[1] "ofn"        "-oTSTES-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/22507048/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22815585/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=578, common to both=578
[1] "Reduce the number of clustering variables from 1268 to 1267."
[1] 1267  578
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           341            237 
  TP53 MUTATED TP53 WILD-TYPE 
           341            237 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
             114              464 
  ARID1A MUTATED ARID1A WILD-TYPE 
             114              464 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            99            479 
  MLL2 MUTATED MLL2 WILD-TYPE 
            99            479 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             47             531 
  RNF43 MUTATED RNF43 WILD-TYPE 
             47             531 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             41             537 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             41             537 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            40            538 
  KRAS MUTATED KRAS WILD-TYPE 
            40            538 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             40             538 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             40             538 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            37            541 
  PTEN MUTATED PTEN WILD-TYPE 
            37            541 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              34              544 
  LARP4B MUTATED LARP4B WILD-TYPE 
              34              544 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             45             533 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             45             533 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            22            556 
  RHOA MUTATED RHOA WILD-TYPE 
            22            556 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           20           558 
  B2M MUTATED B2M WILD-TYPE 
           20           558 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             35             543 
  HLA-B MUTATED HLA-B WILD-TYPE 
             35             543 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               13               565 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               13               565 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
             12             566 
  GNG12 MUTATED GNG12 WILD-TYPE 
             12             566 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               28               550 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               28               550 
[1] "PGM5 MUTATION ANALYSIS"
[1] 3
  PGM5 MUTATED PGM5 WILD-TYPE 
            43            535 
  PGM5 MUTATED PGM5 WILD-TYPE 
            43            535 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            53            525 
  MLL4 MUTATED MLL4 WILD-TYPE 
            53            525 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
            22            556 
  KLF3 MUTATED KLF3 WILD-TYPE 
            22            556 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              42              536 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              42              536 
[1] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            25            553 
  MBD6 MUTATED MBD6 WILD-TYPE 
            25            553 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            59            519 
  MUC6 MUTATED MUC6 WILD-TYPE 
            59            519 
[1] "CBWD1 MUTATION ANALYSIS"
[1] 3
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             22             556 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             22             556 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              33              545 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              33              545 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           62           516 
  APC MUTATED APC WILD-TYPE 
           62           516 
[1] "LARP7 MUTATION ANALYSIS"
[1] 3
  LARP7 MUTATED LARP7 WILD-TYPE 
             22             556 
  LARP7 MUTATED LARP7 WILD-TYPE 
             22             556 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             17             561 
  DDX17 MUTATED DDX17 WILD-TYPE 
             17             561 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           54           524 
  CIC MUTATED CIC WILD-TYPE 
           54           524 
[1] "TENC1 MUTATION ANALYSIS"
[1] 3
  TENC1 MUTATED TENC1 WILD-TYPE 
             23             555 
  TENC1 MUTATED TENC1 WILD-TYPE 
             23             555 
[1] "ARID4A MUTATION ANALYSIS"
[1] 3
  ARID4A MUTATED ARID4A WILD-TYPE 
              24              554 
  ARID4A MUTATED ARID4A WILD-TYPE 
              24              554 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            33            545 
  CDH1 MUTATED CDH1 WILD-TYPE 
            33            545 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            31            547 
  BCOR MUTATED BCOR WILD-TYPE 
            31            547 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                32                546 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                32                546 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              17              561 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              17              561 
[1] "FRMD4A MUTATION ANALYSIS"
[1] 3
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              28              550 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              28              550 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            22            556 
  PAX6 MUTATED PAX6 WILD-TYPE 
            22            556 
[1] "PRSS36 MUTATION ANALYSIS"
[1] 3
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              22              556 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              22              556 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              35              543 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              35              543 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           16           562 
  MVK MUTATED MVK WILD-TYPE 
           16           562 
[1] "KIAA0406 MUTATION ANALYSIS"
[1] 3
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                26                552 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                26                552 
[1] "KIAA1967 MUTATION ANALYSIS"
[1] 3
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                26                552 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                26                552 
[1] "ZMYM4 MUTATION ANALYSIS"
[1] 3
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             24             554 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             24             554 
[1] "LMAN1 MUTATION ANALYSIS"
[1] 3
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             17             561 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             17             561 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              31              547 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              31              547 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
              11              567 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
              11              567 
[1] "FZD3 MUTATION ANALYSIS"
[1] 3
  FZD3 MUTATED FZD3 WILD-TYPE 
            12            566 
  FZD3 MUTATED FZD3 WILD-TYPE 
            12            566 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             20             558 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             20             558 
[1] "NWD1 MUTATION ANALYSIS"
[1] 3
  NWD1 MUTATED NWD1 WILD-TYPE 
            36            542 
  NWD1 MUTATED NWD1 WILD-TYPE 
            36            542 
[1] "CYP27B1 MUTATION ANALYSIS"
[1] 3
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
               11               567 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
               11               567 
[1] "MTG1 MUTATION ANALYSIS"
[1] 3
  MTG1 MUTATED MTG1 WILD-TYPE 
            12            566 
  MTG1 MUTATED MTG1 WILD-TYPE 
            12            566 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             567 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             11             567 
[1] "KIAA1267 MUTATION ANALYSIS"
[1] 3
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                23                555 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                23                555 
[1] "P4HTM MUTATION ANALYSIS"
[1] 3
  P4HTM MUTATED P4HTM WILD-TYPE 
             27             551 
  P4HTM MUTATED P4HTM WILD-TYPE 
             27             551 
[1] "CEP57 MUTATION ANALYSIS"
[1] 3
  CEP57 MUTATED CEP57 WILD-TYPE 
             13             565 
  CEP57 MUTATED CEP57 WILD-TYPE 
             13             565 
[1] "KRT75 MUTATION ANALYSIS"
[1] 3
  KRT75 MUTATED KRT75 WILD-TYPE 
             37             541 
  KRT75 MUTATED KRT75 WILD-TYPE 
             37             541 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
              12              566 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
              12              566 
[1] "DSTN MUTATION ANALYSIS"
[1] 3
  DSTN MUTATED DSTN WILD-TYPE 
             7            571 
  DSTN MUTATED DSTN WILD-TYPE 
             7            571 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               15               563 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               15               563 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
              15              563 
  RNF128 MUTATED RNF128 WILD-TYPE 
              15              563 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             36             542 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             36             542 
[1] "OSBP2 MUTATION ANALYSIS"
[1] 3
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             15             563 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             15             563 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             37             541 
  NFASC MUTATED NFASC WILD-TYPE 
             37             541 
[1] "EPB49 MUTATION ANALYSIS"
[1] 3
  EPB49 MUTATED EPB49 WILD-TYPE 
             17             561 
  EPB49 MUTATED EPB49 WILD-TYPE 
             17             561 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
            11            567 
  WNT1 MUTATED WNT1 WILD-TYPE 
            11            567 
[1] "ATXN2L MUTATION ANALYSIS"
[1] 3
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              25              553 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              25              553 
[1] "C9ORF131 MUTATION ANALYSIS"
[1] 3
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                24                554 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                24                554 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            18            560 
  MFRP MUTATED MFRP WILD-TYPE 
            18            560 
[1] "WASF3 MUTATION ANALYSIS"
[1] 3
  WASF3 MUTATED WASF3 WILD-TYPE 
             22             556 
  WASF3 MUTATED WASF3 WILD-TYPE 
             22             556 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              19              559 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              19              559 
[1] "HOXD8 MUTATION ANALYSIS"
[1] 3
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             14             564 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             14             564 
[1] "PAFAH1B1 MUTATION ANALYSIS"
[1] 3
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                16                562 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                16                562 
[1] "PAX2 MUTATION ANALYSIS"
[1] 3
  PAX2 MUTATED PAX2 WILD-TYPE 
            12            566 
  PAX2 MUTATED PAX2 WILD-TYPE 
            12            566 
[1] "INPPL1 MUTATION ANALYSIS"
[1] 3
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              26              552 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              26              552 
[1] "MCM8 MUTATION ANALYSIS"
[1] 3
  MCM8 MUTATED MCM8 WILD-TYPE 
            26            552 
  MCM8 MUTATED MCM8 WILD-TYPE 
            26            552 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           18           560 
  NLK MUTATED NLK WILD-TYPE 
           18           560 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              18              560 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              18              560 
[1] "NBN MUTATION ANALYSIS"
[1] 3
  NBN MUTATED NBN WILD-TYPE 
           20           558 
  NBN MUTATED NBN WILD-TYPE 
           20           558 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            25            553 
  GLI1 MUTATED GLI1 WILD-TYPE 
            25            553 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             13             565 
  FAM9A MUTATED FAM9A WILD-TYPE 
             13             565 
[1] "HDAC4 MUTATION ANALYSIS"
[1] 3
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             37             541 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             37             541 
[1] "MOBKL1A MUTATION ANALYSIS"
[1] 3
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                7               571 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                7               571 
[1] "KIAA0664 MUTATION ANALYSIS"
[1] 3
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                27                551 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                27                551 
[1] "CR2 MUTATION ANALYSIS"
[1] 3
  CR2 MUTATED CR2 WILD-TYPE 
           27           551 
  CR2 MUTATED CR2 WILD-TYPE 
           27           551 
[1] "RTN2 MUTATION ANALYSIS"
[1] 3
  RTN2 MUTATED RTN2 WILD-TYPE 
            18            560 
  RTN2 MUTATED RTN2 WILD-TYPE 
            18            560 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             25             553 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             25             553 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             15             563 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             15             563 
[1] "IWS1 MUTATION ANALYSIS"
[1] 3
  IWS1 MUTATED IWS1 WILD-TYPE 
            16            562 
  IWS1 MUTATED IWS1 WILD-TYPE 
            16            562 
[1] "SLC12A9 MUTATION ANALYSIS"
[1] 3
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               21               557 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               21               557 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
             13             565 
  IL2RG MUTATED IL2RG WILD-TYPE 
             13             565 
[1] "YY1 MUTATION ANALYSIS"
[1] 3
  YY1 MUTATED YY1 WILD-TYPE 
           12           566 
  YY1 MUTATED YY1 WILD-TYPE 
           12           566 
[1] "OPTN MUTATION ANALYSIS"
[1] 3
  OPTN MUTATED OPTN WILD-TYPE 
            16            562 
  OPTN MUTATED OPTN WILD-TYPE 
            16            562 
[1] "GRK4 MUTATION ANALYSIS"
[1] 3
  GRK4 MUTATED GRK4 WILD-TYPE 
            13            565 
  GRK4 MUTATED GRK4 WILD-TYPE 
            13            565 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            16            562 
  CTCF MUTATED CTCF WILD-TYPE 
            16            562 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             31             547 
  EIF5B MUTATED EIF5B WILD-TYPE 
             31             547 
[1] "RTKN2 MUTATION ANALYSIS"
[1] 3
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             14             564 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             14             564 
[1] "ZNF48 MUTATION ANALYSIS"
[1] 3
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             13             565 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             13             565 
[1] "INF2 MUTATION ANALYSIS"
[1] 3
  INF2 MUTATED INF2 WILD-TYPE 
            26            552 
  INF2 MUTATED INF2 WILD-TYPE 
            26            552 
[1] "NAPEPLD MUTATION ANALYSIS"
[1] 3
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               12               566 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               12               566 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            14            564 
  ELF3 MUTATED ELF3 WILD-TYPE 
            14            564 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
            20            558 
  TTF1 MUTATED TTF1 WILD-TYPE 
            20            558 
[1] "DDC MUTATION ANALYSIS"
[1] 3
  DDC MUTATED DDC WILD-TYPE 
           12           566 
  DDC MUTATED DDC WILD-TYPE 
           12           566 
[1] "KLHDC5 MUTATION ANALYSIS"
[1] 3
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
              13              565 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
              13              565 
[1] "FBXO21 MUTATION ANALYSIS"
[1] 3
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              17              561 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              17              561 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
            19            559 
  IRF2 MUTATED IRF2 WILD-TYPE 
            19            559 
[1] "RHOQ MUTATION ANALYSIS"
[1] 3
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            573 
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            573 
[1] "GRINA MUTATION ANALYSIS"
[1] 3
  GRINA MUTATED GRINA WILD-TYPE 
             10             568 
  GRINA MUTATED GRINA WILD-TYPE 
             10             568 
[1] "EPHX1 MUTATION ANALYSIS"
[1] 3
  EPHX1 MUTATED EPHX1 WILD-TYPE 
             12             566 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
             12             566 
[1] "C13ORF33 MUTATION ANALYSIS"
[1] 3
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 8                570 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 8                570 
[1] "C19ORF40 MUTATION ANALYSIS"
[1] 3
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 7                571 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 7                571 
[1] "MRE11A MUTATION ANALYSIS"
[1] 3
  MRE11A MUTATED MRE11A WILD-TYPE 
               9              569 
  MRE11A MUTATED MRE11A WILD-TYPE 
               9              569 
[1] "ERF MUTATION ANALYSIS"
[1] 3
  ERF MUTATED ERF WILD-TYPE 
           18           560 
  ERF MUTATED ERF WILD-TYPE 
           18           560 
[1] "GYLTL1B MUTATION ANALYSIS"
[1] 3
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               19               559 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               19               559 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            14            564 
  POLM MUTATED POLM WILD-TYPE 
            14            564 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             20             558 
  HLA-A MUTATED HLA-A WILD-TYPE 
             20             558 
[1] "EIF4G3 MUTATION ANALYSIS"
[1] 3
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              24              554 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              24              554 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              33              545 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              33              545 
[1] "TMEM41A MUTATION ANALYSIS"
[1] 3
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                9               569 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                9               569 
[1] "VPS13B MUTATION ANALYSIS"
[1] 3
  VPS13B MUTATED VPS13B WILD-TYPE 
              62              516 
  VPS13B MUTATED VPS13B WILD-TYPE 
              62              516 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             34             544 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             34             544 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             29             549 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             29             549 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
             22             556 
  MED15 MUTATED MED15 WILD-TYPE 
             22             556 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                10                568 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                10                568 
[1] "CDH16 MUTATION ANALYSIS"
[1] 3
  CDH16 MUTATED CDH16 WILD-TYPE 
             17             561 
  CDH16 MUTATED CDH16 WILD-TYPE 
             17             561 
[1] "ANAPC1 MUTATION ANALYSIS"
[1] 3
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              21              557 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              21              557 
[1] "SLC9A11 MUTATION ANALYSIS"
[1] 3
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               30               548 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               30               548 
[1] "C22ORF30 MUTATION ANALYSIS"
[1] 3
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                11                567 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                11                567 
[1] "ANKRD34A MUTATION ANALYSIS"
[1] 3
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                11                567 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                11                567 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            26            552 
  WNK4 MUTATED WNK4 WILD-TYPE 
            26            552 
[1] "PLA2G1B MUTATION ANALYSIS"
[1] 3
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               572 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               572 
[1] "ORC3L MUTATION ANALYSIS"
[1] 3
  ORC3L MUTATED ORC3L WILD-TYPE 
             14             564 
  ORC3L MUTATED ORC3L WILD-TYPE 
             14             564 
[1] "SLC9A10 MUTATION ANALYSIS"
[1] 3
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               20               558 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               20               558 
[1] "ADAMDEC1 MUTATION ANALYSIS"
[1] 3
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                15                563 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                15                563 
[1] "ASAP2 MUTATION ANALYSIS"
[1] 3
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             21             557 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             21             557 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              27              551 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              27              551 
[1] "KCNJ10 MUTATION ANALYSIS"
[1] 3
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              15              563 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              15              563 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
             14             564 
  WNT16 MUTATED WNT16 WILD-TYPE 
             14             564 
[1] "JARID2 MUTATION ANALYSIS"
[1] 3
  JARID2 MUTATED JARID2 WILD-TYPE 
              44              534 
  JARID2 MUTATED JARID2 WILD-TYPE 
              44              534 
[1] "SLC27A3 MUTATION ANALYSIS"
[1] 3
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
               11               567 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
               11               567 
[1] "MICALCL MUTATION ANALYSIS"
[1] 3
  MICALCL MUTATED MICALCL WILD-TYPE 
               19               559 
  MICALCL MUTATED MICALCL WILD-TYPE 
               19               559 
[1] "KLHDC8B MUTATION ANALYSIS"
[1] 3
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
               11               567 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
               11               567 
[1] "B3GNT5 MUTATION ANALYSIS"
[1] 3
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              12              566 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              12              566 
[1] "SPTY2D1 MUTATION ANALYSIS"
[1] 3
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               21               557 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               21               557 
[1] "TP53BP2 MUTATION ANALYSIS"
[1] 3
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               18               560 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               18               560 
[1] "HDLBP MUTATION ANALYSIS"
[1] 3
  HDLBP MUTATED HDLBP WILD-TYPE 
             40             538 
  HDLBP MUTATED HDLBP WILD-TYPE 
             40             538 
[1] "SYNJ1 MUTATION ANALYSIS"
[1] 3
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             18             560 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             18             560 
[1] "PIGT MUTATION ANALYSIS"
[1] 3
  PIGT MUTATED PIGT WILD-TYPE 
            15            563 
  PIGT MUTATED PIGT WILD-TYPE 
            15            563 
[1] "TRIP4 MUTATION ANALYSIS"
[1] 3
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             14             564 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             14             564 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             17             561 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             17             561 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             33             545 
  ARID2 MUTATED ARID2 WILD-TYPE 
             33             545 
[1] "MTMR9 MUTATION ANALYSIS"
[1] 3
  MTMR9 MUTATED MTMR9 WILD-TYPE 
             18             560 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
             18             560 
[1] "CR1L MUTATION ANALYSIS"
[1] 3
  CR1L MUTATED CR1L WILD-TYPE 
            17            561 
  CR1L MUTATED CR1L WILD-TYPE 
            17            561 
[1] "YIPF2 MUTATION ANALYSIS"
[1] 3
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             10             568 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             10             568 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
             16             562 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
             16             562 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                22                556 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                22                556 
[1] "GXYLT1 MUTATION ANALYSIS"
[1] 3
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              15              563 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              15              563 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             32             546 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             32             546 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               30               548 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               30               548 
[1] "BTBD7 MUTATION ANALYSIS"
[1] 3
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             22             556 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             22             556 
[1] "GANAB MUTATION ANALYSIS"
[1] 3
  GANAB MUTATED GANAB WILD-TYPE 
             20             558 
  GANAB MUTATED GANAB WILD-TYPE 
             20             558 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            69            509 
  MLL3 MUTATED MLL3 WILD-TYPE 
            69            509 
[1] "CLDN6 MUTATION ANALYSIS"
[1] 3
  CLDN6 MUTATED CLDN6 WILD-TYPE 
             10             568 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
             10             568 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              34              544 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              34              544 
[1] "FAM133A MUTATION ANALYSIS"
[1] 3
  FAM133A MUTATED FAM133A WILD-TYPE 
               12               566 
  FAM133A MUTATED FAM133A WILD-TYPE 
               12               566 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             25             553 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             25             553 
[1] "CR1 MUTATION ANALYSIS"
[1] 3
  CR1 MUTATED CR1 WILD-TYPE 
           32           546 
  CR1 MUTATED CR1 WILD-TYPE 
           32           546 
[1] "SERPINI1 MUTATION ANALYSIS"
[1] 3
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 9                569 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 9                569 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                22                556 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                22                556 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            20            558 
  PPIG MUTATED PPIG WILD-TYPE 
            20            558 
[1] "HTR7 MUTATION ANALYSIS"
[1] 3
  HTR7 MUTATED HTR7 WILD-TYPE 
            17            561 
  HTR7 MUTATED HTR7 WILD-TYPE 
            17            561 
[1] "PIGB MUTATION ANALYSIS"
[1] 3
  PIGB MUTATED PIGB WILD-TYPE 
            11            567 
  PIGB MUTATED PIGB WILD-TYPE 
            11            567 
[1] "EEF2K MUTATION ANALYSIS"
[1] 3
  EEF2K MUTATED EEF2K WILD-TYPE 
             14             564 
  EEF2K MUTATED EEF2K WILD-TYPE 
             14             564 
[1] "SNRNP35 MUTATION ANALYSIS"
[1] 3
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                7               571 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                7               571 
[1] "ZKSCAN5 MUTATION ANALYSIS"
[1] 3
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               13               565 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               13               565 
[1] "CELSR1 MUTATION ANALYSIS"
[1] 3
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              45              533 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              45              533 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              8             570 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              8             570 
[1] "NPHP1 MUTATION ANALYSIS"
[1] 3
  NPHP1 MUTATED NPHP1 WILD-TYPE 
             12             566 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
             12             566 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               31               547 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               31               547 
[1] "DTX3 MUTATION ANALYSIS"
[1] 3
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            571 
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            571 
[1] "ZNF43 MUTATION ANALYSIS"
[1] 3
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             31             547 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             31             547 
[1] "GLT6D1 MUTATION ANALYSIS"
[1] 3
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              15              563 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              15              563 
[1] "TAC4 MUTATION ANALYSIS"
[1] 3
  TAC4 MUTATED TAC4 WILD-TYPE 
             4            574 
  TAC4 MUTATED TAC4 WILD-TYPE 
             4            574 
[1] "CCDC108 MUTATION ANALYSIS"
[1] 3
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               29               549 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               29               549 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              21              557 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              21              557 
[1] "TATDN1 MUTATION ANALYSIS"
[1] 3
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              572 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              572 
[1] "INO80D MUTATION ANALYSIS"
[1] 3
  INO80D MUTATED INO80D WILD-TYPE 
              23              555 
  INO80D MUTATED INO80D WILD-TYPE 
              23              555 
[1] "WDR7 MUTATION ANALYSIS"
[1] 3
  WDR7 MUTATED WDR7 WILD-TYPE 
            29            549 
  WDR7 MUTATED WDR7 WILD-TYPE 
            29            549 
[1] "FAAH MUTATION ANALYSIS"
[1] 3
  FAAH MUTATED FAAH WILD-TYPE 
             5            573 
  FAAH MUTATED FAAH WILD-TYPE 
             5            573 
[1] "EFNB3 MUTATION ANALYSIS"
[1] 3
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             15             563 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             15             563 
[1] "MAP3K1 MUTATION ANALYSIS"
[1] 3
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              23              555 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              23              555 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
              10              568 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
              10              568 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            34            544 
  SVIL MUTATED SVIL WILD-TYPE 
            34            544 
[1] "TRMT6 MUTATION ANALYSIS"
[1] 3
  TRMT6 MUTATED TRMT6 WILD-TYPE 
             10             568 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
             10             568 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           59           519 
  ATM MUTATED ATM WILD-TYPE 
           59           519 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             574 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             574 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             26             552 
  RASA1 MUTATED RASA1 WILD-TYPE 
             26             552 
[1] "CABP5 MUTATION ANALYSIS"
[1] 3
  CABP5 MUTATED CABP5 WILD-TYPE 
              8             570 
  CABP5 MUTATED CABP5 WILD-TYPE 
              8             570 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
             12             566 
  PALB2 MUTATED PALB2 WILD-TYPE 
             12             566 
[1] "RB1CC1 MUTATION ANALYSIS"
[1] 3
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              17              561 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              17              561 
[1] "C16ORF63 MUTATION ANALYSIS"
[1] 3
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                10                568 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                10                568 
[1] "ZNF878 MUTATION ANALYSIS"
[1] 3
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              16              562 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              16              562 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              84              494 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              84              494 
[1] "SH3KBP1 MUTATION ANALYSIS"
[1] 3
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               19               559 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               19               559 
[1] "C2ORF76 MUTATION ANALYSIS"
[1] 3
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                5               573 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                5               573 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               14               564 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               14               564 
[1] "ANKRD20A4 MUTATION ANALYSIS"
[1] 3
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                 10                 568 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                 10                 568 
[1] "RABGAP1 MUTATION ANALYSIS"
[1] 3
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               25               553 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               25               553 
[1] "PPARG MUTATION ANALYSIS"
[1] 3
  PPARG MUTATED PPARG WILD-TYPE 
              6             572 
  PPARG MUTATED PPARG WILD-TYPE 
              6             572 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
             20             558 
  TOP2A MUTATED TOP2A WILD-TYPE 
             20             558 
[1] "U2AF2 MUTATION ANALYSIS"
[1] 3
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             15             563 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             15             563 
[1] "CCDC153 MUTATION ANALYSIS"
[1] 3
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               571 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               571 
[1] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               39               539 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               39               539 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            20            558 
  JAK1 MUTATED JAK1 WILD-TYPE 
            20            558 
[1] "COIL MUTATION ANALYSIS"
[1] 3
  COIL MUTATED COIL WILD-TYPE 
            11            567 
  COIL MUTATED COIL WILD-TYPE 
            11            567 
[1] "TCF20 MUTATION ANALYSIS"
[1] 3
  TCF20 MUTATED TCF20 WILD-TYPE 
             22             556 
  TCF20 MUTATED TCF20 WILD-TYPE 
             22             556 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            15            563 
  TBX4 MUTATED TBX4 WILD-TYPE 
            15            563 
[1] "PRKAB1 MUTATION ANALYSIS"
[1] 3
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
              12              566 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
              12              566 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
             11             567 
  CETN3 MUTATED CETN3 WILD-TYPE 
             11             567 
[1] "DDX26B MUTATION ANALYSIS"
[1] 3
  DDX26B MUTATED DDX26B WILD-TYPE 
              13              565 
  DDX26B MUTATED DDX26B WILD-TYPE 
              13              565 
[1] "DLAT MUTATION ANALYSIS"
[1] 3
  DLAT MUTATED DLAT WILD-TYPE 
             9            569 
  DLAT MUTATED DLAT WILD-TYPE 
             9            569 
[1] "MPRIP MUTATION ANALYSIS"
[1] 3
  MPRIP MUTATED MPRIP WILD-TYPE 
             18             560 
  MPRIP MUTATED MPRIP WILD-TYPE 
             18             560 
[1] "NCAPD3 MUTATION ANALYSIS"
[1] 3
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              30              548 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              30              548 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             23             555 
  CASP8 MUTATED CASP8 WILD-TYPE 
             23             555 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
            35            543 
  BRD8 MUTATED BRD8 WILD-TYPE 
            35            543 
[1] "PET112L MUTATION ANALYSIS"
[1] 3
  PET112L MUTATED PET112L WILD-TYPE 
               11               567 
  PET112L MUTATED PET112L WILD-TYPE 
               11               567 
[1] "RGS9BP MUTATION ANALYSIS"
[1] 3
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               9              569 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               9              569 
[1] "OR5M3 MUTATION ANALYSIS"
[1] 3
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             25             553 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             25             553 
[1] "FERMT2 MUTATION ANALYSIS"
[1] 3
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              14              564 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              14              564 
[1] "STX2 MUTATION ANALYSIS"
[1] 3
  STX2 MUTATED STX2 WILD-TYPE 
             7            571 
  STX2 MUTATED STX2 WILD-TYPE 
             7            571 
[1] "ABCA6 MUTATION ANALYSIS"
[1] 3
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             23             555 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             23             555 
[1] "PIAS1 MUTATION ANALYSIS"
[1] 3
  PIAS1 MUTATED PIAS1 WILD-TYPE 
             14             564 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
             14             564 
[1] "USP26 MUTATION ANALYSIS"
[1] 3
  USP26 MUTATED USP26 WILD-TYPE 
             25             553 
  USP26 MUTATED USP26 WILD-TYPE 
             25             553 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
            10            568 
  MLH1 MUTATED MLH1 WILD-TYPE 
            10            568 
[1] "SLC22A6 MUTATION ANALYSIS"
[1] 3
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               16               562 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               16               562 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             33             545 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             33             545 
[1] "DAO MUTATION ANALYSIS"
[1] 3
  DAO MUTATED DAO WILD-TYPE 
           15           563 
  DAO MUTATED DAO WILD-TYPE 
           15           563 
[1] "CD79A MUTATION ANALYSIS"
[1] 3
  CD79A MUTATED CD79A WILD-TYPE 
              9             569 
  CD79A MUTATED CD79A WILD-TYPE 
              9             569 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                20                558 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                20                558 
[1] "IPO5 MUTATION ANALYSIS"
[1] 3
  IPO5 MUTATED IPO5 WILD-TYPE 
            25            553 
  IPO5 MUTATED IPO5 WILD-TYPE 
            25            553 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
             13             565 
  MYEOV MUTATED MYEOV WILD-TYPE 
             13             565 
[1] "BCKDHA MUTATION ANALYSIS"
[1] 3
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              11              567 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              11              567 
[1] "TRAM1L1 MUTATION ANALYSIS"
[1] 3
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               21               557 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               21               557 
[1] "KIAA1704 MUTATION ANALYSIS"
[1] 3
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 6                572 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 6                572 
[1] "GPC2 MUTATION ANALYSIS"
[1] 3
  GPC2 MUTATED GPC2 WILD-TYPE 
             9            569 
  GPC2 MUTATED GPC2 WILD-TYPE 
             9            569 
[1] "FILIP1L MUTATION ANALYSIS"
[1] 3
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               23               555 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               23               555 
[1] "GPSM3 MUTATION ANALYSIS"
[1] 3
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             566 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             566 
[1] "FAM82A1 MUTATION ANALYSIS"
[1] 3
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                7               571 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                7               571 
[1] "KNTC1 MUTATION ANALYSIS"
[1] 3
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             26             552 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             26             552 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             66             512 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             66             512 
[1] "NCAPH MUTATION ANALYSIS"
[1] 3
  NCAPH MUTATED NCAPH WILD-TYPE 
             13             565 
  NCAPH MUTATED NCAPH WILD-TYPE 
             13             565 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             30             548 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             30             548 
[1] "ART1 MUTATION ANALYSIS"
[1] 3
  ART1 MUTATED ART1 WILD-TYPE 
             9            569 
  ART1 MUTATED ART1 WILD-TYPE 
             9            569 
[1] "RALGAPB MUTATION ANALYSIS"
[1] 3
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               22               556 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               22               556 
[1] "CDC14A MUTATION ANALYSIS"
[1] 3
  CDC14A MUTATED CDC14A WILD-TYPE 
              17              561 
  CDC14A MUTATED CDC14A WILD-TYPE 
              17              561 
[1] "RIF1 MUTATION ANALYSIS"
[1] 3
  RIF1 MUTATED RIF1 WILD-TYPE 
            26            552 
  RIF1 MUTATED RIF1 WILD-TYPE 
            26            552 
[1] "STK38 MUTATION ANALYSIS"
[1] 3
  STK38 MUTATED STK38 WILD-TYPE 
              8             570 
  STK38 MUTATED STK38 WILD-TYPE 
              8             570 
[1] "PAPD4 MUTATION ANALYSIS"
[1] 3
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             13             565 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             13             565 
[1] "ABCB4 MUTATION ANALYSIS"
[1] 3
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             30             548 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             30             548 
[1] "DIDO1 MUTATION ANALYSIS"
[1] 3
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             50             528 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             50             528 
[1] "ADNP MUTATION ANALYSIS"
[1] 3
  ADNP MUTATED ADNP WILD-TYPE 
            20            558 
  ADNP MUTATED ADNP WILD-TYPE 
            20            558 
[1] "AQP8 MUTATION ANALYSIS"
[1] 3
  AQP8 MUTATED AQP8 WILD-TYPE 
            14            564 
  AQP8 MUTATED AQP8 WILD-TYPE 
            14            564 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              41              537 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              41              537 
[1] "C10ORF76 MUTATION ANALYSIS"
[1] 3
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                13                565 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                13                565 
[1] "SYCP1 MUTATION ANALYSIS"
[1] 3
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             28             550 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             28             550 
[1] "SNRK MUTATION ANALYSIS"
[1] 3
  SNRK MUTATED SNRK WILD-TYPE 
            17            561 
  SNRK MUTATED SNRK WILD-TYPE 
            17            561 
[1] "EAF2 MUTATION ANALYSIS"
[1] 3
  EAF2 MUTATED EAF2 WILD-TYPE 
            11            567 
  EAF2 MUTATED EAF2 WILD-TYPE 
            11            567 
[1] "HSPG2 MUTATION ANALYSIS"
[1] 3
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             75             503 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             75             503 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               27               551 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               27               551 
[1] "KLC2 MUTATION ANALYSIS"
[1] 3
  KLC2 MUTATED KLC2 WILD-TYPE 
            16            562 
  KLC2 MUTATED KLC2 WILD-TYPE 
            16            562 
[1] "SRCIN1 MUTATION ANALYSIS"
[1] 3
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              18              560 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              18              560 
[1] "FAM98C MUTATION ANALYSIS"
[1] 3
  FAM98C MUTATED FAM98C WILD-TYPE 
              10              568 
  FAM98C MUTATED FAM98C WILD-TYPE 
              10              568 
[1] "PDCD1 MUTATION ANALYSIS"
[1] 3
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              6             572 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              6             572 
[1] "TMC4 MUTATION ANALYSIS"
[1] 3
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            558 
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            558 
[1] "ACP1 MUTATION ANALYSIS"
[1] 3
  ACP1 MUTATED ACP1 WILD-TYPE 
             9            569 
  ACP1 MUTATED ACP1 WILD-TYPE 
             9            569 
[1] "PLOD3 MUTATION ANALYSIS"
[1] 3
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             20             558 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             20             558 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                6               572 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                6               572 
[1] "ATP2B4 MUTATION ANALYSIS"
[1] 3
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              22              556 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              22              556 
[1] "LRRN2 MUTATION ANALYSIS"
[1] 3
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             35             543 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             35             543 
[1] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
            114             464 
  OBSCN MUTATED OBSCN WILD-TYPE 
            114             464 
[1] "KIDINS220 MUTATION ANALYSIS"
[1] 3
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 28                 550 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 28                 550 
[1] "NID2 MUTATION ANALYSIS"
[1] 3
  NID2 MUTATED NID2 WILD-TYPE 
            22            556 
  NID2 MUTATED NID2 WILD-TYPE 
            22            556 
[1] "KIRREL MUTATION ANALYSIS"
[1] 3
  KIRREL MUTATED KIRREL WILD-TYPE 
              24              554 
  KIRREL MUTATED KIRREL WILD-TYPE 
              24              554 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             35             543 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             35             543 
[1] "NUP35 MUTATION ANALYSIS"
[1] 3
  NUP35 MUTATED NUP35 WILD-TYPE 
              7             571 
  NUP35 MUTATED NUP35 WILD-TYPE 
              7             571 
[1] "ZC3H18 MUTATION ANALYSIS"
[1] 3
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              25              553 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              25              553 
[1] "GLYR1 MUTATION ANALYSIS"
[1] 3
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             17             561 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             17             561 
[1] "FRYL MUTATION ANALYSIS"
[1] 3
  FRYL MUTATED FRYL WILD-TYPE 
            35            543 
  FRYL MUTATED FRYL WILD-TYPE 
            35            543 
[1] "CNBD1 MUTATION ANALYSIS"
[1] 3
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             22             556 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             22             556 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
             13             565 
  PANK1 MUTATED PANK1 WILD-TYPE 
             13             565 
[1] "UGP2 MUTATION ANALYSIS"
[1] 3
  UGP2 MUTATED UGP2 WILD-TYPE 
             9            569 
  UGP2 MUTATED UGP2 WILD-TYPE 
             9            569 
[1] "CASD1 MUTATION ANALYSIS"
[1] 3
  CASD1 MUTATED CASD1 WILD-TYPE 
             15             563 
  CASD1 MUTATED CASD1 WILD-TYPE 
             15             563 
[1] "NT5M MUTATION ANALYSIS"
[1] 3
  NT5M MUTATED NT5M WILD-TYPE 
             7            571 
  NT5M MUTATED NT5M WILD-TYPE 
             7            571 
[1] "AZGP1 MUTATION ANALYSIS"
[1] 3
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             574 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             574 
[1] "RAB42 MUTATION ANALYSIS"
[1] 3
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             573 
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             573 
[1] "C11ORF80 MUTATION ANALYSIS"
[1] 3
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 9                569 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 9                569 
[1] "OXNAD1 MUTATION ANALYSIS"
[1] 3
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               9              569 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               9              569 
[1] "KLRK1 MUTATION ANALYSIS"
[1] 3
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              8             570 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              8             570 
[1] "IPO11 MUTATION ANALYSIS"
[1] 3
  IPO11 MUTATED IPO11 WILD-TYPE 
             13             565 
  IPO11 MUTATED IPO11 WILD-TYPE 
             13             565 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
            18            560 
  GAS6 MUTATED GAS6 WILD-TYPE 
            18            560 
[1] "DMXL2 MUTATION ANALYSIS"
[1] 3
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             50             528 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             50             528 
[1] "IRS1 MUTATION ANALYSIS"
[1] 3
  IRS1 MUTATED IRS1 WILD-TYPE 
            26            552 
  IRS1 MUTATED IRS1 WILD-TYPE 
            26            552 
[1] "HIST1H1A MUTATION ANALYSIS"
[1] 3
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                11                567 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                11                567 
[1] "CTSO MUTATION ANALYSIS"
[1] 3
  CTSO MUTATED CTSO WILD-TYPE 
             7            571 
  CTSO MUTATED CTSO WILD-TYPE 
             7            571 
[1] "CASC3 MUTATION ANALYSIS"
[1] 3
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             567 
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             567 
[1] "TNFSF10 MUTATION ANALYSIS"
[1] 3
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                9               569 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                9               569 
[1] "RIC3 MUTATION ANALYSIS"
[1] 3
  RIC3 MUTATED RIC3 WILD-TYPE 
             9            569 
  RIC3 MUTATED RIC3 WILD-TYPE 
             9            569 
[1] "FAM108A1 MUTATION ANALYSIS"
[1] 3
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 6                572 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 6                572 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
            13            565 
  GAB2 MUTATED GAB2 WILD-TYPE 
            13            565 
[1] "BAHCC1 MUTATION ANALYSIS"
[1] 3
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              17              561 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              17              561 
[1] "ARHGAP18 MUTATION ANALYSIS"
[1] 3
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                10                568 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                10                568 
[1] "FHDC1 MUTATION ANALYSIS"
[1] 3
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             19             559 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             19             559 
[1] "CCDC148 MUTATION ANALYSIS"
[1] 3
  CCDC148 MUTATED CCDC148 WILD-TYPE 
               10               568 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
               10               568 
[1] "SF3B3 MUTATION ANALYSIS"
[1] 3
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             24             554 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             24             554 
[1] "PPIP5K2 MUTATION ANALYSIS"
[1] 3
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               16               562 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               16               562 
[1] "PTCHD3 MUTATION ANALYSIS"
[1] 3
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              26              552 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              26              552 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              23              555 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              23              555 
[1] "KIN MUTATION ANALYSIS"
[1] 3
  KIN MUTATED KIN WILD-TYPE 
            8           570 
  KIN MUTATED KIN WILD-TYPE 
            8           570 
[1] "KPNA1 MUTATION ANALYSIS"
[1] 3
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             572 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             572 
[1] "KIAA0649 MUTATION ANALYSIS"
[1] 3
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                22                556 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                22                556 
[1] "NIN MUTATION ANALYSIS"
[1] 3
  NIN MUTATED NIN WILD-TYPE 
           33           545 
  NIN MUTATED NIN WILD-TYPE 
           33           545 
[1] "CTSC MUTATION ANALYSIS"
[1] 3
  CTSC MUTATED CTSC WILD-TYPE 
            11            567 
  CTSC MUTATED CTSC WILD-TYPE 
            11            567 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             17             561 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             17             561 
[1] "C2ORF42 MUTATION ANALYSIS"
[1] 3
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               15               563 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               15               563 
[1] "COL12A1 MUTATION ANALYSIS"
[1] 3
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               65               513 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               65               513 
[1] "FAM60A MUTATION ANALYSIS"
[1] 3
  FAM60A MUTATED FAM60A WILD-TYPE 
               4              574 
  FAM60A MUTATED FAM60A WILD-TYPE 
               4              574 
[1] "CBWD6 MUTATION ANALYSIS"
[1] 3
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              7             571 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              7             571 
[1] "SPG20 MUTATION ANALYSIS"
[1] 3
  SPG20 MUTATED SPG20 WILD-TYPE 
             25             553 
  SPG20 MUTATED SPG20 WILD-TYPE 
             25             553 
[1] "BPTF MUTATION ANALYSIS"
[1] 3
  BPTF MUTATED BPTF WILD-TYPE 
            39            539 
  BPTF MUTATED BPTF WILD-TYPE 
            39            539 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               9              569 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               9              569 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
            32            546 
  RAI1 MUTATED RAI1 WILD-TYPE 
            32            546 
[1] "TRUB1 MUTATION ANALYSIS"
[1] 3
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             12             566 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             12             566 
[1] "SPATA20 MUTATION ANALYSIS"
[1] 3
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               18               560 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               18               560 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            20            558 
  NOS3 MUTATED NOS3 WILD-TYPE 
            20            558 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
               14               564 
  FAM155B MUTATED FAM155B WILD-TYPE 
               14               564 
[1] "MDM2 MUTATION ANALYSIS"
[1] 3
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            569 
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            569 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
             11             567 
  ASB11 MUTATED ASB11 WILD-TYPE 
             11             567 
[1] "TAS2R10 MUTATION ANALYSIS"
[1] 3
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                5               573 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                5               573 
[1] "B4GALT6 MUTATION ANALYSIS"
[1] 3
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                9               569 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                9               569 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              569 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              569 
[1] "TCHP MUTATION ANALYSIS"
[1] 3
  TCHP MUTATED TCHP WILD-TYPE 
            13            565 
  TCHP MUTATED TCHP WILD-TYPE 
            13            565 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             21             557 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             21             557 
[1] "PUS7L MUTATION ANALYSIS"
[1] 3
  PUS7L MUTATED PUS7L WILD-TYPE 
             10             568 
  PUS7L MUTATED PUS7L WILD-TYPE 
             10             568 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             18             560 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             18             560 
[1] "RAD50 MUTATION ANALYSIS"
[1] 3
  RAD50 MUTATED RAD50 WILD-TYPE 
             15             563 
  RAD50 MUTATED RAD50 WILD-TYPE 
             15             563 
[1] "KIAA1009 MUTATION ANALYSIS"
[1] 3
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                18                560 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                18                560 
[1] "PFKP MUTATION ANALYSIS"
[1] 3
  PFKP MUTATED PFKP WILD-TYPE 
            20            558 
  PFKP MUTATED PFKP WILD-TYPE 
            20            558 
[1] "NT5DC1 MUTATION ANALYSIS"
[1] 3
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              570 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              570 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              24              554 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              24              554 
[1] "PKN2 MUTATION ANALYSIS"
[1] 3
  PKN2 MUTATED PKN2 WILD-TYPE 
            18            560 
  PKN2 MUTATED PKN2 WILD-TYPE 
            18            560 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
              14              564 
  THEMIS MUTATED THEMIS WILD-TYPE 
              14              564 
[1] "GCC2 MUTATION ANALYSIS"
[1] 3
  GCC2 MUTATED GCC2 WILD-TYPE 
            20            558 
  GCC2 MUTATED GCC2 WILD-TYPE 
            20            558 
[1] "FAM70B MUTATION ANALYSIS"
[1] 3
  FAM70B MUTATED FAM70B WILD-TYPE 
              14              564 
  FAM70B MUTATED FAM70B WILD-TYPE 
              14              564 
[1] "C16ORF74 MUTATION ANALYSIS"
[1] 3
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 3                575 
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 3                575 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              15              563 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              15              563 
[1] "C2CD3 MUTATION ANALYSIS"
[1] 3
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             30             548 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             30             548 
[1] "MASTL MUTATION ANALYSIS"
[1] 3
  MASTL MUTATED MASTL WILD-TYPE 
             17             561 
  MASTL MUTATED MASTL WILD-TYPE 
             17             561 
[1] "CASP7 MUTATION ANALYSIS"
[1] 3
  CASP7 MUTATED CASP7 WILD-TYPE 
              5             573 
  CASP7 MUTATED CASP7 WILD-TYPE 
              5             573 
[1] "HIAT1 MUTATION ANALYSIS"
[1] 3
  HIAT1 MUTATED HIAT1 WILD-TYPE 
             11             567 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
             11             567 
[1] "FAM116A MUTATION ANALYSIS"
[1] 3
  FAM116A MUTATED FAM116A WILD-TYPE 
               10               568 
  FAM116A MUTATED FAM116A WILD-TYPE 
               10               568 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             41             537 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             41             537 
[1] "NDST2 MUTATION ANALYSIS"
[1] 3
  NDST2 MUTATED NDST2 WILD-TYPE 
             16             562 
  NDST2 MUTATED NDST2 WILD-TYPE 
             16             562 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           21           557 
  RB1 MUTATED RB1 WILD-TYPE 
           21           557 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
            49            529 
  GNAS MUTATED GNAS WILD-TYPE 
            49            529 
[1] "SPG11 MUTATION ANALYSIS"
[1] 3
  SPG11 MUTATED SPG11 WILD-TYPE 
             22             556 
  SPG11 MUTATED SPG11 WILD-TYPE 
             22             556 
[1] "FAH MUTATION ANALYSIS"
[1] 3
  FAH MUTATED FAH WILD-TYPE 
            9           569 
  FAH MUTATED FAH WILD-TYPE 
            9           569 
[1] "CNTLN MUTATION ANALYSIS"
[1] 3
  CNTLN MUTATED CNTLN WILD-TYPE 
             45             533 
  CNTLN MUTATED CNTLN WILD-TYPE 
             45             533 
[1] "KIAA0748 MUTATION ANALYSIS"
[1] 3
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                21                557 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                21                557 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             22             556 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             22             556 
[1] "C4ORF6 MUTATION ANALYSIS"
[1] 3
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
              12              566 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
              12              566 
[1] "DPP7 MUTATION ANALYSIS"
[1] 3
  DPP7 MUTATED DPP7 WILD-TYPE 
            11            567 
  DPP7 MUTATED DPP7 WILD-TYPE 
            11            567 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
             10             568 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
             10             568 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             31             547 
  BCL9L MUTATED BCL9L WILD-TYPE 
             31             547 
[1] "SENP3 MUTATION ANALYSIS"
[1] 3
  SENP3 MUTATED SENP3 WILD-TYPE 
             14             564 
  SENP3 MUTATED SENP3 WILD-TYPE 
             14             564 
[1] "MMP3 MUTATION ANALYSIS"
[1] 3
  MMP3 MUTATED MMP3 WILD-TYPE 
            13            565 
  MMP3 MUTATED MMP3 WILD-TYPE 
            13            565 
[1] "RCOR3 MUTATION ANALYSIS"
[1] 3
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             17             561 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             17             561 
[1] "MBD2 MUTATION ANALYSIS"
[1] 3
  MBD2 MUTATED MBD2 WILD-TYPE 
            12            566 
  MBD2 MUTATED MBD2 WILD-TYPE 
            12            566 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             18             560 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             18             560 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              31              547 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              31              547 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            20            558 
  SOX7 MUTATED SOX7 WILD-TYPE 
            20            558 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
              14              564 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
              14              564 
[1] "LARP1B MUTATION ANALYSIS"
[1] 3
  LARP1B MUTATED LARP1B WILD-TYPE 
              14              564 
  LARP1B MUTATED LARP1B WILD-TYPE 
              14              564 
[1] "C17ORF57 MUTATION ANALYSIS"
[1] 3
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                16                562 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                16                562 
[1] "HAUS3 MUTATION ANALYSIS"
[1] 3
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             13             565 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             13             565 
[1] "EHMT2 MUTATION ANALYSIS"
[1] 3
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             23             555 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             23             555 
[1] "PLEKHA5 MUTATION ANALYSIS"
[1] 3
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               23               555 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               23               555 
[1] "ALG10 MUTATION ANALYSIS"
[1] 3
  ALG10 MUTATED ALG10 WILD-TYPE 
             17             561 
  ALG10 MUTATED ALG10 WILD-TYPE 
             17             561 
[1] "NAA16 MUTATION ANALYSIS"
[1] 3
  NAA16 MUTATED NAA16 WILD-TYPE 
             15             563 
  NAA16 MUTATED NAA16 WILD-TYPE 
             15             563 
[1] "C6ORF150 MUTATION ANALYSIS"
[1] 3
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 8                570 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 8                570 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                6               572 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                6               572 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              554 
  KIF21A MUTATED KIF21A WILD-TYPE 
              24              554 
[1] "GPR82 MUTATION ANALYSIS"
[1] 3
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             569 
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             569 
[1] "C14ORF50 MUTATION ANALYSIS"
[1] 3
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                570 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                570 
[1] "ELOVL2 MUTATION ANALYSIS"
[1] 3
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               9              569 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               9              569 
[1] "GPC4 MUTATION ANALYSIS"
[1] 3
  GPC4 MUTATED GPC4 WILD-TYPE 
             9            569 
  GPC4 MUTATED GPC4 WILD-TYPE 
             9            569 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             15             563 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             15             563 
[1] "SETDB2 MUTATION ANALYSIS"
[1] 3
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              17              561 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              17              561 
[1] "CTNNA1 MUTATION ANALYSIS"
[1] 3
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              22              556 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              22              556 
[1] "UBE2Q1 MUTATION ANALYSIS"
[1] 3
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               7              571 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               7              571 
[1] "MAP2K7 MUTATION ANALYSIS"
[1] 3
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              27              551 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              27              551 
[1] "SH3RF1 MUTATION ANALYSIS"
[1] 3
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              15              563 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              15              563 
[1] "GPR161 MUTATION ANALYSIS"
[1] 3
  GPR161 MUTATED GPR161 WILD-TYPE 
              18              560 
  GPR161 MUTATED GPR161 WILD-TYPE 
              18              560 
[1] "KANK4 MUTATION ANALYSIS"
[1] 3
  KANK4 MUTATED KANK4 WILD-TYPE 
             19             559 
  KANK4 MUTATED KANK4 WILD-TYPE 
             19             559 
[1] "ZC3H4 MUTATION ANALYSIS"
[1] 3
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             22             556 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             22             556 
[1] "KYNU MUTATION ANALYSIS"
[1] 3
  KYNU MUTATED KYNU WILD-TYPE 
            14            564 
  KYNU MUTATED KYNU WILD-TYPE 
            14            564 
[1] "MIA2 MUTATION ANALYSIS"
[1] 3
  MIA2 MUTATED MIA2 WILD-TYPE 
            11            567 
  MIA2 MUTATED MIA2 WILD-TYPE 
            11            567 
[1] "PHF1 MUTATION ANALYSIS"
[1] 3
  PHF1 MUTATED PHF1 WILD-TYPE 
             9            569 
  PHF1 MUTATED PHF1 WILD-TYPE 
             9            569 
[1] "TMEFF2 MUTATION ANALYSIS"
[1] 3
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
              13              565 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
              13              565 
[1] "FAM83E MUTATION ANALYSIS"
[1] 3
  FAM83E MUTATED FAM83E WILD-TYPE 
              15              563 
  FAM83E MUTATED FAM83E WILD-TYPE 
              15              563 
[1] "PPP3CA MUTATION ANALYSIS"
[1] 3
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              13              565 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              13              565 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              23              555 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              23              555 
[1] "RRS1 MUTATION ANALYSIS"
[1] 3
  RRS1 MUTATED RRS1 WILD-TYPE 
            10            568 
  RRS1 MUTATED RRS1 WILD-TYPE 
            10            568 
[1] "RBM6 MUTATION ANALYSIS"
[1] 3
  RBM6 MUTATED RBM6 WILD-TYPE 
            26            552 
  RBM6 MUTATED RBM6 WILD-TYPE 
            26            552 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             22             556 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             22             556 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
            10            568 
  TFE3 MUTATED TFE3 WILD-TYPE 
            10            568 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             569 
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             569 
[1] "CDC5L MUTATION ANALYSIS"
[1] 3
  CDC5L MUTATED CDC5L WILD-TYPE 
             17             561 
  CDC5L MUTATED CDC5L WILD-TYPE 
             17             561 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               17               561 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               17               561 
[1] "CRYGA MUTATION ANALYSIS"
[1] 3
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             567 
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             567 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             20             558 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             20             558 
[1] "FAM113B MUTATION ANALYSIS"
[1] 3
  FAM113B MUTATED FAM113B WILD-TYPE 
               17               561 
  FAM113B MUTATED FAM113B WILD-TYPE 
               17               561 
[1] "PTPN4 MUTATION ANALYSIS"
[1] 3
  PTPN4 MUTATED PTPN4 WILD-TYPE 
             17             561 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
             17             561 
[1] "RNF111 MUTATION ANALYSIS"
[1] 3
  RNF111 MUTATED RNF111 WILD-TYPE 
              18              560 
  RNF111 MUTATED RNF111 WILD-TYPE 
              18              560 
[1] "LAT2 MUTATION ANALYSIS"
[1] 3
  LAT2 MUTATED LAT2 WILD-TYPE 
            11            567 
  LAT2 MUTATED LAT2 WILD-TYPE 
            11            567 
[1] "ENTPD2 MUTATION ANALYSIS"
[1] 3
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               7              571 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               7              571 
[1] "CUL2 MUTATION ANALYSIS"
[1] 3
  CUL2 MUTATED CUL2 WILD-TYPE 
            10            568 
  CUL2 MUTATED CUL2 WILD-TYPE 
            10            568 
[1] "CROT MUTATION ANALYSIS"
[1] 3
  CROT MUTATED CROT WILD-TYPE 
            17            561 
  CROT MUTATED CROT WILD-TYPE 
            17            561 
[1] "PDS5B MUTATION ANALYSIS"
[1] 3
  PDS5B MUTATED PDS5B WILD-TYPE 
             27             551 
  PDS5B MUTATED PDS5B WILD-TYPE 
             27             551 
[1] "MTMR6 MUTATION ANALYSIS"
[1] 3
  MTMR6 MUTATED MTMR6 WILD-TYPE 
             13             565 
  MTMR6 MUTATED MTMR6 WILD-TYPE 
             13             565 
[1] "SYCP2L MUTATION ANALYSIS"
[1] 3
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              17              561 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              17              561 
[1] "NUB1 MUTATION ANALYSIS"
[1] 3
  NUB1 MUTATED NUB1 WILD-TYPE 
            12            566 
  NUB1 MUTATED NUB1 WILD-TYPE 
            12            566 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             46             532 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             46             532 
[1] "EVI5 MUTATION ANALYSIS"
[1] 3
  EVI5 MUTATED EVI5 WILD-TYPE 
            13            565 
  EVI5 MUTATED EVI5 WILD-TYPE 
            13            565 
[1] "TIMP3 MUTATION ANALYSIS"
[1] 3
  TIMP3 MUTATED TIMP3 WILD-TYPE 
             11             567 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
             11             567 
[1] "EIF4EBP2 MUTATION ANALYSIS"
[1] 3
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 7                571 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 7                571 
[1] "HOXB7 MUTATION ANALYSIS"
[1] 3
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              9             569 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              9             569 
[1] "CYP4B1 MUTATION ANALYSIS"
[1] 3
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
              11              567 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
              11              567 
[1] "PTOV1 MUTATION ANALYSIS"
[1] 3
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             13             565 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             13             565 
[1] "NOBOX MUTATION ANALYSIS"
[1] 3
  NOBOX MUTATED NOBOX WILD-TYPE 
             12             566 
  NOBOX MUTATED NOBOX WILD-TYPE 
             12             566 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              27              551 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              27              551 
[1] "DNAH5 MUTATION ANALYSIS"
[1] 3
  DNAH5 MUTATED DNAH5 WILD-TYPE 
            106             472 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
            106             472 
[1] "CLMN MUTATION ANALYSIS"
[1] 3
  CLMN MUTATED CLMN WILD-TYPE 
            17            561 
  CLMN MUTATED CLMN WILD-TYPE 
            17            561 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              7             571 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              7             571 
[1] "JHDM1D MUTATION ANALYSIS"
[1] 3
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              11              567 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              11              567 
[1] "FAM123C MUTATION ANALYSIS"
[1] 3
  FAM123C MUTATED FAM123C WILD-TYPE 
               17               561 
  FAM123C MUTATED FAM123C WILD-TYPE 
               17               561 
[1] "GLIPR1L2 MUTATION ANALYSIS"
[1] 3
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                15                563 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                15                563 
[1] "TBC1D26 MUTATION ANALYSIS"
[1] 3
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
                8               570 
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
                8               570 
[1] "BTNL3 MUTATION ANALYSIS"
[1] 3
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              6             572 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              6             572 
[1] "MYO9B MUTATION ANALYSIS"
[1] 3
  MYO9B MUTATED MYO9B WILD-TYPE 
             28             550 
  MYO9B MUTATED MYO9B WILD-TYPE 
             28             550 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             28             550 
  KDM3B MUTATED KDM3B WILD-TYPE 
             28             550 
[1] "USP35 MUTATION ANALYSIS"
[1] 3
  USP35 MUTATED USP35 WILD-TYPE 
             12             566 
  USP35 MUTATED USP35 WILD-TYPE 
             12             566 
[1] "ARAF MUTATION ANALYSIS"
[1] 3
  ARAF MUTATED ARAF WILD-TYPE 
            15            563 
  ARAF MUTATED ARAF WILD-TYPE 
            15            563 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             31             547 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             31             547 
[1] "TXLNG MUTATION ANALYSIS"
[1] 3
  TXLNG MUTATED TXLNG WILD-TYPE 
              9             569 
  TXLNG MUTATED TXLNG WILD-TYPE 
              9             569 
[1] "PIK3R3 MUTATION ANALYSIS"
[1] 3
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
              10              568 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
              10              568 
[1] "UBR3 MUTATION ANALYSIS"
[1] 3
  UBR3 MUTATED UBR3 WILD-TYPE 
            14            564 
  UBR3 MUTATED UBR3 WILD-TYPE 
            14            564 
[1] "RELT MUTATION ANALYSIS"
[1] 3
  RELT MUTATED RELT WILD-TYPE 
             8            570 
  RELT MUTATED RELT WILD-TYPE 
             8            570 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             10             568 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             10             568 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              18              560 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              18              560 
[1] "ADCY10 MUTATION ANALYSIS"
[1] 3
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              27              551 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              27              551 
[1] "INTS12 MUTATION ANALYSIS"
[1] 3
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              572 
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              572 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               11               567 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               11               567 
[1] "DYX1C1 MUTATION ANALYSIS"
[1] 3
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              13              565 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              13              565 
[1] "KIAA1522 MUTATION ANALYSIS"
[1] 3
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                13                565 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                13                565 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            572 
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            572 
[1] "GCDH MUTATION ANALYSIS"
[1] 3
  GCDH MUTATED GCDH WILD-TYPE 
             8            570 
  GCDH MUTATED GCDH WILD-TYPE 
             8            570 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              48              530 
  CREBBP MUTATED CREBBP WILD-TYPE 
              48              530 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             8            570 
  IDH2 MUTATED IDH2 WILD-TYPE 
             8            570 
[1] "POP1 MUTATION ANALYSIS"
[1] 3
  POP1 MUTATED POP1 WILD-TYPE 
            22            556 
  POP1 MUTATED POP1 WILD-TYPE 
            22            556 
[1] "NTAN1 MUTATION ANALYSIS"
[1] 3
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              7             571 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              7             571 
[1] "ZNF776 MUTATION ANALYSIS"
[1] 3
  ZNF776 MUTATED ZNF776 WILD-TYPE 
              10              568 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
              10              568 
[1] "USP15 MUTATION ANALYSIS"
[1] 3
  USP15 MUTATED USP15 WILD-TYPE 
              9             569 
  USP15 MUTATED USP15 WILD-TYPE 
              9             569 
[1] "IGFBP1 MUTATION ANALYSIS"
[1] 3
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              567 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              567 
[1] "GON4L MUTATION ANALYSIS"
[1] 3
  GON4L MUTATED GON4L WILD-TYPE 
             20             558 
  GON4L MUTATED GON4L WILD-TYPE 
             20             558 
[1] "C19ORF26 MUTATION ANALYSIS"
[1] 3
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                10                568 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                10                568 
[1] "PPP1R13B MUTATION ANALYSIS"
[1] 3
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                18                560 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                18                560 
[1] "CDC25C MUTATION ANALYSIS"
[1] 3
  CDC25C MUTATED CDC25C WILD-TYPE 
              11              567 
  CDC25C MUTATED CDC25C WILD-TYPE 
              11              567 
[1] "IFRD1 MUTATION ANALYSIS"
[1] 3
  IFRD1 MUTATED IFRD1 WILD-TYPE 
             10             568 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
             10             568 
[1] "TM6SF1 MUTATION ANALYSIS"
[1] 3
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               9              569 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               9              569 
[1] "CUBN MUTATION ANALYSIS"
[1] 3
  CUBN MUTATED CUBN WILD-TYPE 
            72            506 
  CUBN MUTATED CUBN WILD-TYPE 
            72            506 
[1] "EIF5A2 MUTATION ANALYSIS"
[1] 3
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               6              572 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               6              572 
[1] "HSPA14 MUTATION ANALYSIS"
[1] 3
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               7              571 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               7              571 
[1] "CHPF2 MUTATION ANALYSIS"
[1] 3
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             21             557 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             21             557 
[1] "FCN2 MUTATION ANALYSIS"
[1] 3
  FCN2 MUTATED FCN2 WILD-TYPE 
            14            564 
  FCN2 MUTATED FCN2 WILD-TYPE 
            14            564 
[1] "FGF7 MUTATION ANALYSIS"
[1] 3
  FGF7 MUTATED FGF7 WILD-TYPE 
             7            571 
  FGF7 MUTATED FGF7 WILD-TYPE 
             7            571 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                15                563 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                15                563 
[1] "LRP12 MUTATION ANALYSIS"
[1] 3
  LRP12 MUTATED LRP12 WILD-TYPE 
             39             539 
  LRP12 MUTATED LRP12 WILD-TYPE 
             39             539 
[1] "EFHA1 MUTATION ANALYSIS"
[1] 3
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             16             562 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             16             562 
[1] "GTF3C1 MUTATION ANALYSIS"
[1] 3
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              39              539 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              39              539 
[1] "KIAA0100 MUTATION ANALYSIS"
[1] 3
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                29                549 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                29                549 
[1] "RPS20 MUTATION ANALYSIS"
[1] 3
  RPS20 MUTATED RPS20 WILD-TYPE 
              4             574 
  RPS20 MUTATED RPS20 WILD-TYPE 
              4             574 
[1] "FASTKD1 MUTATION ANALYSIS"
[1] 3
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               14               564 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               14               564 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
             11             567 
  EOMES MUTATED EOMES WILD-TYPE 
             11             567 
[1] "ULK2 MUTATION ANALYSIS"
[1] 3
  ULK2 MUTATED ULK2 WILD-TYPE 
            13            565 
  ULK2 MUTATED ULK2 WILD-TYPE 
            13            565 
[1] "INSIG2 MUTATION ANALYSIS"
[1] 3
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               8              570 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               8              570 
[1] "DPAGT1 MUTATION ANALYSIS"
[1] 3
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               6              572 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               6              572 
[1] "C6ORF165 MUTATION ANALYSIS"
[1] 3
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                18                560 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                18                560 
[1] "YBX2 MUTATION ANALYSIS"
[1] 3
  YBX2 MUTATED YBX2 WILD-TYPE 
             8            570 
  YBX2 MUTATED YBX2 WILD-TYPE 
             8            570 
[1] "CCDC138 MUTATION ANALYSIS"
[1] 3
  CCDC138 MUTATED CCDC138 WILD-TYPE 
               11               567 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
               11               567 
[1] "METTL6 MUTATION ANALYSIS"
[1] 3
  METTL6 MUTATED METTL6 WILD-TYPE 
               5              573 
  METTL6 MUTATED METTL6 WILD-TYPE 
               5              573 
[1] "TRIP10 MUTATION ANALYSIS"
[1] 3
  TRIP10 MUTATED TRIP10 WILD-TYPE 
              15              563 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
              15              563 
[1] "C19ORF70 MUTATION ANALYSIS"
[1] 3
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 7                571 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 7                571 
[1] "C16ORF70 MUTATION ANALYSIS"
[1] 3
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 7                571 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 7                571 
[1] "MARCH7 MUTATION ANALYSIS"
[1] 3
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               9              569 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               9              569 
[1] "PPP1R15A MUTATION ANALYSIS"
[1] 3
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 7                571 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 7                571 
[1] "USP13 MUTATION ANALYSIS"
[1] 3
  USP13 MUTATED USP13 WILD-TYPE 
             13             565 
  USP13 MUTATED USP13 WILD-TYPE 
             13             565 
[1] "DOK1 MUTATION ANALYSIS"
[1] 3
  DOK1 MUTATED DOK1 WILD-TYPE 
             7            571 
  DOK1 MUTATED DOK1 WILD-TYPE 
             7            571 
[1] "CD33 MUTATION ANALYSIS"
[1] 3
  CD33 MUTATED CD33 WILD-TYPE 
            11            567 
  CD33 MUTATED CD33 WILD-TYPE 
            11            567 
[1] "MYLK3 MUTATION ANALYSIS"
[1] 3
  MYLK3 MUTATED MYLK3 WILD-TYPE 
             12             566 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
             12             566 
[1] "GPATCH4 MUTATION ANALYSIS"
[1] 3
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
               13               565 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
               13               565 
[1] "CADPS2 MUTATION ANALYSIS"
[1] 3
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              12              566 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              12              566 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             22             556 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             22             556 
[1] "GALNTL1 MUTATION ANALYSIS"
[1] 3
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               13               565 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               13               565 
[1] "RGS12 MUTATION ANALYSIS"
[1] 3
  RGS12 MUTATED RGS12 WILD-TYPE 
             38             540 
  RGS12 MUTATED RGS12 WILD-TYPE 
             38             540 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
               13               565 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
               13               565 
[1] "SPTA1 MUTATION ANALYSIS"
[1] 3
  SPTA1 MUTATED SPTA1 WILD-TYPE 
             94             484 
  SPTA1 MUTATED SPTA1 WILD-TYPE 
             94             484 
[1] "ZNF292 MUTATION ANALYSIS"
[1] 3
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              40              538 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              40              538 
[1] "ART5 MUTATION ANALYSIS"
[1] 3
  ART5 MUTATED ART5 WILD-TYPE 
             6            572 
  ART5 MUTATED ART5 WILD-TYPE 
             6            572 
[1] "CCDC80 MUTATION ANALYSIS"
[1] 3
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              23              555 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              23              555 
[1] "ACAT1 MUTATION ANALYSIS"
[1] 3
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              9             569 
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              9             569 
[1] "ZCRB1 MUTATION ANALYSIS"
[1] 3
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              7             571 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              7             571 
[1] "PLA2G7 MUTATION ANALYSIS"
[1] 3
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
               8              570 
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
               8              570 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            43            535 
  FBN3 MUTATED FBN3 WILD-TYPE 
            43            535 
[1] "CA2 MUTATION ANALYSIS"
[1] 3
  CA2 MUTATED CA2 WILD-TYPE 
            7           571 
  CA2 MUTATED CA2 WILD-TYPE 
            7           571 
[1] "GTF3C4 MUTATION ANALYSIS"
[1] 3
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              14              564 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              14              564 
[1] "TERF1 MUTATION ANALYSIS"
[1] 3
  TERF1 MUTATED TERF1 WILD-TYPE 
             10             568 
  TERF1 MUTATED TERF1 WILD-TYPE 
             10             568 
[1] "PLEKHO1 MUTATION ANALYSIS"
[1] 3
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                8               570 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                8               570 
[1] "FAM109B MUTATION ANALYSIS"
[1] 3
  FAM109B MUTATED FAM109B WILD-TYPE 
                8               570 
  FAM109B MUTATED FAM109B WILD-TYPE 
                8               570 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             69             509 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             69             509 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              18              560 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              18              560 
[1] "SFRS18 MUTATION ANALYSIS"
[1] 3
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              20              558 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              20              558 
[1] "PRPF4B MUTATION ANALYSIS"
[1] 3
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              12              566 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              12              566 
[1] "SP100 MUTATION ANALYSIS"
[1] 3
  SP100 MUTATED SP100 WILD-TYPE 
             25             553 
  SP100 MUTATED SP100 WILD-TYPE 
             25             553 
[1] "UHRF1BP1 MUTATION ANALYSIS"
[1] 3
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                21                557 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                21                557 
[1] "MRGPRF MUTATION ANALYSIS"
[1] 3
  MRGPRF MUTATED MRGPRF WILD-TYPE 
               7              571 
  MRGPRF MUTATED MRGPRF WILD-TYPE 
               7              571 
[1] "ELL2 MUTATION ANALYSIS"
[1] 3
  ELL2 MUTATED ELL2 WILD-TYPE 
            17            561 
  ELL2 MUTATED ELL2 WILD-TYPE 
            17            561 
[1] "PCGF3 MUTATION ANALYSIS"
[1] 3
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              7             571 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              7             571 
[1] "RSF1 MUTATION ANALYSIS"
[1] 3
  RSF1 MUTATED RSF1 WILD-TYPE 
            16            562 
  RSF1 MUTATED RSF1 WILD-TYPE 
            16            562 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
              37              541 
  ARID1B MUTATED ARID1B WILD-TYPE 
              37              541 
[1] "TNK2 MUTATION ANALYSIS"
[1] 3
  TNK2 MUTATED TNK2 WILD-TYPE 
            22            556 
  TNK2 MUTATED TNK2 WILD-TYPE 
            22            556 
[1] "ABCE1 MUTATION ANALYSIS"
[1] 3
  ABCE1 MUTATED ABCE1 WILD-TYPE 
             12             566 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
             12             566 
[1] "PNMT MUTATION ANALYSIS"
[1] 3
  PNMT MUTATED PNMT WILD-TYPE 
            11            567 
  PNMT MUTATED PNMT WILD-TYPE 
            11            567 
[1] "C8ORF46 MUTATION ANALYSIS"
[1] 3
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
                9               569 
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
                9               569 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
            17            561 
  NOX5 MUTATED NOX5 WILD-TYPE 
            17            561 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
             9            569 
  SGK3 MUTATED SGK3 WILD-TYPE 
             9            569 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              22              556 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              22              556 
[1] "TAS2R42 MUTATION ANALYSIS"
[1] 3
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               572 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               572 
[1] "CDKL3 MUTATION ANALYSIS"
[1] 3
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              8             570 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              8             570 
[1] "USP21 MUTATION ANALYSIS"
[1] 3
  USP21 MUTATED USP21 WILD-TYPE 
             15             563 
  USP21 MUTATED USP21 WILD-TYPE 
             15             563 
[1] "SERPINB12 MUTATION ANALYSIS"
[1] 3
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  9                 569 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  9                 569 
[1] "GCG MUTATION ANALYSIS"
[1] 3
  GCG MUTATED GCG WILD-TYPE 
           10           568 
  GCG MUTATED GCG WILD-TYPE 
           10           568 
[1] "DYRK4 MUTATION ANALYSIS"
[1] 3
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             11             567 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             11             567 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              12              566 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              12              566 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               9              569 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               9              569 
[1] "CNNM2 MUTATION ANALYSIS"
[1] 3
  CNNM2 MUTATED CNNM2 WILD-TYPE 
             18             560 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
             18             560 
[1] "CNNM1 MUTATION ANALYSIS"
[1] 3
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             13             565 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             13             565 
[1] "AFF3 MUTATION ANALYSIS"
[1] 3
  AFF3 MUTATED AFF3 WILD-TYPE 
            34            544 
  AFF3 MUTATED AFF3 WILD-TYPE 
            34            544 
[1] "PPIAL4A MUTATION ANALYSIS"
[1] 3
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               575 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               575 
[1] "MKL2 MUTATION ANALYSIS"
[1] 3
  MKL2 MUTATED MKL2 WILD-TYPE 
            18            560 
  MKL2 MUTATED MKL2 WILD-TYPE 
            18            560 
[1] "PLAG1 MUTATION ANALYSIS"
[1] 3
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             14             564 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             14             564 
[1] "EXPH5 MUTATION ANALYSIS"
[1] 3
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             17             561 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             17             561 
[1] "ARMC4 MUTATION ANALYSIS"
[1] 3
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             26             552 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             26             552 
[1] "MAGEE2 MUTATION ANALYSIS"
[1] 3
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              17              561 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              17              561 
[1] "FGF1 MUTATION ANALYSIS"
[1] 3
  FGF1 MUTATED FGF1 WILD-TYPE 
             5            573 
  FGF1 MUTATED FGF1 WILD-TYPE 
             5            573 
[1] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              25              553 
  KIF13A MUTATED KIF13A WILD-TYPE 
              25              553 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              571 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              571 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               16               562 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               16               562 
[1] "PRRG3 MUTATION ANALYSIS"
[1] 3
  PRRG3 MUTATED PRRG3 WILD-TYPE 
             10             568 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
             10             568 
[1] "CSGALNACT1 MUTATION ANALYSIS"
[1] 3
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  19                  559 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  19                  559 
[1] "BEND3 MUTATION ANALYSIS"
[1] 3
  BEND3 MUTATED BEND3 WILD-TYPE 
             14             564 
  BEND3 MUTATED BEND3 WILD-TYPE 
             14             564 
[1] "TPD52L1 MUTATION ANALYSIS"
[1] 3
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
               13               565 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
               13               565 
[1] "R3HDM2 MUTATION ANALYSIS"
[1] 3
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
              15              563 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
              15              563 
[1] "INPP5F MUTATION ANALYSIS"
[1] 3
  INPP5F MUTATED INPP5F WILD-TYPE 
              21              557 
  INPP5F MUTATED INPP5F WILD-TYPE 
              21              557 
[1] "KIAA1632 MUTATION ANALYSIS"
[1] 3
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                33                545 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                33                545 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
               11               567 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
               11               567 
[1] "PHACTR4 MUTATION ANALYSIS"
[1] 3
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
               12               566 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
               12               566 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              9             569 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              9             569 
[1] "SLC38A6 MUTATION ANALYSIS"
[1] 3
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
               10               568 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
               10               568 
[1] "PDS5A MUTATION ANALYSIS"
[1] 3
  PDS5A MUTATED PDS5A WILD-TYPE 
             24             554 
  PDS5A MUTATED PDS5A WILD-TYPE 
             24             554 
[1] "KLHL14 MUTATION ANALYSIS"
[1] 3
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              20              558 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              20              558 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          38          540 
  F8 MUTATED F8 WILD-TYPE 
          38          540 
[1] "PLAGL2 MUTATION ANALYSIS"
[1] 3
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               9              569 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               9              569 
[1] "C8ORF38 MUTATION ANALYSIS"
[1] 3
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                9               569 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                9               569 
[1] "SIX3 MUTATION ANALYSIS"
[1] 3
  SIX3 MUTATED SIX3 WILD-TYPE 
            12            566 
  SIX3 MUTATED SIX3 WILD-TYPE 
            12            566 
[1] "ACAA2 MUTATION ANALYSIS"
[1] 3
  ACAA2 MUTATED ACAA2 WILD-TYPE 
             12             566 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
             12             566 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             14             564 
  DDX43 MUTATED DDX43 WILD-TYPE 
             14             564 
[1] "ASTE1 MUTATION ANALYSIS"
[1] 3
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             19             559 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             19             559 
[1] "CDC42EP1 MUTATION ANALYSIS"
[1] 3
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                574 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                574 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             15             563 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             15             563 
[1] "NHLRC1 MUTATION ANALYSIS"
[1] 3
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              12              566 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              12              566 
[1] "RNASEH2B MUTATION ANALYSIS"
[1] 3
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 4                574 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 4                574 
[1] "HRNR MUTATION ANALYSIS"
[1] 3
  HRNR MUTATED HRNR WILD-TYPE 
            50            528 
  HRNR MUTATED HRNR WILD-TYPE 
            50            528 
[1] "RDBP MUTATION ANALYSIS"
[1] 3
  RDBP MUTATED RDBP WILD-TYPE 
            13            565 
  RDBP MUTATED RDBP WILD-TYPE 
            13            565 
[1] "TNFSF13 MUTATION ANALYSIS"
[1] 3
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               575 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               575 
[1] "MCEE MUTATION ANALYSIS"
[1] 3
  MCEE MUTATED MCEE WILD-TYPE 
             6            572 
  MCEE MUTATED MCEE WILD-TYPE 
             6            572 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
            11            567 
  OTX2 MUTATED OTX2 WILD-TYPE 
            11            567 
[1] "HAND2 MUTATION ANALYSIS"
[1] 3
  HAND2 MUTATED HAND2 WILD-TYPE 
              7             571 
  HAND2 MUTATED HAND2 WILD-TYPE 
              7             571 
[1] "SLC12A7 MUTATION ANALYSIS"
[1] 3
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               30               548 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               30               548 
[1] "CD1E MUTATION ANALYSIS"
[1] 3
  CD1E MUTATED CD1E WILD-TYPE 
            17            561 
  CD1E MUTATED CD1E WILD-TYPE 
            17            561 
[1] "HEXDC MUTATION ANALYSIS"
[1] 3
  HEXDC MUTATED HEXDC WILD-TYPE 
              9             569 
  HEXDC MUTATED HEXDC WILD-TYPE 
              9             569 
[1] "C11ORF70 MUTATION ANALYSIS"
[1] 3
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 5                573 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 5                573 
[1] "GRXCR1 MUTATION ANALYSIS"
[1] 3
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
              18              560 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
              18              560 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
              13              565 
  GPR141 MUTATED GPR141 WILD-TYPE 
              13              565 
[1] "NEK8 MUTATION ANALYSIS"
[1] 3
  NEK8 MUTATED NEK8 WILD-TYPE 
            14            564 
  NEK8 MUTATED NEK8 WILD-TYPE 
            14            564 
[1] "KRT222 MUTATION ANALYSIS"
[1] 3
  KRT222 MUTATED KRT222 WILD-TYPE 
               9              569 
  KRT222 MUTATED KRT222 WILD-TYPE 
               9              569 
[1] "GIMAP7 MUTATION ANALYSIS"
[1] 3
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               6              572 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               6              572 
[1] "PRMT3 MUTATION ANALYSIS"
[1] 3
  PRMT3 MUTATED PRMT3 WILD-TYPE 
             11             567 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
             11             567 
[1] "C20ORF160 MUTATION ANALYSIS"
[1] 3
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 570 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 570 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              570 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              570 
[1] "PMEPA1 MUTATION ANALYSIS"
[1] 3
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               7              571 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               7              571 
[1] "PTPLA MUTATION ANALYSIS"
[1] 3
  PTPLA MUTATED PTPLA WILD-TYPE 
              7             571 
  PTPLA MUTATED PTPLA WILD-TYPE 
              7             571 
[1] "PNLIPRP3 MUTATION ANALYSIS"
[1] 3
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
                17                561 
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
                17                561 
[1] "KIAA1797 MUTATION ANALYSIS"
[1] 3
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                25                553 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                25                553 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              11              567 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              11              567 
[1] "CYP51A1 MUTATION ANALYSIS"
[1] 3
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
               13               565 
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
               13               565 
[1] "AMZ2 MUTATION ANALYSIS"
[1] 3
  AMZ2 MUTATED AMZ2 WILD-TYPE 
             5            573 
  AMZ2 MUTATED AMZ2 WILD-TYPE 
             5            573 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
             8            570 
  CD58 MUTATED CD58 WILD-TYPE 
             8            570 
[1] "SDAD1 MUTATION ANALYSIS"
[1] 3
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              9             569 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              9             569 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                8               570 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                8               570 
[1] "ACTR8 MUTATION ANALYSIS"
[1] 3
  ACTR8 MUTATED ACTR8 WILD-TYPE 
             12             566 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
             12             566 
[1] "IFT140 MUTATION ANALYSIS"
[1] 3
  IFT140 MUTATED IFT140 WILD-TYPE 
              23              555 
  IFT140 MUTATED IFT140 WILD-TYPE 
              23              555 
[1] "GSDMC MUTATION ANALYSIS"
[1] 3
  GSDMC MUTATED GSDMC WILD-TYPE 
             19             559 
  GSDMC MUTATED GSDMC WILD-TYPE 
             19             559 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            63            515 
  ANK3 MUTATED ANK3 WILD-TYPE 
            63            515 
[1] "TMEM87B MUTATION ANALYSIS"
[1] 3
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                6               572 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                6               572 
[1] "CCDC103 MUTATION ANALYSIS"
[1] 3
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                5               573 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                5               573 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             16             562 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             16             562 
[1] "CTSD MUTATION ANALYSIS"
[1] 3
  CTSD MUTATED CTSD WILD-TYPE 
            11            567 
  CTSD MUTATED CTSD WILD-TYPE 
            11            567 
[1] "BAT4 MUTATION ANALYSIS"
[1] 3
  BAT4 MUTATED BAT4 WILD-TYPE 
             6            572 
  BAT4 MUTATED BAT4 WILD-TYPE 
             6            572 
[1] "OSTALPHA MUTATION ANALYSIS"
[1] 3
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 5                573 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 5                573 
[1] "FNDC4 MUTATION ANALYSIS"
[1] 3
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              6             572 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              6             572 
[1] "FBXO48 MUTATION ANALYSIS"
[1] 3
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               5              573 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               5              573 
[1] "UGT1A4 MUTATION ANALYSIS"
[1] 3
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              12              566 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              12              566 
[1] "FAM113A MUTATION ANALYSIS"
[1] 3
  FAM113A MUTATED FAM113A WILD-TYPE 
               10               568 
  FAM113A MUTATED FAM113A WILD-TYPE 
               10               568 
[1] "BAT3 MUTATION ANALYSIS"
[1] 3
  BAT3 MUTATED BAT3 WILD-TYPE 
            15            563 
  BAT3 MUTATED BAT3 WILD-TYPE 
            15            563 
[1] "TRIML2 MUTATION ANALYSIS"
[1] 3
  TRIML2 MUTATED TRIML2 WILD-TYPE 
              24              554 
  TRIML2 MUTATED TRIML2 WILD-TYPE 
              24              554 
[1] "CTSA MUTATION ANALYSIS"
[1] 3
  CTSA MUTATED CTSA WILD-TYPE 
             5            573 
  CTSA MUTATED CTSA WILD-TYPE 
             5            573 
[1] "ATP6V1C2 MUTATION ANALYSIS"
[1] 3
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                16                562 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                16                562 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              19              559 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              19              559 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            10            568 
  RBMX MUTATED RBMX WILD-TYPE 
            10            568 
[1] "GNPNAT1 MUTATION ANALYSIS"
[1] 3
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                6               572 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                6               572 
[1] "PTPN23 MUTATION ANALYSIS"
[1] 3
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              26              552 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              26              552 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             11             567 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             11             567 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                11                567 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                11                567 
[1] "ACTG2 MUTATION ANALYSIS"
[1] 3
  ACTG2 MUTATED ACTG2 WILD-TYPE 
             12             566 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
             12             566 
[1] "SMTN MUTATION ANALYSIS"
[1] 3
  SMTN MUTATED SMTN WILD-TYPE 
            21            557 
  SMTN MUTATED SMTN WILD-TYPE 
            21            557 
[1] "C9ORF46 MUTATION ANALYSIS"
[1] 3
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                5               573 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                5               573 
[1] "KCNMB2 MUTATION ANALYSIS"
[1] 3
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
              10              568 
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
              10              568 
[1] "C9ORF152 MUTATION ANALYSIS"
[1] 3
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 4                574 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 4                574 
[1] "ZFP36L1 MUTATION ANALYSIS"
[1] 3
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                5               573 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                5               573 
[1] "HTR1F MUTATION ANALYSIS"
[1] 3
  HTR1F MUTATED HTR1F WILD-TYPE 
              9             569 
  HTR1F MUTATED HTR1F WILD-TYPE 
              9             569 
[1] "CDH24 MUTATION ANALYSIS"
[1] 3
  CDH24 MUTATED CDH24 WILD-TYPE 
             14             564 
  CDH24 MUTATED CDH24 WILD-TYPE 
             14             564 
[1] "HERC1 MUTATION ANALYSIS"
[1] 3
  HERC1 MUTATED HERC1 WILD-TYPE 
             49             529 
  HERC1 MUTATED HERC1 WILD-TYPE 
             49             529 
[1] "C1ORF14 MUTATION ANALYSIS"
[1] 3
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               16               562 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               16               562 
[1] "PRPF40B MUTATION ANALYSIS"
[1] 3
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               21               557 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               21               557 
[1] "SERPINA1 MUTATION ANALYSIS"
[1] 3
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 9                569 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 9                569 
[1] "FZR1 MUTATION ANALYSIS"
[1] 3
  FZR1 MUTATED FZR1 WILD-TYPE 
            12            566 
  FZR1 MUTATED FZR1 WILD-TYPE 
            12            566 
[1] "BRF1 MUTATION ANALYSIS"
[1] 3
  BRF1 MUTATED BRF1 WILD-TYPE 
            11            567 
  BRF1 MUTATED BRF1 WILD-TYPE 
            11            567 
[1] "ESRP1 MUTATION ANALYSIS"
[1] 3
  ESRP1 MUTATED ESRP1 WILD-TYPE 
             11             567 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
             11             567 
[1] "P2RY4 MUTATION ANALYSIS"
[1] 3
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             13             565 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             13             565 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             36             542 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             36             542 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
           15           563 
  IDE MUTATED IDE WILD-TYPE 
           15           563 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 7                571 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 7                571 
[1] "MARVELD3 MUTATION ANALYSIS"
[1] 3
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                14                564 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                14                564 
[1] "C1ORF141 MUTATION ANALYSIS"
[1] 3
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                12                566 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                12                566 
[1] "PKN1 MUTATION ANALYSIS"
[1] 3
  PKN1 MUTATED PKN1 WILD-TYPE 
            11            567 
  PKN1 MUTATED PKN1 WILD-TYPE 
            11            567 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
             23             555 
  PCF11 MUTATED PCF11 WILD-TYPE 
             23             555 
[1] "RASSF5 MUTATION ANALYSIS"
[1] 3
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               6              572 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               6              572 
[1] "SLC10A6 MUTATION ANALYSIS"
[1] 3
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
               10               568 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
               10               568 
[1] "OSGEPL1 MUTATION ANALYSIS"
[1] 3
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               574 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               574 
[1] "TSSK2 MUTATION ANALYSIS"
[1] 3
  TSSK2 MUTATED TSSK2 WILD-TYPE 
             10             568 
  TSSK2 MUTATED TSSK2 WILD-TYPE 
             10             568 
[1] "DNAJC1 MUTATION ANALYSIS"
[1] 3
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              14              564 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              14              564 
[1] "KPNA3 MUTATION ANALYSIS"
[1] 3
  KPNA3 MUTATED KPNA3 WILD-TYPE 
             10             568 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
             10             568 
[1] "RRH MUTATION ANALYSIS"
[1] 3
  RRH MUTATED RRH WILD-TYPE 
            5           573 
  RRH MUTATED RRH WILD-TYPE 
            5           573 
[1] "SRP14 MUTATION ANALYSIS"
[1] 3
  SRP14 MUTATED SRP14 WILD-TYPE 
              3             575 
  SRP14 MUTATED SRP14 WILD-TYPE 
              3             575 
[1] "PDE8A MUTATION ANALYSIS"
[1] 3
  PDE8A MUTATED PDE8A WILD-TYPE 
             14             564 
  PDE8A MUTATED PDE8A WILD-TYPE 
             14             564 
[1] "ARPC5L MUTATION ANALYSIS"
[1] 3
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               3              575 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               3              575 
[1] "UPK2 MUTATION ANALYSIS"
[1] 3
  UPK2 MUTATED UPK2 WILD-TYPE 
             5            573 
  UPK2 MUTATED UPK2 WILD-TYPE 
             5            573 
[1] "NEUROD6 MUTATION ANALYSIS"
[1] 3
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                7               571 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                7               571 
[1] "KIF20B MUTATION ANALYSIS"
[1] 3
  KIF20B MUTATED KIF20B WILD-TYPE 
              22              556 
  KIF20B MUTATED KIF20B WILD-TYPE 
              22              556 
[1] "NPHS1 MUTATION ANALYSIS"
[1] 3
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             21             557 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             21             557 
[1] "NUFIP2 MUTATION ANALYSIS"
[1] 3
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               8              570 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               8              570 
[1] "MED23 MUTATION ANALYSIS"
[1] 3
  MED23 MUTATED MED23 WILD-TYPE 
             23             555 
  MED23 MUTATED MED23 WILD-TYPE 
             23             555 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              13              565 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              13              565 
[1] "SH2B1 MUTATION ANALYSIS"
[1] 3
  SH2B1 MUTATED SH2B1 WILD-TYPE 
             13             565 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
             13             565 
[1] "P2RX1 MUTATION ANALYSIS"
[1] 3
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              5             573 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              5             573 
[1] "SAP30BP MUTATION ANALYSIS"
[1] 3
  SAP30BP MUTATED SAP30BP WILD-TYPE 
                7               571 
  SAP30BP MUTATED SAP30BP WILD-TYPE 
                7               571 
[1] "NCEH1 MUTATION ANALYSIS"
[1] 3
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              8             570 
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              8             570 
[1] "ANTXR1 MUTATION ANALYSIS"
[1] 3
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              12              566 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              12              566 
[1] "BLMH MUTATION ANALYSIS"
[1] 3
  BLMH MUTATED BLMH WILD-TYPE 
             5            573 
  BLMH MUTATED BLMH WILD-TYPE 
             5            573 
[1] "ZNF207 MUTATION ANALYSIS"
[1] 3
  ZNF207 MUTATED ZNF207 WILD-TYPE 
              10              568 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
              10              568 
[1] "SIGLEC10 MUTATION ANALYSIS"
[1] 3
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                16                562 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                16                562 
[1] "FAHD2A MUTATION ANALYSIS"
[1] 3
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               9              569 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               9              569 
[1] "NUFIP1 MUTATION ANALYSIS"
[1] 3
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
              13              565 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
              13              565 
[1] "PYHIN1 MUTATION ANALYSIS"
[1] 3
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              14              564 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              14              564 
[1] "KIAA1462 MUTATION ANALYSIS"
[1] 3
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                26                552 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                26                552 
[1] "MGST2 MUTATION ANALYSIS"
[1] 3
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             575 
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             575 
[1] "ZNF285 MUTATION ANALYSIS"
[1] 3
  ZNF285 MUTATED ZNF285 WILD-TYPE 
              14              564 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
              14              564 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
             26             552 
  OPLAH MUTATED OPLAH WILD-TYPE 
             26             552 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           31           547 
  NRK MUTATED NRK WILD-TYPE 
           31           547 
[1] "AP3M2 MUTATION ANALYSIS"
[1] 3
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             13             565 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             13             565 
[1] "CD93 MUTATION ANALYSIS"
[1] 3
  CD93 MUTATED CD93 WILD-TYPE 
            24            554 
  CD93 MUTATED CD93 WILD-TYPE 
            24            554 
[1] "ZBTB38 MUTATION ANALYSIS"
[1] 3
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              22              556 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              22              556 
[1] "PRAMEF14 MUTATION ANALYSIS"
[1] 3
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 6                572 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 6                572 
[1] "ANKRD28 MUTATION ANALYSIS"
[1] 3
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               17               561 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               17               561 
[1] "MKRN3 MUTATION ANALYSIS"
[1] 3
  MKRN3 MUTATED MKRN3 WILD-TYPE 
             24             554 
  MKRN3 MUTATED MKRN3 WILD-TYPE 
             24             554 
[1] "MAN1C1 MUTATION ANALYSIS"
[1] 3
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
              11              567 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
              11              567 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             11             567 
  STK11 MUTATED STK11 WILD-TYPE 
             11             567 
[1] "VPS13A MUTATION ANALYSIS"
[1] 3
  VPS13A MUTATED VPS13A WILD-TYPE 
              42              536 
  VPS13A MUTATED VPS13A WILD-TYPE 
              42              536 
[1] "BEND5 MUTATION ANALYSIS"
[1] 3
  BEND5 MUTATED BEND5 WILD-TYPE 
              9             569 
  BEND5 MUTATED BEND5 WILD-TYPE 
              9             569 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             22             556 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             22             556 
[1] "NFE2L1 MUTATION ANALYSIS"
[1] 3
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
              15              563 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
              15              563 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             23             555 
  ITGAV MUTATED ITGAV WILD-TYPE 
             23             555 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             42             536 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             42             536 
[1] "CWF19L2 MUTATION ANALYSIS"
[1] 3
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               20               558 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               20               558 
[1] "GBP3 MUTATION ANALYSIS"
[1] 3
  GBP3 MUTATED GBP3 WILD-TYPE 
             6            572 
  GBP3 MUTATED GBP3 WILD-TYPE 
             6            572 
[1] "FAM186B MUTATION ANALYSIS"
[1] 3
  FAM186B MUTATED FAM186B WILD-TYPE 
               13               565 
  FAM186B MUTATED FAM186B WILD-TYPE 
               13               565 
[1] "DOCK9 MUTATION ANALYSIS"
[1] 3
  DOCK9 MUTATED DOCK9 WILD-TYPE 
             22             556 
  DOCK9 MUTATED DOCK9 WILD-TYPE 
             22             556 
[1] "TMPRSS5 MUTATION ANALYSIS"
[1] 3
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                4               574 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                4               574 
[1] "FAM104A MUTATION ANALYSIS"
[1] 3
  FAM104A MUTATED FAM104A WILD-TYPE 
                5               573 
  FAM104A MUTATED FAM104A WILD-TYPE 
                5               573 
[1] "EFHD1 MUTATION ANALYSIS"
[1] 3
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              7             571 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              7             571 
[1] "CD4 MUTATION ANALYSIS"
[1] 3
  CD4 MUTATED CD4 WILD-TYPE 
           11           567 
  CD4 MUTATED CD4 WILD-TYPE 
           11           567 
[1] "OR6C65 MUTATION ANALYSIS"
[1] 3
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               5              573 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               5              573 
[1] "SPATA2L MUTATION ANALYSIS"
[1] 3
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                8               570 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                8               570 
[1] "GPR115 MUTATION ANALYSIS"
[1] 3
  GPR115 MUTATED GPR115 WILD-TYPE 
               6              572 
  GPR115 MUTATED GPR115 WILD-TYPE 
               6              572 
[1] "TRPM6 MUTATION ANALYSIS"
[1] 3
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             29             549 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             29             549 
[1] "MKL1 MUTATION ANALYSIS"
[1] 3
  MKL1 MUTATED MKL1 WILD-TYPE 
            17            561 
  MKL1 MUTATED MKL1 WILD-TYPE 
            17            561 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              15              563 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              15              563 
[1] "SOAT1 MUTATION ANALYSIS"
[1] 3
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             11             567 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             11             567 
[1] "TNKS1BP1 MUTATION ANALYSIS"
[1] 3
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                30                548 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                30                548 
[1] "NOB1 MUTATION ANALYSIS"
[1] 3
  NOB1 MUTATED NOB1 WILD-TYPE 
             8            570 
  NOB1 MUTATED NOB1 WILD-TYPE 
             8            570 
[1] "DENND4C MUTATION ANALYSIS"
[1] 3
  DENND4C MUTATED DENND4C WILD-TYPE 
               20               558 
  DENND4C MUTATED DENND4C WILD-TYPE 
               20               558 
[1] "EFNA4 MUTATION ANALYSIS"
[1] 3
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              6             572 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              6             572 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             567 
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             567 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                574 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                574 
[1] "C9ORF41 MUTATION ANALYSIS"
[1] 3
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                7               571 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                7               571 
[1] "EPB41 MUTATION ANALYSIS"
[1] 3
  EPB41 MUTATED EPB41 WILD-TYPE 
             14             564 
  EPB41 MUTATED EPB41 WILD-TYPE 
             14             564 
[1] "DENND2A MUTATION ANALYSIS"
[1] 3
  DENND2A MUTATED DENND2A WILD-TYPE 
               21               557 
  DENND2A MUTATED DENND2A WILD-TYPE 
               21               557 
[1] "SLC45A4 MUTATION ANALYSIS"
[1] 3
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               24               554 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               24               554 
[1] "ALDH3A1 MUTATION ANALYSIS"
[1] 3
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               14               564 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               14               564 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              17              561 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              17              561 
[1] "PCCA MUTATION ANALYSIS"
[1] 3
  PCCA MUTATED PCCA WILD-TYPE 
            15            563 
  PCCA MUTATED PCCA WILD-TYPE 
            15            563 
[1] "WDR11 MUTATION ANALYSIS"
[1] 3
  WDR11 MUTATED WDR11 WILD-TYPE 
             12             566 
  WDR11 MUTATED WDR11 WILD-TYPE 
             12             566 
[1] "PSMC3 MUTATION ANALYSIS"
[1] 3
  PSMC3 MUTATED PSMC3 WILD-TYPE 
             10             568 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
             10             568 
[1] "STEAP2 MUTATION ANALYSIS"
[1] 3
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               7              571 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               7              571 
[1] "CUL1 MUTATION ANALYSIS"
[1] 3
  CUL1 MUTATED CUL1 WILD-TYPE 
            24            554 
  CUL1 MUTATED CUL1 WILD-TYPE 
            24            554 
[1] "TH1L MUTATION ANALYSIS"
[1] 3
  TH1L MUTATED TH1L WILD-TYPE 
            14            564 
  TH1L MUTATED TH1L WILD-TYPE 
            14            564 
[1] "FARSA MUTATION ANALYSIS"
[1] 3
  FARSA MUTATED FARSA WILD-TYPE 
              8             570 
  FARSA MUTATED FARSA WILD-TYPE 
              8             570 
[1] "EDNRB MUTATION ANALYSIS"
[1] 3
  EDNRB MUTATED EDNRB WILD-TYPE 
             31             547 
  EDNRB MUTATED EDNRB WILD-TYPE 
             31             547 
[1] "SMAD7 MUTATION ANALYSIS"
[1] 3
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              7             571 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              7             571 
[1] "PABPC4 MUTATION ANALYSIS"
[1] 3
  PABPC4 MUTATED PABPC4 WILD-TYPE 
              11              567 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
              11              567 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               568 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               568 
[1] "KIAA1539 MUTATION ANALYSIS"
[1] 3
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                14                564 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                14                564 
[1] "DNAJB13 MUTATION ANALYSIS"
[1] 3
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                6               572 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                6               572 
[1] "ZCCHC11 MUTATION ANALYSIS"
[1] 3
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               24               554 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               24               554 
[1] "DDX60 MUTATION ANALYSIS"
[1] 3
  DDX60 MUTATED DDX60 WILD-TYPE 
             23             555 
  DDX60 MUTATED DDX60 WILD-TYPE 
             23             555 
[1] "SCN10A MUTATION ANALYSIS"
[1] 3
  SCN10A MUTATED SCN10A WILD-TYPE 
              47              531 
  SCN10A MUTATED SCN10A WILD-TYPE 
              47              531 
[1] "BRDT MUTATION ANALYSIS"
[1] 3
  BRDT MUTATED BRDT WILD-TYPE 
            14            564 
  BRDT MUTATED BRDT WILD-TYPE 
            14            564 
[1] "CCAR1 MUTATION ANALYSIS"
[1] 3
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             22             556 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             22             556 
[1] "MCCC2 MUTATION ANALYSIS"
[1] 3
  MCCC2 MUTATED MCCC2 WILD-TYPE 
              9             569 
  MCCC2 MUTATED MCCC2 WILD-TYPE 
              9             569 
[1] "AKAP13 MUTATION ANALYSIS"
[1] 3
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              44              534 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              44              534 
[1] "CEP250 MUTATION ANALYSIS"
[1] 3
  CEP250 MUTATED CEP250 WILD-TYPE 
              28              550 
  CEP250 MUTATED CEP250 WILD-TYPE 
              28              550 
[1] "AGAP5 MUTATION ANALYSIS"
[1] 3
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             570 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             570 
[1] "SCLY MUTATION ANALYSIS"
[1] 3
  SCLY MUTATED SCLY WILD-TYPE 
             6            572 
  SCLY MUTATED SCLY WILD-TYPE 
             6            572 
[1] "KRT23 MUTATION ANALYSIS"
[1] 3
  KRT23 MUTATED KRT23 WILD-TYPE 
             17             561 
  KRT23 MUTATED KRT23 WILD-TYPE 
             17             561 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               17               561 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               17               561 
[1] "GTF3C3 MUTATION ANALYSIS"
[1] 3
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              20              558 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              20              558 
[1] "CCDC27 MUTATION ANALYSIS"
[1] 3
  CCDC27 MUTATED CCDC27 WILD-TYPE 
              12              566 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
              12              566 
[1] "SH3BP2 MUTATION ANALYSIS"
[1] 3
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               7              571 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               7              571 
[1] "TIGD7 MUTATION ANALYSIS"
[1] 3
  TIGD7 MUTATED TIGD7 WILD-TYPE 
             12             566 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
             12             566 
[1] "B4GALNT4 MUTATION ANALYSIS"
[1] 3
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                19                559 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                19                559 
[1] "ARHGEF11 MUTATION ANALYSIS"
[1] 3
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                22                556 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                22                556 
[1] "SHMT2 MUTATION ANALYSIS"
[1] 3
  SHMT2 MUTATED SHMT2 WILD-TYPE 
             12             566 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
             12             566 
[1] "USP30 MUTATION ANALYSIS"
[1] 3
  USP30 MUTATED USP30 WILD-TYPE 
             10             568 
  USP30 MUTATED USP30 WILD-TYPE 
             10             568 
[1] "ASPN MUTATION ANALYSIS"
[1] 3
  ASPN MUTATED ASPN WILD-TYPE 
             7            571 
  ASPN MUTATED ASPN WILD-TYPE 
             7            571 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             24             554 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             24             554 
[1] "CNOT6 MUTATION ANALYSIS"
[1] 3
  CNOT6 MUTATED CNOT6 WILD-TYPE 
             10             568 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
             10             568 
[1] "KIFAP3 MUTATION ANALYSIS"
[1] 3
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              15              563 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              15              563 
[1] "MFN1 MUTATION ANALYSIS"
[1] 3
  MFN1 MUTATED MFN1 WILD-TYPE 
            12            566 
  MFN1 MUTATED MFN1 WILD-TYPE 
            12            566 
[1] "MZF1 MUTATION ANALYSIS"
[1] 3
  MZF1 MUTATED MZF1 WILD-TYPE 
            15            563 
  MZF1 MUTATED MZF1 WILD-TYPE 
            15            563 
[1] "SCAMP2 MUTATION ANALYSIS"
[1] 3
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               8              570 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               8              570 
[1] "LCE1A MUTATION ANALYSIS"
[1] 3
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             574 
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             574 
[1] "TMEM55A MUTATION ANALYSIS"
[1] 3
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                5               573 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                5               573 
[1] "PNPLA7 MUTATION ANALYSIS"
[1] 3
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              26              552 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              26              552 
[1] "STAT6 MUTATION ANALYSIS"
[1] 3
  STAT6 MUTATED STAT6 WILD-TYPE 
              9             569 
  STAT6 MUTATED STAT6 WILD-TYPE 
              9             569 
[1] "STK33 MUTATION ANALYSIS"
[1] 3
  STK33 MUTATED STK33 WILD-TYPE 
             13             565 
  STK33 MUTATED STK33 WILD-TYPE 
             13             565 
[1] "DNAJA1 MUTATION ANALYSIS"
[1] 3
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
              12              566 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
              12              566 
[1] "IFITM1 MUTATION ANALYSIS"
[1] 3
  IFITM1 MUTATED IFITM1 WILD-TYPE 
               5              573 
  IFITM1 MUTATED IFITM1 WILD-TYPE 
               5              573 
[1] "FAM151A MUTATION ANALYSIS"
[1] 3
  FAM151A MUTATED FAM151A WILD-TYPE 
                8               570 
  FAM151A MUTATED FAM151A WILD-TYPE 
                8               570 
[1] "HMGCLL1 MUTATION ANALYSIS"
[1] 3
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               568 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               568 
[1] "GIPC3 MUTATION ANALYSIS"
[1] 3
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              9             569 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              9             569 
[1] "EFHA2 MUTATION ANALYSIS"
[1] 3
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             15             563 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             15             563 
[1] "PSD3 MUTATION ANALYSIS"
[1] 3
  PSD3 MUTATED PSD3 WILD-TYPE 
            20            558 
  PSD3 MUTATED PSD3 WILD-TYPE 
            20            558 
[1] "HSPB8 MUTATION ANALYSIS"
[1] 3
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             572 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             572 
[1] "CASKIN2 MUTATION ANALYSIS"
[1] 3
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               16               562 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               16               562 
[1] "IFI27L2 MUTATION ANALYSIS"
[1] 3
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                3               575 
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                3               575 
[1] "PKN3 MUTATION ANALYSIS"
[1] 3
  PKN3 MUTATED PKN3 WILD-TYPE 
            17            561 
  PKN3 MUTATED PKN3 WILD-TYPE 
            17            561 
[1] "GPR160 MUTATION ANALYSIS"
[1] 3
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              570 
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              570 
[1] "OTUD7B MUTATION ANALYSIS"
[1] 3
  OTUD7B MUTATED OTUD7B WILD-TYPE 
              17              561 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
              17              561 
[1] "ICAM4 MUTATION ANALYSIS"
[1] 3
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              8             570 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              8             570 
[1] "ZNF174 MUTATION ANALYSIS"
[1] 3
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               8              570 
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               8              570 
[1] "POMGNT1 MUTATION ANALYSIS"
[1] 3
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               12               566 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               12               566 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
            10            568 
  MEN1 MUTATED MEN1 WILD-TYPE 
            10            568 
[1] "MIA3 MUTATION ANALYSIS"
[1] 3
  MIA3 MUTATED MIA3 WILD-TYPE 
            29            549 
  MIA3 MUTATED MIA3 WILD-TYPE 
            29            549 
[1] "SRP72 MUTATION ANALYSIS"
[1] 3
  SRP72 MUTATED SRP72 WILD-TYPE 
             16             562 
  SRP72 MUTATED SRP72 WILD-TYPE 
             16             562 
[1] "UVRAG MUTATION ANALYSIS"
[1] 3
  UVRAG MUTATED UVRAG WILD-TYPE 
             13             565 
  UVRAG MUTATED UVRAG WILD-TYPE 
             13             565 
[1] "PLXNB2 MUTATION ANALYSIS"
[1] 3
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              31              547 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              31              547 
[1] "KIF2B MUTATION ANALYSIS"
[1] 3
  KIF2B MUTATED KIF2B WILD-TYPE 
             35             543 
  KIF2B MUTATED KIF2B WILD-TYPE 
             35             543 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             573 
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             573 
[1] "CEP290 MUTATION ANALYSIS"
[1] 3
  CEP290 MUTATED CEP290 WILD-TYPE 
              23              555 
  CEP290 MUTATED CEP290 WILD-TYPE 
              23              555 
[1] "COL20A1 MUTATION ANALYSIS"
[1] 3
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               22               556 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               22               556 
[1] "THSD1 MUTATION ANALYSIS"
[1] 3
  THSD1 MUTATED THSD1 WILD-TYPE 
             26             552 
  THSD1 MUTATED THSD1 WILD-TYPE 
             26             552 
[1] "TADA2B MUTATION ANALYSIS"
[1] 3
  TADA2B MUTATED TADA2B WILD-TYPE 
              15              563 
  TADA2B MUTATED TADA2B WILD-TYPE 
              15              563 
[1] "HSP90AA1 MUTATION ANALYSIS"
[1] 3
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                14                564 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                14                564 
[1] "CRAT MUTATION ANALYSIS"
[1] 3
  CRAT MUTATED CRAT WILD-TYPE 
            14            564 
  CRAT MUTATED CRAT WILD-TYPE 
            14            564 
[1] "MON2 MUTATION ANALYSIS"
[1] 3
  MON2 MUTATED MON2 WILD-TYPE 
            21            557 
  MON2 MUTATED MON2 WILD-TYPE 
            21            557 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
               12               566 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
               12               566 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             14             564 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             14             564 
[1] "CHRNA4 MUTATION ANALYSIS"
[1] 3
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
              18              560 
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
              18              560 
[1] "FBXO43 MUTATION ANALYSIS"
[1] 3
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              14              564 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              14              564 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              16              562 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              16              562 
[1] "ZMYND19 MUTATION ANALYSIS"
[1] 3
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
               10               568 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
               10               568 
[1] "DYRK1A MUTATION ANALYSIS"
[1] 3
  DYRK1A MUTATED DYRK1A WILD-TYPE 
              17              561 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
              17              561 
[1] "KIF6 MUTATION ANALYSIS"
[1] 3
  KIF6 MUTATED KIF6 WILD-TYPE 
            18            560 
  KIF6 MUTATED KIF6 WILD-TYPE 
            18            560 
[1] "XPO1 MUTATION ANALYSIS"
[1] 3
  XPO1 MUTATED XPO1 WILD-TYPE 
            14            564 
  XPO1 MUTATED XPO1 WILD-TYPE 
            14            564 
[1] "WHSC1L1 MUTATION ANALYSIS"
[1] 3
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               23               555 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               23               555 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             20             558 
  NAA25 MUTATED NAA25 WILD-TYPE 
             20             558 
[1] "MANEA MUTATION ANALYSIS"
[1] 3
  MANEA MUTATED MANEA WILD-TYPE 
             15             563 
  MANEA MUTATED MANEA WILD-TYPE 
             15             563 
[1] "CCR3 MUTATION ANALYSIS"
[1] 3
  CCR3 MUTATED CCR3 WILD-TYPE 
            13            565 
  CCR3 MUTATED CCR3 WILD-TYPE 
            13            565 
[1] "HAX1 MUTATION ANALYSIS"
[1] 3
  HAX1 MUTATED HAX1 WILD-TYPE 
             7            571 
  HAX1 MUTATED HAX1 WILD-TYPE 
             7            571 
[1] "TAF1D MUTATION ANALYSIS"
[1] 3
  TAF1D MUTATED TAF1D WILD-TYPE 
              8             570 
  TAF1D MUTATED TAF1D WILD-TYPE 
              8             570 
[1] "KLRF1 MUTATION ANALYSIS"
[1] 3
  KLRF1 MUTATED KLRF1 WILD-TYPE 
              6             572 
  KLRF1 MUTATED KLRF1 WILD-TYPE 
              6             572 
[1] "SPOCD1 MUTATION ANALYSIS"
[1] 3
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              17              561 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              17              561 
[1] "DAPK1 MUTATION ANALYSIS"
[1] 3
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             30             548 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             30             548 
[1] "SERPING1 MUTATION ANALYSIS"
[1] 3
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                10                568 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                10                568 
[1] "TMEM165 MUTATION ANALYSIS"
[1] 3
  TMEM165 MUTATED TMEM165 WILD-TYPE 
                5               573 
  TMEM165 MUTATED TMEM165 WILD-TYPE 
                5               573 
[1] "SDC4 MUTATION ANALYSIS"
[1] 3
  SDC4 MUTATED SDC4 WILD-TYPE 
             6            572 
  SDC4 MUTATED SDC4 WILD-TYPE 
             6            572 
[1] "TAF1B MUTATION ANALYSIS"
[1] 3
  TAF1B MUTATED TAF1B WILD-TYPE 
             15             563 
  TAF1B MUTATED TAF1B WILD-TYPE 
             15             563 
[1] "ITGAE MUTATION ANALYSIS"
[1] 3
  ITGAE MUTATED ITGAE WILD-TYPE 
             18             560 
  ITGAE MUTATED ITGAE WILD-TYPE 
             18             560 
[1] "BIN3 MUTATION ANALYSIS"
[1] 3
  BIN3 MUTATED BIN3 WILD-TYPE 
             5            573 
  BIN3 MUTATED BIN3 WILD-TYPE 
             5            573 
[1] "TRIOBP MUTATION ANALYSIS"
[1] 3
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              38              540 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              38              540 
[1] "BRD1 MUTATION ANALYSIS"
[1] 3
  BRD1 MUTATED BRD1 WILD-TYPE 
            22            556 
  BRD1 MUTATED BRD1 WILD-TYPE 
            22            556 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             35             543 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             35             543 
[1] "DDO MUTATION ANALYSIS"
[1] 3
  DDO MUTATED DDO WILD-TYPE 
            7           571 
  DDO MUTATED DDO WILD-TYPE 
            7           571 
[1] "ZNF295 MUTATION ANALYSIS"
[1] 3
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              19              559 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              19              559 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             575 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             575 
[1] "HMMR MUTATION ANALYSIS"
[1] 3
  HMMR MUTATED HMMR WILD-TYPE 
            11            567 
  HMMR MUTATED HMMR WILD-TYPE 
            11            567 
[1] "KIAA1609 MUTATION ANALYSIS"
[1] 3
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                570 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                570 
[1] "RAB14 MUTATION ANALYSIS"
[1] 3
  RAB14 MUTATED RAB14 WILD-TYPE 
              6             572 
  RAB14 MUTATED RAB14 WILD-TYPE 
              6             572 
[1] "AP2A2 MUTATION ANALYSIS"
[1] 3
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             16             562 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             16             562 
[1] "KIAA0427 MUTATION ANALYSIS"
[1] 3
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                17                561 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                17                561 
[1] "CACNA1A MUTATION ANALYSIS"
[1] 3
  CACNA1A MUTATED CACNA1A WILD-TYPE 
               39               539 
  CACNA1A MUTATED CACNA1A WILD-TYPE 
               39               539 
[1] "DCLRE1A MUTATION ANALYSIS"
[1] 3
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               16               562 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               16               562 
[1] "ZNF570 MUTATION ANALYSIS"
[1] 3
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              19              559 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              19              559 
[1] "HAPLN1 MUTATION ANALYSIS"
[1] 3
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               9              569 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               9              569 
[1] "N4BP2 MUTATION ANALYSIS"
[1] 3
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             20             558 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             20             558 
[1] "IPP MUTATION ANALYSIS"
[1] 3
  IPP MUTATED IPP WILD-TYPE 
            9           569 
  IPP MUTATED IPP WILD-TYPE 
            9           569 
[1] "CD6 MUTATION ANALYSIS"
[1] 3
  CD6 MUTATED CD6 WILD-TYPE 
           12           566 
  CD6 MUTATED CD6 WILD-TYPE 
           12           566 
[1] "ATP6V1H MUTATION ANALYSIS"
[1] 3
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               16               562 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               16               562 
[1] "PAMR1 MUTATION ANALYSIS"
[1] 3
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             19             559 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             19             559 
[1] "NLRC5 MUTATION ANALYSIS"
[1] 3
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             29             549 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             29             549 
[1] "CST1 MUTATION ANALYSIS"
[1] 3
  CST1 MUTATED CST1 WILD-TYPE 
             8            570 
  CST1 MUTATED CST1 WILD-TYPE 
             8            570 
[1] "TMEM132D MUTATION ANALYSIS"
[1] 3
  TMEM132D MUTATED TMEM132D WILD-TYPE 
                44                534 
  TMEM132D MUTATED TMEM132D WILD-TYPE 
                44                534 
[1] "XRN1 MUTATION ANALYSIS"
[1] 3
  XRN1 MUTATED XRN1 WILD-TYPE 
            27            551 
  XRN1 MUTATED XRN1 WILD-TYPE 
            27            551 
[1] "OSBPL9 MUTATION ANALYSIS"
[1] 3
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
              12              566 
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
              12              566 
[1] "SYT4 MUTATION ANALYSIS"
[1] 3
  SYT4 MUTATED SYT4 WILD-TYPE 
            18            560 
  SYT4 MUTATED SYT4 WILD-TYPE 
            18            560 
[1] "PHF13 MUTATION ANALYSIS"
[1] 3
  PHF13 MUTATED PHF13 WILD-TYPE 
              7             571 
  PHF13 MUTATED PHF13 WILD-TYPE 
              7             571 
[1] "SMAP2 MUTATION ANALYSIS"
[1] 3
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             573 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             573 
[1] "GLYATL2 MUTATION ANALYSIS"
[1] 3
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
               10               568 
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
               10               568 
[1] "C9ORF98 MUTATION ANALYSIS"
[1] 3
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
               12               566 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
               12               566 
[1] "ZNF341 MUTATION ANALYSIS"
[1] 3
  ZNF341 MUTATED ZNF341 WILD-TYPE 
              20              558 
  ZNF341 MUTATED ZNF341 WILD-TYPE 
              20              558 
[1] "MRPL24 MUTATION ANALYSIS"
[1] 3
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              572 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              572 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             5            573 
  NRAS MUTATED NRAS WILD-TYPE 
             5            573 
[1] "RSPH4A MUTATION ANALYSIS"
[1] 3
  RSPH4A MUTATED RSPH4A WILD-TYPE 
              10              568 
  RSPH4A MUTATED RSPH4A WILD-TYPE 
              10              568 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
              9             569 
  RING1 MUTATED RING1 WILD-TYPE 
              9             569 
[1] "KCNH4 MUTATION ANALYSIS"
[1] 3
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             15             563 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             15             563 
[1] "ZNF23 MUTATION ANALYSIS"
[1] 3
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              5             573 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              5             573 
[1] "MYO3A MUTATION ANALYSIS"
[1] 3
  MYO3A MUTATED MYO3A WILD-TYPE 
             39             539 
  MYO3A MUTATED MYO3A WILD-TYPE 
             39             539 
[1] "C7ORF49 MUTATION ANALYSIS"
[1] 3
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                8               570 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                8               570 
[1] "C1RL MUTATION ANALYSIS"
[1] 3
  C1RL MUTATED C1RL WILD-TYPE 
             8            570 
  C1RL MUTATED C1RL WILD-TYPE 
             8            570 
[1] "C9ORF25 MUTATION ANALYSIS"
[1] 3
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               573 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               573 
[1] "LRFN3 MUTATION ANALYSIS"
[1] 3
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             22             556 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             22             556 
[1] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
             8            570 
  ING1 MUTATED ING1 WILD-TYPE 
             8            570 
[1] "FAM26E MUTATION ANALYSIS"
[1] 3
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              575 
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              575 
[1] "USP1 MUTATION ANALYSIS"
[1] 3
  USP1 MUTATED USP1 WILD-TYPE 
             7            571 
  USP1 MUTATED USP1 WILD-TYPE 
             7            571 
[1] "CRYBG3 MUTATION ANALYSIS"
[1] 3
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              18              560 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              18              560 
[1] "HCFC1R1 MUTATION ANALYSIS"
[1] 3
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               572 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               572 
[1] "ZNF142 MUTATION ANALYSIS"
[1] 3
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              25              553 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              25              553 
[1] "POLE3 MUTATION ANALYSIS"
[1] 3
  POLE3 MUTATED POLE3 WILD-TYPE 
              3             575 
  POLE3 MUTATED POLE3 WILD-TYPE 
              3             575 
[1] "HGF MUTATION ANALYSIS"
[1] 3
  HGF MUTATED HGF WILD-TYPE 
           20           558 
  HGF MUTATED HGF WILD-TYPE 
           20           558 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
           10           568 
  PAM MUTATED PAM WILD-TYPE 
           10           568 
[1] "TMEM116 MUTATION ANALYSIS"
[1] 3
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               575 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               575 
[1] "DNER MUTATION ANALYSIS"
[1] 3
  DNER MUTATED DNER WILD-TYPE 
            18            560 
  DNER MUTATED DNER WILD-TYPE 
            18            560 
[1] "TEX15 MUTATION ANALYSIS"
[1] 3
  TEX15 MUTATED TEX15 WILD-TYPE 
             34             544 
  TEX15 MUTATED TEX15 WILD-TYPE 
             34             544 
[1] "C1ORF63 MUTATION ANALYSIS"
[1] 3
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
                3               575 
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
                3               575 
[1] "FOLH1 MUTATION ANALYSIS"
[1] 3
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             24             554 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             24             554 
[1] "MOCS2 MUTATION ANALYSIS"
[1] 3
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              8             570 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              8             570 
[1] "MICALL1 MUTATION ANALYSIS"
[1] 3
  MICALL1 MUTATED MICALL1 WILD-TYPE 
               10               568 
  MICALL1 MUTATED MICALL1 WILD-TYPE 
               10               568 
[1] "CLCA4 MUTATION ANALYSIS"
[1] 3
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             19             559 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             19             559 
[1] "SMO MUTATION ANALYSIS"
[1] 3
  SMO MUTATED SMO WILD-TYPE 
           18           560 
  SMO MUTATED SMO WILD-TYPE 
           18           560 
[1] "MSL1 MUTATION ANALYSIS"
[1] 3
  MSL1 MUTATED MSL1 WILD-TYPE 
             7            571 
  MSL1 MUTATED MSL1 WILD-TYPE 
             7            571 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            28            550 
  IRS4 MUTATED IRS4 WILD-TYPE 
            28            550 
[1] "AARS2 MUTATION ANALYSIS"
[1] 3
  AARS2 MUTATED AARS2 WILD-TYPE 
             21             557 
  AARS2 MUTATED AARS2 WILD-TYPE 
             21             557 
[1] "DDHD1 MUTATION ANALYSIS"
[1] 3
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             17             561 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             17             561 
[1] "PSD MUTATION ANALYSIS"
[1] 3
  PSD MUTATED PSD WILD-TYPE 
           19           559 
  PSD MUTATED PSD WILD-TYPE 
           19           559 
[1] "NOP2 MUTATION ANALYSIS"
[1] 3
  NOP2 MUTATED NOP2 WILD-TYPE 
             9            569 
  NOP2 MUTATED NOP2 WILD-TYPE 
             9            569 
[1] "GPR45 MUTATION ANALYSIS"
[1] 3
  GPR45 MUTATED GPR45 WILD-TYPE 
             17             561 
  GPR45 MUTATED GPR45 WILD-TYPE 
             17             561 
[1] "IFI44 MUTATION ANALYSIS"
[1] 3
  IFI44 MUTATED IFI44 WILD-TYPE 
              6             572 
  IFI44 MUTATED IFI44 WILD-TYPE 
              6             572 
[1] "BEST3 MUTATION ANALYSIS"
[1] 3
  BEST3 MUTATED BEST3 WILD-TYPE 
             14             564 
  BEST3 MUTATED BEST3 WILD-TYPE 
             14             564 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            32            546 
  FLNB MUTATED FLNB WILD-TYPE 
            32            546 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             11             567 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             11             567 
[1] "ERN2 MUTATION ANALYSIS"
[1] 3
  ERN2 MUTATED ERN2 WILD-TYPE 
            19            559 
  ERN2 MUTATED ERN2 WILD-TYPE 
            19            559 
[1] "PTGER4 MUTATION ANALYSIS"
[1] 3
  PTGER4 MUTATED PTGER4 WILD-TYPE 
              15              563 
  PTGER4 MUTATED PTGER4 WILD-TYPE 
              15              563 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             23             555 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             23             555 
[1] "IGF2BP3 MUTATION ANALYSIS"
[1] 3
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                9               569 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                9               569 
[1] "QRFPR MUTATION ANALYSIS"
[1] 3
  QRFPR MUTATED QRFPR WILD-TYPE 
             17             561 
  QRFPR MUTATED QRFPR WILD-TYPE 
             17             561 
[1] "GGT6 MUTATION ANALYSIS"
[1] 3
  GGT6 MUTATED GGT6 WILD-TYPE 
             6            572 
  GGT6 MUTATED GGT6 WILD-TYPE 
             6            572 
[1] "SCIN MUTATION ANALYSIS"
[1] 3
  SCIN MUTATED SCIN WILD-TYPE 
            14            564 
  SCIN MUTATED SCIN WILD-TYPE 
            14            564 
[1] "SLC6A11 MUTATION ANALYSIS"
[1] 3
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
               13               565 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
               13               565 
[1] "SMCHD1 MUTATION ANALYSIS"
[1] 3
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              17              561 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              17              561 
[1] "PGCP MUTATION ANALYSIS"
[1] 3
  PGCP MUTATED PGCP WILD-TYPE 
            10            568 
  PGCP MUTATED PGCP WILD-TYPE 
            10            568 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               11               567 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               11               567 
[1] "TMEM127 MUTATION ANALYSIS"
[1] 3
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                6               572 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                6               572 
[1] "APITD1 MUTATION ANALYSIS"
[1] 3
  APITD1 MUTATED APITD1 WILD-TYPE 
               6              572 
  APITD1 MUTATED APITD1 WILD-TYPE 
               6              572 
[1] "UGT2A3 MUTATION ANALYSIS"
[1] 3
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               8              570 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               8              570 
[1] "ATP8B1 MUTATION ANALYSIS"
[1] 3
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              21              557 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              21              557 
[1] "HIVEP1 MUTATION ANALYSIS"
[1] 3
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              30              548 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              30              548 
[1] "RINT1 MUTATION ANALYSIS"
[1] 3
  RINT1 MUTATED RINT1 WILD-TYPE 
             10             568 
  RINT1 MUTATED RINT1 WILD-TYPE 
             10             568 
[1] "H2AFY MUTATION ANALYSIS"
[1] 3
  H2AFY MUTATED H2AFY WILD-TYPE 
              9             569 
  H2AFY MUTATED H2AFY WILD-TYPE 
              9             569 
[1] "TAF1L MUTATION ANALYSIS"
[1] 3
  TAF1L MUTATED TAF1L WILD-TYPE 
             38             540 
  TAF1L MUTATED TAF1L WILD-TYPE 
             38             540 
[1] "C1ORF177 MUTATION ANALYSIS"
[1] 3
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                566 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                566 
[1] "DGKD MUTATION ANALYSIS"
[1] 3
  DGKD MUTATED DGKD WILD-TYPE 
             8            570 
  DGKD MUTATED DGKD WILD-TYPE 
             8            570 
[1] "TNFRSF25 MUTATION ANALYSIS"
[1] 3
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
                 8                570 
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
                 8                570 
[1] "CFI MUTATION ANALYSIS"
[1] 3
  CFI MUTATED CFI WILD-TYPE 
           14           564 
  CFI MUTATED CFI WILD-TYPE 
           14           564 
[1] "EMILIN3 MUTATION ANALYSIS"
[1] 3
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               15               563 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               15               563 
[1] "EHBP1 MUTATION ANALYSIS"
[1] 3
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             19             559 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             19             559 
[1] "HIC2 MUTATION ANALYSIS"
[1] 3
  HIC2 MUTATED HIC2 WILD-TYPE 
            19            559 
  HIC2 MUTATED HIC2 WILD-TYPE 
            19            559 
[1] "C9ORF86 MUTATION ANALYSIS"
[1] 3
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
               13               565 
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
               13               565 
[1] "ABCC1 MUTATION ANALYSIS"
[1] 3
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             17             561 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             17             561 
[1] "ZNF750 MUTATION ANALYSIS"
[1] 3
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              17              561 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              17              561 
[1] "ZNF7 MUTATION ANALYSIS"
[1] 3
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             9            569 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             9            569 
[1] "TMEM64 MUTATION ANALYSIS"
[1] 3
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               8              570 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               8              570 
[1] "HSP90B1 MUTATION ANALYSIS"
[1] 3
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
               11               567 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
               11               567 
[1] "OR10J1 MUTATION ANALYSIS"
[1] 3
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              14              564 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              14              564 
[1] "CPSF2 MUTATION ANALYSIS"
[1] 3
  CPSF2 MUTATED CPSF2 WILD-TYPE 
             10             568 
  CPSF2 MUTATED CPSF2 WILD-TYPE 
             10             568 
[1] "ZBTB40 MUTATION ANALYSIS"
[1] 3
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              13              565 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              13              565 
[1] "RPS6KA6 MUTATION ANALYSIS"
[1] 3
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               22               556 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               22               556 
[1] "ICAM3 MUTATION ANALYSIS"
[1] 3
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              6             572 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              6             572 
[1] "PAX4 MUTATION ANALYSIS"
[1] 3
  PAX4 MUTATED PAX4 WILD-TYPE 
            14            564 
  PAX4 MUTATED PAX4 WILD-TYPE 
            14            564 
[1] "ZNF514 MUTATION ANALYSIS"
[1] 3
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               9              569 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               9              569 
[1] "MSN MUTATION ANALYSIS"
[1] 3
  MSN MUTATED MSN WILD-TYPE 
           16           562 
  MSN MUTATED MSN WILD-TYPE 
           16           562 
[1] "ANKRD36 MUTATION ANALYSIS"
[1] 3
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               555 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               555 
[1] "SIGLEC1 MUTATION ANALYSIS"
[1] 3
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
               29               549 
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
               29               549 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
            10            568 
  CLGN MUTATED CLGN WILD-TYPE 
            10            568 
[1] "IL7R MUTATION ANALYSIS"
[1] 3
  IL7R MUTATED IL7R WILD-TYPE 
            17            561 
  IL7R MUTATED IL7R WILD-TYPE 
            17            561 
[1] "AVEN MUTATION ANALYSIS"
[1] 3
  AVEN MUTATED AVEN WILD-TYPE 
             7            571 
  AVEN MUTATED AVEN WILD-TYPE 
             7            571 
[1] "CCDC37 MUTATION ANALYSIS"
[1] 3
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              17              561 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              17              561 
[1] "SPATA5L1 MUTATION ANALYSIS"
[1] 3
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 8                570 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 8                570 
[1] "SERPINB10 MUTATION ANALYSIS"
[1] 3
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 568 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 568 
[1] "PIWIL2 MUTATION ANALYSIS"
[1] 3
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
              12              566 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
              12              566 
[1] "FAM46D MUTATION ANALYSIS"
[1] 3
  FAM46D MUTATED FAM46D WILD-TYPE 
              13              565 
  FAM46D MUTATED FAM46D WILD-TYPE 
              13              565 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
             9            569 
  LIPH MUTATED LIPH WILD-TYPE 
             9            569 
[1] "GOLT1B MUTATION ANALYSIS"
[1] 3
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              573 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              573 
[1] "HMCN1 MUTATION ANALYSIS"
[1] 3
  HMCN1 MUTATED HMCN1 WILD-TYPE 
            105             473 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
            105             473 
[1] "SERPINB7 MUTATION ANALYSIS"
[1] 3
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                572 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                572 
[1] "TLE1 MUTATION ANALYSIS"
[1] 3
  TLE1 MUTATED TLE1 WILD-TYPE 
            14            564 
  TLE1 MUTATED TLE1 WILD-TYPE 
            14            564 
[1] "BRMS1 MUTATION ANALYSIS"
[1] 3
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             572 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             572 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             21             557 
  GATA3 MUTATED GATA3 WILD-TYPE 
             21             557 
[1] "FAM18A MUTATION ANALYSIS"
[1] 3
  FAM18A MUTATED FAM18A WILD-TYPE 
               4              574 
  FAM18A MUTATED FAM18A WILD-TYPE 
               4              574 
[1] "GPATCH2 MUTATION ANALYSIS"
[1] 3
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
               10               568 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
               10               568 
[1] "OR6C70 MUTATION ANALYSIS"
[1] 3
  OR6C70 MUTATED OR6C70 WILD-TYPE 
               6              572 
  OR6C70 MUTATED OR6C70 WILD-TYPE 
               6              572 
[1] "SPIB MUTATION ANALYSIS"
[1] 3
  SPIB MUTATED SPIB WILD-TYPE 
             9            569 
  SPIB MUTATED SPIB WILD-TYPE 
             9            569 
[1] "SULF1 MUTATION ANALYSIS"
[1] 3
  SULF1 MUTATED SULF1 WILD-TYPE 
             31             547 
  SULF1 MUTATED SULF1 WILD-TYPE 
             31             547 
[1] "LPHN2 MUTATION ANALYSIS"
[1] 3
  LPHN2 MUTATED LPHN2 WILD-TYPE 
             26             552 
  LPHN2 MUTATED LPHN2 WILD-TYPE 
             26             552 
[1] "TMEM161A MUTATION ANALYSIS"
[1] 3
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                10                568 
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                10                568 
[1] "PLXNB1 MUTATION ANALYSIS"
[1] 3
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
              31              547 
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
              31              547 
[1] "MYOCD MUTATION ANALYSIS"
[1] 3
  MYOCD MUTATED MYOCD WILD-TYPE 
             18             560 
  MYOCD MUTATED MYOCD WILD-TYPE 
             18             560 
[1] "EIF4E1B MUTATION ANALYSIS"
[1] 3
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
                9               569 
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
                9               569 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
            13            565 
  PKD2 MUTATED PKD2 WILD-TYPE 
            13            565 
[1] "APOA1BP MUTATION ANALYSIS"
[1] 3
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                6               572 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                6               572 
[1] "ATP2C1 MUTATION ANALYSIS"
[1] 3
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              20              558 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              20              558 
[1] "FER1L6 MUTATION ANALYSIS"
[1] 3
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              31              547 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              31              547 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           41           537 
  MGA MUTATED MGA WILD-TYPE 
           41           537 
[1] "MYCT1 MUTATION ANALYSIS"
[1] 3
  MYCT1 MUTATED MYCT1 WILD-TYPE 
             11             567 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
             11             567 
[1] "KCNQ1 MUTATION ANALYSIS"
[1] 3
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             572 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             572 
[1] "LIMCH1 MUTATION ANALYSIS"
[1] 3
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              16              562 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              16              562 
[1] "KRTAP5-1 MUTATION ANALYSIS"
[1] 3
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
                10                568 
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
                10                568 
[1] "C20ORF7 MUTATION ANALYSIS"
[1] 3
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               572 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               572 
[1] "KCNH2 MUTATION ANALYSIS"
[1] 3
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             15             563 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             15             563 
[1] "XRCC2 MUTATION ANALYSIS"
[1] 3
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              7             571 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              7             571 
[1] "EIF4G1 MUTATION ANALYSIS"
[1] 3
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
              26              552 
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
              26              552 
[1] "PTPN3 MUTATION ANALYSIS"
[1] 3
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             20             558 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             20             558 
[1] "CRYBB1 MUTATION ANALYSIS"
[1] 3
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
              13              565 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
              13              565 
[1] "DHX9 MUTATION ANALYSIS"
[1] 3
  DHX9 MUTATED DHX9 WILD-TYPE 
            20            558 
  DHX9 MUTATED DHX9 WILD-TYPE 
            20            558 
[1] "RELB MUTATION ANALYSIS"
[1] 3
  RELB MUTATED RELB WILD-TYPE 
            14            564 
  RELB MUTATED RELB WILD-TYPE 
            14            564 
[1] "GPATCH8 MUTATION ANALYSIS"
[1] 3
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               32               546 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               32               546 
[1] "ZCCHC7 MUTATION ANALYSIS"
[1] 3
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
               7              571 
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
               7              571 
[1] "VWA3A MUTATION ANALYSIS"
[1] 3
  VWA3A MUTATED VWA3A WILD-TYPE 
             15             563 
  VWA3A MUTATED VWA3A WILD-TYPE 
             15             563 
[1] "SET MUTATION ANALYSIS"
[1] 3
  SET MUTATED SET WILD-TYPE 
           10           568 
  SET MUTATED SET WILD-TYPE 
           10           568 
[1] "RAVER1 MUTATION ANALYSIS"
[1] 3
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               9              569 
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               9              569 
[1] "PTPRU MUTATION ANALYSIS"
[1] 3
  PTPRU MUTATED PTPRU WILD-TYPE 
             30             548 
  PTPRU MUTATED PTPRU WILD-TYPE 
             30             548 
[1] "SOS2 MUTATION ANALYSIS"
[1] 3
  SOS2 MUTATED SOS2 WILD-TYPE 
            19            559 
  SOS2 MUTATED SOS2 WILD-TYPE 
            19            559 
[1] "HSF4 MUTATION ANALYSIS"
[1] 3
  HSF4 MUTATED HSF4 WILD-TYPE 
            10            568 
  HSF4 MUTATED HSF4 WILD-TYPE 
            10            568 
[1] "OR51F1 MUTATION ANALYSIS"
[1] 3
  OR51F1 MUTATED OR51F1 WILD-TYPE 
              12              566 
  OR51F1 MUTATED OR51F1 WILD-TYPE 
              12              566 
[1] "DNAH10 MUTATION ANALYSIS"
[1] 3
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              63              515 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              63              515 
[1] "PTX4 MUTATION ANALYSIS"
[1] 3
  PTX4 MUTATED PTX4 WILD-TYPE 
            16            562 
  PTX4 MUTATED PTX4 WILD-TYPE 
            16            562 
[1] "AMELX MUTATION ANALYSIS"
[1] 3
  AMELX MUTATED AMELX WILD-TYPE 
              6             572 
  AMELX MUTATED AMELX WILD-TYPE 
              6             572 
[1] "CHD3 MUTATION ANALYSIS"
[1] 3
  CHD3 MUTATED CHD3 WILD-TYPE 
            38            540 
  CHD3 MUTATED CHD3 WILD-TYPE 
            38            540 
[1] "PCDH15 MUTATION ANALYSIS"
[1] 3
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              81              497 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              81              497 
[1] "NKD2 MUTATION ANALYSIS"
[1] 3
  NKD2 MUTATED NKD2 WILD-TYPE 
             6            572 
  NKD2 MUTATED NKD2 WILD-TYPE 
             6            572 
[1] "BUB1B MUTATION ANALYSIS"
[1] 3
  BUB1B MUTATED BUB1B WILD-TYPE 
             15             563 
  BUB1B MUTATED BUB1B WILD-TYPE 
             15             563 
[1] "EXOSC10 MUTATION ANALYSIS"
[1] 3
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               15               563 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               15               563 
[1] "KCNN3 MUTATION ANALYSIS"
[1] 3
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             15             563 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             15             563 
[1] "TIE1 MUTATION ANALYSIS"
[1] 3
  TIE1 MUTATED TIE1 WILD-TYPE 
            28            550 
  TIE1 MUTATED TIE1 WILD-TYPE 
            28            550 
[1] "MBOAT2 MUTATION ANALYSIS"
[1] 3
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               4              574 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               4              574 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                9               569 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                9               569 
[1] "KIAA1549 MUTATION ANALYSIS"
[1] 3
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                33                545 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                33                545 
[1] "COL4A3BP MUTATION ANALYSIS"
[1] 3
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
                 6                572 
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
                 6                572 
[1] "HCRTR1 MUTATION ANALYSIS"
[1] 3
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               6              572 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               6              572 
[1] "DHRS9 MUTATION ANALYSIS"
[1] 3
  DHRS9 MUTATED DHRS9 WILD-TYPE 
             10             568 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
             10             568 
[1] "MBD3 MUTATION ANALYSIS"
[1] 3
  MBD3 MUTATED MBD3 WILD-TYPE 
            14            564 
  MBD3 MUTATED MBD3 WILD-TYPE 
            14            564 
[1] "ERI1 MUTATION ANALYSIS"
[1] 3
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            574 
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            574 
[1] "POU5F1B MUTATION ANALYSIS"
[1] 3
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                9               569 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                9               569 
[1] "MYCN MUTATION ANALYSIS"
[1] 3
  MYCN MUTATED MYCN WILD-TYPE 
             8            570 
  MYCN MUTATED MYCN WILD-TYPE 
             8            570 
[1] "TCN2 MUTATION ANALYSIS"
[1] 3
  TCN2 MUTATED TCN2 WILD-TYPE 
            12            566 
  TCN2 MUTATED TCN2 WILD-TYPE 
            12            566 
[1] "IFT74 MUTATION ANALYSIS"
[1] 3
  IFT74 MUTATED IFT74 WILD-TYPE 
             12             566 
  IFT74 MUTATED IFT74 WILD-TYPE 
             12             566 
[1] "EVI2B MUTATION ANALYSIS"
[1] 3
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             569 
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             569 
[1] "PTPRJ MUTATION ANALYSIS"
[1] 3
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             34             544 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             34             544 
[1] "GPR114 MUTATION ANALYSIS"
[1] 3
  GPR114 MUTATED GPR114 WILD-TYPE 
              10              568 
  GPR114 MUTATED GPR114 WILD-TYPE 
              10              568 
[1] "TUBGCP4 MUTATION ANALYSIS"
[1] 3
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
                8               570 
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
                8               570 
[1] "F13A1 MUTATION ANALYSIS"
[1] 3
  F13A1 MUTATED F13A1 WILD-TYPE 
             19             559 
  F13A1 MUTATED F13A1 WILD-TYPE 
             19             559 
[1] "ZBTB49 MUTATION ANALYSIS"
[1] 3
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
              11              567 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
              11              567 
[1] "NUPL2 MUTATION ANALYSIS"
[1] 3
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              9             569 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              9             569 
[1] "RAI2 MUTATION ANALYSIS"
[1] 3
  RAI2 MUTATED RAI2 WILD-TYPE 
             9            569 
  RAI2 MUTATED RAI2 WILD-TYPE 
             9            569 
[1] "LEFTY1 MUTATION ANALYSIS"
[1] 3
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              575 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              575 
[1] "IKBIP MUTATION ANALYSIS"
[1] 3
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             575 
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             575 
[1] "SLC12A1 MUTATION ANALYSIS"
[1] 3
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
               29               549 
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
               29               549 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              29              549 
  CARD11 MUTATED CARD11 WILD-TYPE 
              29              549 
[1] "OLFM1 MUTATION ANALYSIS"
[1] 3
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             15             563 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             15             563 
[1] "KIF27 MUTATION ANALYSIS"
[1] 3
  KIF27 MUTATED KIF27 WILD-TYPE 
             20             558 
  KIF27 MUTATED KIF27 WILD-TYPE 
             20             558 
[1] "ARSJ MUTATION ANALYSIS"
[1] 3
  ARSJ MUTATED ARSJ WILD-TYPE 
            10            568 
  ARSJ MUTATED ARSJ WILD-TYPE 
            10            568 
[1] "PRICKLE4 MUTATION ANALYSIS"
[1] 3
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 7                571 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 7                571 
[1] "PIGO MUTATION ANALYSIS"
[1] 3
  PIGO MUTATED PIGO WILD-TYPE 
            12            566 
  PIGO MUTATED PIGO WILD-TYPE 
            12            566 
[1] "EFHC1 MUTATION ANALYSIS"
[1] 3
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             568 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             568 
[1] "EPB41L5 MUTATION ANALYSIS"
[1] 3
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               11               567 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               11               567 
[1] "OR52A5 MUTATION ANALYSIS"
[1] 3
  OR52A5 MUTATED OR52A5 WILD-TYPE 
              11              567 
  OR52A5 MUTATED OR52A5 WILD-TYPE 
              11              567 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
            11            567 
  ASB5 MUTATED ASB5 WILD-TYPE 
            11            567 
[1] "MMP10 MUTATION ANALYSIS"
[1] 3
  MMP10 MUTATED MMP10 WILD-TYPE 
             10             568 
  MMP10 MUTATED MMP10 WILD-TYPE 
             10             568 
[1] "FGF5 MUTATION ANALYSIS"
[1] 3
  FGF5 MUTATED FGF5 WILD-TYPE 
             8            570 
  FGF5 MUTATED FGF5 WILD-TYPE 
             8            570 
[1] "CWH43 MUTATION ANALYSIS"
[1] 3
  CWH43 MUTATED CWH43 WILD-TYPE 
             12             566 
  CWH43 MUTATED CWH43 WILD-TYPE 
             12             566 
[1] "MTSS1 MUTATION ANALYSIS"
[1] 3
  MTSS1 MUTATED MTSS1 WILD-TYPE 
             15             563 
  MTSS1 MUTATED MTSS1 WILD-TYPE 
             15             563 
[1] "KIAA2018 MUTATION ANALYSIS"
[1] 3
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                32                546 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                32                546 
[1] "SMC5 MUTATION ANALYSIS"
[1] 3
  SMC5 MUTATED SMC5 WILD-TYPE 
            13            565 
  SMC5 MUTATED SMC5 WILD-TYPE 
            13            565 
[1] "BAG4 MUTATION ANALYSIS"
[1] 3
  BAG4 MUTATED BAG4 WILD-TYPE 
             5            573 
  BAG4 MUTATED BAG4 WILD-TYPE 
             5            573 
[1] "ZMYND8 MUTATION ANALYSIS"
[1] 3
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              21              557 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              21              557 
[1] "MPP5 MUTATION ANALYSIS"
[1] 3
  MPP5 MUTATED MPP5 WILD-TYPE 
             9            569 
  MPP5 MUTATED MPP5 WILD-TYPE 
             9            569 
[1] "ECSIT MUTATION ANALYSIS"
[1] 3
  ECSIT MUTATED ECSIT WILD-TYPE 
              8             570 
  ECSIT MUTATED ECSIT WILD-TYPE 
              8             570 
[1] "CSNK2A2 MUTATION ANALYSIS"
[1] 3
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                9               569 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                9               569 
[1] "CCR9 MUTATION ANALYSIS"
[1] 3
  CCR9 MUTATED CCR9 WILD-TYPE 
             8            570 
  CCR9 MUTATED CCR9 WILD-TYPE 
             8            570 
[1] "PODN MUTATION ANALYSIS"
[1] 3
  PODN MUTATED PODN WILD-TYPE 
            15            563 
  PODN MUTATED PODN WILD-TYPE 
            15            563 
[1] "VWA1 MUTATION ANALYSIS"
[1] 3
  VWA1 MUTATED VWA1 WILD-TYPE 
             8            570 
  VWA1 MUTATED VWA1 WILD-TYPE 
             8            570 
[1] "PADI3 MUTATION ANALYSIS"
[1] 3
  PADI3 MUTATED PADI3 WILD-TYPE 
             15             563 
  PADI3 MUTATED PADI3 WILD-TYPE 
             15             563 
[1] "BMPR2 MUTATION ANALYSIS"
[1] 3
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             22             556 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             22             556 
[1] "SETD6 MUTATION ANALYSIS"
[1] 3
  SETD6 MUTATED SETD6 WILD-TYPE 
              8             570 
  SETD6 MUTATED SETD6 WILD-TYPE 
              8             570 
[1] "GPR84 MUTATION ANALYSIS"
[1] 3
  GPR84 MUTATED GPR84 WILD-TYPE 
              5             573 
  GPR84 MUTATED GPR84 WILD-TYPE 
              5             573 
[1] "TTC3 MUTATION ANALYSIS"
[1] 3
  TTC3 MUTATED TTC3 WILD-TYPE 
            32            546 
  TTC3 MUTATED TTC3 WILD-TYPE 
            32            546 
[1] "PLK2 MUTATION ANALYSIS"
[1] 3
  PLK2 MUTATED PLK2 WILD-TYPE 
             8            570 
  PLK2 MUTATED PLK2 WILD-TYPE 
             8            570 
[1] "ABCC2 MUTATION ANALYSIS"
[1] 3
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             22             556 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             22             556 
[1] "CXXC1 MUTATION ANALYSIS"
[1] 3
  CXXC1 MUTATED CXXC1 WILD-TYPE 
             16             562 
  CXXC1 MUTATED CXXC1 WILD-TYPE 
             16             562 
[1] "DGAT1 MUTATION ANALYSIS"
[1] 3
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             569 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             569 
[1] "ZNF506 MUTATION ANALYSIS"
[1] 3
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               9              569 
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               9              569 
[1] "ATP2B1 MUTATION ANALYSIS"
[1] 3
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
              19              559 
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
              19              559 
[1] "PI16 MUTATION ANALYSIS"
[1] 3
  PI16 MUTATED PI16 WILD-TYPE 
             6            572 
  PI16 MUTATED PI16 WILD-TYPE 
             6            572 
[1] "TOPBP1 MUTATION ANALYSIS"
[1] 3
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              22              556 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              22              556 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             17             561 
  CSF3R MUTATED CSF3R WILD-TYPE 
             17             561 
[1] "LRP4 MUTATION ANALYSIS"
[1] 3
  LRP4 MUTATED LRP4 WILD-TYPE 
            25            553 
  LRP4 MUTATED LRP4 WILD-TYPE 
            25            553 
[1] "UGDH MUTATION ANALYSIS"
[1] 3
  UGDH MUTATED UGDH WILD-TYPE 
            11            567 
  UGDH MUTATED UGDH WILD-TYPE 
            11            567 
[1] "C1QA MUTATION ANALYSIS"
[1] 3
  C1QA MUTATED C1QA WILD-TYPE 
             5            573 
  C1QA MUTATED C1QA WILD-TYPE 
             5            573 
[1] "ZC3H3 MUTATION ANALYSIS"
[1] 3
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             22             556 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             22             556 
[1] "CHMP7 MUTATION ANALYSIS"
[1] 3
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              6             572 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              6             572 
[1] "PTPRT MUTATION ANALYSIS"
[1] 3
  PTPRT MUTATED PTPRT WILD-TYPE 
             57             521 
  PTPRT MUTATED PTPRT WILD-TYPE 
             57             521 
[1] "ZNF687 MUTATION ANALYSIS"
[1] 3
  ZNF687 MUTATED ZNF687 WILD-TYPE 
              14              564 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
              14              564 
[1] "FAM111A MUTATION ANALYSIS"
[1] 3
  FAM111A MUTATED FAM111A WILD-TYPE 
               13               565 
  FAM111A MUTATED FAM111A WILD-TYPE 
               13               565 
[1] "INTS8 MUTATION ANALYSIS"
[1] 3
  INTS8 MUTATED INTS8 WILD-TYPE 
             20             558 
  INTS8 MUTATED INTS8 WILD-TYPE 
             20             558 
[1] "IL1R2 MUTATION ANALYSIS"
[1] 3
  IL1R2 MUTATED IL1R2 WILD-TYPE 
             12             566 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
             12             566 
[1] "ALCAM MUTATION ANALYSIS"
[1] 3
  ALCAM MUTATED ALCAM WILD-TYPE 
             14             564 
  ALCAM MUTATED ALCAM WILD-TYPE 
             14             564 
[1] "TIA1 MUTATION ANALYSIS"
[1] 3
  TIA1 MUTATED TIA1 WILD-TYPE 
             6            572 
  TIA1 MUTATED TIA1 WILD-TYPE 
             6            572 
[1] "C6ORF72 MUTATION ANALYSIS"
[1] 3
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                8               570 
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                8               570 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            9           569 
  DEK MUTATED DEK WILD-TYPE 
            9           569 
[1] "UBXN6 MUTATION ANALYSIS"
[1] 3
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             14             564 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             14             564 
[1] "FGF13 MUTATION ANALYSIS"
[1] 3
  FGF13 MUTATED FGF13 WILD-TYPE 
             19             559 
  FGF13 MUTATED FGF13 WILD-TYPE 
             19             559 
[1] "CHD1 MUTATION ANALYSIS"
[1] 3
  CHD1 MUTATED CHD1 WILD-TYPE 
            20            558 
  CHD1 MUTATED CHD1 WILD-TYPE 
            20            558 
[1] "SLC30A5 MUTATION ANALYSIS"
[1] 3
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                8               570 
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                8               570 
[1] "PHACTR2 MUTATION ANALYSIS"
[1] 3
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               18               560 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               18               560 
[1] "YIF1A MUTATION ANALYSIS"
[1] 3
  YIF1A MUTATED YIF1A WILD-TYPE 
              5             573 
  YIF1A MUTATED YIF1A WILD-TYPE 
              5             573 
[1] "ARID3A MUTATION ANALYSIS"
[1] 3
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              572 
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              572 
[1] "IRF2BP2 MUTATION ANALYSIS"
[1] 3
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               571 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               571 
[1] "ABCF3 MUTATION ANALYSIS"
[1] 3
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             13             565 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             13             565 
[1] "DTNBP1 MUTATION ANALYSIS"
[1] 3
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               7              571 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               7              571 
[1] "CHST15 MUTATION ANALYSIS"
[1] 3
  CHST15 MUTATED CHST15 WILD-TYPE 
              17              561 
  CHST15 MUTATED CHST15 WILD-TYPE 
              17              561 
[1] "SI MUTATION ANALYSIS"
[1] 3
  SI MUTATED SI WILD-TYPE 
          48          530 
  SI MUTATED SI WILD-TYPE 
          48          530 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             40             538 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             40             538 
[1] "ITGAL MUTATION ANALYSIS"
[1] 3
  ITGAL MUTATED ITGAL WILD-TYPE 
             26             552 
  ITGAL MUTATED ITGAL WILD-TYPE 
             26             552 
[1] "PCLO MUTATION ANALYSIS"
[1] 3
  PCLO MUTATED PCLO WILD-TYPE 
           109            469 
  PCLO MUTATED PCLO WILD-TYPE 
           109            469 
[1] "NPR3 MUTATION ANALYSIS"
[1] 3
  NPR3 MUTATED NPR3 WILD-TYPE 
            11            567 
  NPR3 MUTATED NPR3 WILD-TYPE 
            11            567 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              13              565 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              13              565 
[1] "MTSS1L MUTATION ANALYSIS"
[1] 3
  MTSS1L MUTATED MTSS1L WILD-TYPE 
              12              566 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
              12              566 
[1] "ABCA7 MUTATION ANALYSIS"
[1] 3
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             25             553 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             25             553 
[1] "OR1L3 MUTATION ANALYSIS"
[1] 3
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              8             570 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              8             570 
[1] "HOOK1 MUTATION ANALYSIS"
[1] 3
  HOOK1 MUTATED HOOK1 WILD-TYPE 
             11             567 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
             11             567 
[1] "MAP7D1 MUTATION ANALYSIS"
[1] 3
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              17              561 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              17              561 
[1] "VPRBP MUTATION ANALYSIS"
[1] 3
  VPRBP MUTATED VPRBP WILD-TYPE 
             11             567 
  VPRBP MUTATED VPRBP WILD-TYPE 
             11             567 
[1] "OR2M5 MUTATION ANALYSIS"
[1] 3
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             16             562 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             16             562 
[1] "RANBP3 MUTATION ANALYSIS"
[1] 3
  RANBP3 MUTATED RANBP3 WILD-TYPE 
              14              564 
  RANBP3 MUTATED RANBP3 WILD-TYPE 
              14              564 
[1] "PLK1 MUTATION ANALYSIS"
[1] 3
  PLK1 MUTATED PLK1 WILD-TYPE 
            18            560 
  PLK1 MUTATED PLK1 WILD-TYPE 
            18            560 
[1] "BRPF3 MUTATION ANALYSIS"
[1] 3
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             13             565 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             13             565 
[1] "CSNK1G3 MUTATION ANALYSIS"
[1] 3
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                9               569 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                9               569 
[1] "STX12 MUTATION ANALYSIS"
[1] 3
  STX12 MUTATED STX12 WILD-TYPE 
              4             574 
  STX12 MUTATED STX12 WILD-TYPE 
              4             574 
[1] "KRTAP10-9 MUTATION ANALYSIS"
[1] 3
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  9                 569 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  9                 569 
[1] "LOXL2 MUTATION ANALYSIS"
[1] 3
  LOXL2 MUTATED LOXL2 WILD-TYPE 
             18             560 
  LOXL2 MUTATED LOXL2 WILD-TYPE 
             18             560 
[1] "SLC25A41 MUTATION ANALYSIS"
[1] 3
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
                 6                572 
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
                 6                572 
[1] "MAP9 MUTATION ANALYSIS"
[1] 3
  MAP9 MUTATED MAP9 WILD-TYPE 
            14            564 
  MAP9 MUTATED MAP9 WILD-TYPE 
            14            564 
[1] "SLC9A2 MUTATION ANALYSIS"
[1] 3
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              15              563 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              15              563 
[1] "SEC31B MUTATION ANALYSIS"
[1] 3
  SEC31B MUTATED SEC31B WILD-TYPE 
              22              556 
  SEC31B MUTATED SEC31B WILD-TYPE 
              22              556 
[1] "MINA MUTATION ANALYSIS"
[1] 3
  MINA MUTATED MINA WILD-TYPE 
             8            570 
  MINA MUTATED MINA WILD-TYPE 
             8            570 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              570 
  CAB39L MUTATED CAB39L WILD-TYPE 
               8              570 
[1] "GPR137B MUTATION ANALYSIS"
[1] 3
  GPR137B MUTATED GPR137B WILD-TYPE 
                8               570 
  GPR137B MUTATED GPR137B WILD-TYPE 
                8               570 
[1] "IL1F7 MUTATION ANALYSIS"
[1] 3
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              4             574 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              4             574 
[1] "TM7SF3 MUTATION ANALYSIS"
[1] 3
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               7              571 
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               7              571 
[1] "TTK MUTATION ANALYSIS"
[1] 3
  TTK MUTATED TTK WILD-TYPE 
           22           556 
  TTK MUTATED TTK WILD-TYPE 
           22           556 
[1] "SLFN13 MUTATION ANALYSIS"
[1] 3
  SLFN13 MUTATED SLFN13 WILD-TYPE 
              10              568 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
              10              568 
[1] "RBBP8 MUTATION ANALYSIS"
[1] 3
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              8             570 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              8             570 
[1] "SPANXC MUTATION ANALYSIS"
[1] 3
  SPANXC MUTATED SPANXC WILD-TYPE 
              11              567 
  SPANXC MUTATED SPANXC WILD-TYPE 
              11              567 
[1] "MSL3 MUTATION ANALYSIS"
[1] 3
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            569 
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            569 
[1] "EGLN1 MUTATION ANALYSIS"
[1] 3
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              6             572 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              6             572 
[1] "ARNT MUTATION ANALYSIS"
[1] 3
  ARNT MUTATED ARNT WILD-TYPE 
             8            570 
  ARNT MUTATED ARNT WILD-TYPE 
             8            570 
[1] "SCN9A MUTATION ANALYSIS"
[1] 3
  SCN9A MUTATED SCN9A WILD-TYPE 
             43             535 
  SCN9A MUTATED SCN9A WILD-TYPE 
             43             535 
[1] "AMHR2 MUTATION ANALYSIS"
[1] 3
  AMHR2 MUTATED AMHR2 WILD-TYPE 
             10             568 
  AMHR2 MUTATED AMHR2 WILD-TYPE 
             10             568 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             21             557 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             21             557 
[1] "AMICA1 MUTATION ANALYSIS"
[1] 3
  AMICA1 MUTATED AMICA1 WILD-TYPE 
               8              570 
  AMICA1 MUTATED AMICA1 WILD-TYPE 
               8              570 
[1] "OXCT2 MUTATION ANALYSIS"
[1] 3
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              6             572 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              6             572 
[1] "WWC1 MUTATION ANALYSIS"
[1] 3
  WWC1 MUTATED WWC1 WILD-TYPE 
            20            558 
  WWC1 MUTATED WWC1 WILD-TYPE 
            20            558 
[1] "ATF5 MUTATION ANALYSIS"
[1] 3
  ATF5 MUTATED ATF5 WILD-TYPE 
             5            573 
  ATF5 MUTATED ATF5 WILD-TYPE 
             5            573 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             36             542 
  EP300 MUTATED EP300 WILD-TYPE 
             36             542 
[1] "DLD MUTATION ANALYSIS"
[1] 3
  DLD MUTATED DLD WILD-TYPE 
           14           564 
  DLD MUTATED DLD WILD-TYPE 
           14           564 
[1] "BIRC3 MUTATION ANALYSIS"
[1] 3
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             12             566 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             12             566 
[1] "NOS1 MUTATION ANALYSIS"
[1] 3
  NOS1 MUTATED NOS1 WILD-TYPE 
            37            541 
  NOS1 MUTATED NOS1 WILD-TYPE 
            37            541 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              45              533 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              45              533 
[1] "C16ORF7 MUTATION ANALYSIS"
[1] 3
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               16               562 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               16               562 
[1] "HIVEP3 MUTATION ANALYSIS"
[1] 3
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              36              542 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              36              542 
[1] "FBXO32 MUTATION ANALYSIS"
[1] 3
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               7              571 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               7              571 
[1] "BIRC7 MUTATION ANALYSIS"
[1] 3
  BIRC7 MUTATED BIRC7 WILD-TYPE 
              6             572 
  BIRC7 MUTATED BIRC7 WILD-TYPE 
              6             572 
[1] "AFP MUTATION ANALYSIS"
[1] 3
  AFP MUTATED AFP WILD-TYPE 
            4           574 
  AFP MUTATED AFP WILD-TYPE 
            4           574 
[1] "COL11A1 MUTATION ANALYSIS"
[1] 3
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               61               517 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               61               517 
[1] "FAM166B MUTATION ANALYSIS"
[1] 3
  FAM166B MUTATED FAM166B WILD-TYPE 
                9               569 
  FAM166B MUTATED FAM166B WILD-TYPE 
                9               569 
[1] "ARHGEF17 MUTATION ANALYSIS"
[1] 3
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                25                553 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                25                553 
[1] "RRBP1 MUTATION ANALYSIS"
[1] 3
  RRBP1 MUTATED RRBP1 WILD-TYPE 
             20             558 
  RRBP1 MUTATED RRBP1 WILD-TYPE 
             20             558 
[1] "PROK2 MUTATION ANALYSIS"
[1] 3
  PROK2 MUTATED PROK2 WILD-TYPE 
              4             574 
  PROK2 MUTATED PROK2 WILD-TYPE 
              4             574 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              19              559 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              19              559 
[1] "PSMC4 MUTATION ANALYSIS"
[1] 3
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             16             562 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             16             562 
[1] "ITGB8 MUTATION ANALYSIS"
[1] 3
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             15             563 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             15             563 
[1] "ARHGEF5 MUTATION ANALYSIS"
[1] 3
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                8               570 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                8               570 
[1] "INVS MUTATION ANALYSIS"
[1] 3
  INVS MUTATED INVS WILD-TYPE 
            23            555 
  INVS MUTATED INVS WILD-TYPE 
            23            555 
[1] "E2F5 MUTATION ANALYSIS"
[1] 3
  E2F5 MUTATED E2F5 WILD-TYPE 
             5            573 
  E2F5 MUTATED E2F5 WILD-TYPE 
             5            573 
[1] "MKI67IP MUTATION ANALYSIS"
[1] 3
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                9               569 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                9               569 
[1] "TMEM63A MUTATION ANALYSIS"
[1] 3
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               15               563 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               15               563 
[1] "ZCCHC2 MUTATION ANALYSIS"
[1] 3
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               8              570 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               8              570 
[1] "EPHB6 MUTATION ANALYSIS"
[1] 3
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             22             556 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             22             556 
[1] "GPR1 MUTATION ANALYSIS"
[1] 3
  GPR1 MUTATED GPR1 WILD-TYPE 
             7            571 
  GPR1 MUTATED GPR1 WILD-TYPE 
             7            571 
[1] "PCDHGC3 MUTATION ANALYSIS"
[1] 3
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
               15               563 
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
               15               563 
[1] "CACNA1H MUTATION ANALYSIS"
[1] 3
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               40               538 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               40               538 
[1] "RPS6KA5 MUTATION ANALYSIS"
[1] 3
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                9               569 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                9               569 
[1] "NAGPA MUTATION ANALYSIS"
[1] 3
  NAGPA MUTATED NAGPA WILD-TYPE 
              9             569 
  NAGPA MUTATED NAGPA WILD-TYPE 
              9             569 
[1] "KCNJ6 MUTATION ANALYSIS"
[1] 3
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
             12             566 
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
             12             566 
[1] "PIGZ MUTATION ANALYSIS"
[1] 3
  PIGZ MUTATED PIGZ WILD-TYPE 
            10            568 
  PIGZ MUTATED PIGZ WILD-TYPE 
            10            568 
[1] "DBF4 MUTATION ANALYSIS"
[1] 3
  DBF4 MUTATED DBF4 WILD-TYPE 
             9            569 
  DBF4 MUTATED DBF4 WILD-TYPE 
             9            569 
[1] "DOK7 MUTATION ANALYSIS"
[1] 3
  DOK7 MUTATED DOK7 WILD-TYPE 
             7            571 
  DOK7 MUTATED DOK7 WILD-TYPE 
             7            571 
[1] "HECA MUTATION ANALYSIS"
[1] 3
  HECA MUTATED HECA WILD-TYPE 
            19            559 
  HECA MUTATED HECA WILD-TYPE 
            19            559 
[1] "IGBP1 MUTATION ANALYSIS"
[1] 3
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             572 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             572 
[1] "INSM2 MUTATION ANALYSIS"
[1] 3
  INSM2 MUTATED INSM2 WILD-TYPE 
             13             565 
  INSM2 MUTATED INSM2 WILD-TYPE 
             13             565 
[1] "SAE1 MUTATION ANALYSIS"
[1] 3
  SAE1 MUTATED SAE1 WILD-TYPE 
             6            572 
  SAE1 MUTATED SAE1 WILD-TYPE 
             6            572 
[1] "SUCLG2 MUTATION ANALYSIS"
[1] 3
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               8              570 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               8              570 
[1] "CDC6 MUTATION ANALYSIS"
[1] 3
  CDC6 MUTATED CDC6 WILD-TYPE 
            13            565 
  CDC6 MUTATED CDC6 WILD-TYPE 
            13            565 
[1] "CUL5 MUTATION ANALYSIS"
[1] 3
  CUL5 MUTATED CUL5 WILD-TYPE 
            15            563 
  CUL5 MUTATED CUL5 WILD-TYPE 
            15            563 
[1] "SERPINB8 MUTATION ANALYSIS"
[1] 3
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                570 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                570 
[1] "HSP90AB1 MUTATION ANALYSIS"
[1] 3
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                13                565 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                13                565 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               540 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               540 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             24             554 
  SETD2 MUTATED SETD2 WILD-TYPE 
             24             554 
[1] "ZC3H8 MUTATION ANALYSIS"
[1] 3
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              5             573 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              5             573 
[1] "NARG2 MUTATION ANALYSIS"
[1] 3
  NARG2 MUTATED NARG2 WILD-TYPE 
             14             564 
  NARG2 MUTATED NARG2 WILD-TYPE 
             14             564 
[1] "C3ORF33 MUTATION ANALYSIS"
[1] 3
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                8               570 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                8               570 
[1] "ZNF2 MUTATION ANALYSIS"
[1] 3
  ZNF2 MUTATED ZNF2 WILD-TYPE 
             9            569 
  ZNF2 MUTATED ZNF2 WILD-TYPE 
             9            569 
[1] "ETV1 MUTATION ANALYSIS"
[1] 3
  ETV1 MUTATED ETV1 WILD-TYPE 
             9            569 
  ETV1 MUTATED ETV1 WILD-TYPE 
             9            569 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
            15            563 
  TAF6 MUTATED TAF6 WILD-TYPE 
            15            563 
[1] "BCL2L2 MUTATION ANALYSIS"
[1] 3
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
               5              573 
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
               5              573 
[1] "SPTLC3 MUTATION ANALYSIS"
[1] 3
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
              15              563 
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
              15              563 
[1] "PPRC1 MUTATION ANALYSIS"
[1] 3
  PPRC1 MUTATED PPRC1 WILD-TYPE 
             20             558 
  PPRC1 MUTATED PPRC1 WILD-TYPE 
             20             558 
[1] "KCNT2 MUTATION ANALYSIS"
[1] 3
  KCNT2 MUTATED KCNT2 WILD-TYPE 
             41             537 
  KCNT2 MUTATED KCNT2 WILD-TYPE 
             41             537 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              14              564 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              14              564 
[1] "PCDH19 MUTATION ANALYSIS"
[1] 3
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              30              548 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              30              548 
[1] "LRRC4 MUTATION ANALYSIS"
[1] 3
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             22             556 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             22             556 
[1] "THYN1 MUTATION ANALYSIS"
[1] 3
  THYN1 MUTATED THYN1 WILD-TYPE 
             10             568 
  THYN1 MUTATED THYN1 WILD-TYPE 
             10             568 
[1] "BZW1 MUTATION ANALYSIS"
[1] 3
  BZW1 MUTATED BZW1 WILD-TYPE 
             9            569 
  BZW1 MUTATED BZW1 WILD-TYPE 
             9            569 
[1] "CEP110 MUTATION ANALYSIS"
[1] 3
  CEP110 MUTATED CEP110 WILD-TYPE 
              19              559 
  CEP110 MUTATED CEP110 WILD-TYPE 
              19              559 
[1] "UACA MUTATION ANALYSIS"
[1] 3
  UACA MUTATED UACA WILD-TYPE 
            17            561 
  UACA MUTATED UACA WILD-TYPE 
            17            561 
[1] "PAPOLB MUTATION ANALYSIS"
[1] 3
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              15              563 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              15              563 
[1] "TBC1D22B MUTATION ANALYSIS"
[1] 3
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 9                569 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 9                569 
[1] "HTR1E MUTATION ANALYSIS"
[1] 3
  HTR1E MUTATED HTR1E WILD-TYPE 
             17             561 
  HTR1E MUTATED HTR1E WILD-TYPE 
             17             561 
[1] "SALL2 MUTATION ANALYSIS"
[1] 3
  SALL2 MUTATED SALL2 WILD-TYPE 
             16             562 
  SALL2 MUTATED SALL2 WILD-TYPE 
             16             562 
[1] "BTAF1 MUTATION ANALYSIS"
[1] 3
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             25             553 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             25             553 
[1] "ARV1 MUTATION ANALYSIS"
[1] 3
  ARV1 MUTATED ARV1 WILD-TYPE 
             7            571 
  ARV1 MUTATED ARV1 WILD-TYPE 
             7            571 
[1] "DOPEY2 MUTATION ANALYSIS"
[1] 3
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              35              543 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              35              543 
[1] "ZNF800 MUTATION ANALYSIS"
[1] 3
  ZNF800 MUTATED ZNF800 WILD-TYPE 
              14              564 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
              14              564 
[1] "SRPK3 MUTATION ANALYSIS"
[1] 3
  SRPK3 MUTATED SRPK3 WILD-TYPE 
             13             565 
  SRPK3 MUTATED SRPK3 WILD-TYPE 
             13             565 
[1] "CIB3 MUTATION ANALYSIS"
[1] 3
  CIB3 MUTATED CIB3 WILD-TYPE 
             5            573 
  CIB3 MUTATED CIB3 WILD-TYPE 
             5            573 
[1] "PDK3 MUTATION ANALYSIS"
[1] 3
  PDK3 MUTATED PDK3 WILD-TYPE 
             8            570 
  PDK3 MUTATED PDK3 WILD-TYPE 
             8            570 
[1] "NRIP3 MUTATION ANALYSIS"
[1] 3
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              7             571 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              7             571 
[1] "ZKSCAN3 MUTATION ANALYSIS"
[1] 3
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
               13               565 
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
               13               565 
[1] "ZNF167 MUTATION ANALYSIS"
[1] 3
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              15              563 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              15              563 
[1] "ABCA5 MUTATION ANALYSIS"
[1] 3
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             23             555 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             23             555 
[1] "PPM1D MUTATION ANALYSIS"
[1] 3
  PPM1D MUTATED PPM1D WILD-TYPE 
             10             568 
  PPM1D MUTATED PPM1D WILD-TYPE 
             10             568 
[1] "CSNK1G1 MUTATION ANALYSIS"
[1] 3
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                7               571 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                7               571 
[1] "TMC2 MUTATION ANALYSIS"
[1] 3
  TMC2 MUTATED TMC2 WILD-TYPE 
            19            559 
  TMC2 MUTATED TMC2 WILD-TYPE 
            19            559 
[1] "XRCC5 MUTATION ANALYSIS"
[1] 3
  XRCC5 MUTATED XRCC5 WILD-TYPE 
             13             565 
  XRCC5 MUTATED XRCC5 WILD-TYPE 
             13             565 
[1] "ZNF828 MUTATION ANALYSIS"
[1] 3
  ZNF828 MUTATED ZNF828 WILD-TYPE 
              12              566 
  ZNF828 MUTATED ZNF828 WILD-TYPE 
              12              566 
[1] "CHST4 MUTATION ANALYSIS"
[1] 3
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             571 
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             571 
[1] "SMARCC2 MUTATION ANALYSIS"
[1] 3
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               22               556 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               22               556 
[1] "ZNF98 MUTATION ANALYSIS"
[1] 3
  ZNF98 MUTATED ZNF98 WILD-TYPE 
             18             560 
  ZNF98 MUTATED ZNF98 WILD-TYPE 
             18             560 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
             23             555 
  RGS22 MUTATED RGS22 WILD-TYPE 
             23             555 
[1] "ATOH1 MUTATION ANALYSIS"
[1] 3
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             572 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             572 
[1] "RBM33 MUTATION ANALYSIS"
[1] 3
  RBM33 MUTATED RBM33 WILD-TYPE 
             21             557 
  RBM33 MUTATED RBM33 WILD-TYPE 
             21             557 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                12                566 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                12                566 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             11             567 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             11             567 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              12              566 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              12              566 
[1] "KDELR2 MUTATION ANALYSIS"
[1] 3
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               5              573 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               5              573 
[1] "NOLC1 MUTATION ANALYSIS"
[1] 3
  NOLC1 MUTATED NOLC1 WILD-TYPE 
             15             563 
  NOLC1 MUTATED NOLC1 WILD-TYPE 
             15             563 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           35           543 
  NF1 MUTATED NF1 WILD-TYPE 
           35           543 
[1] "GSDMB MUTATION ANALYSIS"
[1] 3
  GSDMB MUTATED GSDMB WILD-TYPE 
              5             573 
  GSDMB MUTATED GSDMB WILD-TYPE 
              5             573 
[1] "PPP1R12C MUTATION ANALYSIS"
[1] 3
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                11                567 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                11                567 
[1] "PELI2 MUTATION ANALYSIS"
[1] 3
  PELI2 MUTATED PELI2 WILD-TYPE 
             11             567 
  PELI2 MUTATED PELI2 WILD-TYPE 
             11             567 
[1] "UNC93B1 MUTATION ANALYSIS"
[1] 3
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                9               569 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                9               569 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
             12             566 
  PRKCD MUTATED PRKCD WILD-TYPE 
             12             566 
[1] "TESK1 MUTATION ANALYSIS"
[1] 3
  TESK1 MUTATED TESK1 WILD-TYPE 
             13             565 
  TESK1 MUTATED TESK1 WILD-TYPE 
             13             565 
[1] "GLTPD1 MUTATION ANALYSIS"
[1] 3
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              574 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              574 
[1] "ST8SIA6 MUTATION ANALYSIS"
[1] 3
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               568 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               10               568 
[1] "ATP11B MUTATION ANALYSIS"
[1] 3
  ATP11B MUTATED ATP11B WILD-TYPE 
              13              565 
  ATP11B MUTATED ATP11B WILD-TYPE 
              13              565 
[1] "SRP68 MUTATION ANALYSIS"
[1] 3
  SRP68 MUTATED SRP68 WILD-TYPE 
              8             570 
  SRP68 MUTATED SRP68 WILD-TYPE 
              8             570 
[1] "ABCD1 MUTATION ANALYSIS"
[1] 3
  ABCD1 MUTATED ABCD1 WILD-TYPE 
             10             568 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
             10             568 
[1] "MCTP1 MUTATION ANALYSIS"
[1] 3
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             10             568 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             10             568 
[1] "TCERG1 MUTATION ANALYSIS"
[1] 3
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              12              566 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              12              566 
[1] "SETBP1 MUTATION ANALYSIS"
[1] 3
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              47              531 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              47              531 
[1] "WEE1 MUTATION ANALYSIS"
[1] 3
  WEE1 MUTATED WEE1 WILD-TYPE 
             7            571 
  WEE1 MUTATED WEE1 WILD-TYPE 
             7            571 
[1] "IGSF21 MUTATION ANALYSIS"
[1] 3
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               5              573 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               5              573 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            23            555 
  IBTK MUTATED IBTK WILD-TYPE 
            23            555 
[1] "EEA1 MUTATION ANALYSIS"
[1] 3
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            562 
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            562 
[1] "PBX2 MUTATION ANALYSIS"
[1] 3
  PBX2 MUTATED PBX2 WILD-TYPE 
            11            567 
  PBX2 MUTATED PBX2 WILD-TYPE 
            11            567 
[1] "C2ORF67 MUTATION ANALYSIS"
[1] 3
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
               18               560 
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
               18               560 
[1] "ZNF740 MUTATION ANALYSIS"
[1] 3
  ZNF740 MUTATED ZNF740 WILD-TYPE 
               3              575 
  ZNF740 MUTATED ZNF740 WILD-TYPE 
               3              575 
[1] "SLA MUTATION ANALYSIS"
[1] 3
  SLA MUTATED SLA WILD-TYPE 
            9           569 
  SLA MUTATED SLA WILD-TYPE 
            9           569 
[1] "CC2D2A MUTATION ANALYSIS"
[1] 3
  CC2D2A MUTATED CC2D2A WILD-TYPE 
              17              561 
  CC2D2A MUTATED CC2D2A WILD-TYPE 
              17              561 
[1] "GZF1 MUTATION ANALYSIS"
[1] 3
  GZF1 MUTATED GZF1 WILD-TYPE 
            21            557 
  GZF1 MUTATED GZF1 WILD-TYPE 
            21            557 
[1] "AGXT2L1 MUTATION ANALYSIS"
[1] 3
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               10               568 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               10               568 
[1] "EPN1 MUTATION ANALYSIS"
[1] 3
  EPN1 MUTATED EPN1 WILD-TYPE 
            12            566 
  EPN1 MUTATED EPN1 WILD-TYPE 
            12            566 
[1] "CCT6A MUTATION ANALYSIS"
[1] 3
  CCT6A MUTATED CCT6A WILD-TYPE 
              9             569 
  CCT6A MUTATED CCT6A WILD-TYPE 
              9             569 
[1] "PJA1 MUTATION ANALYSIS"
[1] 3
  PJA1 MUTATED PJA1 WILD-TYPE 
            13            565 
  PJA1 MUTATED PJA1 WILD-TYPE 
            13            565 
[1] "GALK1 MUTATION ANALYSIS"
[1] 3
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             574 
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             574 
[1] "PEG3 MUTATION ANALYSIS"
[1] 3
  PEG3 MUTATED PEG3 WILD-TYPE 
            43            535 
  PEG3 MUTATED PEG3 WILD-TYPE 
            43            535 
[1] "GPR120 MUTATION ANALYSIS"
[1] 3
  GPR120 MUTATED GPR120 WILD-TYPE 
               7              571 
  GPR120 MUTATED GPR120 WILD-TYPE 
               7              571 
[1] "RRP7A MUTATION ANALYSIS"
[1] 3
  RRP7A MUTATED RRP7A WILD-TYPE 
              5             573 
  RRP7A MUTATED RRP7A WILD-TYPE 
              5             573 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              18              560 
  ARID5B MUTATED ARID5B WILD-TYPE 
              18              560 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"              "VITAL_STATUS"               
 [3] "DAYS_TO_DEATH"               "DAYS_TO_LAST_FOLLOWUP"      
 [5] "PATHOLOGIC_STAGE"            "PATHOLOGY_T_STAGE"          
 [7] "PATHOLOGY_N_STAGE"           "PATHOLOGY_M_STAGE"          
 [9] "GENDER"                      "RADIATION_THERAPY"          
[11] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
[13] "RACE"                        "ETHNICITY"                  

Input Data has 14 rows and 578 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=191,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=285,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 578 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=55, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  53 135 261 102 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   54   135   261   102 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  53 135 261 102 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   54   135   261   102 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
195 173  89  85 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
195 173  89  85 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
195 173  89  85 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
195 173  89  85 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=46, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   212 121
  TP53 WILD-TYPE 126  95
  TP53 MUTATED TP53 WILD-TYPE 
           333            221 
  TP53 MUTATED TP53 WILD-TYPE 
           121             95 
$`TP53 MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
       35.97        27.12         5.16        20.02        47.05        21.99 
TCGA-CG-5727 TCGA-KB-A93G TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       79.07        20.15        20.05        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       26.33        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        3.16         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.75         3.02        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55        13.22        21.37        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        16.31         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.66        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.97         4.08         9.34        17.29        13.68        19.33 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
        9.17        31.20        44.94         9.21        36.16        33.63 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       39.78        28.73         3.45        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       32.25        29.42         2.66         7.40         6.18        31.10 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
       14.04        14.79         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        1.12         9.34        24.79        32.58         9.86        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
       13.87         7.53        34.98         1.48        27.55        12.89 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       13.51        20.65        20.42         1.15        21.44        13.02 
TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 
       12.33        12.39        12.59        15.39         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       11.31        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       54.08         4.01        19.07        18.97         7.07        30.97 
TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 
       36.00         6.02       105.07         4.01        69.04        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       20.91        19.13        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       12.33        14.66        21.14        11.24        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       15.65         7.13         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
        3.48        19.53        17.06         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        6.21        77.29        26.47         1.51         5.92        24.39 
TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN 
       22.82         3.25        22.75        25.81        11.77        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         0.10         6.58        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       29.00        23.84        33.40        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J 
        6.51        10.62        11.70         2.53         5.56        36.95 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 
       14.04        45.67        18.21         8.52        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        38.14        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-AA68 TCGA-VQ-AA6A 
       17.85         1.87         1.71        42.64        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        26.04        16.14 

$`TP53 WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-CG-4475 
       15.68         8.94        19.99        22.82         0.36        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GI TCGA-IG-A4QT 
       16.24         0.23         9.86        25.78        14.30         9.30 
TCGA-IG-A7DP TCGA-JY-A6FE TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OH TCGA-L5-A4OO 
       14.86         3.68        24.03         6.28        32.61         3.32 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NM 
       58.59         7.43        25.12        55.50         2.66         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.49         8.71        83.24         7.82         7.04        38.40 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-AA7I TCGA-ZR-A9CJ 
        2.30         7.00        15.35         1.55        15.91        19.73 
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         9.47         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       15.95        13.87        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       21.90        35.24        35.84        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8284 
       29.56        33.21        37.25        14.43        29.59         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        0.56        19.96         2.20         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 
        7.36        25.05         9.21        12.79        27.12        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        26.73        31.96        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       34.13         6.08        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53        28.34         0.66        32.52        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 
       13.41        13.18        13.35        11.21         7.17        12.30 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       11.64        12.07        12.82        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 
       14.01        29.98        12.03         0.00         9.01         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
       65.10        21.07         7.99        25.71        20.55        18.61 
TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       17.85        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       19.96         0.62        21.27        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 
        5.03        13.58        63.06        52.21        30.51        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H5 
       22.68        24.20        21.37         6.51         2.10        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1V 
       21.17        14.07        15.68         3.39        19.53        15.75 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR 
       13.51        63.62         3.72        19.73        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EA 
      122.30        40.64       116.38        71.38        57.44        19.04 
TCGA-VQ-A8P3 TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       37.22        15.65        20.81        66.81        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        54.12        27.55        12.43        17.26 

  TP53 MUTATED TP53 WILD-TYPE 
           0.1            0.0 
  TP53 MUTATED TP53 WILD-TYPE 
         122.1          122.3 
  TP53 MUTATED TP53 WILD-TYPE 
         13.15          15.65 
[1] "0.1 - 122.1 (13.2)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53 MUTATED         8       10       23       17        64        49
  TP53 WILD-TYPE       2       10       23       14        20        34
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED          20         51         31         19       19         3
  TP53 WILD-TYPE         9         33         31         20       24         1
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               8              2
  STAGE IA             10             10
  STAGE IB             23             23
  STAGE II             17             14
  STAGE IIA            64             20
  STAGE IIB            49             34
  STAGE III            20              9
  STAGE IIIA           51             33
  STAGE IIIB           31             31
  STAGE IIIC           19             20
  STAGE IV             19             24
  STAGE IVA             3              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TP53 MUTATED      36  82 163  44
  TP53 WILD-TYPE    18  53  98  58
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T0+T1           36             18
  T2              82             53
  T3             163             98
  T4              44             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TP53 MUTATED   124 108  48  39
  TP53 WILD-TYPE  71  65  41  46
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          124             71
  N1          108             65
  N2           48             41
  N3           39             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED   282  18
  TP53 WILD-TYPE 200  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    282   18
  TP53 WILD-TYPE  200   20
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          282            200
  1           18             20
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    87 254
  TP53 WILD-TYPE  85 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     87  254
  TP53 WILD-TYPE   85  152
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           87             85
  MALE            254            152
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   245  68
  TP53 WILD-TYPE 171  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    245   68
  TP53 WILD-TYPE  171   34
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           245            171
  YES           68             34
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TP53 MUTATED      90                         9
  TP53 WILD-TYPE    43                         5
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53 MUTATED                                           0   205
  TP53 WILD-TYPE                                         1   152
D1V11, multiclass
                                           clus
vv                                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                               90             43
  BLACK OR AFRICAN AMERICAN                            9              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                              205            152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                cls
clus               0   1
  TP53 MUTATED     7 225
  TP53 WILD-TYPE   3 173
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      7  225
  TP53 WILD-TYPE    3  173
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                7              3
  NOT HISPANIC OR LATINO          225            173
[1] 2 2
[1] FALSE

Clustering(2) Variable = ARID1A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    64  42
  ARID1A WILD-TYPE 274 174
  ARID1A MUTATED ARID1A WILD-TYPE 
             106              448 
  ARID1A MUTATED ARID1A WILD-TYPE 
              42              174 
$`ARID1A MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-CG-4460 TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GR 
       24.00        19.99        21.99         9.86        25.78        32.45 
TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F TCGA-L5-A4OJ TCGA-L5-A4OX 
       44.75        47.38        21.70        24.03        21.01         7.43 
TCGA-L5-A88Z TCGA-L5-A8NL TCGA-R6-A6DQ TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-B7-5816 
        7.40        13.22         7.59         9.30         7.00        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
       19.56         9.47         6.97         7.43        30.90         4.08 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-6802 
        9.34        34.68        13.87        17.29        19.89        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-8059 
       44.94        21.90        35.84        33.63        15.32        14.43 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8368 
       29.59         8.05        31.10         0.26        17.52         4.31 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 
       31.27         7.36        25.05         1.12        27.12        28.14 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J5 
       31.96        20.88         8.22         6.08         0.72        28.34 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5803 TCGA-CD-8536 TCGA-CG-4305 
       13.51        20.42        16.14        11.21        12.43        15.95 
TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 
        1.02         9.01         7.07         6.02        65.10        21.07 
TCGA-D7-5577 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       25.71        18.54        17.85        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-F1-6874 TCGA-F1-A448 
        5.92        36.43        11.44        20.32        14.47        21.27 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       17.06         0.56        11.08        77.29        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       26.47        21.07         5.59        24.26        22.68        24.20 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       11.77        29.98         0.10         6.58        20.25        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 
       23.84        14.07        63.62        19.73        74.53         4.60 
TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA6J 
       16.67        19.04        38.14        27.55 

$`ARID1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24         4.21         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93C 
       12.16       122.10        68.02         3.68        41.52        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        11.70        11.01         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.64        18.35         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
        6.61        15.95        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 
       40.21        31.20         9.21        36.16        35.24        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       37.25        11.44         0.69         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58         9.86        10.68        34.13        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
       14.17         0.53         0.66        32.52        20.65         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       69.04         7.99        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.61        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       13.78        14.76        26.43        11.24        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM 
       22.29        59.54         5.03        13.58         5.52         6.21 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       63.06         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       22.82         0.76        24.30         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37         8.98         6.51         0.26         2.10        12.95 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       14.04        45.67        18.21         8.52         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        17.26 

  ARID1A MUTATED ARID1A WILD-TYPE 
             0.1              0.0 
  ARID1A MUTATED ARID1A WILD-TYPE 
           77.29           122.30 
  ARID1A MUTATED ARID1A WILD-TYPE 
          19.645           13.165 
[1] "0.1 - 77.3 (19.6)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.2"
D2V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1A MUTATED         2        4       12        5        12        19
  ARID1A WILD-TYPE       8       16       34       26        72        64
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           3         14         10         12       11
  ARID1A WILD-TYPE        26         70         52         27       32
                  vv
clus               STAGE IVA
  ARID1A MUTATED           0
  ARID1A WILD-TYPE         4
D2V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 2                8
  STAGE IA                4               16
  STAGE IB               12               34
  STAGE II                5               26
  STAGE IIA              12               72
  STAGE IIB              19               64
  STAGE III               3               26
  STAGE IIIA             14               70
  STAGE IIIB             10               52
  STAGE IIIC             12               27
  STAGE IV               11               32
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ARID1A MUTATED      12  25  40  31
  ARID1A WILD-TYPE    42 110 221  71
D2V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T0+T1             12               42
  T2                25              110
  T3                40              221
  T4                31               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1A MUTATED    31  37  20  19
  ARID1A WILD-TYPE 164 136  69  66
D2V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             31              164
  N1             37              136
  N2             20               69
  N3             19               66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    96   8
  ARID1A WILD-TYPE 386  30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     96    8
  ARID1A WILD-TYPE  386   30
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             96              386
  1              8               30
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    51  63
  ARID1A WILD-TYPE 121 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     51   63
  ARID1A WILD-TYPE  121  343
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             51              121
  MALE               63              343
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    91   8
  ARID1A WILD-TYPE 325  94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     91    8
  ARID1A WILD-TYPE  325   94
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              91              325
  YES              8               94
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID1A MUTATED      21                         4
  ARID1A WILD-TYPE   112                        10
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1A MUTATED                                           0    75
  ARID1A WILD-TYPE                                         1   282
D2V11, multiclass
                                           clus
vv                                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                                 21              112
  BLACK OR AFRICAN AMERICAN                              4               10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 75              282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                  cls
clus                 0   1
  ARID1A MUTATED     3  85
  ARID1A WILD-TYPE   7 313
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3   85
  ARID1A WILD-TYPE    7  313
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  3                7
  NOT HISPANIC OR LATINO             85              313
[1] 2 2
[1] FALSE

Clustering(3) Variable = MLL2 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    61  32
  MLL2 WILD-TYPE 277 184
  MLL2 MUTATED MLL2 WILD-TYPE 
            93            461 
  MLL2 MUTATED MLL2 WILD-TYPE 
            32            184 
$`MLL2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OG TCGA-CG-4460 TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
        4.31         4.70        21.99         7.63        13.94         8.94 
TCGA-IG-A625 TCGA-JY-A6FD TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       12.82        68.02        31.56        24.03         6.28        30.25 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49R 
        2.60        25.12         7.76         8.71        46.09        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A5U5 TCGA-LN-A7HX 
       13.15        15.35        12.59        12.76         4.47        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6XG 
       13.18        12.33        13.18         0.13        12.03        38.40 
TCGA-VR-A8EU TCGA-XP-A8T7 TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 
       18.31        41.23         2.66        26.70        19.56        30.90 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 
        9.34         9.67         6.18         6.61        34.68        13.87 
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 
       32.78        30.90        35.84        29.59         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        0.26         4.31        31.27         7.36        25.05         1.12 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI 
       27.12        28.14         7.53        16.14         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-5721 
       12.62        15.95         1.02        54.08        29.98         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-A4YV 
      105.07        28.96        65.10        17.19        24.72         5.92 
TCGA-D7-A6EY TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 
       11.44        77.29        30.51        26.47        22.32        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       29.98         0.10         6.51         6.58        20.25        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-A6RN TCGA-IN-A6RR TCGA-R5-A7ZI TCGA-R5-A804 
       14.07        33.40        19.53         6.74        74.53         4.60 
TCGA-RD-A8MV TCGA-VQ-A8P2 TCGA-VQ-A91Q 
      122.30        38.14        20.81 

$`MLL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         5.92        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       23.18        25.22         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37        13.41        83.24        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 
       12.59        13.25        12.62        12.46        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I0 
       12.33        25.25        10.52        12.00        12.03        13.38 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        3.42         2.10         1.32        19.73        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6456 
       18.35         4.08         4.08         9.57        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.96         2.20         7.40        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 
       26.33        14.04         3.32        11.80        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
       27.02         7.99         8.05         4.01        14.01        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        5.52         6.21        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       11.77        21.37         8.98         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.84        23.80        21.17        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       14.04        45.67        18.21         8.52         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        15.65         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MLL2 MUTATED MLL2 WILD-TYPE 
           0.1            0.0 
  MLL2 MUTATED MLL2 WILD-TYPE 
         122.3          122.1 
  MLL2 MUTATED MLL2 WILD-TYPE 
         15.35          13.48 
[1] "0.1 - 122.3 (15.3)" "0.0 - 122.1 (13.5)"
[1] "hr=" "1.3"
D3V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL2 MUTATED         3        3       11        3        21        11
  MLL2 WILD-TYPE       7       17       35       28        63        72
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL2 MUTATED           7          7          7         10       10         0
  MLL2 WILD-TYPE        22         77         55         29       33         4
D3V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               3              7
  STAGE IA              3             17
  STAGE IB             11             35
  STAGE II              3             28
  STAGE IIA            21             63
  STAGE IIB            11             72
  STAGE III             7             22
  STAGE IIIA            7             77
  STAGE IIIB            7             55
  STAGE IIIC           10             29
  STAGE IV             10             33
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLL2 MUTATED      10  25  40  20
  MLL2 WILD-TYPE    44 110 221  82
D3V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T0+T1           10             44
  T2              25            110
  T3              40            221
  T4              20             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL2 MUTATED    38  32  13  12
  MLL2 WILD-TYPE 157 141  76  73
D3V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           38            157
  N1           32            141
  N2           13             76
  N3           12             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus               0   1
  MLL2 MUTATED    86   6
  MLL2 WILD-TYPE 396  32
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     86    6
  MLL2 WILD-TYPE  396   32
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           86            396
  1            6             32
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  MLL2 MUTATED    40  59
  MLL2 WILD-TYPE 132 347
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     40   59
  MLL2 WILD-TYPE  132  347
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           40            132
  MALE             59            347
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus               0   1
  MLL2 MUTATED    69  17
  MLL2 WILD-TYPE 347  85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     69   17
  MLL2 WILD-TYPE  347   85
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            69            347
  YES           17             85
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL2 MUTATED      27                         2
  MLL2 WILD-TYPE   106                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL2 MUTATED                                           0    53
  MLL2 WILD-TYPE                                         1   304
D3V11, multiclass
                                           clus
vv                                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                               27            106
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               53            304
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                cls
clus               0   1
  MLL2 MUTATED     2  68
  MLL2 WILD-TYPE   8 330
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   68
  MLL2 WILD-TYPE    8  330
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2              8
  NOT HISPANIC OR LATINO           68            330
[1] 2 2
[1] FALSE

Clustering(4) Variable = RNF43 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  RNF43 MUTATED    27  14
  RNF43 WILD-TYPE 311 202
  RNF43 MUTATED RNF43 WILD-TYPE 
             41             513 
  RNF43 MUTATED RNF43 WILD-TYPE 
             14             202 
$`RNF43 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 
        4.31        19.99        11.01         6.97        30.90         9.34 
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8361 
       34.68        44.94        35.84        32.25         6.18        31.10 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-A4QL 
        4.31        31.27        25.05         1.12        12.79        16.14 
TCGA-BR-A4QM TCGA-CG-4306 TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 
        5.13         1.02         7.07         6.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-A4YT TCGA-F1-A448 TCGA-HF-A5NB TCGA-HJ-7597 
       21.07         7.99        14.27        21.27        30.51        26.47 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
       24.20        29.98         0.10         6.51        29.00        14.07 
TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A91U 
       19.73        19.04        48.79        38.14         1.71 

$`RNF43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        19.56         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       31.20        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42         1.15        21.44        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        15.02         4.01        69.04 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37         8.98         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RNF43 MUTATED RNF43 WILD-TYPE 
            0.1             0.0 
  RNF43 MUTATED RNF43 WILD-TYPE 
           65.1           122.3 
  RNF43 MUTATED RNF43 WILD-TYPE 
          19.73           13.41 
[1] "0.1 - 65.1 (19.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D4V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF43 MUTATED         0        2        7        0         6         5
  RNF43 WILD-TYPE      10       18       39       31        78        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF43 MUTATED           0          9          3          7        4         0
  RNF43 WILD-TYPE        29         75         59         32       39         4
D4V3, multiclass
            clus
vv           RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               7              39
  STAGE II               0              31
  STAGE IIA              6              78
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             9              75
  STAGE IIIB             3              59
  STAGE IIIC             7              32
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RNF43 MUTATED       4  10  17  14
  RNF43 WILD-TYPE    50 125 244  88
D4V4, multiclass
       clus
vv      RNF43 MUTATED RNF43 WILD-TYPE
  T0+T1             4              50
  T2               10             125
  T3               17             244
  T4               14              88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RNF43 MUTATED    18   9   7  10
  RNF43 WILD-TYPE 177 164  82  75
D4V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            18             177
  N1             9             164
  N2             7              82
  N3            10              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                 cls
clus                0   1
  RNF43 MUTATED    42   1
  RNF43 WILD-TYPE 440  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     42    1
  RNF43 WILD-TYPE  440   37
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            42             440
  1             1              37
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  RNF43 MUTATED    24  23
  RNF43 WILD-TYPE 148 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     24   23
  RNF43 WILD-TYPE  148  383
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE            24             148
  MALE              23             383
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus                0   1
  RNF43 MUTATED    31   4
  RNF43 WILD-TYPE 385  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     31    4
  RNF43 WILD-TYPE  385   98
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO             31             385
  YES             4              98
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "RNF43 MUTATED"         
clus
  RNF43 MUTATED RNF43 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL      TCGA-IG-A3Y9 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" "RNF43 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RNF43 MUTATED       7                         0
  RNF43 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF43 MUTATED                                           0    30
  RNF43 WILD-TYPE                                         1   327
D4V11, multiclass
                                           clus
vv                                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                30             327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                 cls
clus                0   1
  RNF43 MUTATED     1  32
  RNF43 WILD-TYPE   9 366
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      1   32
  RNF43 WILD-TYPE    9  366
                        clus
vv                       RNF43 MUTATED RNF43 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            32             366
[1] 2 2
[1] FALSE

Clustering(5) Variable = SMAD4 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    23  18
  SMAD4 WILD-TYPE 315 198
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             41             513 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             198 
$`SMAD4 MUTATED`
TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-2H-A9GN TCGA-IC-A6RE TCGA-JY-A93C TCGA-L5-A4OR 
       24.00         5.16         8.94         7.69        23.18         3.16 
TCGA-L5-A8NU TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-VR-A8EQ TCGA-VR-AA7D 
       83.24         5.06        53.95         2.30        22.82         9.17 
TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7722 
        2.66         6.97         6.18         9.57        26.10        15.32 
TCGA-BR-7958 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 
       29.56        31.10         0.95         3.32        31.27         1.12 
TCGA-BR-A4J6 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8529 TCGA-CG-4469 TCGA-CG-5719 
        0.66        11.21        12.10        12.30         7.07         1.02 
TCGA-D7-6815 TCGA-D7-A6EV TCGA-F1-A72C TCGA-FP-7829 TCGA-HU-8243 TCGA-HU-A4G2 
       15.98        11.24        11.38        19.53         5.92        24.30 
TCGA-HU-A4H4 TCGA-IN-8462 TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-VQ-A91U 
       23.84        18.81        63.62         8.52         1.71 

$`SMAD4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
       38.40         6.35         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05        11.24        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.67         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        6.18         0.26        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       14.04        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18        13.35        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 
       19.07        12.03         0.00         9.01        18.97        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.66            0.00 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          83.24          122.30 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          11.21           13.87 
[1] "0.7 - 83.2 (11.2)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD4 MUTATED         0        1        2        2         6         8
  SMAD4 WILD-TYPE      10       19       44       29        78        75
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED           2          3          5          4        4         0
  SMAD4 WILD-TYPE        27         81         57         35       39         4
D5V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              8              75
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             5              57
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SMAD4 MUTATED       3   7  21   7
  SMAD4 WILD-TYPE    51 128 240  95
D5V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T0+T1             3              51
  T2                7             128
  T3               21             240
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SMAD4 MUTATED    12  13   8   5
  SMAD4 WILD-TYPE 183 160  81  80
D5V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            12             183
  N1            13             160
  N2             8              81
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED    32   3
  SMAD4 WILD-TYPE 450  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     32    3
  SMAD4 WILD-TYPE  450   35
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            32             450
  1             3              35
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED    13  28
  SMAD4 WILD-TYPE 159 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     13   28
  SMAD4 WILD-TYPE  159  378
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            13             159
  MALE              28             378
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    32   5
  SMAD4 WILD-TYPE 384  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     32    5
  SMAD4 WILD-TYPE  384   97
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO             32             384
  YES             5              97
[1] 2 2
[1] FALSE
D5V9, continuous
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D5V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD4 MUTATED       9                         1
  SMAD4 WILD-TYPE   124                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD4 MUTATED                                           0    26
  SMAD4 WILD-TYPE                                         1   331
D5V11, multiclass
                                           clus
vv                                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                26             331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  30
  SMAD4 WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   30
  SMAD4 WILD-TYPE   10  368
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(6) Variable = KRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    24  12
  KRAS WILD-TYPE 314 204
  KRAS MUTATED KRAS WILD-TYPE 
            36            518 
  KRAS MUTATED KRAS WILD-TYPE 
            12            204 
$`KRAS MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NT TCGA-CG-5727 TCGA-EQ-A4SO TCGA-IC-A6RE TCGA-B7-A5TJ 
       24.00        27.12        79.07        16.24         7.69        11.01 
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 
        9.47         6.97        30.90         9.67         6.18         6.61 
TCGA-BR-6705 TCGA-BR-6802 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 
       25.61        30.90        36.16        35.84        14.43        29.59 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CQ 
        0.95         4.31         3.32        31.96         8.22        34.98 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-8535 TCGA-CD-A4MJ TCGA-D7-A74A TCGA-HF-A5NB 
       16.14        13.41        12.82        12.62        19.96        30.51 
TCGA-HU-8604 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-SW-A7EA TCGA-VQ-A94T TCGA-VQ-AA69 
       22.82         0.10        29.00        19.04        11.24        28.41 

$`KRAS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        47.05        21.99        22.98         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
        2.66        19.73        26.70        11.70        19.56         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.34         9.57        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       44.94        21.90         9.21        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15        21.44         5.13        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        42.64        66.81        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KRAS MUTATED KRAS WILD-TYPE 
           0.1            0.0 
  KRAS MUTATED KRAS WILD-TYPE 
         79.07         122.30 
  KRAS MUTATED KRAS WILD-TYPE 
         16.19          13.51 
[1] "0.1 - 79.1 (16.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D6V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED         0        1        7        2         2         4
  KRAS WILD-TYPE      10       19       39       29        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED           2          8          6          4        2         0
  KRAS WILD-TYPE        27         76         56         35       41         4
D6V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              7             39
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             2             27
  STAGE IIIA            8             76
  STAGE IIIB            6             56
  STAGE IIIC            4             35
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  KRAS MUTATED       2   9  15  13
  KRAS WILD-TYPE    52 126 246  89
D6V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T0+T1            2             52
  T2               9            126
  T3              15            246
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KRAS MUTATED    15   7   9   5
  KRAS WILD-TYPE 180 166  80  80
D6V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           15            180
  N1            7            166
  N2            9             80
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                cls
clus               0   1
  KRAS MUTATED    36   1
  KRAS WILD-TYPE 446  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     36    1
  KRAS WILD-TYPE  446   37
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           36            446
  1            1             37
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  KRAS MUTATED    18  22
  KRAS WILD-TYPE 154 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     18   22
  KRAS WILD-TYPE  154  384
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           18            154
  MALE             22            384
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  KRAS MUTATED    32   4
  KRAS WILD-TYPE 384  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     32    4
  KRAS WILD-TYPE  384   98
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            32            384
  YES            4             98
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KRAS MUTATED       7                         0
  KRAS WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRAS MUTATED                                           0    29
  KRAS WILD-TYPE                                         1   328
D6V11, multiclass
                                           clus
vv                                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               29            328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                cls
clus               0   1
  KRAS MUTATED     0  33
  KRAS WILD-TYPE  10 365
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   33
  KRAS WILD-TYPE   10  365
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           33            365
[1] 2 2
[1] FALSE

Clustering(7) Variable = XYLT2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    25  10
  XYLT2 WILD-TYPE 313 206
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             35             519 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             10             206 
$`XYLT2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A8NM TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-6566 
       19.99        21.99         7.76        19.56        34.68        32.78 
TCGA-BR-7707 TCGA-BR-7723 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8360 
       35.84        28.73        29.59        32.25         8.05         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 
       31.10         0.26        25.05         1.12        28.14        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5728 
        6.58        11.77        12.62         1.02       105.07        65.10 
TCGA-CG-5733 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GU 
       21.07        11.08        77.29        30.51        22.32         6.58 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       20.25        29.00        14.07        19.73        38.14 

$`XYLT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.24        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.69         9.60         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        2.20         7.40        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.61        12.20        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
           0.26            0.00 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
         105.07          122.30 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          21.07           13.41 
[1] "0.3 - 105.1 (21.1)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.9"
D7V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XYLT2 MUTATED         1        0        5        3         6         6
  XYLT2 WILD-TYPE       9       20       41       28        78        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XYLT2 MUTATED           0          5          1          9        3         0
  XYLT2 WILD-TYPE        29         79         61         30       40         4
D7V3, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               5              41
  STAGE II               3              28
  STAGE IIA              6              78
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             1              61
  STAGE IIIC             9              30
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  XYLT2 MUTATED       3   8  13  16
  XYLT2 WILD-TYPE    51 127 248  86
D7V4, multiclass
       clus
vv      XYLT2 MUTATED XYLT2 WILD-TYPE
  T0+T1             3              51
  T2                8             127
  T3               13             248
  T4               16              86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  XYLT2 MUTATED    16   9   6   8
  XYLT2 WILD-TYPE 179 164  83  77
D7V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            16             179
  N1             9             164
  N2             6              83
  N3             8              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                 cls
clus                0   1
  XYLT2 MUTATED    36   2
  XYLT2 WILD-TYPE 446  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     36    2
  XYLT2 WILD-TYPE  446   36
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            36             446
  1             2              36
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  XYLT2 MUTATED    22  18
  XYLT2 WILD-TYPE 150 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     22   18
  XYLT2 WILD-TYPE  150  388
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  FEMALE            22             150
  MALE              18             388
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  XYLT2 MUTATED    30   4
  XYLT2 WILD-TYPE 386  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     30    4
  XYLT2 WILD-TYPE  386   98
     clus
vv    XYLT2 MUTATED XYLT2 WILD-TYPE
  NO             30             386
  YES             4              98
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
[1] "Remove cluster labels:" "XYLT2 MUTATED"         
clus
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" "XYLT2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"XYLT2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XYLT2 MUTATED       9                         2
  XYLT2 WILD-TYPE   124                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XYLT2 MUTATED                                           0    22
  XYLT2 WILD-TYPE                                         1   335
D7V11, multiclass
                                           clus
vv                                          XYLT2 MUTATED XYLT2 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                22             335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                 cls
clus                0   1
  XYLT2 MUTATED     0  30
  XYLT2 WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED      0   30
  XYLT2 WILD-TYPE   10  368
                        clus
vv                       XYLT2 MUTATED XYLT2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(8) Variable = PTEN MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    23  12
  PTEN WILD-TYPE 315 204
  PTEN MUTATED PTEN WILD-TYPE 
            35            519 
  PTEN MUTATED PTEN WILD-TYPE 
            12            204 
$`PTEN MUTATED`
TCGA-JY-A93F TCGA-L5-A88V TCGA-L5-A8NM TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV 
       24.03         2.60         7.76        12.33        13.22        10.52 
TCGA-VR-A8EP TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
       27.09        26.70        19.56        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8284 
        9.67        34.68        19.89        35.24        29.59         8.05 
TCGA-BR-8368 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8531 TCGA-CG-4305 
        4.31         7.36         1.12        28.14        12.59        15.95 
TCGA-CG-5725 TCGA-CG-5728 TCGA-D7-5577 TCGA-FP-7735 TCGA-FP-8211 TCGA-FP-A4BE 
       15.02        65.10        25.71         3.48        13.58        11.08 
TCGA-HU-A4GT TCGA-IN-A6RN TCGA-R5-A7O7 TCGA-R5-A805 TCGA-VQ-A8DL 
        6.51        19.53        45.67         9.24         0.92 

$`PTEN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        25.22         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
       12.59        22.39        12.85        15.52        11.54         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.39        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44         8.94        35.61        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PTEN MUTATED PTEN WILD-TYPE 
          0.92           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
          65.1          122.3 
  PTEN MUTATED PTEN WILD-TYPE 
         13.22          13.68 
[1] "0.9 - 65.1 (13.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D8V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTEN MUTATED         0        0        5        2         9         6
  PTEN WILD-TYPE      10       20       41       29        75        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED           2          3          2          3        1         0
  PTEN WILD-TYPE        27         81         60         36       42         4
D8V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              5             41
  STAGE II              2             29
  STAGE IIA             9             75
  STAGE IIB             6             77
  STAGE III             2             27
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PTEN MUTATED       1  11  16   6
  PTEN WILD-TYPE    53 124 245  96
D8V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T0+T1            1             53
  T2              11            124
  T3              16            245
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTEN MUTATED    17  11   3   4
  PTEN WILD-TYPE 178 162  86  81
D8V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           17            178
  N1           11            162
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                cls
clus               0   1
  PTEN MUTATED    33   1
  PTEN WILD-TYPE 449  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     33    1
  PTEN WILD-TYPE  449   37
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           33            449
  1            1             37
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  PTEN MUTATED    19  18
  PTEN WILD-TYPE 153 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     19   18
  PTEN WILD-TYPE  153  388
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           19            153
  MALE             18            388
[1] 2 2
[1] FALSE
D8V8, binary
                cls
clus               0   1
  PTEN MUTATED    30   4
  PTEN WILD-TYPE 386  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     30    4
  PTEN WILD-TYPE  386   98
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            30            386
  YES            4             98
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PTEN MUTATED       5                         2
  PTEN WILD-TYPE   128                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTEN MUTATED                                           0    27
  PTEN WILD-TYPE                                         1   330
D8V11, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               27            330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                cls
clus               0   1
  PTEN MUTATED     1  28
  PTEN WILD-TYPE   9 370
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   28
  PTEN WILD-TYPE    9  370
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           28            370
[1] 2 2
[1] FALSE

Clustering(9) Variable = LARP4B MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    20   9
  LARP4B WILD-TYPE 318 207
  LARP4B MUTATED LARP4B WILD-TYPE 
              29              525 
  LARP4B MUTATED LARP4B WILD-TYPE 
               9              207 
$`LARP4B MUTATED`
TCGA-IG-A8O2 TCGA-L5-A8NM TCGA-L5-A8NS TCGA-Z6-A8JE TCGA-BR-4201 TCGA-BR-4257 
        4.67         7.76        13.41         2.10        30.90         9.67 
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8680 
       32.78        35.84         4.31        31.27        28.14        31.96 
TCGA-BR-A4QL TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 
       16.14        12.82         6.58        11.77         6.02        65.10 
TCGA-CG-5733 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN 
       21.07        14.47        30.51        22.32        22.68        29.98 
TCGA-HU-A4GT TCGA-IN-A6RN TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-VQ-A8P2 
        6.51        19.53        74.53        16.67        38.14 

$`LARP4B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  LARP4B MUTATED LARP4B WILD-TYPE 
             2.1              0.0 
  LARP4B MUTATED LARP4B WILD-TYPE 
           74.53           122.30 
  LARP4B MUTATED LARP4B WILD-TYPE 
           19.53            13.48 
[1] "2.1 - 74.5 (19.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D9V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP4B MUTATED         0        0        5        0         5         4
  LARP4B WILD-TYPE      10       20       41       31        79        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           0          6          2          3        4
  LARP4B WILD-TYPE        29         78         60         36       39
                  vv
clus               STAGE IVA
  LARP4B MUTATED           0
  LARP4B WILD-TYPE         4
D9V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                5               41
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              6               78
  STAGE IIIB              2               60
  STAGE IIIC              3               36
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  LARP4B MUTATED       2   9  11  10
  LARP4B WILD-TYPE    52 126 250  92
D9V4, multiclass
       clus
vv      LARP4B MUTATED LARP4B WILD-TYPE
  T0+T1              2               52
  T2                 9              126
  T3                11              250
  T4                10               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LARP4B MUTATED    11   9   5   4
  LARP4B WILD-TYPE 184 164  84  81
D9V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0             11              184
  N1              9              164
  N2              5               84
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                  cls
clus                 0   1
  LARP4B MUTATED    31   2
  LARP4B WILD-TYPE 451  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     31    2
  LARP4B WILD-TYPE  451   36
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             31              451
  1              2               36
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                 0   1
  LARP4B MUTATED    20  14
  LARP4B WILD-TYPE 152 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     20   14
  LARP4B WILD-TYPE  152  392
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE             20              152
  MALE               14              392
[1] 2 2
[1] FALSE
D9V8, binary
                  cls
clus                 0   1
  LARP4B MUTATED    24   3
  LARP4B WILD-TYPE 392  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     24    3
  LARP4B WILD-TYPE  392   99
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO              24              392
  YES              3               99
[1] 2 2
[1] FALSE
D9V9, continuous
[1] "Remove cluster labels:" "LARP4B MUTATED"        
clus
  LARP4B MUTATED LARP4B WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JD 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
D9V10, continuous
[1] "Remove cluster labels:" "LARP4B MUTATED"        
clus
  LARP4B MUTATED LARP4B WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LARP4B MUTATED       9                         0
  LARP4B WILD-TYPE   124                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP4B MUTATED                                           0    21
  LARP4B WILD-TYPE                                         1   336
D9V11, multiclass
                                           clus
vv                                          LARP4B MUTATED LARP4B WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 21              336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                  cls
clus                 0   1
  LARP4B MUTATED     1  26
  LARP4B WILD-TYPE   9 372
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      1   26
  LARP4B WILD-TYPE    9  372
                        clus
vv                       LARP4B MUTATED LARP4B WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             26              372
[1] 2 2
[1] FALSE

Clustering(10) Variable = FBXW7 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    29  13
  FBXW7 WILD-TYPE 309 203
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             42             512 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             203 
$`FBXW7 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GN TCGA-IG-A3YB TCGA-IG-A7DP TCGA-L5-A88Z TCGA-L5-A8NI 
       19.99         8.94         2.63        14.86         7.40        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-LN-A8HZ TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-V5-A7RB 
        7.76         5.49        12.33        16.31        15.78         5.29 
TCGA-XP-A8T7 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8360 
       41.23        30.90         9.34        44.94        35.84         6.18 
TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4QL 
       31.27         9.21         1.12        24.79        31.96        16.14 
TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       12.43        12.62         6.02       105.07        65.10        21.07 
TCGA-D7-A4YV TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 
        5.92        11.44        21.27        77.29        30.51        22.32 
TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-KB-A6F5 TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
       29.98        29.00         5.56        19.73         5.46        38.14 

$`FBXW7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.12            0.00 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         105.07          122.30 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          15.96           13.51 
[1] "1.1 - 105.1 (16.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D10V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXW7 MUTATED         0        0        4        3         7         4
  FBXW7 WILD-TYPE      10       20       42       28        77        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED           3          7          3          6        2         1
  FBXW7 WILD-TYPE        26         77         59         33       41         3
D10V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               4              42
  STAGE II               3              28
  STAGE IIA              7              77
  STAGE IIB              4              79
  STAGE III              3              26
  STAGE IIIA             7              77
  STAGE IIIB             3              59
  STAGE IIIC             6              33
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FBXW7 MUTATED       2  13  17  11
  FBXW7 WILD-TYPE    52 122 244  91
D10V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T0+T1             2              52
  T2               13             122
  T3               17             244
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FBXW7 MUTATED    12  15   5   9
  FBXW7 WILD-TYPE 183 158  84  76
D10V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            12             183
  N1            15             158
  N2             5              84
  N3             9              76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED    39   2
  FBXW7 WILD-TYPE 443  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     39    2
  FBXW7 WILD-TYPE  443   36
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            39             443
  1             2              36
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    19  26
  FBXW7 WILD-TYPE 153 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     19   26
  FBXW7 WILD-TYPE  153  380
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            19             153
  MALE              26             380
[1] 2 2
[1] FALSE
D10V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    36   6
  FBXW7 WILD-TYPE 380  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     36    6
  FBXW7 WILD-TYPE  380   96
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             36             380
  YES             6              96
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FBXW7 MUTATED       7                         0
  FBXW7 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXW7 MUTATED                                           0    29
  FBXW7 WILD-TYPE                                         1   328
D10V11, multiclass
                                           clus
vv                                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                29             328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                 cls
clus                0   1
  FBXW7 MUTATED     3  27
  FBXW7 WILD-TYPE   7 371
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      3   27
  FBXW7 WILD-TYPE    7  371
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 3               7
  NOT HISPANIC OR LATINO            27             371
[1] 2 2
[1] FALSE

Clustering(11) Variable = RHOA MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  RHOA MUTATED    12  10
  RHOA WILD-TYPE 326 206
  RHOA MUTATED RHOA WILD-TYPE 
            22            532 
  RHOA MUTATED RHOA WILD-TYPE 
            10            206 
$`RHOA MUTATED`
TCGA-2H-A9GK TCGA-JY-A6FG TCGA-LN-A4A9 TCGA-BR-4188 TCGA-BR-6563 TCGA-BR-6802 
        7.63        41.52        11.54         7.43        39.12        30.90 
TCGA-BR-7722 TCGA-BR-8366 TCGA-BR-A4IV TCGA-BR-A4QM TCGA-CG-4465 TCGA-CG-5720 
       15.32         0.95        28.57         5.13         9.01         0.99 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-8574 TCGA-D7-A4YU TCGA-F1-A448 TCGA-HU-A4H0 
       18.84        18.54        17.19        16.44        21.27         2.10 
TCGA-R5-A804 TCGA-VQ-A8P2 TCGA-VQ-A8PM TCGA-ZA-A8F6 
        4.60        38.14         1.87        17.26 

$`RHOA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        18.15        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        31.10         0.26        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
        7.53         6.08        34.98         1.48        27.55        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         6.08         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        27.55        12.43 

  RHOA MUTATED RHOA WILD-TYPE 
          0.95           0.00 
  RHOA MUTATED RHOA WILD-TYPE 
         41.52         122.30 
  RHOA MUTATED RHOA WILD-TYPE 
         15.88          13.53 
[1] "0.9 - 41.5 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOA MUTATED         0        0        2        0         2         2
  RHOA WILD-TYPE      10       20       44       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHOA MUTATED           2          5          3          1        3         0
  RHOA WILD-TYPE        27         79         59         38       40         4
D11V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            5             79
  STAGE IIIB            3             59
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RHOA MUTATED       0   6  10   5
  RHOA WILD-TYPE    54 129 251  97
D11V4, multiclass
       clus
vv      RHOA MUTATED RHOA WILD-TYPE
  T0+T1            0             54
  T2               6            129
  T3              10            251
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RHOA MUTATED     4   6   6   6
  RHOA WILD-TYPE 191 167  83  79
D11V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            4            191
  N1            6            167
  N2            6             83
  N3            6             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                cls
clus               0   1
  RHOA MUTATED    19   2
  RHOA WILD-TYPE 463  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     19    2
  RHOA WILD-TYPE  463   36
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0           19            463
  1            2             36
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  RHOA MUTATED     3  19
  RHOA WILD-TYPE 169 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      3   19
  RHOA WILD-TYPE  169  387
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            3            169
  MALE             19            387
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  RHOA MUTATED    18   2
  RHOA WILD-TYPE 398 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     18    2
  RHOA WILD-TYPE  398  100
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO            18            398
  YES            2            100
[1] 2 2
[1] FALSE
D11V9, continuous
[1] "Remove cluster labels:" "RHOA MUTATED"          
clus
  RHOA MUTATED RHOA WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
D11V10, continuous
[1] "Remove cluster labels:" "RHOA MUTATED"          
clus
  RHOA MUTATED RHOA WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RHOA MUTATED       3                         1
  RHOA WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHOA MUTATED                                           0    15
  RHOA WILD-TYPE                                         1   342
D11V11, multiclass
                                           clus
vv                                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                cls
clus               0   1
  RHOA MUTATED     1  15
  RHOA WILD-TYPE   9 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      1   15
  RHOA WILD-TYPE    9  383
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(12) Variable = B2M MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  B2M MUTATED    14   4
  B2M WILD-TYPE 324 212
  B2M MUTATED B2M WILD-TYPE 
           18           536 
  B2M MUTATED B2M WILD-TYPE 
            4           212 
$`B2M MUTATED`
TCGA-L5-A4OI TCGA-V5-AASX TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8382 
       19.99         8.98        32.78        44.94        35.84        25.05 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 
        1.12        28.14        16.14        12.43        11.77         6.02 
TCGA-CG-5728 TCGA-D7-8570 TCGA-D7-A6EY TCGA-D7-A74A TCGA-HU-A4GX TCGA-HU-A4H8 
       65.10        24.72        11.44        19.96        20.25        14.07 

$`B2M WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  B2M MUTATED B2M WILD-TYPE 
         1.12          0.00 
  B2M MUTATED B2M WILD-TYPE 
         65.1         122.3 
  B2M MUTATED B2M WILD-TYPE 
       19.975        13.495 
[1] "1.1 - 65.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D12V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B2M MUTATED         1        0        3        1         3         0
  B2M WILD-TYPE       9       20       43       30        81        83
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  B2M MUTATED           0          2          3          4        1         0
  B2M WILD-TYPE        29         82         59         35       42         4
D12V3, multiclass
            clus
vv           B2M MUTATED B2M WILD-TYPE
  STAGE I              1             9
  STAGE IA             0            20
  STAGE IB             3            43
  STAGE II             1            30
  STAGE IIA            3            81
  STAGE IIB            0            83
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           3            59
  STAGE IIIC           4            35
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  B2M MUTATED       2   2  10   4
  B2M WILD-TYPE    52 133 251  98
D12V4, multiclass
       clus
vv      B2M MUTATED B2M WILD-TYPE
  T0+T1           2            52
  T2              2           133
  T3             10           251
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  B2M MUTATED     6   5   2   6
  B2M WILD-TYPE 189 168  87  79
D12V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0           6           189
  N1           5           168
  N2           2            87
  N3           6            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
               cls
clus              0   1
  B2M MUTATED    17   0
  B2M WILD-TYPE 465  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     17    0
  B2M WILD-TYPE  465   38
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          17           465
  1           0            38
[1] 2 2
[1] FALSE
D12V7, binary
               cls
clus              0   1
  B2M MUTATED    11   9
  B2M WILD-TYPE 161 397
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     11    9
  B2M WILD-TYPE  161  397
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE          11           161
  MALE             9           397
[1] 2 2
[1] FALSE
D12V8, binary
               cls
clus              0   1
  B2M MUTATED    17   0
  B2M WILD-TYPE 399 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     17    0
  B2M WILD-TYPE  399  102
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO           17           399
  YES           0           102
[1] 2 2
[1] FALSE
D12V9, continuous
[1] "Remove cluster labels:" "B2M MUTATED"           
clus
  B2M MUTATED B2M WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-V5-AASW    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"B2M WILD-TYPE" "B2M WILD-TYPE" 
D12V10, continuous
[1] "Remove cluster labels:" "B2M MUTATED"           
clus
  B2M MUTATED B2M WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" "B2M WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"B2M WILD-TYPE" "B2M WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  B2M MUTATED       4                         1
  B2M WILD-TYPE   129                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B2M MUTATED                                           0    13
  B2M WILD-TYPE                                         1   344
D12V11, multiclass
                                           clus
vv                                          B2M MUTATED B2M WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              13           344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
               cls
clus              0   1
  B2M MUTATED     0  17
  B2M WILD-TYPE  10 381
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      0   17
  B2M WILD-TYPE   10  381
                        clus
vv                       B2M MUTATED B2M WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          17           381
[1] 2 2
[1] FALSE

Clustering(13) Variable = HLA-B MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    23   9
  HLA-B WILD-TYPE 315 207
  HLA-B MUTATED HLA-B WILD-TYPE 
             32             522 
  HLA-B MUTATED HLA-B WILD-TYPE 
              9             207 
$`HLA-B MUTATED`
TCGA-CG-4460 TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A4OP TCGA-L5-A8NJ TCGA-V5-AASX 
       21.99        41.52        24.03         7.17        16.47         8.98 
TCGA-VR-A8EP TCGA-Z6-AAPN TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8078 
       27.09         2.66        26.70         6.61        44.94        29.59 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8591 TCGA-CD-8531 
        0.26         0.95        31.27        27.12        28.14        12.59 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 
        6.58        12.62         1.02         9.01         6.02        28.96 
TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-KB-A93J 
       65.10        14.47        22.68         0.10        29.00        36.95 
TCGA-MX-A5UJ TCGA-SW-A7EA 
       19.73        19.04 

$`HLA-B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 
       14.37         3.42         2.10         1.32        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        7.40         6.18        31.10        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  HLA-B MUTATED HLA-B WILD-TYPE 
            0.1             0.0 
  HLA-B MUTATED HLA-B WILD-TYPE 
           65.1           122.3 
  HLA-B MUTATED HLA-B WILD-TYPE 
         19.385          13.495 
[1] "0.1 - 65.1 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D13V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-B MUTATED         0        3        7        1         4         3
  HLA-B WILD-TYPE      10       17       39       30        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-B MUTATED           3          2          2          4        4         0
  HLA-B WILD-TYPE        26         82         60         35       39         4
D13V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0              10
  STAGE IA               3              17
  STAGE IB               7              39
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              3              26
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HLA-B MUTATED       3   9  12  10
  HLA-B WILD-TYPE    51 126 249  92
D13V4, multiclass
       clus
vv      HLA-B MUTATED HLA-B WILD-TYPE
  T0+T1             3              51
  T2                9             126
  T3               12             249
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HLA-B MUTATED    16   9   4   4
  HLA-B WILD-TYPE 179 164  85  81
D13V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            16             179
  N1             9             164
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    29   3
  HLA-B WILD-TYPE 453  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     29    3
  HLA-B WILD-TYPE  453   35
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0            29             453
  1             3              35
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  HLA-B MUTATED    17  18
  HLA-B WILD-TYPE 155 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     17   18
  HLA-B WILD-TYPE  155  388
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE            17             155
  MALE              18             388
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  HLA-B MUTATED    23   3
  HLA-B WILD-TYPE 393  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     23    3
  HLA-B WILD-TYPE  393   99
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO             23             393
  YES             3              99
[1] 2 2
[1] FALSE
D13V9, continuous
[1] "Remove cluster labels:" "HLA-B MUTATED"         
clus
  HLA-B MUTATED HLA-B WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EQ 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"HLA-B WILD-TYPE" "HLA-B WILD-TYPE" 
D13V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HLA-B MUTATED       7                         0
  HLA-B WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-B MUTATED                                           0    21
  HLA-B WILD-TYPE                                         1   336
D13V11, multiclass
                                           clus
vv                                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  22
  HLA-B WILD-TYPE  10 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   22
  HLA-B WILD-TYPE   10  376
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(14) Variable = C7ORF50 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     7   6
  C7ORF50 WILD-TYPE 331 210
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               13               541 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                6               210 
$`C7ORF50 MUTATED`
TCGA-CG-4460 TCGA-IG-A6QS TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 
       21.99         9.96        34.68         6.18        31.10         1.12 
TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4G8 
       16.14        28.96        13.78        11.44        14.47        22.68 
TCGA-HU-A4GQ 
        0.10 

$`C7ORF50 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         2.20         7.40         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
              0.1               0.0 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            34.68            122.30 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            14.47             13.51 
[1] "0.1 - 34.7 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF50 MUTATED         0        1        1        0         3         2
  C7ORF50 WILD-TYPE      10       19       45       31        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          3          2        1
  C7ORF50 WILD-TYPE        29         84         59         37       42
                   vv
clus                STAGE IVA
  C7ORF50 MUTATED           0
  C7ORF50 WILD-TYPE         4
D14V3, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               3                59
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C7ORF50 MUTATED       1   2   7   3
  C7ORF50 WILD-TYPE    53 133 254  99
D14V4, multiclass
       clus
vv      C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  7               254
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C7ORF50 MUTATED     5   3   2   3
  C7ORF50 WILD-TYPE 190 170  87  82
D14V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               5               190
  N1               3               170
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED    12   1
  C7ORF50 WILD-TYPE 470  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED     12    1
  C7ORF50 WILD-TYPE  470   37
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0              12               470
  1               1                37
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     7   6
  C7ORF50 WILD-TYPE 165 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      7    6
  C7ORF50 WILD-TYPE  165  400
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  FEMALE               7               165
  MALE                 6               400
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED    11   1
  C7ORF50 WILD-TYPE 405 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED     11    1
  C7ORF50 WILD-TYPE  405  101
     clus
vv    C7ORF50 MUTATED C7ORF50 WILD-TYPE
  NO               11               405
  YES               1               101
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
[1] "Remove cluster labels:" "C7ORF50 MUTATED"       
clus
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" "C7ORF50 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C7ORF50 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C7ORF50 MUTATED       2                         0
  C7ORF50 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C7ORF50 MUTATED                                           0     9
  C7ORF50 WILD-TYPE                                         1   348
D14V11, multiclass
                                           clus
vv                                          C7ORF50 MUTATED C7ORF50 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     0  11
  C7ORF50 WILD-TYPE  10 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      0   11
  C7ORF50 WILD-TYPE   10  387
                        clus
vv                       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(15) Variable = GNG12 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     7   3
  GNG12 WILD-TYPE 331 213
  GNG12 MUTATED GNG12 WILD-TYPE 
             10             544 
  GNG12 MUTATED GNG12 WILD-TYPE 
              3             213 
$`GNG12 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-4305 
        6.97        34.68        29.59         0.26         6.58        15.95 
TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4GT TCGA-SW-A7EA 
        6.02        22.32         6.51        19.04 

$`GNG12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GNG12 MUTATED GNG12 WILD-TYPE 
           0.26            0.00 
  GNG12 MUTATED GNG12 WILD-TYPE 
          34.68          122.30 
  GNG12 MUTATED GNG12 WILD-TYPE 
         11.460          13.565 
[1] "0.3 - 34.7 (11.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D15V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNG12 MUTATED         0        0        2        1         3         2
  GNG12 WILD-TYPE      10       20       44       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNG12 MUTATED           0          1          0          0        2         0
  GNG12 WILD-TYPE        29         83         62         39       41         4
D15V3, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GNG12 MUTATED       0   3   4   4
  GNG12 WILD-TYPE    54 132 257  98
D15V4, multiclass
       clus
vv      GNG12 MUTATED GNG12 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                4             257
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GNG12 MUTATED     7   4   1   0
  GNG12 WILD-TYPE 188 169  88  85
D15V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             7             188
  N1             4             169
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                 cls
clus                0   1
  GNG12 MUTATED    11   0
  GNG12 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED     11    0
  GNG12 WILD-TYPE  471   38
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  GNG12 MUTATED     8   4
  GNG12 WILD-TYPE 164 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      8    4
  GNG12 WILD-TYPE  164  402
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  FEMALE             8             164
  MALE               4             402
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  GNG12 MUTATED    10   0
  GNG12 WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED     10    0
  GNG12 WILD-TYPE  406  102
     clus
vv    GNG12 MUTATED GNG12 WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GNG12 MUTATED       3                         0
  GNG12 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNG12 MUTATED                                           0     7
  GNG12 WILD-TYPE                                         1   350
D15V11, multiclass
                                           clus
vv                                          GNG12 MUTATED GNG12 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                 cls
clus                0   1
  GNG12 MUTATED     0  10
  GNG12 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      0   10
  GNG12 WILD-TYPE   10  388
                        clus
vv                       GNG12 MUTATED GNG12 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(16) Variable = PLEKHA6 MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    12  13
  PLEKHA6 WILD-TYPE 326 203
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               25               529 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               13               203 
$`PLEKHA6 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3Y9 TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NM TCGA-BR-4184 
       19.99         0.85         4.90         2.60         7.76         6.97 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8363 
       34.68        32.78        33.63        14.43        31.10         0.26 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 
        4.31        25.05        16.14        11.77         1.02         6.02 
TCGA-CG-5733 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GT TCGA-IN-A6RR TCGA-R5-A7ZI 
       21.07         5.92        11.08         6.51         6.74        74.53 
TCGA-VQ-A8P2 
       38.14 

$`PLEKHA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         6.18        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
             0.26              0.00 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            74.53            122.30 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            11.08             13.68 
[1] "0.3 - 74.5 (11.1)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.5"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA6 MUTATED         0        0        2        0         5         3
  PLEKHA6 WILD-TYPE      10       20       44       31        79        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           2          7          1          3        5
  PLEKHA6 WILD-TYPE        27         77         61         36       38
                   vv
clus                STAGE IVA
  PLEKHA6 MUTATED           0
  PLEKHA6 WILD-TYPE         4
D16V3, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                5                79
  STAGE IIB                3                80
  STAGE III                2                27
  STAGE IIIA               7                77
  STAGE IIIB               1                61
  STAGE IIIC               3                36
  STAGE IV                 5                38
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PLEKHA6 MUTATED       0   4  14  10
  PLEKHA6 WILD-TYPE    54 131 247  92
D16V4, multiclass
       clus
vv      PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T0+T1               0                54
  T2                  4               131
  T3                 14               247
  T4                 10                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PLEKHA6 MUTATED    10  11   4   3
  PLEKHA6 WILD-TYPE 185 162  85  82
D16V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0              10               185
  N1              11               162
  N2               4                85
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    22   3
  PLEKHA6 WILD-TYPE 460  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     22    3
  PLEKHA6 WILD-TYPE  460   35
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              22               460
  1               3                35
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    14  14
  PLEKHA6 WILD-TYPE 158 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     14   14
  PLEKHA6 WILD-TYPE  158  392
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE              14               158
  MALE                14               392
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    23   2
  PLEKHA6 WILD-TYPE 393 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     23    2
  PLEKHA6 WILD-TYPE  393  100
     clus
vv    PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  NO               23               393
  YES               2               100
[1] 2 2
[1] FALSE
D16V9, continuous
[1] "Remove cluster labels:" "PLEKHA6 MUTATED"       
clus
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" "PLEKHA6 WILD-TYPE" 
D16V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHA6 MUTATED       2                         1
  PLEKHA6 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHA6 MUTATED                                           0    22
  PLEKHA6 WILD-TYPE                                         1   335
D16V11, multiclass
                                           clus
vv                                          PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     1  19
  PLEKHA6 WILD-TYPE   9 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      1   19
  PLEKHA6 WILD-TYPE    9  379
                        clus
vv                       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              19               379
[1] 2 2
[1] FALSE

Clustering(17) Variable = PGM5 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  PGM5 MUTATED    24  14
  PGM5 WILD-TYPE 314 202
  PGM5 MUTATED PGM5 WILD-TYPE 
            38            516 
  PGM5 MUTATED PGM5 WILD-TYPE 
            14            202 
$`PGM5 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-L5-A8NM TCGA-LN-A49U TCGA-VR-A8EQ TCGA-BR-4201 
        4.31        21.99         7.76        15.35        22.82        30.90 
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 
       34.68        36.16        35.84        29.59        32.25        31.10 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 
        0.26         4.31        31.27        25.05         1.12        31.96 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4462 
       16.14        12.43         6.58        15.95         1.02         0.00 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6521 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-FP-A4BE 
      105.07        21.07        18.54         5.92        13.78        11.08 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT 
       30.51        22.32        22.68        24.20         0.10         6.51 
TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.00        14.07 

$`PGM5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       31.20        44.94        21.90         9.21        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       11.77        12.62        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27        16.44        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.26         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PGM5 MUTATED PGM5 WILD-TYPE 
          0.00           0.13 
  PGM5 MUTATED PGM5 WILD-TYPE 
        105.07         122.30 
  PGM5 MUTATED PGM5 WILD-TYPE 
        19.805         13.410 
[1] "0.0 - 105.1 (19.8)" "0.1 - 122.3 (13.4)"
[1] "hr=" "1.2"
D17V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGM5 MUTATED         1        2        5        3         6         7
  PGM5 WILD-TYPE       9       18       41       28        78        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGM5 MUTATED           1          1          2          6        4         0
  PGM5 WILD-TYPE        28         83         60         33       39         4
D17V3, multiclass
            clus
vv           PGM5 MUTATED PGM5 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              5             41
  STAGE II              3             28
  STAGE IIA             6             78
  STAGE IIB             7             76
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            6             33
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PGM5 MUTATED       5  10  15  11
  PGM5 WILD-TYPE    49 125 246  91
D17V4, multiclass
       clus
vv      PGM5 MUTATED PGM5 WILD-TYPE
  T0+T1            5             49
  T2              10            125
  T3              15            246
  T4              11             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PGM5 MUTATED    17  10   6   7
  PGM5 WILD-TYPE 178 163  83  78
D17V5, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  N0           17            178
  N1           10            163
  N2            6             83
  N3            7             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                cls
clus               0   1
  PGM5 MUTATED    37   4
  PGM5 WILD-TYPE 445  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     37    4
  PGM5 WILD-TYPE  445   34
   clus
vv  PGM5 MUTATED PGM5 WILD-TYPE
  0           37            445
  1            4             34
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  PGM5 MUTATED    25  18
  PGM5 WILD-TYPE 147 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     25   18
  PGM5 WILD-TYPE  147  388
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  FEMALE           25            147
  MALE             18            388
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus               0   1
  PGM5 MUTATED    30   5
  PGM5 WILD-TYPE 386  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     30    5
  PGM5 WILD-TYPE  386   97
     clus
vv    PGM5 MUTATED PGM5 WILD-TYPE
  NO            30            386
  YES            5             97
[1] 2 2
[1] FALSE
D17V9, continuous
[1] "Remove cluster labels:" "PGM5 MUTATED"          
clus
  PGM5 MUTATED PGM5 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49V     TCGA-LN-A49W 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
D17V10, continuous
[1] "Remove cluster labels:" "PGM5 MUTATED"          
clus
  PGM5 MUTATED PGM5 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49V 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" "PGM5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PGM5 MUTATED      11                         2
  PGM5 WILD-TYPE   122                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PGM5 MUTATED                                           0    22
  PGM5 WILD-TYPE                                         1   335
D17V11, multiclass
                                           clus
vv                                          PGM5 MUTATED PGM5 WILD-TYPE
  ASIAN                                               11            122
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               22            335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                cls
clus               0   1
  PGM5 MUTATED     0  32
  PGM5 WILD-TYPE  10 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED      0   32
  PGM5 WILD-TYPE   10  366
                        clus
vv                       PGM5 MUTATED PGM5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           32            366
[1] 2 2
[1] FALSE

Clustering(18) Variable = MLL4 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    29  20
  MLL4 WILD-TYPE 309 196
  MLL4 MUTATED MLL4 WILD-TYPE 
            49            505 
  MLL4 MUTATED MLL4 WILD-TYPE 
            20            196 
$`MLL4 MUTATED`
TCGA-L5-A43I TCGA-L5-A4OI TCGA-JY-A6FA TCGA-L5-A4OR TCGA-L5-A8NM TCGA-LN-A4A4 
       18.28        19.99        44.75         3.16         7.76        12.59 
TCGA-LN-A4A9 TCGA-V5-AASV TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4280 
       11.54        15.35        19.56         6.97         7.43         6.61 
TCGA-BR-6452 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8078 
       34.68        17.29        19.33        32.78        44.94        29.59 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       32.25         0.26         4.31        31.27         7.36        25.05 
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        1.12        28.14        12.43         6.58        11.77        12.62 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YV 
       15.95         1.02         0.99         6.02        28.96         5.92 
TCGA-D7-A6EY TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 
       11.44        21.27        11.08        30.51        26.47        22.32 
TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-RD-A8MV TCGA-SW-A7EA 
       29.98        20.25        29.00        14.07       122.30        19.04 
TCGA-VQ-A8P2 
       38.14 

$`MLL4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.18         9.57        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44         0.69         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
       14.04         3.32        11.80        14.79         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.30        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        52.21         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MLL4 MUTATED MLL4 WILD-TYPE 
          0.26           0.00 
  MLL4 MUTATED MLL4 WILD-TYPE 
         122.3          122.1 
  MLL4 MUTATED MLL4 WILD-TYPE 
         17.29          13.48 
[1] "0.3 - 122.3 (17.3)" "0.0 - 122.1 (13.5)"
[1] "hr=" "1"  
D18V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL4 MUTATED         1        2        8        2         8        11
  MLL4 WILD-TYPE       9       18       38       29        76        72
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL4 MUTATED           2          5          3          8        2         0
  MLL4 WILD-TYPE        27         79         59         31       41         4
D18V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              8             38
  STAGE II              2             29
  STAGE IIA             8             76
  STAGE IIB            11             72
  STAGE III             2             27
  STAGE IIIA            5             79
  STAGE IIIB            3             59
  STAGE IIIC            8             31
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLL4 MUTATED       4  13  21  14
  MLL4 WILD-TYPE    50 122 240  88
D18V4, multiclass
       clus
vv      MLL4 MUTATED MLL4 WILD-TYPE
  T0+T1            4             50
  T2              13            122
  T3              21            240
  T4              14             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL4 MUTATED    23  18   3   9
  MLL4 WILD-TYPE 172 155  86  76
D18V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           23            172
  N1           18            155
  N2            3             86
  N3            9             76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                cls
clus               0   1
  MLL4 MUTATED    45   1
  MLL4 WILD-TYPE 437  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     45    1
  MLL4 WILD-TYPE  437   37
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           45            437
  1            1             37
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  MLL4 MUTATED    23  30
  MLL4 WILD-TYPE 149 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     23   30
  MLL4 WILD-TYPE  149  376
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           23            149
  MALE             30            376
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus               0   1
  MLL4 MUTATED    39   8
  MLL4 WILD-TYPE 377  94
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     39    8
  MLL4 WILD-TYPE  377   94
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            39            377
  YES            8             94
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL4 MUTATED      12                         3
  MLL4 WILD-TYPE   121                        11
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL4 MUTATED                                           0    31
  MLL4 WILD-TYPE                                         1   326
D18V11, multiclass
                                           clus
vv                                          MLL4 MUTATED MLL4 WILD-TYPE
  ASIAN                                               12            121
  BLACK OR AFRICAN AMERICAN                            3             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               31            326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                cls
clus               0   1
  MLL4 MUTATED     1  39
  MLL4 WILD-TYPE   9 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      1   39
  MLL4 WILD-TYPE    9  359
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           39            359
[1] 2 2
[1] FALSE

Clustering(19) Variable = KLF3 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED    13   7
  KLF3 WILD-TYPE 325 209
  KLF3 MUTATED KLF3 WILD-TYPE 
            20            534 
  KLF3 MUTATED KLF3 WILD-TYPE 
             7            209 
$`KLF3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NG TCGA-MX-A663 TCGA-L5-A8NM TCGA-BR-6566 TCGA-BR-6852 
       19.99        35.97         9.86         7.76        32.78        44.94 
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8680 
       35.84        29.59         8.05         2.66         7.40        31.96 
TCGA-BR-8682 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4GN 
       32.58         6.58         5.92        77.29        22.32        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H2 
        0.10        12.95 

$`KLF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60        32.25         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KLF3 MUTATED KLF3 WILD-TYPE 
           0.1            0.0 
  KLF3 MUTATED KLF3 WILD-TYPE 
         77.29         122.30 
  KLF3 MUTATED KLF3 WILD-TYPE 
        21.155         13.530 
[1] "0.1 - 77.3 (21.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D19V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLF3 MUTATED         0        0        1        1         5         6
  KLF3 WILD-TYPE      10       20       45       30        79        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF3 MUTATED           1          1          1          4        2         0
  KLF3 WILD-TYPE        28         83         61         35       41         4
D19V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             6             77
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            4             35
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  KLF3 MUTATED       0   4   8  10
  KLF3 WILD-TYPE    54 131 253  92
D19V4, multiclass
       clus
vv      KLF3 MUTATED KLF3 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               8            253
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KLF3 MUTATED    10   5   2   5
  KLF3 WILD-TYPE 185 168  87  80
D19V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0           10            185
  N1            5            168
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                cls
clus               0   1
  KLF3 MUTATED    19   2
  KLF3 WILD-TYPE 463  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     19    2
  KLF3 WILD-TYPE  463   36
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0           19            463
  1            2             36
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus               0   1
  KLF3 MUTATED    10  12
  KLF3 WILD-TYPE 162 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     10   12
  KLF3 WILD-TYPE  162  394
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE           10            162
  MALE             12            394
[1] 2 2
[1] FALSE
D19V8, binary
                cls
clus               0   1
  KLF3 MUTATED    20   1
  KLF3 WILD-TYPE 396 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     20    1
  KLF3 WILD-TYPE  396  101
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO            20            396
  YES            1            101
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
[1] "Remove cluster labels:" "KLF3 MUTATED"          
clus
  KLF3 MUTATED KLF3 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL     TCGA-IG-A3Y9 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" "KLF3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KLF3 MUTATED       7                         0
  KLF3 WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLF3 MUTATED                                           0    14
  KLF3 WILD-TYPE                                         1   343
D19V11, multiclass
                                           clus
vv                                          KLF3 MUTATED KLF3 WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                cls
clus               0   1
  KLF3 MUTATED     0  18
  KLF3 WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      0   18
  KLF3 WILD-TYPE   10  380
                        clus
vv                       KLF3 MUTATED KLF3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(20) Variable = ZBTB20 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    23  14
  ZBTB20 WILD-TYPE 315 202
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              37              517 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              14              202 
$`ZBTB20 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GI TCGA-L5-A8NM TCGA-L5-A8NR TCGA-VR-A8ET TCGA-BR-4201 
       19.99        14.30         7.76         8.71         1.55        30.90 
TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7958 
        9.34         6.61        34.68        36.16        35.84        29.56 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG 
       25.05         1.12        12.79        28.14        16.14         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       12.62         1.02         9.01         6.02       105.07        28.96 
TCGA-CG-5733 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       21.07        13.78        11.44        30.51        22.68        29.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.51         6.58        29.00        14.07        19.73        74.53 
TCGA-VQ-A8P2 
       38.14 

$`ZBTB20 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        9.21        20.22        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       25.81        11.77        21.37         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
            1.02             0.00 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          105.07           122.30 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           16.14            13.48 
[1] "1.0 - 105.1 (16.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D20V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB20 MUTATED         1        2        4        1         6         4
  ZBTB20 WILD-TYPE       9       18       42       30        78        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           3          4          4          5        5
  ZBTB20 WILD-TYPE        26         80         58         34       38
                  vv
clus               STAGE IVA
  ZBTB20 MUTATED           0
  ZBTB20 WILD-TYPE         4
D20V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                2               18
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               4               79
  STAGE III               3               26
  STAGE IIIA              4               80
  STAGE IIIB              4               58
  STAGE IIIC              5               34
  STAGE IV                5               38
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZBTB20 MUTATED       4  10  14  12
  ZBTB20 WILD-TYPE    50 125 247  90
D20V4, multiclass
       clus
vv      ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T0+T1              4               50
  T2                10              125
  T3                14              247
  T4                12               90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB20 MUTATED    13  15   4   9
  ZBTB20 WILD-TYPE 182 158  85  76
D20V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             13              182
  N1             15              158
  N2              4               85
  N3              9               76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    37   3
  ZBTB20 WILD-TYPE 445  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     37    3
  ZBTB20 WILD-TYPE  445   35
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             37              445
  1              3               35
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    22  20
  ZBTB20 WILD-TYPE 150 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     22   20
  ZBTB20 WILD-TYPE  150  386
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE             22              150
  MALE               20              386
[1] 2 2
[1] FALSE
D20V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    31   3
  ZBTB20 WILD-TYPE 385  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     31    3
  ZBTB20 WILD-TYPE  385   99
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO              31              385
  YES              3               99
[1] 2 2
[1] FALSE
D20V9, continuous
[1] "Remove cluster labels:" "ZBTB20 MUTATED"        
clus
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
D20V10, continuous
[1] "Remove cluster labels:" "ZBTB20 MUTATED"        
clus
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" "ZBTB20 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB20 MUTATED       8                         1
  ZBTB20 WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB20 MUTATED                                           0    23
  ZBTB20 WILD-TYPE                                         1   334
D20V11, multiclass
                                           clus
vv                                          ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 23              334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     1  27
  ZBTB20 WILD-TYPE   9 371
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      1   27
  ZBTB20 WILD-TYPE    9  371
                        clus
vv                       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             27              371
[1] 2 2
[1] FALSE

Clustering(21) Variable = MBD6 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED    14   7
  MBD6 WILD-TYPE 324 209
  MBD6 MUTATED MBD6 WILD-TYPE 
            21            533 
  MBD6 MUTATED MBD6 WILD-TYPE 
             7            209 
$`MBD6 MUTATED`
TCGA-IC-A6RE TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 
        7.69        30.90         9.67        44.94         1.12        28.14 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6815 TCGA-F1-6874 
       16.14         6.58       105.07        65.10        15.98        14.47 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GU TCGA-IN-A6RR 
       11.08        26.47        28.96        22.32         6.58         6.74 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-VQ-A8P2 
       19.73         4.60        38.14 

$`MBD6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        24.39        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         6.08         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MBD6 MUTATED MBD6 WILD-TYPE 
          1.12           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
        105.07         122.30 
  MBD6 MUTATED MBD6 WILD-TYPE 
         16.14          13.51 
[1] "1.1 - 105.1 (16.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D21V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD6 MUTATED         0        0        4        1         4         4
  MBD6 WILD-TYPE      10       20       42       30        80        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBD6 MUTATED           0          5          1          1        1         0
  MBD6 WILD-TYPE        29         79         61         38       42         4
D21V3, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            5             79
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MBD6 MUTATED       2   7  10   4
  MBD6 WILD-TYPE    52 128 251  98
D21V4, multiclass
       clus
vv      MBD6 MUTATED MBD6 WILD-TYPE
  T0+T1            2             52
  T2               7            128
  T3              10            251
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MBD6 MUTATED    10   6   4   2
  MBD6 WILD-TYPE 185 167  85  83
D21V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           10            185
  N1            6            167
  N2            4             85
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  MBD6 MUTATED    23   1
  MBD6 WILD-TYPE 459  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     23    1
  MBD6 WILD-TYPE  459   37
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           23            459
  1            1             37
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  MBD6 MUTATED    13  12
  MBD6 WILD-TYPE 159 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     13   12
  MBD6 WILD-TYPE  159  394
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE           13            159
  MALE             12            394
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus               0   1
  MBD6 MUTATED    18   2
  MBD6 WILD-TYPE 398 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     18    2
  MBD6 WILD-TYPE  398  100
     clus
vv    MBD6 MUTATED MBD6 WILD-TYPE
  NO            18            398
  YES            2            100
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
[1] "Remove cluster labels:" "MBD6 MUTATED"          
clus
  MBD6 MUTATED MBD6 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IG-A3QL 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" "MBD6 WILD-TYPE" 
    TCGA-Z6-AAPN 
"MBD6 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MBD6 MUTATED       4                         2
  MBD6 WILD-TYPE   129                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBD6 MUTATED                                           0    16
  MBD6 WILD-TYPE                                         1   341
D21V11, multiclass
                                           clus
vv                                          MBD6 MUTATED MBD6 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                cls
clus               0   1
  MBD6 MUTATED     0  21
  MBD6 WILD-TYPE  10 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      0   21
  MBD6 WILD-TYPE   10  377
                        clus
vv                       MBD6 MUTATED MBD6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           21            377
[1] 2 2
[1] FALSE

Clustering(22) Variable = MUC6 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  MUC6 MUTATED    33  23
  MUC6 WILD-TYPE 305 193
  MUC6 MUTATED MUC6 WILD-TYPE 
            56            498 
  MUC6 MUTATED MUC6 WILD-TYPE 
            23            193 
$`MUC6 MUTATED`
TCGA-L5-A8NG TCGA-CG-4475 TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       35.97        22.98        25.78         5.92        13.94         4.21 
TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A93C TCGA-JY-A93D TCGA-R6-A6XG TCGA-R6-A8W8 
       12.82        14.50        23.18        31.56        38.40         2.89 
TCGA-R6-A8WC TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6801 
        2.30        19.73        26.70         6.97        34.68        40.21 
TCGA-BR-7703 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8382 
       36.16        11.44        29.59        32.25        31.10        25.05 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-8525 
        1.12        28.14        31.96        20.42        16.14        12.59 
TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
       12.30         6.58        11.77         1.02         6.02       105.07 
TCGA-D7-8578 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GX 
       21.14        13.58         0.56        24.30         3.25        20.25 
TCGA-HU-A4H3 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1V TCGA-R5-A7ZE 
       29.00        36.36         3.39        19.53        15.75        18.21 
TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       74.53         8.61         5.13         8.94        13.25        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A94T 
       38.14        11.24 

$`MUC6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        21.99        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       58.55         7.63         8.94        16.24        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       23.41         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5818 
       14.37         3.42         2.10         1.32         2.66        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       32.52        13.51        20.65         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.39        12.76        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
       17.06        59.54         5.03        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       48.79         5.46        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MUC6 MUTATED MUC6 WILD-TYPE 
          0.56           0.00 
  MUC6 MUTATED MUC6 WILD-TYPE 
        105.07         122.30 
  MUC6 MUTATED MUC6 WILD-TYPE 
        17.175         13.410 
[1] "0.6 - 105.1 (17.2)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D22V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC6 MUTATED         0        2        4        1         6        10
  MUC6 WILD-TYPE      10       18       42       30        78        73
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC6 MUTATED           4          8          5          7        7         0
  MUC6 WILD-TYPE        25         76         57         32       36         4
D22V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             6             78
  STAGE IIB            10             73
  STAGE III             4             25
  STAGE IIIA            8             76
  STAGE IIIB            5             57
  STAGE IIIC            7             32
  STAGE IV              7             36
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MUC6 MUTATED       5   9  25  16
  MUC6 WILD-TYPE    49 126 236  86
D22V4, multiclass
       clus
vv      MUC6 MUTATED MUC6 WILD-TYPE
  T0+T1            5             49
  T2               9            126
  T3              25            236
  T4              16             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MUC6 MUTATED    15  17  14   8
  MUC6 WILD-TYPE 180 156  75  77
D22V5, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  N0           15            180
  N1           17            156
  N2           14             75
  N3            8             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                cls
clus               0   1
  MUC6 MUTATED    47   5
  MUC6 WILD-TYPE 435  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     47    5
  MUC6 WILD-TYPE  435   33
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           47            435
  1            5             33
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  MUC6 MUTATED    21  38
  MUC6 WILD-TYPE 151 368
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     21   38
  MUC6 WILD-TYPE  151  368
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  FEMALE           21            151
  MALE             38            368
[1] 2 2
[1] FALSE
D22V8, binary
                cls
clus               0   1
  MUC6 MUTATED    44   6
  MUC6 WILD-TYPE 372  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     44    6
  MUC6 WILD-TYPE  372   96
     clus
vv    MUC6 MUTATED MUC6 WILD-TYPE
  NO            44            372
  YES            6             96
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MUC6 MUTATED      12                         1
  MUC6 WILD-TYPE   121                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MUC6 MUTATED                                           1    36
  MUC6 WILD-TYPE                                         0   321
D22V11, multiclass
                                           clus
vv                                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                               12            121
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               36            321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                cls
clus               0   1
  MUC6 MUTATED     1  43
  MUC6 WILD-TYPE   9 355
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      1   43
  MUC6 WILD-TYPE    9  355
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           43            355
[1] 2 2
[1] FALSE

Clustering(23) Variable = CBWD1 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  CBWD1 MUTATED    13   6
  CBWD1 WILD-TYPE 325 210
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             19             535 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              6             210 
$`CBWD1 MUTATED`
TCGA-LN-A49Y TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 
       12.46        26.70        34.68        32.78        35.84        29.59 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 
       31.27        25.05        28.14         6.58        12.62        15.95 
TCGA-CG-4306 TCGA-CG-5733 TCGA-F1-A448 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GQ 
        1.02        21.07        21.27        77.29        26.47         0.10 
TCGA-HU-A4GT 
        6.51 

$`CBWD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       25.81        11.77        21.37        29.98         8.98         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CBWD1 MUTATED CBWD1 WILD-TYPE 
            0.1             0.0 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          77.29          122.30 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          25.05           13.48 
[1] "0.1 - 77.3 (25.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D23V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBWD1 MUTATED         0        0        3        2         5         3
  CBWD1 WILD-TYPE      10       20       43       29        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBWD1 MUTATED           0          1          1          4        2         0
  CBWD1 WILD-TYPE        29         83         61         35       41         4
D23V3, multiclass
            clus
vv           CBWD1 MUTATED CBWD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               2              29
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CBWD1 MUTATED       0   6   7   8
  CBWD1 WILD-TYPE    54 129 254  94
D23V4, multiclass
       clus
vv      CBWD1 MUTATED CBWD1 WILD-TYPE
  T0+T1             0              54
  T2                6             129
  T3                7             254
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CBWD1 MUTATED    11   3   4   4
  CBWD1 WILD-TYPE 184 170  85  81
D23V5, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  N0            11             184
  N1             3             170
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                 cls
clus                0   1
  CBWD1 MUTATED    20   1
  CBWD1 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     20    1
  CBWD1 WILD-TYPE  462   37
   clus
vv  CBWD1 MUTATED CBWD1 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D23V7, binary
                 cls
clus                0   1
  CBWD1 MUTATED    11  11
  CBWD1 WILD-TYPE 161 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     11   11
  CBWD1 WILD-TYPE  161  395
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  FEMALE            11             161
  MALE              11             395
[1] 2 2
[1] FALSE
D23V8, binary
                 cls
clus                0   1
  CBWD1 MUTATED    17   2
  CBWD1 WILD-TYPE 399 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     17    2
  CBWD1 WILD-TYPE  399  100
     clus
vv    CBWD1 MUTATED CBWD1 WILD-TYPE
  NO             17             399
  YES             2             100
[1] 2 2
[1] FALSE
D23V9, continuous
[1] "Remove cluster labels:" "CBWD1 MUTATED"         
clus
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A4A1      TCGA-LN-A4A2 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" "CBWD1 WILD-TYPE" 
D23V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBWD1 MUTATED       5                         0
  CBWD1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBWD1 MUTATED                                           0    13
  CBWD1 WILD-TYPE                                         1   344
D23V11, multiclass
                                           clus
vv                                          CBWD1 MUTATED CBWD1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                 cls
clus                0   1
  CBWD1 MUTATED     1  17
  CBWD1 WILD-TYPE   9 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      1   17
  CBWD1 WILD-TYPE    9  381
                        clus
vv                       CBWD1 MUTATED CBWD1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(24) Variable = CTNND1 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    22   9
  CTNND1 WILD-TYPE 316 207
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              31              523 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               9              207 
$`CTNND1 MUTATED`
TCGA-JY-A938 TCGA-IG-A5B8 TCGA-IG-A625 TCGA-L5-A4OH TCGA-L5-A8NN TCGA-LN-A49S 
       34.85         0.79        12.82        32.61         5.49        13.15 
TCGA-LN-A7HW TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6452 
       12.00         7.04         9.30         9.44         6.97        34.68 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-8284 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 
       21.90        36.16         8.05         0.26        31.27        25.05 
TCGA-BR-8678 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 
       24.79        31.96        12.43        12.62        15.95         6.02 
TCGA-CG-5733 TCGA-D7-A4Z0 TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-VQ-A8P2 
       21.07        14.76        30.51        29.98        29.00        38.14 
TCGA-VQ-A91V 
       42.64 

$`CTNND1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.47         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       30.90        31.20        44.94         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       11.77        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.26             0.00 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           42.64           122.30 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           15.95            13.51 
[1] "0.3 - 42.6 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D24V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNND1 MUTATED         2        1        4        2         4         4
  CTNND1 WILD-TYPE       8       19       42       29        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           1          4          1          5        3
  CTNND1 WILD-TYPE        28         80         61         34       40
                  vv
clus               STAGE IVA
  CTNND1 MUTATED           0
  CTNND1 WILD-TYPE         4
D24V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                1               19
  STAGE IB                4               42
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              5               34
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CTNND1 MUTATED       3   8  10  10
  CTNND1 WILD-TYPE    51 127 251  92
D24V4, multiclass
       clus
vv      CTNND1 MUTATED CTNND1 WILD-TYPE
  T0+T1              3               51
  T2                 8              127
  T3                10              251
  T4                10               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CTNND1 MUTATED    12   7   5   6
  CTNND1 WILD-TYPE 183 166  84  79
D24V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0             12              183
  N1              7              166
  N2              5               84
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    27   2
  CTNND1 WILD-TYPE 455  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     27    2
  CTNND1 WILD-TYPE  455   36
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             27              455
  1              2               36
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     8  25
  CTNND1 WILD-TYPE 164 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      8   25
  CTNND1 WILD-TYPE  164  381
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              8              164
  MALE               25              381
[1] 2 2
[1] FALSE
D24V8, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    26   5
  CTNND1 WILD-TYPE 390  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     26    5
  CTNND1 WILD-TYPE  390   97
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO              26              390
  YES              5               97
[1] 2 2
[1] FALSE
D24V9, continuous
[1] "Remove cluster labels:" "CTNND1 MUTATED"        
clus
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CTNND1 WILD-TYPE" "CTNND1 WILD-TYPE" 
D24V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNND1 MUTATED       8                         1
  CTNND1 WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNND1 MUTATED                                           0    19
  CTNND1 WILD-TYPE                                         1   338
D24V11, multiclass
                                           clus
vv                                          CTNND1 MUTATED CTNND1 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 19              338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     1  23
  CTNND1 WILD-TYPE   9 375
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      1   23
  CTNND1 WILD-TYPE    9  375
                        clus
vv                       CTNND1 MUTATED CTNND1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             23              375
[1] 2 2
[1] FALSE

Clustering(25) Variable = APC MUTATION ANALYSIS
D25V1, survival
               sevent
clus2             0   1
  APC MUTATED    34  24
  APC WILD-TYPE 304 192
  APC MUTATED APC WILD-TYPE 
           58           496 
  APC MUTATED APC WILD-TYPE 
           24           192 
$`APC MUTATED`
TCGA-JY-A6FB TCGA-S8-A6BV TCGA-KB-A93G TCGA-IC-A6RE TCGA-IG-A4QS TCGA-IG-A97I 
       60.39        20.02        20.15         7.69         3.88        12.16 
TCGA-JY-A6FH TCGA-L5-A4OP TCGA-L5-A88V TCGA-L5-A8NN TCGA-L5-A8NR TCGA-LN-A7HX 
       47.38         7.17         2.60         5.49         8.71        12.23 
TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-VR-A8Q7 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 
        9.30        12.69        52.27         6.97        18.35         6.18 
TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7197 TCGA-BR-7703 
       34.68        39.12         9.17        30.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A452 
       35.24        32.25         0.26         1.12        31.96         7.53 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 
       12.82        12.43         6.58        12.62         1.02         9.01 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6528 
        7.07        36.00         6.02       105.07        21.07        15.22 
TCGA-D7-A4YV TCGA-D7-A6EY TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8211 TCGA-HU-8243 
        5.92        11.44        72.23         3.48        13.58         5.92 
TCGA-HU-8604 TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-IN-A6RP TCGA-MX-A666 TCGA-R5-A7ZF 
       22.82         6.58        29.00         6.44        14.04         8.52 
TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A91U 
       13.25        38.14        22.19         1.71 

$`APC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
        4.90        29.00         7.13         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       19.33        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       11.77        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00        18.97        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.41        37.22        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  APC MUTATED APC WILD-TYPE 
         0.26          0.00 
  APC MUTATED APC WILD-TYPE 
       105.07        122.30 
  APC MUTATED APC WILD-TYPE 
       12.330        13.975 
[1] "0.3 - 105.1 (12.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D25V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APC MUTATED         1        3        8        5         7         8
  APC WILD-TYPE       9       17       38       26        77        75
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED           3         10          3          4        6         0
  APC WILD-TYPE        26         74         59         35       37         4
D25V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              1             9
  STAGE IA             3            17
  STAGE IB             8            38
  STAGE II             5            26
  STAGE IIA            7            77
  STAGE IIB            8            75
  STAGE III            3            26
  STAGE IIIA          10            74
  STAGE IIIB           3            59
  STAGE IIIC           4            35
  STAGE IV             6            37
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  APC MUTATED       5  16  25  12
  APC WILD-TYPE    49 119 236  90
D25V4, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  T0+T1           5            49
  T2             16           119
  T3             25           236
  T4             12            90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  APC MUTATED    24  22   5   8
  APC WILD-TYPE 171 151  84  77
D25V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          24           171
  N1          22           151
  N2           5            84
  N3           8            77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
               cls
clus              0   1
  APC MUTATED    49   4
  APC WILD-TYPE 433  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     49    4
  APC WILD-TYPE  433   34
   clus
vv  APC MUTATED APC WILD-TYPE
  0          49           433
  1           4            34
[1] 2 2
[1] FALSE
D25V7, binary
               cls
clus              0   1
  APC MUTATED    18  44
  APC WILD-TYPE 154 362
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     18   44
  APC WILD-TYPE  154  362
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          18           154
  MALE            44           362
[1] 2 2
[1] FALSE
D25V8, binary
               cls
clus              0   1
  APC MUTATED    48   5
  APC WILD-TYPE 368  97
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     48    5
  APC WILD-TYPE  368   97
     clus
vv    APC MUTATED APC WILD-TYPE
  NO           48           368
  YES           5            97
[1] 2 2
[1] FALSE
D25V9, continuous
[1] "Remove cluster labels:" "APC MUTATED"           
clus
  APC MUTATED APC WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-Z6-A8JE 
"APC WILD-TYPE" 
D25V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  APC MUTATED      12                         3
  APC WILD-TYPE   121                        11
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APC MUTATED                                           0    37
  APC WILD-TYPE                                         1   320
D25V11, multiclass
                                           clus
vv                                          APC MUTATED APC WILD-TYPE
  ASIAN                                              12           121
  BLACK OR AFRICAN AMERICAN                           3            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              37           320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
               cls
clus              0   1
  APC MUTATED     2  39
  APC WILD-TYPE   8 359
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      2   39
  APC WILD-TYPE    8  359
                        clus
vv                       APC MUTATED APC WILD-TYPE
  HISPANIC OR LATINO               2             8
  NOT HISPANIC OR LATINO          39           359
[1] 2 2
[1] FALSE

Clustering(26) Variable = LARP7 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  LARP7 MUTATED    14   4
  LARP7 WILD-TYPE 324 212
  LARP7 MUTATED LARP7 WILD-TYPE 
             18             536 
  LARP7 MUTATED LARP7 WILD-TYPE 
              4             212 
$`LARP7 MUTATED`
TCGA-2H-A9GF TCGA-LN-A9FP TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-B7-A5TI TCGA-BR-6803 
       25.78        12.03        14.37         1.32        19.56        31.20 
TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8372 TCGA-CD-A486 TCGA-D7-A6EY TCGA-HU-8602 
       44.94         6.18        31.27         6.31        11.44        22.32 
TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-SW-A7EA TCGA-VQ-A8DU 
       22.68        23.84        19.73        45.67        19.04         5.46 

$`LARP7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        2.10         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        30.90        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  LARP7 MUTATED LARP7 WILD-TYPE 
           1.32            0.00 
  LARP7 MUTATED LARP7 WILD-TYPE 
          45.67          122.30 
  LARP7 MUTATED LARP7 WILD-TYPE 
         19.645          13.495 
[1] "1.3 - 45.7 (19.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D26V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP7 MUTATED         1        0        2        0         5         4
  LARP7 WILD-TYPE       9       20       44       31        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LARP7 MUTATED           1          4          1          2        1         0
  LARP7 WILD-TYPE        28         80         61         37       42         4
D26V3, multiclass
            clus
vv           LARP7 MUTATED LARP7 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LARP7 MUTATED       2   4  11   4
  LARP7 WILD-TYPE    52 131 250  98
D26V4, multiclass
       clus
vv      LARP7 MUTATED LARP7 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3               11             250
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LARP7 MUTATED     9   7   3   3
  LARP7 WILD-TYPE 186 166  86  82
D26V5, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  N0             9             186
  N1             7             166
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                 cls
clus                0   1
  LARP7 MUTATED    20   1
  LARP7 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     20    1
  LARP7 WILD-TYPE  462   37
   clus
vv  LARP7 MUTATED LARP7 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  LARP7 MUTATED    11  11
  LARP7 WILD-TYPE 161 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     11   11
  LARP7 WILD-TYPE  161  395
        clus
vv       LARP7 MUTATED LARP7 WILD-TYPE
  FEMALE            11             161
  MALE              11             395
[1] 2 2
[1] FALSE
D26V8, binary
                 cls
clus                0   1
  LARP7 MUTATED    17   2
  LARP7 WILD-TYPE 399 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     17    2
  LARP7 WILD-TYPE  399  100
     clus
vv    LARP7 MUTATED LARP7 WILD-TYPE
  NO             17             399
  YES             2             100
[1] 2 2
[1] FALSE
D26V9, continuous
[1] "Remove cluster labels:" "LARP7 MUTATED"         
clus
  LARP7 MUTATED LARP7 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
D26V10, continuous
[1] "Remove cluster labels:" "LARP7 MUTATED"         
clus
  LARP7 MUTATED LARP7 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" "LARP7 WILD-TYPE" 
     TCGA-Z6-AAPN 
"LARP7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LARP7 MUTATED       5                         2
  LARP7 WILD-TYPE   128                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP7 MUTATED                                           0    13
  LARP7 WILD-TYPE                                         1   344
D26V11, multiclass
                                           clus
vv                                          LARP7 MUTATED LARP7 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                 cls
clus                0   1
  LARP7 MUTATED     2  17
  LARP7 WILD-TYPE   8 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      2   17
  LARP7 WILD-TYPE    8  381
                        clus
vv                       LARP7 MUTATED LARP7 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(27) Variable = DDX17 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     8   6
  DDX17 WILD-TYPE 330 210
  DDX17 MUTATED DDX17 WILD-TYPE 
             14             540 
  DDX17 MUTATED DDX17 WILD-TYPE 
              6             210 
$`DDX17 MUTATED`
TCGA-2H-A9GI TCGA-L5-A4OJ TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 
       14.30        21.01        29.59        32.25        31.10         0.26 
TCGA-BR-8372 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-CG-5733 
       31.27        12.30         6.58         9.01        28.96        21.07 
TCGA-HF-A5NB TCGA-HU-A4H8 
       30.51        14.07 

$`DDX17 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         6.18        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DDX17 MUTATED DDX17 WILD-TYPE 
           0.26            0.00 
  DDX17 MUTATED DDX17 WILD-TYPE 
          32.25          122.30 
  DDX17 MUTATED DDX17 WILD-TYPE 
         21.040          13.495 
[1] "0.3 - 32.2 (21.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D27V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX17 MUTATED         1        1        2        0         1         3
  DDX17 WILD-TYPE       9       19       44       31        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX17 MUTATED           1          2          0          3        2         0
  DDX17 WILD-TYPE        28         82         62         36       41         4
D27V3, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DDX17 MUTATED       3   2   3   9
  DDX17 WILD-TYPE    51 133 258  93
D27V4, multiclass
       clus
vv      DDX17 MUTATED DDX17 WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3                3             258
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX17 MUTATED     9   2   2   3
  DDX17 WILD-TYPE 186 171  87  82
D27V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             9             186
  N1             2             171
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                 cls
clus                0   1
  DDX17 MUTATED    14   2
  DDX17 WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED     14    2
  DDX17 WILD-TYPE  468   36
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus                0   1
  DDX17 MUTATED    10   7
  DDX17 WILD-TYPE 162 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED     10    7
  DDX17 WILD-TYPE  162  399
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE            10             162
  MALE               7             399
[1] 2 2
[1] FALSE
D27V8, binary
                 cls
clus                0   1
  DDX17 MUTATED    11   2
  DDX17 WILD-TYPE 405 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED     11    2
  DDX17 WILD-TYPE  405  100
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO             11             405
  YES             2             100
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX17 MUTATED       3                         0
  DDX17 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX17 MUTATED                                           0     9
  DDX17 WILD-TYPE                                         1   348
D27V11, multiclass
                                           clus
vv                                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                 cls
clus                0   1
  DDX17 MUTATED     0  11
  DDX17 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0   11
  DDX17 WILD-TYPE   10  387
                        clus
vv                       DDX17 MUTATED DDX17 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(28) Variable = CIC MUTATION ANALYSIS
D28V1, survival
               sevent
clus2             0   1
  CIC MUTATED    34  16
  CIC WILD-TYPE 304 200
  CIC MUTATED CIC WILD-TYPE 
           50           504 
  CIC MUTATED CIC WILD-TYPE 
           16           200 
$`CIC MUTATED`
TCGA-EQ-A4SO TCGA-JY-A93E TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NM TCGA-LN-A4A8 
       16.24        25.22         3.75         2.66         7.76        15.52 
TCGA-R6-A8W5 TCGA-VR-A8Q7 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8077 
       15.78        52.27        30.90        34.68        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8372 
       29.59        32.25         6.18         0.95        26.33        31.27 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4J2 TCGA-BR-A4QL TCGA-CD-8524 TCGA-CD-8526 
       25.05         1.12        14.17        16.14        12.76        12.53 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A4MI TCGA-CG-4465 
       12.33        12.39        11.64        12.07        11.77         9.01 
TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A6EY 
      105.07        65.10        21.07        19.50        17.19        11.44 
TCGA-F1-6874 TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8602 
       14.47        17.06        59.54        26.47         5.92        22.32 
TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H3 
        0.76        22.68        11.77         8.98         6.58        29.00 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`CIC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       33.21        37.25        11.44         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19        17.52         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.39        12.59         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.59        15.39        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
       77.29        63.06        52.21        30.51         1.51        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       28.96        22.82        21.07        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CIC MUTATED CIC WILD-TYPE 
         0.69          0.00 
  CIC MUTATED CIC WILD-TYPE 
       105.07        122.30 
  CIC MUTATED CIC WILD-TYPE 
       15.650        13.445 
[1] "0.7 - 105.1 (15.6)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D28V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CIC MUTATED         1        2        5        5         8         7
  CIC WILD-TYPE       9       18       41       26        76        76
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIC MUTATED           1          8          5          4        3         2
  CIC WILD-TYPE        28         76         57         35       40         2
D28V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              1             9
  STAGE IA             2            18
  STAGE IB             5            41
  STAGE II             5            26
  STAGE IIA            8            76
  STAGE IIB            7            76
  STAGE III            1            28
  STAGE IIIA           8            76
  STAGE IIIB           5            57
  STAGE IIIC           4            35
  STAGE IV             3            40
  STAGE IVA            2             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CIC MUTATED       4  12  22  16
  CIC WILD-TYPE    50 123 239  86
D28V4, multiclass
       clus
vv      CIC MUTATED CIC WILD-TYPE
  T0+T1           4            50
  T2             12           123
  T3             22           239
  T4             16            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CIC MUTATED    24  17   2   9
  CIC WILD-TYPE 171 156  87  76
D28V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          24           171
  N1          17           156
  N2           2            87
  N3           9            76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
               cls
clus              0   1
  CIC MUTATED    45   4
  CIC WILD-TYPE 437  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     45    4
  CIC WILD-TYPE  437   34
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          45           437
  1           4            34
[1] 2 2
[1] FALSE
D28V7, binary
               cls
clus              0   1
  CIC MUTATED    25  29
  CIC WILD-TYPE 147 377
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     25   29
  CIC WILD-TYPE  147  377
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE          25           147
  MALE            29           377
[1] 2 2
[1] FALSE
D28V8, binary
               cls
clus              0   1
  CIC MUTATED    41   5
  CIC WILD-TYPE 375  97
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     41    5
  CIC WILD-TYPE  375   97
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           41           375
  YES           5            97
[1] 2 2
[1] FALSE
D28V9, continuous
[1] "Remove cluster labels:" "CIC MUTATED"           
clus
  CIC MUTATED CIC WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A9 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" "CIC WILD-TYPE" 
   TCGA-Z6-A8JE 
"CIC WILD-TYPE" 
D28V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CIC MUTATED      17                         1
  CIC WILD-TYPE   116                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CIC MUTATED                                           0    31
  CIC WILD-TYPE                                         1   326
D28V11, multiclass
                                           clus
vv                                          CIC MUTATED CIC WILD-TYPE
  ASIAN                                              17           116
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              31           326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
               cls
clus              0   1
  CIC MUTATED     1  42
  CIC WILD-TYPE   9 356
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      1   42
  CIC WILD-TYPE    9  356
                        clus
vv                       CIC MUTATED CIC WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          42           356
[1] 2 2
[1] FALSE

Clustering(29) Variable = TENC1 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  TENC1 MUTATED    14   8
  TENC1 WILD-TYPE 324 208
  TENC1 MUTATED TENC1 WILD-TYPE 
             22             532 
  TENC1 MUTATED TENC1 WILD-TYPE 
              8             208 
$`TENC1 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-JY-A6FD TCGA-LN-A4A3 TCGA-B7-5816 TCGA-BR-4280 
       21.99         5.92        68.02        12.76        26.70         6.61 
TCGA-BR-6852 TCGA-BR-8297 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 
       44.94         7.40        31.27         6.58        15.95         6.02 
TCGA-D7-6526 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ 
       17.19         5.92        30.51        26.47        29.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-RD-A7BT TCGA-VQ-A8P2 
       20.25        29.00         8.61        38.14 

$`TENC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TENC1 MUTATED TENC1 WILD-TYPE 
            0.1             0.0 
  TENC1 MUTATED TENC1 WILD-TYPE 
          68.02          122.30 
  TENC1 MUTATED TENC1 WILD-TYPE 
          18.72           13.51 
[1] "0.1 - 68.0 (18.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D29V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TENC1 MUTATED         0        0        1        1         4         2
  TENC1 WILD-TYPE      10       20       45       30        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TENC1 MUTATED           3          2          0          6        3         0
  TENC1 WILD-TYPE        26         82         62         33       40         4
D29V3, multiclass
            clus
vv           TENC1 MUTATED TENC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              3              26
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             6              33
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TENC1 MUTATED       0   4   8  10
  TENC1 WILD-TYPE    54 131 253  92
D29V4, multiclass
       clus
vv      TENC1 MUTATED TENC1 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                8             253
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TENC1 MUTATED     5   9   3   5
  TENC1 WILD-TYPE 190 164  86  80
D29V5, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  N0             5             190
  N1             9             164
  N2             3              86
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                 cls
clus                0   1
  TENC1 MUTATED    21   1
  TENC1 WILD-TYPE 461  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     21    1
  TENC1 WILD-TYPE  461   37
   clus
vv  TENC1 MUTATED TENC1 WILD-TYPE
  0            21             461
  1             1              37
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus                0   1
  TENC1 MUTATED    12  11
  TENC1 WILD-TYPE 160 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     12   11
  TENC1 WILD-TYPE  160  395
        clus
vv       TENC1 MUTATED TENC1 WILD-TYPE
  FEMALE            12             160
  MALE              11             395
[1] 2 2
[1] FALSE
D29V8, binary
                 cls
clus                0   1
  TENC1 MUTATED    18   3
  TENC1 WILD-TYPE 398  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     18    3
  TENC1 WILD-TYPE  398   99
     clus
vv    TENC1 MUTATED TENC1 WILD-TYPE
  NO             18             398
  YES             3              99
[1] 2 2
[1] FALSE
D29V9, continuous
[1] "Remove cluster labels:" "TENC1 MUTATED"         
clus
  TENC1 MUTATED TENC1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
D29V10, continuous
[1] "Remove cluster labels:" "TENC1 MUTATED"         
clus
  TENC1 MUTATED TENC1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A6 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" "TENC1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"TENC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TENC1 MUTATED       7                         0
  TENC1 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TENC1 MUTATED                                           1    10
  TENC1 WILD-TYPE                                         0   347
D29V11, multiclass
                                           clus
vv                                          TENC1 MUTATED TENC1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                 cls
clus                0   1
  TENC1 MUTATED     0  16
  TENC1 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED      0   16
  TENC1 WILD-TYPE   10  382
                        clus
vv                       TENC1 MUTATED TENC1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(30) Variable = ARID4A MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2                0   1
  ARID4A MUTATED    16   6
  ARID4A WILD-TYPE 322 210
  ARID4A MUTATED ARID4A WILD-TYPE 
              22              532 
  ARID4A MUTATED ARID4A WILD-TYPE 
               6              210 
$`ARID4A MUTATED`
TCGA-JY-A6FA TCGA-Z6-A8JD TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8368 
       44.75         3.42        34.68        44.94         8.05         4.31 
TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J2 TCGA-CD-5813 TCGA-CD-8536 
       31.27        28.14        31.96        14.17        12.39        12.43 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5723 TCGA-CG-5728 
       12.62        15.95         1.02         4.01       105.07        65.10 
TCGA-D7-A6EY TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-VQ-A8P2 
       11.44         6.58        14.07        38.14 

$`ARID4A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
       27.02         7.99         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ARID4A MUTATED ARID4A WILD-TYPE 
            1.02             0.00 
  ARID4A MUTATED ARID4A WILD-TYPE 
          105.07           122.30 
  ARID4A MUTATED ARID4A WILD-TYPE 
           14.12            13.53 
[1] "1.0 - 105.1 (14.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D30V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID4A MUTATED         0        0        4        4         2         4
  ARID4A WILD-TYPE      10       20       42       27        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID4A MUTATED           0          1          1          4        3
  ARID4A WILD-TYPE        29         83         61         35       40
                  vv
clus               STAGE IVA
  ARID4A MUTATED           0
  ARID4A WILD-TYPE         4
D30V3, multiclass
            clus
vv           ARID4A MUTATED ARID4A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                4               27
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ARID4A MUTATED       1   6   9   7
  ARID4A WILD-TYPE    53 129 252  95
D30V4, multiclass
       clus
vv      ARID4A MUTATED ARID4A WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 9              252
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID4A MUTATED     9   6   2   6
  ARID4A WILD-TYPE 186 167  87  79
D30V5, multiclass
    clus
vv   ARID4A MUTATED ARID4A WILD-TYPE
  N0              9              186
  N1              6              167
  N2              2               87
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                  cls
clus                 0   1
  ARID4A MUTATED    21   3
  ARID4A WILD-TYPE 461  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED     21    3
  ARID4A WILD-TYPE  461   35
   clus
vv  ARID4A MUTATED ARID4A WILD-TYPE
  0             21              461
  1              3               35
[1] 2 2
[1] FALSE
D30V7, binary
                  cls
clus                 0   1
  ARID4A MUTATED     7  17
  ARID4A WILD-TYPE 165 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED      7   17
  ARID4A WILD-TYPE  165  389
        clus
vv       ARID4A MUTATED ARID4A WILD-TYPE
  FEMALE              7              165
  MALE               17              389
[1] 2 2
[1] FALSE
D30V8, binary
                  cls
clus                 0   1
  ARID4A MUTATED    19   1
  ARID4A WILD-TYPE 397 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED     19    1
  ARID4A WILD-TYPE  397  101
     clus
vv    ARID4A MUTATED ARID4A WILD-TYPE
  NO              19              397
  YES              1              101
[1] 2 2
[1] FALSE
D30V9, continuous
[1] "Remove cluster labels:" "ARID4A MUTATED"        
clus
  ARID4A MUTATED ARID4A WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "ARID4A MUTATED"        
clus
  ARID4A MUTATED ARID4A WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" "ARID4A WILD-TYPE" 
      TCGA-Z6-AAPN 
"ARID4A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID4A MUTATED       8                         0
  ARID4A WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID4A MUTATED                                           0    11
  ARID4A WILD-TYPE                                         1   346
D30V11, multiclass
                                           clus
vv                                          ARID4A MUTATED ARID4A WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                  cls
clus                 0   1
  ARID4A MUTATED     0  17
  ARID4A WILD-TYPE  10 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED      0   17
  ARID4A WILD-TYPE   10  381
                        clus
vv                       ARID4A MUTATED ARID4A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             17              381
[1] 2 2
[1] FALSE

Clustering(31) Variable = CDH1 MUTATION ANALYSIS
D31V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    17  14
  CDH1 WILD-TYPE 321 202
  CDH1 MUTATED CDH1 WILD-TYPE 
            31            523 
  CDH1 MUTATED CDH1 WILD-TYPE 
            14            202 
$`CDH1 MUTATED`
TCGA-FP-A8CX TCGA-X8-AAAR TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6452 
        0.23        18.21        19.56         7.43         9.57        34.68 
TCGA-BR-6566 TCGA-BR-6803 TCGA-BR-8058 TCGA-BR-8364 TCGA-BR-8370 TCGA-BR-8592 
       32.78        31.20        37.25        22.19         3.32         6.28 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4QM TCGA-CD-5799 
       20.88        34.13         6.08        28.57         5.13        13.02 
TCGA-CD-5813 TCGA-CD-A4MG TCGA-D7-6518 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4YU 
       12.39         6.58        19.13        16.80        17.19        16.44 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-F1-6874 TCGA-FP-8210 TCGA-IN-7808 TCGA-MX-A5UG 
       11.44         4.34        14.47         5.03         3.45         3.72 
TCGA-R5-A804 
        4.60 

$`CDH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       31.96        32.58         9.86         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53        34.98         1.48        27.55        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A 
       11.31        20.32        22.29        15.65         8.38        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         6.08         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.23           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
         37.25         122.30 
  CDH1 MUTATED CDH1 WILD-TYPE 
         13.02          13.58 
[1] "0.2 - 37.2 (13.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D31V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH1 MUTATED         0        0        1        3         5         1
  CDH1 WILD-TYPE      10       20       45       28        79        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH1 MUTATED           0          5          7          3        4         0
  CDH1 WILD-TYPE        29         79         55         36       39         4
D31V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              3             28
  STAGE IIA             5             79
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            5             79
  STAGE IIIB            7             55
  STAGE IIIC            3             36
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CDH1 MUTATED       2   6  14  10
  CDH1 WILD-TYPE    52 129 247  92
D31V4, multiclass
       clus
vv      CDH1 MUTATED CDH1 WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3              14            247
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CDH1 MUTATED     7   8   7  10
  CDH1 WILD-TYPE 188 165  82  75
D31V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            7            188
  N1            8            165
  N2            7             82
  N3           10             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                cls
clus               0   1
  CDH1 MUTATED    26   5
  CDH1 WILD-TYPE 456  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     26    5
  CDH1 WILD-TYPE  456   33
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           26            456
  1            5             33
[1] 2 2
[1] FALSE
D31V7, binary
                cls
clus               0   1
  CDH1 MUTATED    12  21
  CDH1 WILD-TYPE 160 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     12   21
  CDH1 WILD-TYPE  160  385
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE           12            160
  MALE             21            385
[1] 2 2
[1] FALSE
D31V8, binary
                cls
clus               0   1
  CDH1 MUTATED    28   2
  CDH1 WILD-TYPE 388 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     28    2
  CDH1 WILD-TYPE  388  100
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO            28            388
  YES            2            100
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
[1] "Remove cluster labels:" "CDH1 MUTATED"          
clus
  CDH1 MUTATED CDH1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" "CDH1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"CDH1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CDH1 MUTATED       8                         1
  CDH1 WILD-TYPE   125                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH1 MUTATED                                           0    23
  CDH1 WILD-TYPE                                         1   334
D31V11, multiclass
                                           clus
vv                                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               23            334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                cls
clus               0   1
  CDH1 MUTATED     0  32
  CDH1 WILD-TYPE  10 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      0   32
  CDH1 WILD-TYPE   10  366
                        clus
vv                       CDH1 MUTATED CDH1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           32            366
[1] 2 2
[1] FALSE

Clustering(32) Variable = BCOR MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    18  10
  BCOR WILD-TYPE 320 206
  BCOR MUTATED BCOR WILD-TYPE 
            28            526 
  BCOR MUTATED BCOR WILD-TYPE 
            10            206 
$`BCOR MUTATED`
TCGA-2H-A9GF TCGA-L5-A8NQ TCGA-V5-AASX TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6455 
       25.78        21.37         8.98        26.70         6.97        13.87 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-8366 TCGA-BR-8487 
       32.78        19.89        21.90        35.84         0.95         1.12 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5724 
       12.43        11.77         1.02        12.03         6.02        12.03 
TCGA-D7-A6ET TCGA-D7-A6F0 TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-8608 
       26.43        22.29        21.27        26.47        22.82        21.07 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-SW-A7EA TCGA-VQ-A8P2 
        0.10         6.51        19.04        38.14 

$`BCOR WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       44.94         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        14.76        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        28.96        22.32         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BCOR MUTATED BCOR WILD-TYPE 
           0.1            0.0 
  BCOR MUTATED BCOR WILD-TYPE 
         38.14         122.30 
  BCOR MUTATED BCOR WILD-TYPE 
        19.465         13.510 
[1] "0.1 - 38.1 (19.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D32V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCOR MUTATED         0        0        5        2         7         2
  BCOR WILD-TYPE      10       20       41       29        77        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED           1          4          3          1        4         0
  BCOR WILD-TYPE        28         80         59         38       39         4
D32V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              5             41
  STAGE II              2             29
  STAGE IIA             7             77
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            3             59
  STAGE IIIC            1             38
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BCOR MUTATED       0   7  17   6
  BCOR WILD-TYPE    54 128 244  96
D32V4, multiclass
       clus
vv      BCOR MUTATED BCOR WILD-TYPE
  T0+T1            0             54
  T2               7            128
  T3              17            244
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BCOR MUTATED    15   7   3   4
  BCOR WILD-TYPE 180 166  86  81
D32V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           15            180
  N1            7            166
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                cls
clus               0   1
  BCOR MUTATED    24   3
  BCOR WILD-TYPE 458  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     24    3
  BCOR WILD-TYPE  458   35
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           24            458
  1            3             35
[1] 2 2
[1] FALSE
D32V7, binary
                cls
clus               0   1
  BCOR MUTATED    12  19
  BCOR WILD-TYPE 160 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     12   19
  BCOR WILD-TYPE  160  387
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE           12            160
  MALE             19            387
[1] 2 2
[1] FALSE
D32V8, binary
                cls
clus               0   1
  BCOR MUTATED    23   3
  BCOR WILD-TYPE 393  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     23    3
  BCOR WILD-TYPE  393   99
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            23            393
  YES            3             99
[1] 2 2
[1] FALSE
D32V9, continuous
[1] "Remove cluster labels:" "BCOR MUTATED"          
clus
  BCOR MUTATED BCOR WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-VR-A8EO     TCGA-VR-A8EP 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
D32V10, continuous
[1] "Remove cluster labels:" "BCOR MUTATED"          
clus
  BCOR MUTATED BCOR WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" "BCOR WILD-TYPE" 
    TCGA-Z6-AAPN 
"BCOR WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BCOR MUTATED       6                         0
  BCOR WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCOR MUTATED                                           0    19
  BCOR WILD-TYPE                                         1   338
D32V11, multiclass
                                           clus
vv                                          BCOR MUTATED BCOR WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                cls
clus               0   1
  BCOR MUTATED     1  22
  BCOR WILD-TYPE   9 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      1   22
  BCOR WILD-TYPE    9  376
                        clus
vv                       BCOR MUTATED BCOR WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           22            376
[1] 2 2
[1] FALSE

Clustering(33) Variable = C14ORF43 MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    22   7
  C14ORF43 WILD-TYPE 316 209
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                29                525 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 7                209 
$`C14ORF43 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4QS TCGA-L5-A8NW TCGA-LN-A7HY TCGA-R6-A6XG TCGA-VR-A8EY 
       19.99         3.88        46.09        12.03        38.40        33.70 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8372 
        6.61        34.68        29.59         6.18        14.04        31.27 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 
       31.96        16.14        12.43        11.77         6.02        65.10 
TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
       11.44        26.47        22.32        22.68        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        6.58        29.00        23.80        74.53        38.14 

$`C14ORF43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              3.88               0.00 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             74.53             122.30 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             22.68              13.41 
[1] "3.9 - 74.5 (22.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C14ORF43 MUTATED         0        0        4        1         5         4
  C14ORF43 WILD-TYPE      10       20       42       30        79        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           2          2          4          3        4
  C14ORF43 WILD-TYPE        27         82         58         36       39
                    vv
clus                 STAGE IVA
  C14ORF43 MUTATED           0
  C14ORF43 WILD-TYPE         4
D33V3, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  4                 42
  STAGE II                  1                 30
  STAGE IIA                 5                 79
  STAGE IIB                 4                 79
  STAGE III                 2                 27
  STAGE IIIA                2                 82
  STAGE IIIB                4                 58
  STAGE IIIC                3                 36
  STAGE IV                  4                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C14ORF43 MUTATED       1   6  15   9
  C14ORF43 WILD-TYPE    53 129 246  93
D33V4, multiclass
       clus
vv      C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T0+T1                1                 53
  T2                   6                129
  T3                  15                246
  T4                   9                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C14ORF43 MUTATED    10  10   3   6
  C14ORF43 WILD-TYPE 185 163  86  79
D33V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0               10                185
  N1               10                163
  N2                3                 86
  N3                6                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    26   2
  C14ORF43 WILD-TYPE 456  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     26    2
  C14ORF43 WILD-TYPE  456   36
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               26                456
  1                2                 36
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    17  15
  C14ORF43 WILD-TYPE 155 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     17   15
  C14ORF43 WILD-TYPE  155  391
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE               17                155
  MALE                 15                391
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    26   1
  C14ORF43 WILD-TYPE 390 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     26    1
  C14ORF43 WILD-TYPE  390  101
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                26                390
  YES                1                101
[1] 2 2
[1] FALSE
D33V9, continuous
[1] "Remove cluster labels:" "C14ORF43 MUTATED"      
clus
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
D33V10, continuous
[1] "Remove cluster labels:" "C14ORF43 MUTATED"      
clus
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-LN-A49O 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" "C14ORF43 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C14ORF43 MUTATED      11                         0
  C14ORF43 WILD-TYPE   122                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF43 MUTATED                                           0    19
  C14ORF43 WILD-TYPE                                         1   338
D33V11, multiclass
                                           clus
vv                                          C14ORF43 MUTATED C14ORF43 WILD-TYPE
  ASIAN                                                   11                122
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   19                338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED     1  25
  C14ORF43 WILD-TYPE   9 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      1   25
  C14ORF43 WILD-TYPE    9  373
                        clus
vv                       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               25                373
[1] 2 2
[1] FALSE

Clustering(34) Variable = ZBTB7C MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED    10   4
  ZBTB7C WILD-TYPE 328 212
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              540 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               4              212 
$`ZBTB7C MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-A4QL 
       34.68        29.59         6.18         4.31         1.12        16.14 
TCGA-CD-A4MG TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV TCGA-HU-A4G8 TCGA-MX-A5UJ 
        6.58        28.96        65.10         5.92        22.68        19.73 
TCGA-VQ-A8P2 TCGA-VQ-AA68 
       38.14        43.66 

$`ZBTB7C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
            1.12             0.00 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
            65.1            122.3 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
          21.205           13.510 
[1] "1.1 - 65.1 (21.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D34V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB7C MUTATED         1        1        2        0         4         4
  ZBTB7C WILD-TYPE       9       19       44       31        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          2          1          1        0
  ZBTB7C WILD-TYPE        29         82         61         38       43
                  vv
clus               STAGE IVA
  ZBTB7C MUTATED           0
  ZBTB7C WILD-TYPE         4
D34V3, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZBTB7C MUTATED       3   2   8   4
  ZBTB7C WILD-TYPE    51 133 253  98
D34V4, multiclass
       clus
vv      ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                 8              253
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB7C MUTATED     9   4   1   2
  ZBTB7C WILD-TYPE 186 169  88  83
D34V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0              9              186
  N1              4              169
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    16   0
  ZBTB7C WILD-TYPE 466  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     16    0
  ZBTB7C WILD-TYPE  466   38
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             16              466
  1              0               38
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    11   6
  ZBTB7C WILD-TYPE 161 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     11    6
  ZBTB7C WILD-TYPE  161  400
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  FEMALE             11              161
  MALE                6              400
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   2
  ZBTB7C WILD-TYPE 404 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    2
  ZBTB7C WILD-TYPE  404  100
     clus
vv    ZBTB7C MUTATED ZBTB7C WILD-TYPE
  NO              12              404
  YES              2              100
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB7C MUTATED       2                         1
  ZBTB7C WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB7C MUTATED                                           0    12
  ZBTB7C WILD-TYPE                                         1   345
D34V11, multiclass
                                           clus
vv                                          ZBTB7C MUTATED ZBTB7C WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     0  13
  ZBTB7C WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      0   13
  ZBTB7C WILD-TYPE   10  385
                        clus
vv                       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(35) Variable = FRMD4A MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  FRMD4A MUTATED    20   6
  FRMD4A WILD-TYPE 318 210
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              26              528 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
               6              210 
$`FRMD4A MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OI TCGA-IG-A4P3 TCGA-JY-A6F8 TCGA-LN-A49S TCGA-R6-A6DN 
       60.39        19.99        18.64       122.10        13.15         8.02 
TCGA-R6-A6Y0 TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8361 
       53.95        26.70        11.01         9.34        35.84        31.10 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 
        1.12        28.14        31.96         6.58         6.02        28.96 
TCGA-D7-6822 TCGA-F1-6874 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GQ 
       12.33        14.47        11.08        77.29        30.51         0.10 
TCGA-HU-A4H6 TCGA-HU-A4H8 
       21.17        14.07 

$`FRMD4A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        23.80        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FRMD4A MUTATED FRMD4A WILD-TYPE 
             0.1              0.0 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
           122.1            122.3 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
          19.315           13.495 
[1] "0.1 - 122.1 (19.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D35V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FRMD4A MUTATED         2        2        4        1         4         3
  FRMD4A WILD-TYPE       8       18       42       30        80        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMD4A MUTATED           0          1          0          5        2
  FRMD4A WILD-TYPE        29         83         62         34       41
                  vv
clus               STAGE IVA
  FRMD4A MUTATED           0
  FRMD4A WILD-TYPE         4
D35V3, multiclass
            clus
vv           FRMD4A MUTATED FRMD4A WILD-TYPE
  STAGE I                 2                8
  STAGE IA                2               18
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              5               34
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FRMD4A MUTATED       5   5   6   8
  FRMD4A WILD-TYPE    49 130 255  94
D35V4, multiclass
       clus
vv      FRMD4A MUTATED FRMD4A WILD-TYPE
  T0+T1              5               49
  T2                 5              130
  T3                 6              255
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FRMD4A MUTATED    12   6   4   3
  FRMD4A WILD-TYPE 183 167  85  82
D35V5, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  N0             12              183
  N1              6              167
  N2              4               85
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                  cls
clus                 0   1
  FRMD4A MUTATED    24   1
  FRMD4A WILD-TYPE 458  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED     24    1
  FRMD4A WILD-TYPE  458   37
   clus
vv  FRMD4A MUTATED FRMD4A WILD-TYPE
  0             24              458
  1              1               37
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     7  21
  FRMD4A WILD-TYPE 165 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      7   21
  FRMD4A WILD-TYPE  165  385
        clus
vv       FRMD4A MUTATED FRMD4A WILD-TYPE
  FEMALE              7              165
  MALE               21              385
[1] 2 2
[1] FALSE
D35V8, binary
                  cls
clus                 0   1
  FRMD4A MUTATED    19   6
  FRMD4A WILD-TYPE 397  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED     19    6
  FRMD4A WILD-TYPE  397   96
     clus
vv    FRMD4A MUTATED FRMD4A WILD-TYPE
  NO              19              397
  YES              6               96
[1] 2 2
[1] FALSE
D35V9, continuous
[1] "Remove cluster labels:" "FRMD4A MUTATED"        
clus
  FRMD4A MUTATED FRMD4A WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" "FRMD4A WILD-TYPE" 
D35V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FRMD4A MUTATED       7                         1
  FRMD4A WILD-TYPE   126                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FRMD4A MUTATED                                           0    16
  FRMD4A WILD-TYPE                                         1   341
D35V11, multiclass
                                           clus
vv                                          FRMD4A MUTATED FRMD4A WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     0  21
  FRMD4A WILD-TYPE  10 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      0   21
  FRMD4A WILD-TYPE   10  377
                        clus
vv                       FRMD4A MUTATED FRMD4A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(36) Variable = PAX6 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    14   6
  PAX6 WILD-TYPE 324 210
  PAX6 MUTATED PAX6 WILD-TYPE 
            20            534 
  PAX6 MUTATED PAX6 WILD-TYPE 
             6            210 
$`PAX6 MUTATED`
TCGA-2H-A9GH TCGA-L5-A8NS TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8078 
       31.27        13.41         9.67        32.78        36.16        29.59 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-A4CQ TCGA-CD-8529 TCGA-CG-5721 
       31.10        31.27        25.05        34.98        12.30         6.02 
TCGA-CG-5733 TCGA-FP-7916 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU 
       21.07        14.07        30.51        22.68         6.51         6.58 
TCGA-R5-A7ZI TCGA-RD-A7BT 
       74.53         8.61 

$`PAX6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PAX6 MUTATED PAX6 WILD-TYPE 
          6.02           0.00 
  PAX6 MUTATED PAX6 WILD-TYPE 
         74.53         122.30 
  PAX6 MUTATED PAX6 WILD-TYPE 
        23.865         13.495 
[1] "6.0 - 74.5 (23.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D36V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX6 MUTATED         0        1        1        0         2         5
  PAX6 WILD-TYPE      10       19       45       31        82        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX6 MUTATED           0          2          0          5        4         0
  PAX6 WILD-TYPE        29         82         62         34       39         4
D36V3, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            5             34
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PAX6 MUTATED       2   2   7  10
  PAX6 WILD-TYPE    52 133 254  92
D36V4, multiclass
       clus
vv      PAX6 MUTATED PAX6 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               7            254
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PAX6 MUTATED     7   6   2   5
  PAX6 WILD-TYPE 188 167  87  80
D36V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0            7            188
  N1            6            167
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                cls
clus               0   1
  PAX6 MUTATED    18   2
  PAX6 WILD-TYPE 464  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     18    2
  PAX6 WILD-TYPE  464   36
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           18            464
  1            2             36
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus               0   1
  PAX6 MUTATED    11  11
  PAX6 WILD-TYPE 161 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     11   11
  PAX6 WILD-TYPE  161  395
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  FEMALE           11            161
  MALE             11            395
[1] 2 2
[1] FALSE
D36V8, binary
                cls
clus               0   1
  PAX6 MUTATED    17   3
  PAX6 WILD-TYPE 399  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     17    3
  PAX6 WILD-TYPE  399   99
     clus
vv    PAX6 MUTATED PAX6 WILD-TYPE
  NO            17            399
  YES            3             99
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
[1] "Remove cluster labels:" "PAX6 MUTATED"          
clus
  PAX6 MUTATED PAX6 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NW     TCGA-LN-A49O 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" "PAX6 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PAX6 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PAX6 MUTATED       5                         0
  PAX6 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAX6 MUTATED                                           1    11
  PAX6 WILD-TYPE                                         0   346
D36V11, multiclass
                                           clus
vv                                          PAX6 MUTATED PAX6 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                cls
clus               0   1
  PAX6 MUTATED     1  15
  PAX6 WILD-TYPE   9 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      1   15
  PAX6 WILD-TYPE    9  383
                        clus
vv                       PAX6 MUTATED PAX6 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(37) Variable = PRSS36 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  PRSS36 MUTATED    10  11
  PRSS36 WILD-TYPE 328 205
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              21              533 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              11              205 
$`PRSS36 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NS TCGA-LN-A8HZ TCGA-VR-A8EQ TCGA-VR-AA7B 
        4.31        19.99        13.41        12.33        22.82        11.24 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 
       30.90         9.34        32.78        44.94        29.59        31.10 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV 
       16.14        15.95         1.02        28.96        65.10         5.92 
TCGA-D7-A6EY TCGA-HU-A4GQ TCGA-IN-A6RL 
       11.44         0.10        13.35 

$`PRSS36 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PRSS36 MUTATED PRSS36 WILD-TYPE 
             0.1              0.0 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
            65.1            122.3 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
           15.95            13.55 
[1] "0.1 - 65.1 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D37V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRSS36 MUTATED         0        1        2        1         3         4
  PRSS36 WILD-TYPE      10       19       44       30        81        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS36 MUTATED           1          1          2          3        2
  PRSS36 WILD-TYPE        28         83         60         36       41
                  vv
clus               STAGE IVA
  PRSS36 MUTATED           0
  PRSS36 WILD-TYPE         4
D37V3, multiclass
            clus
vv           PRSS36 MUTATED PRSS36 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PRSS36 MUTATED       1   6  11   3
  PRSS36 WILD-TYPE    53 129 250  99
D37V4, multiclass
       clus
vv      PRSS36 MUTATED PRSS36 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                11              250
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PRSS36 MUTATED     9   5   3   4
  PRSS36 WILD-TYPE 186 168  86  81
D37V5, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  N0              9              186
  N1              5              168
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    18   2
  PRSS36 WILD-TYPE 464  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     18    2
  PRSS36 WILD-TYPE  464   36
   clus
vv  PRSS36 MUTATED PRSS36 WILD-TYPE
  0             18              464
  1              2               36
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    10  12
  PRSS36 WILD-TYPE 162 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     10   12
  PRSS36 WILD-TYPE  162  394
        clus
vv       PRSS36 MUTATED PRSS36 WILD-TYPE
  FEMALE             10              162
  MALE               12              394
[1] 2 2
[1] FALSE
D37V8, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    14   3
  PRSS36 WILD-TYPE 402  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     14    3
  PRSS36 WILD-TYPE  402   99
     clus
vv    PRSS36 MUTATED PRSS36 WILD-TYPE
  NO              14              402
  YES              3               99
[1] 2 2
[1] FALSE
D37V9, continuous
[1] "Remove cluster labels:" "PRSS36 MUTATED"        
clus
  PRSS36 MUTATED PRSS36 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7D 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PRSS36 WILD-TYPE" "PRSS36 WILD-TYPE" 
D37V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRSS36 MUTATED       2                         0
  PRSS36 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRSS36 MUTATED                                           0    15
  PRSS36 WILD-TYPE                                         1   342
D37V11, multiclass
                                           clus
vv                                          PRSS36 MUTATED PRSS36 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                  cls
clus                 0   1
  PRSS36 MUTATED     0  12
  PRSS36 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED      0   12
  PRSS36 WILD-TYPE   10  386
                        clus
vv                       PRSS36 MUTATED PRSS36 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(38) Variable = CDKN2A MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    22  10
  CDKN2A WILD-TYPE 316 206
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              32              522 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              10              206 
$`CDKN2A MUTATED`
TCGA-L5-A8NG TCGA-MX-A663 TCGA-2H-A9GN TCGA-JY-A93D TCGA-L5-A4OF TCGA-L5-A4OO 
       35.97         9.86         8.94        31.56        26.33         3.32 
TCGA-L5-A4OP TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A6VZ 
        7.17        13.22         7.76         5.49        13.41        10.36 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-V5-A7RC 
       13.41        13.38        13.18        33.11        38.40         3.42 
TCGA-VR-AA4D TCGA-XP-A8T7 TCGA-BR-8487 TCGA-CD-5799 TCGA-CD-A489 TCGA-FP-8099 
       46.19        41.23         1.12        13.02        11.31        17.06 
TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-A7NT TCGA-R5-A7O7 TCGA-VQ-A91V 
       22.68        20.25        14.07        10.62        45.67        42.64 
TCGA-VQ-AA64 TCGA-VQ-AA6I 
       18.41        16.14 

$`CDKN2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        21.01        47.93        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NQ 
        2.66        12.92        13.48        16.47        13.55        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        8.71        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        1.71        66.81        11.24        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        27.55        12.43        17.26 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.12             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           46.19           122.30 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           13.41            13.63 
[1] "1.1 - 46.2 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D38V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKN2A MUTATED         0        1        1        1         8         6
  CDKN2A WILD-TYPE      10       19       45       30        76        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED           5          2          2          4        1
  CDKN2A WILD-TYPE        24         82         60         35       42
                  vv
clus               STAGE IVA
  CDKN2A MUTATED           0
  CDKN2A WILD-TYPE         4
D38V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               8               76
  STAGE IIB               6               77
  STAGE III               5               24
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              4               35
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CDKN2A MUTATED       4   5  21   1
  CDKN2A WILD-TYPE    50 130 240 101
D38V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T0+T1              4               50
  T2                 5              130
  T3                21              240
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDKN2A MUTATED    10  14   3   4
  CDKN2A WILD-TYPE 185 159  86  81
D38V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0             10              185
  N1             14              159
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    28   1
  CDKN2A WILD-TYPE 454  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     28    1
  CDKN2A WILD-TYPE  454   37
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             28              454
  1              1               37
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     9  26
  CDKN2A WILD-TYPE 163 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      9   26
  CDKN2A WILD-TYPE  163  380
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              9              163
  MALE               26              380
[1] 2 2
[1] FALSE
D38V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    19  11
  CDKN2A WILD-TYPE 397  91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     19   11
  CDKN2A WILD-TYPE  397   91
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              19              397
  YES             11               91
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDKN2A MUTATED       8                         1
  CDKN2A WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKN2A MUTATED                                           0    22
  CDKN2A WILD-TYPE                                         1   335
D38V11, multiclass
                                           clus
vv                                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     2  17
  CDKN2A WILD-TYPE   8 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2   17
  CDKN2A WILD-TYPE    8  381
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             17              381
[1] 2 2
[1] FALSE

Clustering(39) Variable = MVK MUTATION ANALYSIS
D39V1, survival
               sevent
clus2             0   1
  MVK MUTATED     9   5
  MVK WILD-TYPE 329 211
  MVK MUTATED MVK WILD-TYPE 
           14           540 
  MVK MUTATED MVK WILD-TYPE 
            5           211 
$`MVK MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8589 
       19.99         6.97         6.61        35.84        31.10        27.12 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GU 
        6.58        11.77        21.07        30.51        22.68         6.58 
TCGA-HU-A4H3 TCGA-MX-A5UJ 
       29.00        19.73 

$`MVK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MVK MUTATED MVK WILD-TYPE 
         6.58          0.00 
  MVK MUTATED MVK WILD-TYPE 
        35.84        122.30 
  MVK MUTATED MVK WILD-TYPE 
        20.53         13.51 
[1] "6.6 - 35.8 (20.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D39V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MVK MUTATED         0        0        2        0         1         2
  MVK WILD-TYPE      10       20       44       31        83        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MVK MUTATED           1          4          1          4        0         0
  MVK WILD-TYPE        28         80         61         35       43         4
D39V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             2            44
  STAGE II             0            31
  STAGE IIA            1            83
  STAGE IIB            2            81
  STAGE III            1            28
  STAGE IIIA           4            80
  STAGE IIIB           1            61
  STAGE IIIC           4            35
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  MVK MUTATED       1   4   7   4
  MVK WILD-TYPE    53 131 254  98
D39V4, multiclass
       clus
vv      MVK MUTATED MVK WILD-TYPE
  T0+T1           1            53
  T2              4           131
  T3              7           254
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  MVK MUTATED     3   6   3   3
  MVK WILD-TYPE 192 167  86  82
D39V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0           3           192
  N1           6           167
  N2           3            86
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
               cls
clus              0   1
  MVK MUTATED    14   0
  MVK WILD-TYPE 468  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     14    0
  MVK WILD-TYPE  468   38
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          14           468
  1           0            38
[1] 2 2
[1] FALSE
D39V7, binary
               cls
clus              0   1
  MVK MUTATED     9   7
  MVK WILD-TYPE 163 399
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      9    7
  MVK WILD-TYPE  163  399
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           9           163
  MALE             7           399
[1] 2 2
[1] FALSE
D39V8, binary
               cls
clus              0   1
  MVK MUTATED    12   1
  MVK WILD-TYPE 404 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     12    1
  MVK WILD-TYPE  404  101
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO           12           404
  YES           1           101
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
[1] "Remove cluster labels:" "MVK MUTATED"           
clus
  MVK MUTATED MVK WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" "MVK WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"MVK WILD-TYPE" "MVK WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  MVK MUTATED       5                         0
  MVK WILD-TYPE   128                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MVK MUTATED                                           0     8
  MVK WILD-TYPE                                         1   349
D39V11, multiclass
                                           clus
vv                                          MVK MUTATED MVK WILD-TYPE
  ASIAN                                               5           128
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               8           349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
               cls
clus              0   1
  MVK MUTATED     0  12
  MVK WILD-TYPE  10 386
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      0   12
  MVK WILD-TYPE   10  386
                        clus
vv                       MVK MUTATED MVK WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          12           386
[1] 2 2
[1] FALSE

Clustering(40) Variable = KIAA0406 MUTATION ANALYSIS
D40V1, survival
                    sevent
clus2                  0   1
  KIAA0406 MUTATED    12  13
  KIAA0406 WILD-TYPE 326 203
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                25                529 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                13                203 
$`KIAA0406 MUTATED`
TCGA-L5-A4OI TCGA-CG-4475 TCGA-L5-A8NM TCGA-LN-A4A5 TCGA-BR-4256 TCGA-BR-6452 
       19.99        22.98         7.76        22.39         9.34        34.68 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8589 TCGA-BR-8591 
       11.44        29.59        32.25         0.26        27.12        28.14 
TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       31.96         1.48        16.14        12.43         6.58        11.77 
TCGA-CG-4306 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HU-A4GN TCGA-HU-A4GX 
        1.02        28.96        65.10        11.44        29.98        20.25 
TCGA-VQ-A8PE 
       22.19 

$`KIAA0406 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        21.99        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43         0.69         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        34.98        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
              0.26               0.00 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
              65.1              122.3 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             20.25              13.51 
[1] "0.3 - 65.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D40V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0406 MUTATED         0        1        3        1         4         5
  KIAA0406 WILD-TYPE      10       19       43       30        80        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0406 MUTATED           0          1          4          4        2
  KIAA0406 WILD-TYPE        29         83         58         35       41
                    vv
clus                 STAGE IVA
  KIAA0406 MUTATED           0
  KIAA0406 WILD-TYPE         4
D40V3, multiclass
            clus
vv           KIAA0406 MUTATED KIAA0406 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  3                 43
  STAGE II                  1                 30
  STAGE IIA                 4                 80
  STAGE IIB                 5                 78
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                4                 58
  STAGE IIIC                4                 35
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0406 MUTATED       1   7  10   7
  KIAA0406 WILD-TYPE    53 128 251  95
D40V4, multiclass
       clus
vv      KIAA0406 MUTATED KIAA0406 WILD-TYPE
  T0+T1                1                 53
  T2                   7                128
  T3                  10                251
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0406 MUTATED    10   6   4   6
  KIAA0406 WILD-TYPE 185 167  85  79
D40V5, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  N0               10                185
  N1                6                167
  N2                4                 85
  N3                6                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    23   2
  KIAA0406 WILD-TYPE 459  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     23    2
  KIAA0406 WILD-TYPE  459   36
   clus
vv  KIAA0406 MUTATED KIAA0406 WILD-TYPE
  0               23                459
  1                2                 36
[1] 2 2
[1] FALSE
D40V7, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    10  16
  KIAA0406 WILD-TYPE 162 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     10   16
  KIAA0406 WILD-TYPE  162  390
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  FEMALE               10                162
  MALE                 16                390
[1] 2 2
[1] FALSE
D40V8, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    22   0
  KIAA0406 WILD-TYPE 394 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     22    0
  KIAA0406 WILD-TYPE  394  102
     clus
vv    KIAA0406 MUTATED KIAA0406 WILD-TYPE
  NO                22                394
  YES                0                102
[1] 2 2
[1] FALSE
D40V9, continuous
[1] "Remove cluster labels:" "KIAA0406 MUTATED"      
clus
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA0406 WILD-TYPE" 
D40V10, continuous
[1] "Remove cluster labels:" "KIAA0406 MUTATED"      
clus
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" "KIAA0406 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KIAA0406 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0406 MUTATED       7                         0
  KIAA0406 WILD-TYPE   126                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0406 MUTATED                                           0    14
  KIAA0406 WILD-TYPE                                         1   343
D40V11, multiclass
                                           clus
vv                                          KIAA0406 MUTATED KIAA0406 WILD-TYPE
  ASIAN                                                    7                126
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     0  18
  KIAA0406 WILD-TYPE  10 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      0   18
  KIAA0406 WILD-TYPE   10  380
                        clus
vv                       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               18                380
[1] 2 2
[1] FALSE

Clustering(41) Variable = KIAA1967 MUTATION ANALYSIS
D41V1, survival
                    sevent
clus2                  0   1
  KIAA1967 MUTATED    17   8
  KIAA1967 WILD-TYPE 321 208
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                25                529 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 8                208 
$`KIAA1967 MUTATED`
TCGA-IG-A3I8 TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-BR-4184 TCGA-BR-4201 
       33.27        13.22         7.76        13.41         6.97        30.90 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8081 
        9.67        34.68        44.94        35.84        14.43        32.25 
TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5733 TCGA-D7-A6EY TCGA-F1-A448 
       31.27        11.77        15.95        21.07        11.44        21.27 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-SW-A7EA 
       30.51        22.32        22.68         6.51        29.00        19.04 
TCGA-VQ-A8P2 
       38.14 

$`KIAA1967 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
        2.66        12.92        13.48        16.47        13.55         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
              6.51               0.00 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             44.94             122.30 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             21.27              13.41 
[1] "6.5 - 44.9 (21.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D41V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1967 MUTATED         0        0        2        1         4         5
  KIAA1967 WILD-TYPE      10       20       44       30        80        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1967 MUTATED           2          4          2          3        0
  KIAA1967 WILD-TYPE        27         80         60         36       43
                    vv
clus                 STAGE IVA
  KIAA1967 MUTATED           0
  KIAA1967 WILD-TYPE         4
D41V3, multiclass
            clus
vv           KIAA1967 MUTATED KIAA1967 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 4                 80
  STAGE IIB                 5                 78
  STAGE III                 2                 27
  STAGE IIIA                4                 80
  STAGE IIIB                2                 60
  STAGE IIIC                3                 36
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1967 MUTATED       0   6  11   7
  KIAA1967 WILD-TYPE    54 129 250  95
D41V4, multiclass
       clus
vv      KIAA1967 MUTATED KIAA1967 WILD-TYPE
  T0+T1                0                 54
  T2                   6                129
  T3                  11                250
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1967 MUTATED     9   9   1   5
  KIAA1967 WILD-TYPE 186 164  88  80
D41V5, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  N0                9                186
  N1                9                164
  N2                1                 88
  N3                5                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    25   0
  KIAA1967 WILD-TYPE 457  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     25    0
  KIAA1967 WILD-TYPE  457   38
   clus
vv  KIAA1967 MUTATED KIAA1967 WILD-TYPE
  0               25                457
  1                0                 38
[1] 2 2
[1] FALSE
D41V7, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    17   9
  KIAA1967 WILD-TYPE 155 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     17    9
  KIAA1967 WILD-TYPE  155  397
        clus
vv       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  FEMALE               17                155
  MALE                  9                397
[1] 2 2
[1] FALSE
D41V8, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    19   4
  KIAA1967 WILD-TYPE 397  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     19    4
  KIAA1967 WILD-TYPE  397   98
     clus
vv    KIAA1967 MUTATED KIAA1967 WILD-TYPE
  NO                19                397
  YES                4                 98
[1] 2 2
[1] FALSE
D41V9, continuous
[1] "Remove cluster labels:" "KIAA1967 MUTATED"      
clus
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A51D 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A7DP         TCGA-KH-A6WC 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1967 WILD-TYPE" 
D41V10, continuous
[1] "Remove cluster labels:" "KIAA1967 MUTATED"      
clus
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NW 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" "KIAA1967 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KIAA1967 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1967 MUTATED       5                         0
  KIAA1967 WILD-TYPE   128                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1967 MUTATED                                           0    18
  KIAA1967 WILD-TYPE                                         1   339
D41V11, multiclass
                                           clus
vv                                          KIAA1967 MUTATED KIAA1967 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   18                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED     1  18
  KIAA1967 WILD-TYPE   9 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED      1   18
  KIAA1967 WILD-TYPE    9  380
                        clus
vv                       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               18                380
[1] 2 2
[1] FALSE

Clustering(42) Variable = ZMYM4 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  ZMYM4 MUTATED    13   8
  ZMYM4 WILD-TYPE 325 208
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             21             533 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              8             208 
$`ZMYM4 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-IG-A50L TCGA-JY-A6FH TCGA-L5-A8NI TCGA-R6-A8W5 
        4.31        21.99         0.53        47.38        13.48        15.78 
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8589 
       26.70        11.01         6.97        35.84        25.05        27.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4466 TCGA-CG-5721 
       28.14        31.96         6.58        15.95        18.97         6.02 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-VQ-A8P2 
        0.10        20.25        38.14 

$`ZMYM4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       19.73        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
            0.1             0.0 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          47.38          122.30 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          18.97           13.51 
[1] "0.1 - 47.4 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D42V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYM4 MUTATED         0        0        2        1         1         5
  ZMYM4 WILD-TYPE      10       20       44       30        83        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMYM4 MUTATED           1          4          1          4        4         1
  ZMYM4 WILD-TYPE        28         80         61         35       39         3
D42V3, multiclass
            clus
vv           ZMYM4 MUTATED ZMYM4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZMYM4 MUTATED       0   4   6  14
  ZMYM4 WILD-TYPE    54 131 255  88
D42V4, multiclass
       clus
vv      ZMYM4 MUTATED ZMYM4 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                6             255
  T4               14              88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZMYM4 MUTATED     7  10   4   2
  ZMYM4 WILD-TYPE 188 163  85  83
D42V5, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  N0             7             188
  N1            10             163
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    19   3
  ZMYM4 WILD-TYPE 463  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     19    3
  ZMYM4 WILD-TYPE  463   35
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0            19             463
  1             3              35
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     8  16
  ZMYM4 WILD-TYPE 164 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      8   16
  ZMYM4 WILD-TYPE  164  390
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  FEMALE             8             164
  MALE              16             390
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    19   1
  ZMYM4 WILD-TYPE 397 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     19    1
  ZMYM4 WILD-TYPE  397  101
     clus
vv    ZMYM4 MUTATED ZMYM4 WILD-TYPE
  NO             19             397
  YES             1             101
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZMYM4 MUTATED       5                         0
  ZMYM4 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYM4 MUTATED                                           0    15
  ZMYM4 WILD-TYPE                                         1   342
D42V11, multiclass
                                           clus
vv                                          ZMYM4 MUTATED ZMYM4 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     0  16
  ZMYM4 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      0   16
  ZMYM4 WILD-TYPE   10  382
                        clus
vv                       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(43) Variable = LMAN1 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  LMAN1 MUTATED    12   2
  LMAN1 WILD-TYPE 326 214
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             14             540 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
              2             214 
$`LMAN1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-BR-8078 TCGA-BR-8680 
       19.99         7.76        22.39        15.52        29.59        31.96 
TCGA-CG-5728 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       65.10        21.27        29.98         6.51        20.25        29.00 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`LMAN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        12.59        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LMAN1 MUTATED LMAN1 WILD-TYPE 
           6.51            0.00 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
          74.53          122.30 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
          21.83           13.41 
[1] "6.5 - 74.5 (21.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "4.2"
D43V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LMAN1 MUTATED         0        0        3        0         4         2
  LMAN1 WILD-TYPE      10       20       43       31        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LMAN1 MUTATED           0          1          1          3        3         0
  LMAN1 WILD-TYPE        29         83         61         36       40         4
D43V3, multiclass
            clus
vv           LMAN1 MUTATED LMAN1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LMAN1 MUTATED       1   6   3   7
  LMAN1 WILD-TYPE    53 129 258  95
D43V4, multiclass
       clus
vv      LMAN1 MUTATED LMAN1 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                3             258
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LMAN1 MUTATED     7   4   3   3
  LMAN1 WILD-TYPE 188 169  86  82
D43V5, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  N0             7             188
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                 cls
clus                0   1
  LMAN1 MUTATED    14   2
  LMAN1 WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED     14    2
  LMAN1 WILD-TYPE  468   36
   clus
vv  LMAN1 MUTATED LMAN1 WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  LMAN1 MUTATED     9   8
  LMAN1 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      9    8
  LMAN1 WILD-TYPE  163  398
        clus
vv       LMAN1 MUTATED LMAN1 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus                0   1
  LMAN1 MUTATED    11   1
  LMAN1 WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED     11    1
  LMAN1 WILD-TYPE  405  101
     clus
vv    LMAN1 MUTATED LMAN1 WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D43V9, continuous
[1] "Remove cluster labels:" "LMAN1 MUTATED"         
clus
  LMAN1 MUTATED LMAN1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A6 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
D43V10, continuous
[1] "Remove cluster labels:" "LMAN1 MUTATED"         
clus
  LMAN1 MUTATED LMAN1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" "LMAN1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"LMAN1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LMAN1 MUTATED       8                         0
  LMAN1 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LMAN1 MUTATED                                           0     7
  LMAN1 WILD-TYPE                                         1   350
D43V11, multiclass
                                           clus
vv                                          LMAN1 MUTATED LMAN1 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                 cls
clus                0   1
  LMAN1 MUTATED     2  11
  LMAN1 WILD-TYPE   8 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      2   11
  LMAN1 WILD-TYPE    8  387
                        clus
vv                       LMAN1 MUTATED LMAN1 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(44) Variable = TGFBR2 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    20  10
  TGFBR2 WILD-TYPE 318 206
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              30              524 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              10              206 
$`TGFBR2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A4OO TCGA-L5-A88W 
        4.31        19.99        24.03        30.25         3.32        25.12 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A7HZ 
        7.76         8.71        10.36        12.43        12.33        13.18 
TCGA-VR-A8EX TCGA-VR-AA4G TCGA-Z6-A9VB TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6563 
       28.11        18.05         1.32        18.35        34.68        39.12 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-A453 TCGA-CD-8531 TCGA-CG-4465 TCGA-CG-5726 
        1.12        12.79         6.08        12.59         9.01        28.96 
TCGA-D7-6522 TCGA-D7-A4YT TCGA-HU-A4HD TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BW 
       18.61        14.27        33.40        19.73         4.60         5.13 

$`TGFBR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       23.18        31.56        25.22         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43        15.48         2.60         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.85         5.92        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1.12             0.00 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           39.12           122.30 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          12.985           13.630 
[1] "1.1 - 39.1 (13.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D44V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TGFBR2 MUTATED         1        1        3        0         5         5
  TGFBR2 WILD-TYPE       9       19       43       31        79        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           1          6          0          3        3
  TGFBR2 WILD-TYPE        28         78         62         36       40
                  vv
clus               STAGE IVA
  TGFBR2 MUTATED           1
  TGFBR2 WILD-TYPE         3
D44V3, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              6               78
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TGFBR2 MUTATED       3   8  15   3
  TGFBR2 WILD-TYPE    51 127 246  99
D44V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T0+T1              3               51
  T2                 8              127
  T3                15              246
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TGFBR2 MUTATED    12   9   4   6
  TGFBR2 WILD-TYPE 183 164  85  79
D44V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0             12              183
  N1              9              164
  N2              4               85
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    23   4
  TGFBR2 WILD-TYPE 459  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     23    4
  TGFBR2 WILD-TYPE  459   34
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             23              459
  1              4               34
[1] 2 2
[1] FALSE
D44V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    12  19
  TGFBR2 WILD-TYPE 160 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     12   19
  TGFBR2 WILD-TYPE  160  387
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE             12              160
  MALE               19              387
[1] 2 2
[1] FALSE
D44V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    21   5
  TGFBR2 WILD-TYPE 395  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     21    5
  TGFBR2 WILD-TYPE  395   97
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO              21              395
  YES              5               97
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TGFBR2 MUTATED       6                         1
  TGFBR2 WILD-TYPE   127                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TGFBR2 MUTATED                                           0    20
  TGFBR2 WILD-TYPE                                         1   337
D44V11, multiclass
                                           clus
vv                                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0  19
  TGFBR2 WILD-TYPE  10 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0   19
  TGFBR2 WILD-TYPE   10  379
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             19              379
[1] 2 2
[1] FALSE

Clustering(45) Variable = SNAPC1 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     7   4
  SNAPC1 WILD-TYPE 331 212
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
              11              543 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               4              212 
$`SNAPC1 MUTATED`
TCGA-L5-A8NM TCGA-LN-A9FQ TCGA-VR-A8EQ TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8361 
        7.76        12.85        22.82        26.70        29.59        31.10 
TCGA-BR-8487 TCGA-CG-5726 TCGA-D7-A4YV TCGA-HU-A4G9 TCGA-SW-A7EA 
        1.12        28.96         5.92        24.20        19.04 

$`SNAPC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            1.12             0.00 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            31.1            122.3 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
           22.82            13.51 
[1] "1.1 - 31.1 (22.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D45V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNAPC1 MUTATED         0        2        1        0         2         4
  SNAPC1 WILD-TYPE      10       18       45       31        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           1          0          0          1        0
  SNAPC1 WILD-TYPE        28         84         62         38       43
                  vv
clus               STAGE IVA
  SNAPC1 MUTATED           0
  SNAPC1 WILD-TYPE         4
D45V3, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SNAPC1 MUTATED       2   2   4   3
  SNAPC1 WILD-TYPE    52 133 257  99
D45V4, multiclass
       clus
vv      SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T0+T1              2               52
  T2                 2              133
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SNAPC1 MUTATED     7   3   1   0
  SNAPC1 WILD-TYPE 188 170  88  85
D45V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              7              188
  N1              3              170
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED    11   0
  SNAPC1 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED     11    0
  SNAPC1 WILD-TYPE  471   38
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D45V7, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     8   3
  SNAPC1 WILD-TYPE 164 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      8    3
  SNAPC1 WILD-TYPE  164  403
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  FEMALE              8              164
  MALE                3              403
[1] 2 2
[1] FALSE
D45V8, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     9   1
  SNAPC1 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      9    1
  SNAPC1 WILD-TYPE  407  101
     clus
vv    SNAPC1 MUTATED SNAPC1 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D45V9, continuous
[1] "Remove cluster labels:" "SNAPC1 MUTATED"        
clus
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" "SNAPC1 WILD-TYPE" 
D45V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SNAPC1 MUTATED       2                         0
  SNAPC1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNAPC1 MUTATED                                           0     8
  SNAPC1 WILD-TYPE                                         1   349
D45V11, multiclass
                                           clus
vv                                          SNAPC1 MUTATED SNAPC1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     0   8
  SNAPC1 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      0    8
  SNAPC1 WILD-TYPE   10  390
                        clus
vv                       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(46) Variable = FZD3 MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  FZD3 MUTATED     5   6
  FZD3 WILD-TYPE 333 210
  FZD3 MUTATED FZD3 WILD-TYPE 
            11            543 
  FZD3 MUTATED FZD3 WILD-TYPE 
             6            210 
$`FZD3 MUTATED`
TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-6458 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 
        7.76         6.97        19.33        29.59         6.18         4.31 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A6EY TCGA-MX-A5UJ 
       16.14         6.58       105.07        11.44        19.73 

$`FZD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FZD3 MUTATED FZD3 WILD-TYPE 
          4.31           0.00 
  FZD3 MUTATED FZD3 WILD-TYPE 
        105.07         122.30 
  FZD3 MUTATED FZD3 WILD-TYPE 
         11.44          13.58 
[1] "4.3 - 105.1 (11.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D46V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FZD3 MUTATED         0        0        1        1         2         4
  FZD3 WILD-TYPE      10       20       45       30        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FZD3 MUTATED           0          2          2          0        0         0
  FZD3 WILD-TYPE        29         82         60         39       43         4
D46V3, multiclass
            clus
vv           FZD3 MUTATED FZD3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FZD3 MUTATED       0   3   7   2
  FZD3 WILD-TYPE    54 132 254 100
D46V4, multiclass
       clus
vv      FZD3 MUTATED FZD3 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               7            254
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FZD3 MUTATED     5   4   1   2
  FZD3 WILD-TYPE 190 169  88  83
D46V5, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  N0            5            190
  N1            4            169
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                cls
clus               0   1
  FZD3 MUTATED    11   0
  FZD3 WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     11    0
  FZD3 WILD-TYPE  471   38
   clus
vv  FZD3 MUTATED FZD3 WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  FZD3 MUTATED     7   5
  FZD3 WILD-TYPE 165 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      7    5
  FZD3 WILD-TYPE  165  401
        clus
vv       FZD3 MUTATED FZD3 WILD-TYPE
  FEMALE            7            165
  MALE              5            401
[1] 2 2
[1] FALSE
D46V8, binary
                cls
clus               0   1
  FZD3 MUTATED    12   0
  FZD3 WILD-TYPE 404 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     12    0
  FZD3 WILD-TYPE  404  102
     clus
vv    FZD3 MUTATED FZD3 WILD-TYPE
  NO            12            404
  YES            0            102
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FZD3 MUTATED       1                         0
  FZD3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FZD3 MUTATED                                           0    10
  FZD3 WILD-TYPE                                         1   347
D46V11, multiclass
                                           clus
vv                                          FZD3 MUTATED FZD3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                cls
clus               0   1
  FZD3 MUTATED     0  10
  FZD3 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      0   10
  FZD3 WILD-TYPE   10  388
                        clus
vv                       FZD3 MUTATED FZD3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(47) Variable = SCLT1 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED    12   6
  SCLT1 WILD-TYPE 326 210
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             18             536 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              6             210 
$`SCLT1 MUTATED`
TCGA-LN-A49R TCGA-LN-A4A6 TCGA-LN-A9FQ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
       13.38        12.85        12.85         6.97        30.90        34.68 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A48A TCGA-CG-4306 TCGA-CG-5728 
       25.18         1.12        16.14        12.43         1.02        65.10 
TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX 
       11.44        77.29        22.32        22.68         6.58        20.25 

$`SCLT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
           1.02            0.00 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          77.29          122.30 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         14.760          13.565 
[1] "1.0 - 77.3 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D47V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCLT1 MUTATED         0        0        2        2         4         3
  SCLT1 WILD-TYPE      10       20       44       29        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCLT1 MUTATED           1          2          2          1        2         0
  SCLT1 WILD-TYPE        28         82         60         38       41         4
D47V3, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SCLT1 MUTATED       0   5  11   4
  SCLT1 WILD-TYPE    54 130 250  98
D47V4, multiclass
       clus
vv      SCLT1 MUTATED SCLT1 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3               11             250
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SCLT1 MUTATED     8   6   3   2
  SCLT1 WILD-TYPE 187 167  86  83
D47V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0             8             187
  N1             6             167
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                 cls
clus                0   1
  SCLT1 MUTATED    18   1
  SCLT1 WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     18    1
  SCLT1 WILD-TYPE  464   37
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  SCLT1 MUTATED    10  10
  SCLT1 WILD-TYPE 162 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     10   10
  SCLT1 WILD-TYPE  162  396
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE            10             162
  MALE              10             396
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  SCLT1 MUTATED    13   3
  SCLT1 WILD-TYPE 403  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     13    3
  SCLT1 WILD-TYPE  403   99
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO             13             403
  YES             3              99
[1] 2 2
[1] FALSE
D47V9, continuous
[1] "Remove cluster labels:" "SCLT1 MUTATED"         
clus
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A8 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
D47V10, continuous
[1] "Remove cluster labels:" "SCLT1 MUTATED"         
clus
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49S      TCGA-LN-A49U 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A9 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SCLT1 MUTATED       8                         0
  SCLT1 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCLT1 MUTATED                                           0     8
  SCLT1 WILD-TYPE                                         1   349
D47V11, multiclass
                                           clus
vv                                          SCLT1 MUTATED SCLT1 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                 cls
clus                0   1
  SCLT1 MUTATED     0  16
  SCLT1 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      0   16
  SCLT1 WILD-TYPE   10  382
                        clus
vv                       SCLT1 MUTATED SCLT1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(48) Variable = NWD1 MUTATION ANALYSIS
D48V1, survival
                sevent
clus2              0   1
  NWD1 MUTATED    22  12
  NWD1 WILD-TYPE 316 204
  NWD1 MUTATED NWD1 WILD-TYPE 
            34            520 
  NWD1 MUTATED NWD1 WILD-TYPE 
            12            204 
$`NWD1 MUTATED`
TCGA-JY-A93E TCGA-L5-A8NM TCGA-LN-A9FP TCGA-R6-A8WC TCGA-B7-5818 TCGA-BR-4184 
       25.22         7.76        12.03         2.30        11.70         6.97 
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8078 
       34.68        44.94         9.21        18.15         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8687 
       32.25        26.33        11.80        25.05         1.12         8.22 
TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8534 TCGA-CD-A48C 
       21.44        12.76        12.33        12.30        12.07        11.61 
TCGA-CD-A4MG TCGA-CG-5726 TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8211 TCGA-FP-A4BE 
        6.58        28.96        19.53        59.54        13.58        11.08 
TCGA-HU-A4G6 TCGA-HU-A4GY TCGA-VQ-A8P2 TCGA-VQ-AA69 
       24.26         0.26        38.14        28.41 

$`NWD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        21.90        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 
       33.21        37.25        14.43        11.44         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       24.79        31.96        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.59        12.53         7.17        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        17.06         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NWD1 MUTATED NWD1 WILD-TYPE 
          0.26           0.00 
  NWD1 MUTATED NWD1 WILD-TYPE 
         59.54         122.30 
  NWD1 MUTATED NWD1 WILD-TYPE 
        12.545         13.730 
[1] "0.3 - 59.5 (12.5)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D48V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NWD1 MUTATED         1        2        2        3         7         6
  NWD1 WILD-TYPE       9       18       44       28        77        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NWD1 MUTATED           0          6          3          2        2         0
  NWD1 WILD-TYPE        29         78         59         37       41         4
D48V3, multiclass
            clus
vv           NWD1 MUTATED NWD1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              2             44
  STAGE II              3             28
  STAGE IIA             7             77
  STAGE IIB             6             77
  STAGE III             0             29
  STAGE IIIA            6             78
  STAGE IIIB            3             59
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NWD1 MUTATED       4   4  17  10
  NWD1 WILD-TYPE    50 131 244  92
D48V4, multiclass
       clus
vv      NWD1 MUTATED NWD1 WILD-TYPE
  T0+T1            4             50
  T2               4            131
  T3              17            244
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NWD1 MUTATED    18  11   2   3
  NWD1 WILD-TYPE 177 162  87  82
D48V5, multiclass
    clus
vv   NWD1 MUTATED NWD1 WILD-TYPE
  N0           18            177
  N1           11            162
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                cls
clus               0   1
  NWD1 MUTATED    31   1
  NWD1 WILD-TYPE 451  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     31    1
  NWD1 WILD-TYPE  451   37
   clus
vv  NWD1 MUTATED NWD1 WILD-TYPE
  0           31            451
  1            1             37
[1] 2 2
[1] FALSE
D48V7, binary
                cls
clus               0   1
  NWD1 MUTATED    16  20
  NWD1 WILD-TYPE 156 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     16   20
  NWD1 WILD-TYPE  156  386
        clus
vv       NWD1 MUTATED NWD1 WILD-TYPE
  FEMALE           16            156
  MALE             20            386
[1] 2 2
[1] FALSE
D48V8, binary
                cls
clus               0   1
  NWD1 MUTATED    23   9
  NWD1 WILD-TYPE 393  93
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     23    9
  NWD1 WILD-TYPE  393   93
     clus
vv    NWD1 MUTATED NWD1 WILD-TYPE
  NO            23            393
  YES            9             93
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
[1] "Remove cluster labels:" "NWD1 MUTATED"          
clus
  NWD1 MUTATED NWD1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-RE-A7BO     TCGA-V5-A7RB 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"NWD1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NWD1 MUTATED       9                         2
  NWD1 WILD-TYPE   124                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NWD1 MUTATED                                           0    24
  NWD1 WILD-TYPE                                         1   333
D48V11, multiclass
                                           clus
vv                                          NWD1 MUTATED NWD1 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               24            333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                cls
clus               0   1
  NWD1 MUTATED     0  31
  NWD1 WILD-TYPE  10 367
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      0   31
  NWD1 WILD-TYPE   10  367
                        clus
vv                       NWD1 MUTATED NWD1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           31            367
[1] 2 2
[1] FALSE

Clustering(49) Variable = CYP27B1 MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  CYP27B1 MUTATED     4   7
  CYP27B1 WILD-TYPE 334 209
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
               11               543 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                7               209 
$`CYP27B1 MUTATED`
TCGA-2H-A9GI TCGA-VR-A8ER TCGA-BR-4184 TCGA-BR-8059 TCGA-BR-8680 TCGA-CD-A4MG 
       14.30        12.43         6.97        14.43        31.96         6.58 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-A6EY TCGA-HU-A4GX TCGA-HU-A4H4 
       65.10        21.07        11.44        20.25        23.84 

$`CYP27B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        28.96         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
             6.58              0.00 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
             65.1             122.3 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            14.43             13.51 
[1] "6.6 - 65.1 (14.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP27B1 MUTATED         0        0        1        0         1         1
  CYP27B1 WILD-TYPE      10       20       45       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP27B1 MUTATED           3          2          1          1        1
  CYP27B1 WILD-TYPE        26         82         61         38       42
                   vv
clus                STAGE IVA
  CYP27B1 MUTATED           0
  CYP27B1 WILD-TYPE         4
D49V3, multiclass
            clus
vv           CYP27B1 MUTATED CYP27B1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                3                26
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CYP27B1 MUTATED       0   3   4   4
  CYP27B1 WILD-TYPE    54 132 257  98
D49V4, multiclass
       clus
vv      CYP27B1 MUTATED CYP27B1 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  4               257
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CYP27B1 MUTATED     2   4   4   1
  CYP27B1 WILD-TYPE 193 169  85  84
D49V5, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  N0               2               193
  N1               4               169
  N2               4                85
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     9   1
  CYP27B1 WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      9    1
  CYP27B1 WILD-TYPE  473   37
   clus
vv  CYP27B1 MUTATED CYP27B1 WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     5   6
  CYP27B1 WILD-TYPE 167 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      5    6
  CYP27B1 WILD-TYPE  167  400
        clus
vv       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  FEMALE               5               167
  MALE                 6               400
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     9   1
  CYP27B1 WILD-TYPE 407 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      9    1
  CYP27B1 WILD-TYPE  407  101
     clus
vv    CYP27B1 MUTATED CYP27B1 WILD-TYPE
  NO                9               407
  YES               1               101
[1] 2 2
[1] FALSE
D49V9, continuous
[1] "Remove cluster labels:" "CYP27B1 MUTATED"       
clus
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ET        TCGA-VR-A8EU 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
D49V10, continuous
[1] "Remove cluster labels:" "CYP27B1 MUTATED"       
clus
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" "CYP27B1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"CYP27B1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CYP27B1 MUTATED       4                         0
  CYP27B1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP27B1 MUTATED                                           0     3
  CYP27B1 WILD-TYPE                                         1   354
D49V11, multiclass
                                           clus
vv                                          CYP27B1 MUTATED CYP27B1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     0   7
  CYP27B1 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      0    7
  CYP27B1 WILD-TYPE   10  391
                        clus
vv                       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(50) Variable = MTG1 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2              0   1
  MTG1 MUTATED     7   5
  MTG1 WILD-TYPE 331 211
  MTG1 MUTATED MTG1 WILD-TYPE 
            12            542 
  MTG1 MUTATED MTG1 WILD-TYPE 
             5            211 
$`MTG1 MUTATED`
TCGA-IG-A3QL TCGA-L5-A8NI TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-8081 TCGA-CG-4306 
       35.21        13.48         2.66         6.97        32.25         1.02 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 
        5.92        14.47        11.08        22.32         0.10        38.14 

$`MTG1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MTG1 MUTATED MTG1 WILD-TYPE 
           0.1            0.0 
  MTG1 MUTATED MTG1 WILD-TYPE 
         38.14         122.30 
  MTG1 MUTATED MTG1 WILD-TYPE 
         12.28          13.63 
[1] "0.1 - 38.1 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D50V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTG1 MUTATED         0        0        1        0         3         3
  MTG1 WILD-TYPE      10       20       45       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTG1 MUTATED           1          2          0          1        1         0
  MTG1 WILD-TYPE        28         82         62         38       42         4
D50V3, multiclass
            clus
vv           MTG1 MUTATED MTG1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MTG1 MUTATED       0   2   6   4
  MTG1 WILD-TYPE    54 133 255  98
D50V4, multiclass
       clus
vv      MTG1 MUTATED MTG1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               6            255
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MTG1 MUTATED     6   4   2   0
  MTG1 WILD-TYPE 189 169  87  85
D50V5, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                cls
clus               0   1
  MTG1 MUTATED    10   1
  MTG1 WILD-TYPE 472  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED     10    1
  MTG1 WILD-TYPE  472   37
   clus
vv  MTG1 MUTATED MTG1 WILD-TYPE
  0           10            472
  1            1             37
[1] 2 2
[1] FALSE
D50V7, binary
                cls
clus               0   1
  MTG1 MUTATED     3   9
  MTG1 WILD-TYPE 169 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      3    9
  MTG1 WILD-TYPE  169  397
        clus
vv       MTG1 MUTATED MTG1 WILD-TYPE
  FEMALE            3            169
  MALE              9            397
[1] 2 2
[1] FALSE
D50V8, binary
                cls
clus               0   1
  MTG1 MUTATED     9   2
  MTG1 WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      9    2
  MTG1 WILD-TYPE  407  100
     clus
vv    MTG1 MUTATED MTG1 WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D50V9, continuous
[1] "Remove cluster labels:" "MTG1 MUTATED"          
clus
  MTG1 MUTATED MTG1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YB 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3     TCGA-IG-A7DP 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
D50V10, continuous
[1] "Remove cluster labels:" "MTG1 MUTATED"          
clus
  MTG1 MUTATED MTG1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" "MTG1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MTG1 MUTATED       2                         1
  MTG1 WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTG1 MUTATED                                           0     8
  MTG1 WILD-TYPE                                         1   349
D50V11, multiclass
                                           clus
vv                                          MTG1 MUTATED MTG1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                cls
clus               0   1
  MTG1 MUTATED     0   9
  MTG1 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      0    9
  MTG1 WILD-TYPE   10  389
                        clus
vv                       MTG1 MUTATED MTG1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(51) Variable = PRRG1 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  PRRG1 MUTATED     5   3
  PRRG1 WILD-TYPE 333 213
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              8             546 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              3             213 
$`PRRG1 MUTATED`
TCGA-IG-A3YB TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5726 TCGA-HU-8602 
        2.63        29.59         0.26         6.58        28.96        22.32 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`PRRG1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21         0.85        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
           0.26            0.00 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          38.14          122.30 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
         21.025          13.530 
[1] "0.3 - 38.1 (21.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D51V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRRG1 MUTATED         0        1        1        0         1         2
  PRRG1 WILD-TYPE      10       19       45       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRG1 MUTATED           0          4          0          0        1         0
  PRRG1 WILD-TYPE        29         80         62         39       42         4
D51V3, multiclass
            clus
vv           PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PRRG1 MUTATED       1   1   3   5
  PRRG1 WILD-TYPE    53 134 258  97
D51V4, multiclass
       clus
vv      PRRG1 MUTATED PRRG1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                3             258
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PRRG1 MUTATED     6   3   2   0
  PRRG1 WILD-TYPE 189 170  87  85
D51V5, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                 cls
clus                0   1
  PRRG1 MUTATED    11   0
  PRRG1 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED     11    0
  PRRG1 WILD-TYPE  471   38
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   4
  PRRG1 WILD-TYPE 165 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    4
  PRRG1 WILD-TYPE  165  402
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  FEMALE             7             165
  MALE               4             402
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  PRRG1 MUTATED     5   2
  PRRG1 WILD-TYPE 411 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      5    2
  PRRG1 WILD-TYPE  411  100
     clus
vv    PRRG1 MUTATED PRRG1 WILD-TYPE
  NO              5             411
  YES             2             100
[1] 2 2
[1] FALSE
D51V9, continuous
[1] "Remove cluster labels:" "PRRG1 MUTATED"         
clus
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
D51V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRRG1 MUTATED       2                         0
  PRRG1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRRG1 MUTATED                                           0     8
  PRRG1 WILD-TYPE                                         1   349
D51V11, multiclass
                                           clus
vv                                          PRRG1 MUTATED PRRG1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                 cls
clus                0   1
  PRRG1 MUTATED     0   9
  PRRG1 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      0    9
  PRRG1 WILD-TYPE   10  389
                        clus
vv                       PRRG1 MUTATED PRRG1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(52) Variable = KIAA1267 MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                  0   1
  KIAA1267 MUTATED    10   9
  KIAA1267 WILD-TYPE 328 207
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                535 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 9                207 
$`KIAA1267 MUTATED`
TCGA-CG-4460 TCGA-L5-A88W TCGA-L5-A8NQ TCGA-LN-A9FP TCGA-V5-AASV TCGA-B7-5816 
       21.99        25.12        21.37        12.03        15.35        26.70 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6563 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8363 
        6.97        30.90        39.12        36.16        14.43         0.26 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 TCGA-IN-7808 
       31.27        25.05         1.12        28.14        12.43         3.45 
TCGA-VQ-A8P2 
       38.14 

$`KIAA1267 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
              0.26               0.00 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
             39.12             122.30 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
             21.99              13.48 
[1] "0.3 - 39.1 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D52V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1267 MUTATED         1        1        2        1         4         3
  KIAA1267 WILD-TYPE       9       19       44       30        80        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1267 MUTATED           1          2          0          3        1
  KIAA1267 WILD-TYPE        28         82         62         36       42
                    vv
clus                 STAGE IVA
  KIAA1267 MUTATED           0
  KIAA1267 WILD-TYPE         4
D52V3, multiclass
            clus
vv           KIAA1267 MUTATED KIAA1267 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 4                 80
  STAGE IIB                 3                 80
  STAGE III                 1                 28
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1267 MUTATED       2   5   7   7
  KIAA1267 WILD-TYPE    52 130 254  95
D52V4, multiclass
       clus
vv      KIAA1267 MUTATED KIAA1267 WILD-TYPE
  T0+T1                2                 52
  T2                   5                130
  T3                   7                254
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1267 MUTATED    10   7   0   4
  KIAA1267 WILD-TYPE 185 166  89  81
D52V5, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  N0               10                185
  N1                7                166
  N2                0                 89
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    17   2
  KIAA1267 WILD-TYPE 465  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     17    2
  KIAA1267 WILD-TYPE  465   36
   clus
vv  KIAA1267 MUTATED KIAA1267 WILD-TYPE
  0               17                465
  1                2                 36
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     9  14
  KIAA1267 WILD-TYPE 163 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      9   14
  KIAA1267 WILD-TYPE  163  392
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  FEMALE                9                163
  MALE                 14                392
[1] 2 2
[1] FALSE
D52V8, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    16   4
  KIAA1267 WILD-TYPE 400  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     16    4
  KIAA1267 WILD-TYPE  400   98
     clus
vv    KIAA1267 MUTATED KIAA1267 WILD-TYPE
  NO                16                400
  YES                4                 98
[1] 2 2
[1] FALSE
D52V9, continuous
[1] "Remove cluster labels:" "KIAA1267 MUTATED"      
clus
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASW 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1267 WILD-TYPE" 
D52V10, continuous
[1] "Remove cluster labels:" "KIAA1267 MUTATED"      
clus
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" "KIAA1267 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1267 MUTATED       2                         2
  KIAA1267 WILD-TYPE   131                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1267 MUTATED                                           0    17
  KIAA1267 WILD-TYPE                                         1   340
D52V11, multiclass
                                           clus
vv                                          KIAA1267 MUTATED KIAA1267 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   17                340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     0  18
  KIAA1267 WILD-TYPE  10 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      0   18
  KIAA1267 WILD-TYPE   10  380
                        clus
vv                       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               18                380
[1] 2 2
[1] FALSE

Clustering(53) Variable = P4HTM MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  P4HTM MUTATED    18   7
  P4HTM WILD-TYPE 320 209
  P4HTM MUTATED P4HTM WILD-TYPE 
             25             529 
  P4HTM MUTATED P4HTM WILD-TYPE 
              7             209 
$`P4HTM MUTATED`
TCGA-XP-A8T6 TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-7197 TCGA-BR-8059 
       25.08        26.70         9.67         6.61         9.21        14.43 
TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-A44U TCGA-BR-A4J2 TCGA-CD-8524 TCGA-CD-8525 
       29.59        31.27        13.87        14.17        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CG-5723 
       12.53        12.33        12.30        12.59        11.64       105.07 
TCGA-CG-5728 TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP 
       65.10        14.66        13.58         0.76        11.77         8.98 
TCGA-HU-A4GY 
        0.26 

$`P4HTM WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        9.86        20.88         8.22        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 
       11.21        12.10        12.39         7.17        12.39        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  P4HTM MUTATED P4HTM WILD-TYPE 
           0.26            0.00 
  P4HTM MUTATED P4HTM WILD-TYPE 
         105.07          122.30 
  P4HTM MUTATED P4HTM WILD-TYPE 
          12.59           13.78 
[1] "0.3 - 105.1 (12.6)" "0.0 - 122.3 (13.8)"
[1] "hr=" "1.4"
D53V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P4HTM MUTATED         0        2        1        4         1         5
  P4HTM WILD-TYPE      10       18       45       27        83        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P4HTM MUTATED           2          5          2          1        2         0
  P4HTM WILD-TYPE        27         79         60         38       41         4
D53V3, multiclass
            clus
vv           P4HTM MUTATED P4HTM WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               4              27
  STAGE IIA              1              83
  STAGE IIB              5              78
  STAGE III              2              27
  STAGE IIIA             5              79
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  P4HTM MUTATED       2   5   9   9
  P4HTM WILD-TYPE    52 130 252  93
D53V4, multiclass
       clus
vv      P4HTM MUTATED P4HTM WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3                9             252
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  P4HTM MUTATED    11  10   1   3
  P4HTM WILD-TYPE 184 163  88  82
D53V5, multiclass
    clus
vv   P4HTM MUTATED P4HTM WILD-TYPE
  N0            11             184
  N1            10             163
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                 cls
clus                0   1
  P4HTM MUTATED    25   1
  P4HTM WILD-TYPE 457  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     25    1
  P4HTM WILD-TYPE  457   37
   clus
vv  P4HTM MUTATED P4HTM WILD-TYPE
  0            25             457
  1             1              37
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus                0   1
  P4HTM MUTATED    14  13
  P4HTM WILD-TYPE 158 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     14   13
  P4HTM WILD-TYPE  158  393
        clus
vv       P4HTM MUTATED P4HTM WILD-TYPE
  FEMALE            14             158
  MALE              13             393
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus                0   1
  P4HTM MUTATED    19   5
  P4HTM WILD-TYPE 397  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     19    5
  P4HTM WILD-TYPE  397   97
     clus
vv    P4HTM MUTATED P4HTM WILD-TYPE
  NO             19             397
  YES             5              97
[1] 2 2
[1] FALSE
D53V9, continuous
[1] "Remove cluster labels:" "P4HTM MUTATED"         
clus
  P4HTM MUTATED P4HTM WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T7 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
D53V10, continuous
[1] "Remove cluster labels:" "P4HTM MUTATED"         
clus
  P4HTM MUTATED P4HTM WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T7      TCGA-XP-A8T8 
"P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" "P4HTM WILD-TYPE" 
     TCGA-Z6-AAPN 
"P4HTM WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P4HTM MUTATED      12                         1
  P4HTM WILD-TYPE   121                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P4HTM MUTATED                                           0    12
  P4HTM WILD-TYPE                                         1   345
D53V11, multiclass
                                           clus
vv                                          P4HTM MUTATED P4HTM WILD-TYPE
  ASIAN                                                12             121
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                 cls
clus                0   1
  P4HTM MUTATED     1  24
  P4HTM WILD-TYPE   9 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED      1   24
  P4HTM WILD-TYPE    9  374
                        clus
vv                       P4HTM MUTATED P4HTM WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            24             374
[1] 2 2
[1] FALSE

Clustering(54) Variable = CEP57 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  CEP57 MUTATED     7   5
  CEP57 WILD-TYPE 331 211
  CEP57 MUTATED CEP57 WILD-TYPE 
             12             542 
  CEP57 MUTATED CEP57 WILD-TYPE 
              5             211 
$`CEP57 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-6566 TCGA-BR-8382 TCGA-CG-4306 
       21.99         6.97         4.64        32.78        25.05         1.02 
TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-8238 TCGA-HU-A4H3 TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.02        14.47         1.51        29.00        19.04        38.14 

$`CEP57 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.61         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CEP57 MUTATED CEP57 WILD-TYPE 
           1.02            0.00 
  CEP57 MUTATED CEP57 WILD-TYPE 
          38.14          122.30 
  CEP57 MUTATED CEP57 WILD-TYPE 
         16.755          13.530 
[1] "1.0 - 38.1 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D54V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP57 MUTATED         0        0        2        0         1         0
  CEP57 WILD-TYPE      10       20       44       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CEP57 MUTATED           0          3          0          2        3         0
  CEP57 WILD-TYPE        29         81         62         37       40         4
D54V3, multiclass
            clus
vv           CEP57 MUTATED CEP57 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CEP57 MUTATED       0   2   4   6
  CEP57 WILD-TYPE    54 133 257  96
D54V4, multiclass
       clus
vv      CEP57 MUTATED CEP57 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CEP57 MUTATED     4   4   2   2
  CEP57 WILD-TYPE 191 169  87  83
D54V5, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                 cls
clus                0   1
  CEP57 MUTATED    10   2
  CEP57 WILD-TYPE 472  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED     10    2
  CEP57 WILD-TYPE  472   36
   clus
vv  CEP57 MUTATED CEP57 WILD-TYPE
  0            10             472
  1             2              36
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  CEP57 MUTATED     6   7
  CEP57 WILD-TYPE 166 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      6    7
  CEP57 WILD-TYPE  166  399
        clus
vv       CEP57 MUTATED CEP57 WILD-TYPE
  FEMALE             6             166
  MALE               7             399
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus                0   1
  CEP57 MUTATED     9   1
  CEP57 WILD-TYPE 407 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      9    1
  CEP57 WILD-TYPE  407  101
     clus
vv    CEP57 MUTATED CEP57 WILD-TYPE
  NO              9             407
  YES             1             101
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CEP57 MUTATED       2                         0
  CEP57 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP57 MUTATED                                           0     8
  CEP57 WILD-TYPE                                         1   349
D54V11, multiclass
                                           clus
vv                                          CEP57 MUTATED CEP57 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                 cls
clus                0   1
  CEP57 MUTATED     0   9
  CEP57 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      0    9
  CEP57 WILD-TYPE   10  389
                        clus
vv                       CEP57 MUTATED CEP57 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(55) Variable = KRT75 MUTATION ANALYSIS
D55V1, survival
                 sevent
clus2               0   1
  KRT75 MUTATED    26  10
  KRT75 WILD-TYPE 312 206
  KRT75 MUTATED KRT75 WILD-TYPE 
             36             518 
  KRT75 MUTATED KRT75 WILD-TYPE 
             10             206 
$`KRT75 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-8059 TCGA-BR-8078 
        6.97        30.90        44.94         9.21        14.43        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8367 TCGA-BR-8368 
       32.25         8.05         2.20         6.18        26.33         4.31 
TCGA-BR-8371 TCGA-BR-A44U TCGA-BR-A4J2 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.80        13.87        14.17        12.76        12.59        12.53 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-D7-8573 TCGA-D7-8574 
       12.30        12.39        12.59        11.64        19.50        17.19 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       17.06        59.54        13.58         0.76        24.30        24.26 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GY TCGA-R5-A7ZI TCGA-VQ-A8P2 
        3.25        11.77         8.98         0.26        74.53        38.14 

$`KRT75 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 
       33.21        37.25        11.44         0.69         9.60         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       29.42         2.66        19.96         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
       22.19        17.52         0.95        14.04         3.32        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8527 TCGA-CD-8528 
       13.35        11.21        12.10        12.39         7.17        12.33 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
       22.29         5.03         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        22.68        24.20        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       29.98         0.10         6.51         6.58        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KRT75 MUTATED KRT75 WILD-TYPE 
           0.26            0.00 
  KRT75 MUTATED KRT75 WILD-TYPE 
          74.53          122.30 
  KRT75 MUTATED KRT75 WILD-TYPE 
         12.675          13.730 
[1] "0.3 - 74.5 (12.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.4"
D55V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT75 MUTATED         0        3        3        4         5         6
  KRT75 WILD-TYPE      10       17       43       27        79        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT75 MUTATED           1          7          4          1        2         0
  KRT75 WILD-TYPE        28         77         58         38       41         4
D55V3, multiclass
            clus
vv           KRT75 MUTATED KRT75 WILD-TYPE
  STAGE I                0              10
  STAGE IA               3              17
  STAGE IB               3              43
  STAGE II               4              27
  STAGE IIA              5              79
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             7              77
  STAGE IIIB             4              58
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KRT75 MUTATED       3   6  17  11
  KRT75 WILD-TYPE    51 129 244  91
D55V4, multiclass
       clus
vv      KRT75 MUTATED KRT75 WILD-TYPE
  T0+T1             3              51
  T2                6             129
  T3               17             244
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KRT75 MUTATED    19  11   1   5
  KRT75 WILD-TYPE 176 162  88  80
D55V5, multiclass
    clus
vv   KRT75 MUTATED KRT75 WILD-TYPE
  N0            19             176
  N1            11             162
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                 cls
clus                0   1
  KRT75 MUTATED    32   2
  KRT75 WILD-TYPE 450  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     32    2
  KRT75 WILD-TYPE  450   36
   clus
vv  KRT75 MUTATED KRT75 WILD-TYPE
  0            32             450
  1             2              36
[1] 2 2
[1] FALSE
D55V7, binary
                 cls
clus                0   1
  KRT75 MUTATED    14  23
  KRT75 WILD-TYPE 158 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     14   23
  KRT75 WILD-TYPE  158  383
        clus
vv       KRT75 MUTATED KRT75 WILD-TYPE
  FEMALE            14             158
  MALE              23             383
[1] 2 2
[1] FALSE
D55V8, binary
                 cls
clus                0   1
  KRT75 MUTATED    29   7
  KRT75 WILD-TYPE 387  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     29    7
  KRT75 WILD-TYPE  387   95
     clus
vv    KRT75 MUTATED KRT75 WILD-TYPE
  NO             29             387
  YES             7              95
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KRT75 MUTATED      15                         0
  KRT75 WILD-TYPE   118                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRT75 MUTATED                                           0    21
  KRT75 WILD-TYPE                                         1   336
D55V11, multiclass
                                           clus
vv                                          KRT75 MUTATED KRT75 WILD-TYPE
  ASIAN                                                15             118
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                 cls
clus                0   1
  KRT75 MUTATED     1  34
  KRT75 WILD-TYPE   9 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED      1   34
  KRT75 WILD-TYPE    9  364
                        clus
vv                       KRT75 MUTATED KRT75 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            34             364
[1] 2 2
[1] FALSE

Clustering(56) Variable = FAHD2B MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     6   5
  FAHD2B WILD-TYPE 332 211
  FAHD2B MUTATED FAHD2B WILD-TYPE 
              11              543 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              211 
$`FAHD2B MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-L5-A8NU TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8360 
       19.99         7.76        83.24        30.90        32.78         6.18 
TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4306 
       25.05        31.96        12.43        12.62         1.02 

$`FAHD2B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       11.77        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
            1.02             0.00 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           83.24           122.30 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           19.99            13.55 
[1] "1.0 - 83.2 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D56V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAHD2B MUTATED         0        0        1        1         3         2
  FAHD2B WILD-TYPE      10       20       45       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          2        2
  FAHD2B WILD-TYPE        29         84         62         37       41
                  vv
clus               STAGE IVA
  FAHD2B MUTATED           0
  FAHD2B WILD-TYPE         4
D56V3, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAHD2B MUTATED       0   4   5   3
  FAHD2B WILD-TYPE    54 131 256  99
D56V4, multiclass
       clus
vv      FAHD2B MUTATED FAHD2B WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 5              256
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAHD2B MUTATED     6   1   2   2
  FAHD2B WILD-TYPE 189 172  87  83
D56V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              6              189
  N1              1              172
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     9   2
  FAHD2B WILD-TYPE 473  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      9    2
  FAHD2B WILD-TYPE  473   36
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              9              473
  1              2               36
[1] 2 2
[1] FALSE
D56V7, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   8
  FAHD2B WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    8
  FAHD2B WILD-TYPE  168  398
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  FAHD2B MUTATED    10   0
  FAHD2B WILD-TYPE 406 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED     10    0
  FAHD2B WILD-TYPE  406  102
     clus
vv    FAHD2B MUTATED FAHD2B WILD-TYPE
  NO              10              406
  YES              0              102
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
[1] "Remove cluster labels:" "FAHD2B MUTATED"        
clus
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" "FAHD2B WILD-TYPE" 
      TCGA-Z6-AAPN 
"FAHD2B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAHD2B MUTATED       3                         0
  FAHD2B WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAHD2B MUTATED                                           0     8
  FAHD2B WILD-TYPE                                         1   349
D56V11, multiclass
                                           clus
vv                                          FAHD2B MUTATED FAHD2B WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     0   8
  FAHD2B WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      0    8
  FAHD2B WILD-TYPE   10  390
                        clus
vv                       FAHD2B MUTATED FAHD2B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(57) Variable = DSTN MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  DSTN MUTATED     3   3
  DSTN WILD-TYPE 335 213
  DSTN MUTATED DSTN WILD-TYPE 
             6            548 
  DSTN MUTATED DSTN WILD-TYPE 
             3            213 
$`DSTN MUTATED`
TCGA-BR-8291 TCGA-BR-A4QL TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-A4GU TCGA-HU-A4H8 
       19.96        16.14        21.07        11.08         6.58        14.07 

$`DSTN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56        29.42         2.66         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DSTN MUTATED DSTN WILD-TYPE 
          6.58           0.00 
  DSTN MUTATED DSTN WILD-TYPE 
         21.07         122.30 
  DSTN MUTATED DSTN WILD-TYPE 
        15.105         13.530 
[1] "6.6 - 21.1 (15.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D57V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DSTN MUTATED         0        0        1        0         1         2
  DSTN WILD-TYPE      10       20       45       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSTN MUTATED           0          1          1          0        1         0
  DSTN WILD-TYPE        29         83         61         39       42         4
D57V3, multiclass
            clus
vv           DSTN MUTATED DSTN WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DSTN MUTATED       1   1   4   1
  DSTN WILD-TYPE    53 134 257 101
D57V4, multiclass
       clus
vv      DSTN MUTATED DSTN WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               4            257
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DSTN MUTATED     1   3   2   1
  DSTN WILD-TYPE 194 170  87  84
D57V5, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  N0            1            194
  N1            3            170
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                cls
clus               0   1
  DSTN MUTATED     7   0
  DSTN WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      7    0
  DSTN WILD-TYPE  475   38
   clus
vv  DSTN MUTATED DSTN WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  DSTN MUTATED     3   4
  DSTN WILD-TYPE 169 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      3    4
  DSTN WILD-TYPE  169  402
        clus
vv       DSTN MUTATED DSTN WILD-TYPE
  FEMALE            3            169
  MALE              4            402
[1] 2 2
[1] FALSE
D57V8, binary
                cls
clus               0   1
  DSTN MUTATED     5   1
  DSTN WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      5    1
  DSTN WILD-TYPE  411  101
     clus
vv    DSTN MUTATED DSTN WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DSTN MUTATED       2                         1
  DSTN WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DSTN MUTATED                                           0     3
  DSTN WILD-TYPE                                         1   354
D57V11, multiclass
                                           clus
vv                                          DSTN MUTATED DSTN WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                cls
clus               0   1
  DSTN MUTATED     0   6
  DSTN WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      0    6
  DSTN WILD-TYPE   10  392
                        clus
vv                       DSTN MUTATED DSTN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(58) Variable = ZFP36L2 MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    11   2
  ZFP36L2 WILD-TYPE 327 214
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               13               541 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                2               214 
$`ZFP36L2 MUTATED`
TCGA-LN-A4A3 TCGA-BR-7716 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8487 
       12.76        39.78         8.05        31.10        26.33         1.12 
TCGA-D7-6521 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-IP-7968 TCGA-MX-A5UJ 
       18.54        24.20         6.51        14.07         2.53        19.73 
TCGA-VQ-A8P2 
       38.14 

$`ZFP36L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             1.12              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            39.78            122.30 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            18.54             13.51 
[1] "1.1 - 39.8 (18.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFP36L2 MUTATED         0        1        2        0         2         1
  ZFP36L2 WILD-TYPE      10       19       44       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           1          2          2          2        0
  ZFP36L2 WILD-TYPE        28         82         60         37       43
                   vv
clus                STAGE IVA
  ZFP36L2 MUTATED           0
  ZFP36L2 WILD-TYPE         4
D58V3, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZFP36L2 MUTATED       2   2   7   3
  ZFP36L2 WILD-TYPE    52 133 254  99
D58V4, multiclass
       clus
vv      ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  7               254
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L2 MUTATED     4   4   4   2
  ZFP36L2 WILD-TYPE 191 169  85  83
D58V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0               4               191
  N1               4               169
  N2               4                85
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    14   0
  ZFP36L2 WILD-TYPE 468  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     14    0
  ZFP36L2 WILD-TYPE  468   38
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0              14               468
  1               0                38
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     7   8
  ZFP36L2 WILD-TYPE 165 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      7    8
  ZFP36L2 WILD-TYPE  165  398
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               7               165
  MALE                 8               398
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    10   2
  ZFP36L2 WILD-TYPE 406 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     10    2
  ZFP36L2 WILD-TYPE  406  100
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO               10               406
  YES               2               100
[1] 2 2
[1] FALSE
D58V9, continuous
[1] "Remove cluster labels:" "ZFP36L2 MUTATED"       
clus
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
D58V10, continuous
[1] "Remove cluster labels:" "ZFP36L2 MUTATED"       
clus
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A6 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-Z6-AAPN 
"ZFP36L2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZFP36L2 MUTATED       4                         0
  ZFP36L2 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFP36L2 MUTATED                                           0    10
  ZFP36L2 WILD-TYPE                                         1   347
D58V11, multiclass
                                           clus
vv                                          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     0  13
  ZFP36L2 WILD-TYPE  10 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      0   13
  ZFP36L2 WILD-TYPE   10  385
                        clus
vv                       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              13               385
[1] 2 2
[1] FALSE

Clustering(59) Variable = RNF128 MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED    11   3
  RNF128 WILD-TYPE 327 213
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              540 
  RNF128 MUTATED RNF128 WILD-TYPE 
               3              213 
$`RNF128 MUTATED`
TCGA-L5-A4OI TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-A4QL 
       19.99        34.68         0.26         4.31        31.27        16.14 
TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H3 
        6.02        22.32        24.26        24.20         6.51        29.00 
TCGA-VQ-A8DU TCGA-VQ-A8P2 
        5.46        38.14 

$`RNF128 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       31.10        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       35.61        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.26             0.00 
  RNF128 MUTATED RNF128 WILD-TYPE 
           38.14           122.30 
  RNF128 MUTATED RNF128 WILD-TYPE 
          21.155           13.510 
[1] "0.3 - 38.1 (21.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D59V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF128 MUTATED         0        2        2        0         2         1
  RNF128 WILD-TYPE      10       18       44       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF128 MUTATED           0          2          1          3        1
  RNF128 WILD-TYPE        29         82         61         36       42
                  vv
clus               STAGE IVA
  RNF128 MUTATED           0
  RNF128 WILD-TYPE         4
D59V3, multiclass
            clus
vv           RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RNF128 MUTATED       2   2   5   5
  RNF128 WILD-TYPE    52 133 256  97
D59V4, multiclass
       clus
vv      RNF128 MUTATED RNF128 WILD-TYPE
  T0+T1              2               52
  T2                 2              133
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RNF128 MUTATED     7   2   1   4
  RNF128 WILD-TYPE 188 171  88  81
D59V5, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  N0              7              188
  N1              2              171
  N2              1               88
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                  cls
clus                 0   1
  RNF128 MUTATED    14   0
  RNF128 WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     14    0
  RNF128 WILD-TYPE  468   38
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D59V7, binary
                  cls
clus                 0   1
  RNF128 MUTATED     9   6
  RNF128 WILD-TYPE 163 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      9    6
  RNF128 WILD-TYPE  163  400
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              9              163
  MALE                6              400
[1] 2 2
[1] FALSE
D59V8, binary
                  cls
clus                 0   1
  RNF128 MUTATED    12   1
  RNF128 WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     12    1
  RNF128 WILD-TYPE  404  101
     clus
vv    RNF128 MUTATED RNF128 WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-Z6-AAPN 
"RNF128 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RNF128 MUTATED       5                         0
  RNF128 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF128 MUTATED                                           0     9
  RNF128 WILD-TYPE                                         1   348
D59V11, multiclass
                                           clus
vv                                          RNF128 MUTATED RNF128 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                  cls
clus                 0   1
  RNF128 MUTATED     0  11
  RNF128 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      0   11
  RNF128 WILD-TYPE   10  387
                        clus
vv                       RNF128 MUTATED RNF128 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(60) Variable = FHOD3 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    24   9
  FHOD3 WILD-TYPE 314 207
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             33             521 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              9             207 
$`FHOD3 MUTATED`
TCGA-L5-A43M TCGA-L5-A4OI TCGA-CG-4460 TCGA-LN-A4A2 TCGA-R6-A6L4 TCGA-X8-AAAR 
        8.94        19.99        21.99        12.49        16.31        18.21 
TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7197 
        2.10         6.97         9.34         6.61        34.68         9.21 
TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8368 
       29.56        29.59         8.05         6.18         0.26         4.31 
TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4466 
        1.12         6.58        15.95         1.02         8.05        18.97 
TCGA-CG-5722 TCGA-FP-7829 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-A6RP 
        0.99        19.53        24.20         6.58        14.07         6.44 
TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       19.04        37.41        38.14 

$`FHOD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.59        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        4.08         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 
        2.66        19.96         2.20         7.40        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
           0.26            0.00 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          38.14          122.30 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
           9.34           13.68 
[1] "0.3 - 38.1 (9.3)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D60V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHOD3 MUTATED         0        1        5        3         5         3
  FHOD3 WILD-TYPE      10       19       41       28        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FHOD3 MUTATED           1          4          1          3        5         0
  FHOD3 WILD-TYPE        28         80         61         36       38         4
D60V3, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               3              28
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FHOD3 MUTATED       5   7  15   7
  FHOD3 WILD-TYPE    49 128 246  95
D60V4, multiclass
       clus
vv      FHOD3 MUTATED FHOD3 WILD-TYPE
  T0+T1             5              49
  T2                7             128
  T3               15             246
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FHOD3 MUTATED    14  13   4   3
  FHOD3 WILD-TYPE 181 160  85  82
D60V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            14             181
  N1            13             160
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                 cls
clus                0   1
  FHOD3 MUTATED    27   4
  FHOD3 WILD-TYPE 455  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     27    4
  FHOD3 WILD-TYPE  455   34
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            27             455
  1             4              34
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus                0   1
  FHOD3 MUTATED    16  20
  FHOD3 WILD-TYPE 156 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     16   20
  FHOD3 WILD-TYPE  156  386
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  FEMALE            16             156
  MALE              20             386
[1] 2 2
[1] FALSE
D60V8, binary
                 cls
clus                0   1
  FHOD3 MUTATED    27   4
  FHOD3 WILD-TYPE 389  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     27    4
  FHOD3 WILD-TYPE  389   98
     clus
vv    FHOD3 MUTATED FHOD3 WILD-TYPE
  NO             27             389
  YES             4              98
[1] 2 2
[1] FALSE
D60V9, continuous
[1] "Remove cluster labels:" "FHOD3 MUTATED"         
clus
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD 
"FHOD3 WILD-TYPE" "FHOD3 WILD-TYPE" 
D60V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FHOD3 MUTATED       5                         0
  FHOD3 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FHOD3 MUTATED                                           0    24
  FHOD3 WILD-TYPE                                         1   333
D60V11, multiclass
                                           clus
vv                                          FHOD3 MUTATED FHOD3 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                24             333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                 cls
clus                0   1
  FHOD3 MUTATED     0  26
  FHOD3 WILD-TYPE  10 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED      0   26
  FHOD3 WILD-TYPE   10  372
                        clus
vv                       FHOD3 MUTATED FHOD3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            26             372
[1] 2 2
[1] FALSE

Clustering(61) Variable = OSBP2 MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2               0   1
  OSBP2 MUTATED     9   5
  OSBP2 WILD-TYPE 329 211
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             14             540 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
              5             211 
$`OSBP2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8382 
       30.90        34.68        32.78        44.94        35.84        25.05 
TCGA-BR-A4QL TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX 
       16.14         1.02        22.32        22.68         6.58        20.25 
TCGA-VQ-A8E7 TCGA-VQ-AA64 
       37.41        18.41 

$`OSBP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  OSBP2 MUTATED OSBP2 WILD-TYPE 
           1.02            0.00 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
          44.94          122.30 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
         23.865          13.410 
[1] "1.0 - 44.9 (23.9)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D61V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSBP2 MUTATED         0        0        1        0         3         3
  OSBP2 WILD-TYPE      10       20       45       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSBP2 MUTATED           0          0          2          2        3         0
  OSBP2 WILD-TYPE        29         84         60         37       40         4
D61V3, multiclass
            clus
vv           OSBP2 MUTATED OSBP2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OSBP2 MUTATED       0   2   9   4
  OSBP2 WILD-TYPE    54 133 252  98
D61V4, multiclass
       clus
vv      OSBP2 MUTATED OSBP2 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                9             252
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OSBP2 MUTATED     5   3   4   2
  OSBP2 WILD-TYPE 190 170  85  83
D61V5, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                 cls
clus                0   1
  OSBP2 MUTATED    13   2
  OSBP2 WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     13    2
  OSBP2 WILD-TYPE  469   36
   clus
vv  OSBP2 MUTATED OSBP2 WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D61V7, binary
                 cls
clus                0   1
  OSBP2 MUTATED    11   4
  OSBP2 WILD-TYPE 161 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     11    4
  OSBP2 WILD-TYPE  161  402
        clus
vv       OSBP2 MUTATED OSBP2 WILD-TYPE
  FEMALE            11             161
  MALE               4             402
[1] 2 2
[1] FALSE
D61V8, binary
                 cls
clus                0   1
  OSBP2 MUTATED    12   1
  OSBP2 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     12    1
  OSBP2 WILD-TYPE  404  101
     clus
vv    OSBP2 MUTATED OSBP2 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OSBP2 MUTATED       4                         0
  OSBP2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSBP2 MUTATED                                           0    10
  OSBP2 WILD-TYPE                                         1   347
D61V11, multiclass
                                           clus
vv                                          OSBP2 MUTATED OSBP2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                 cls
clus                0   1
  OSBP2 MUTATED     0  12
  OSBP2 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED      0   12
  OSBP2 WILD-TYPE   10  386
                        clus
vv                       OSBP2 MUTATED OSBP2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(62) Variable = NFASC MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    22  10
  NFASC WILD-TYPE 316 206
  NFASC MUTATED NFASC WILD-TYPE 
             32             522 
  NFASC MUTATED NFASC WILD-TYPE 
             10             206 
$`NFASC MUTATED`
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-L5-A8NM TCGA-R6-A6DQ TCGA-V5-AASV TCGA-ZR-A9CJ 
        4.21        32.45         7.76         7.59        15.35        19.73 
TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8381 TCGA-BR-8382 
       11.01         9.67        34.68        29.59         7.36        25.05 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5721 
        1.12        31.96        16.14        15.95         8.05         6.02 
TCGA-CG-5733 TCGA-D7-6518 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G2 
       21.07        19.13        11.08        77.29        22.32        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       24.26        22.68         6.58        23.80        18.21        74.53 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`NFASC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94         8.94        16.24         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        2.66        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        31.27        14.79         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       24.39        28.96        22.82        21.07         0.76         5.59 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NFASC MUTATED NFASC WILD-TYPE 
           1.12            0.00 
  NFASC MUTATED NFASC WILD-TYPE 
          77.29          122.30 
  NFASC MUTATED NFASC WILD-TYPE 
         19.085          13.410 
[1] "1.1 - 77.3 (19.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D62V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFASC MUTATED         0        1        3        3         4        10
  NFASC WILD-TYPE      10       19       43       28        80        73
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFASC MUTATED           1          4          1          2        3         0
  NFASC WILD-TYPE        28         80         61         37       40         4
D62V3, multiclass
            clus
vv           NFASC MUTATED NFASC WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               3              28
  STAGE IIA              4              80
  STAGE IIB             10              73
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NFASC MUTATED       1   9  14   9
  NFASC WILD-TYPE    53 126 247  93
D62V4, multiclass
       clus
vv      NFASC MUTATED NFASC WILD-TYPE
  T0+T1             1              53
  T2                9             126
  T3               14             247
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NFASC MUTATED    12  13   3   4
  NFASC WILD-TYPE 183 160  86  81
D62V5, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            12             183
  N1            13             160
  N2             3              86
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                 cls
clus                0   1
  NFASC MUTATED    31   2
  NFASC WILD-TYPE 451  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     31    2
  NFASC WILD-TYPE  451   36
   clus
vv  NFASC MUTATED NFASC WILD-TYPE
  0            31             451
  1             2              36
[1] 2 2
[1] FALSE
D62V7, binary
                 cls
clus                0   1
  NFASC MUTATED    17  20
  NFASC WILD-TYPE 155 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     17   20
  NFASC WILD-TYPE  155  386
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE            17             155
  MALE              20             386
[1] 2 2
[1] FALSE
D62V8, binary
                 cls
clus                0   1
  NFASC MUTATED    28   4
  NFASC WILD-TYPE 388  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     28    4
  NFASC WILD-TYPE  388   98
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO             28             388
  YES             4              98
[1] 2 2
[1] FALSE
D62V9, continuous
[1] "Remove cluster labels:" "NFASC MUTATED"         
clus
  NFASC MUTATED NFASC WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
D62V10, continuous
[1] "Remove cluster labels:" "NFASC MUTATED"         
clus
  NFASC MUTATED NFASC WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" "NFASC WILD-TYPE" 
     TCGA-Z6-AAPN 
"NFASC WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NFASC MUTATED       7                         2
  NFASC WILD-TYPE   126                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFASC MUTATED                                           0    20
  NFASC WILD-TYPE                                         1   337
D62V11, multiclass
                                           clus
vv                                          NFASC MUTATED NFASC WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                20             337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                 cls
clus                0   1
  NFASC MUTATED     1  26
  NFASC WILD-TYPE   9 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      1   26
  NFASC WILD-TYPE    9  372
                        clus
vv                       NFASC MUTATED NFASC WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            26             372
[1] 2 2
[1] FALSE

Clustering(63) Variable = EPB49 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  EPB49 MUTATED    11   3
  EPB49 WILD-TYPE 327 213
  EPB49 MUTATED EPB49 WILD-TYPE 
             14             540 
  EPB49 MUTATED EPB49 WILD-TYPE 
              3             213 
$`EPB49 MUTATED`
TCGA-L5-A43J TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A7HW TCGA-BR-4201 TCGA-BR-8368 
        4.31        10.36        12.43        12.00        30.90         4.31 
TCGA-BR-8487 TCGA-CG-5723 TCGA-FP-7916 TCGA-HU-8602 TCGA-HU-A4H4 TCGA-MX-A5UJ 
        1.12       105.07        14.07        22.32        23.84        19.73 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`EPB49 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  EPB49 MUTATED EPB49 WILD-TYPE 
           1.12            0.00 
  EPB49 MUTATED EPB49 WILD-TYPE 
         105.07          122.30 
  EPB49 MUTATED EPB49 WILD-TYPE 
          16.90           13.53 
[1] "1.1 - 105.1 (16.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D63V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB49 MUTATED         0        0        1        1         2         4
  EPB49 WILD-TYPE      10       20       45       30        82        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPB49 MUTATED           0          3          0          2        1         0
  EPB49 WILD-TYPE        29         81         62         37       42         4
D63V3, multiclass
            clus
vv           EPB49 MUTATED EPB49 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPB49 MUTATED       1   6   4   5
  EPB49 WILD-TYPE    53 129 257  97
D63V4, multiclass
       clus
vv      EPB49 MUTATED EPB49 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                4             257
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPB49 MUTATED     6   5   2   2
  EPB49 WILD-TYPE 189 168  87  83
D63V5, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  N0             6             189
  N1             5             168
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                 cls
clus                0   1
  EPB49 MUTATED    13   1
  EPB49 WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED     13    1
  EPB49 WILD-TYPE  469   37
   clus
vv  EPB49 MUTATED EPB49 WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus                0   1
  EPB49 MUTATED    10   7
  EPB49 WILD-TYPE 162 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED     10    7
  EPB49 WILD-TYPE  162  399
        clus
vv       EPB49 MUTATED EPB49 WILD-TYPE
  FEMALE            10             162
  MALE               7             399
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  EPB49 MUTATED    11   2
  EPB49 WILD-TYPE 405 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED     11    2
  EPB49 WILD-TYPE  405  100
     clus
vv    EPB49 MUTATED EPB49 WILD-TYPE
  NO             11             405
  YES             2             100
[1] 2 2
[1] FALSE
D63V9, continuous
[1] "Remove cluster labels:" "EPB49 MUTATED"         
clus
  EPB49 MUTATED EPB49 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
D63V10, continuous
[1] "Remove cluster labels:" "EPB49 MUTATED"         
clus
  EPB49 MUTATED EPB49 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" "EPB49 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPB49 MUTATED       5                         0
  EPB49 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB49 MUTATED                                           0    11
  EPB49 WILD-TYPE                                         1   346
D63V11, multiclass
                                           clus
vv                                          EPB49 MUTATED EPB49 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                 cls
clus                0   1
  EPB49 MUTATED     1  13
  EPB49 WILD-TYPE   9 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      1   13
  EPB49 WILD-TYPE    9  385
                        clus
vv                       EPB49 MUTATED EPB49 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(64) Variable = WNT1 MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     7   3
  WNT1 WILD-TYPE 331 213
  WNT1 MUTATED WNT1 WILD-TYPE 
            10            544 
  WNT1 MUTATED WNT1 WILD-TYPE 
             3            213 
$`WNT1 MUTATED`
TCGA-EQ-A4SO TCGA-L5-A8NM TCGA-BR-6565 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8487 
       16.24         7.76         9.17        44.94        29.59         1.12 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4H8 
        5.92        11.08        77.29        14.07 

$`WNT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  WNT1 MUTATED WNT1 WILD-TYPE 
          1.12           0.00 
  WNT1 MUTATED WNT1 WILD-TYPE 
         77.29         122.30 
  WNT1 MUTATED WNT1 WILD-TYPE 
        12.575         13.565 
[1] "1.1 - 77.3 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D64V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT1 MUTATED         1        0        1        1         3         4
  WNT1 WILD-TYPE       9       20       45       30        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNT1 MUTATED           0          0          1          0        0         0
  WNT1 WILD-TYPE        29         84         61         39       43         4
D64V3, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WNT1 MUTATED       2   2   4   3
  WNT1 WILD-TYPE    52 133 257  99
D64V4, multiclass
       clus
vv      WNT1 MUTATED WNT1 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WNT1 MUTATED     5   6   0   0
  WNT1 WILD-TYPE 190 167  89  85
D64V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            5            190
  N1            6            167
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                cls
clus               0   1
  WNT1 MUTATED     9   0
  WNT1 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      9    0
  WNT1 WILD-TYPE  473   38
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D64V7, binary
                cls
clus               0   1
  WNT1 MUTATED     5   6
  WNT1 WILD-TYPE 167 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      5    6
  WNT1 WILD-TYPE  167  400
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  FEMALE            5            167
  MALE              6            400
[1] 2 2
[1] FALSE
D64V8, binary
                cls
clus               0   1
  WNT1 MUTATED     8   3
  WNT1 WILD-TYPE 408  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      8    3
  WNT1 WILD-TYPE  408   99
     clus
vv    WNT1 MUTATED WNT1 WILD-TYPE
  NO             8            408
  YES            3             99
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WNT1 MUTATED       1                         2
  WNT1 WILD-TYPE   132                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNT1 MUTATED                                           0     7
  WNT1 WILD-TYPE                                         1   350
D64V11, multiclass
                                           clus
vv                                          WNT1 MUTATED WNT1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                cls
clus               0   1
  WNT1 MUTATED     0   9
  WNT1 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      0    9
  WNT1 WILD-TYPE   10  389
                        clus
vv                       WNT1 MUTATED WNT1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(65) Variable = ATXN2L MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  ATXN2L MUTATED    15   8
  ATXN2L WILD-TYPE 323 208
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              23              531 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               8              208 
$`ATXN2L MUTATED`
TCGA-CG-4460 TCGA-2H-A9GG TCGA-LN-A9FQ TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 
       21.99        20.05        12.85        34.68        32.78        36.16 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 
       14.43        29.59        29.42        31.10        31.27         1.12 
TCGA-CD-5813 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4465 TCGA-D7-A6EY 
       12.39        11.77        12.62        20.02         9.01        11.44 
TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-MX-A5UJ 
       22.32        29.98         6.51        29.00        19.73 

$`ATXN2L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        6.58        12.20         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ATXN2L MUTATED ATXN2L WILD-TYPE 
            1.12             0.00 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
           36.16           122.30 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
           20.05            13.48 
[1] "1.1 - 36.2 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D65V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATXN2L MUTATED         0        1        1        2         6         2
  ATXN2L WILD-TYPE      10       19       45       29        78        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN2L MUTATED           2          2          2          3        2
  ATXN2L WILD-TYPE        27         82         60         36       41
                  vv
clus               STAGE IVA
  ATXN2L MUTATED           0
  ATXN2L WILD-TYPE         4
D65V3, multiclass
            clus
vv           ATXN2L MUTATED ATXN2L WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               6               78
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATXN2L MUTATED       2   2  12   8
  ATXN2L WILD-TYPE    52 133 249  94
D65V4, multiclass
       clus
vv      ATXN2L MUTATED ATXN2L WILD-TYPE
  T0+T1              2               52
  T2                 2              133
  T3                12              249
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATXN2L MUTATED    11   6   3   4
  ATXN2L WILD-TYPE 184 167  86  81
D65V5, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  N0             11              184
  N1              6              167
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    23   2
  ATXN2L WILD-TYPE 459  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     23    2
  ATXN2L WILD-TYPE  459   36
   clus
vv  ATXN2L MUTATED ATXN2L WILD-TYPE
  0             23              459
  1              2               36
[1] 2 2
[1] FALSE
D65V7, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    14  11
  ATXN2L WILD-TYPE 158 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     14   11
  ATXN2L WILD-TYPE  158  395
        clus
vv       ATXN2L MUTATED ATXN2L WILD-TYPE
  FEMALE             14              158
  MALE               11              395
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    20   0
  ATXN2L WILD-TYPE 396 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     20    0
  ATXN2L WILD-TYPE  396  102
     clus
vv    ATXN2L MUTATED ATXN2L WILD-TYPE
  NO              20              396
  YES              0              102
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATXN2L MUTATED       8                         0
  ATXN2L WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATXN2L MUTATED                                           0    13
  ATXN2L WILD-TYPE                                         1   344
D65V11, multiclass
                                           clus
vv                                          ATXN2L MUTATED ATXN2L WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                  cls
clus                 0   1
  ATXN2L MUTATED     0  21
  ATXN2L WILD-TYPE  10 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      0   21
  ATXN2L WILD-TYPE   10  377
                        clus
vv                       ATXN2L MUTATED ATXN2L WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(66) Variable = C9ORF131 MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED    16   6
  C9ORF131 WILD-TYPE 322 210
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                22                532 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 6                210 
$`C9ORF131 MUTATED`
TCGA-L5-A43J TCGA-JY-A93E TCGA-L5-A4OS TCGA-L5-A8NJ TCGA-XP-A8T8 TCGA-BR-4184 
        4.31        25.22        58.59        16.47        14.37         6.97 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8680 
       30.90         9.34        34.68        11.44        29.59        31.96 
TCGA-CD-5802 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H3 
       13.35        65.10        11.44        30.51        24.20        29.00 
TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       14.07        19.73        74.53        38.14 

$`C9ORF131 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 
       29.56        33.21        37.25        14.43         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.18        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
              4.31               0.00 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             74.53             122.30 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             24.71              13.41 
[1] "4.3 - 74.5 (24.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF131 MUTATED         1        1        2        1         1         5
  C9ORF131 WILD-TYPE       9       19       44       30        83        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           1          5          1          2        2
  C9ORF131 WILD-TYPE        28         79         61         37       41
                    vv
clus                 STAGE IVA
  C9ORF131 MUTATED           0
  C9ORF131 WILD-TYPE         4
D66V3, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 1                 83
  STAGE IIB                 5                 78
  STAGE III                 1                 28
  STAGE IIIA                5                 79
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C9ORF131 MUTATED       4   4   8   7
  C9ORF131 WILD-TYPE    50 131 253  95
D66V4, multiclass
       clus
vv      C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T0+T1                4                 50
  T2                   4                131
  T3                   8                253
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C9ORF131 MUTATED     7  10   3   3
  C9ORF131 WILD-TYPE 188 163  86  82
D66V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0                7                188
  N1               10                163
  N2                3                 86
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    19   2
  C9ORF131 WILD-TYPE 463  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     19    2
  C9ORF131 WILD-TYPE  463   36
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0               19                463
  1                2                 36
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    13  11
  C9ORF131 WILD-TYPE 159 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     13   11
  C9ORF131 WILD-TYPE  159  395
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  FEMALE               13                159
  MALE                 11                395
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    16   4
  C9ORF131 WILD-TYPE 400  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     16    4
  C9ORF131 WILD-TYPE  400   98
     clus
vv    C9ORF131 MUTATED C9ORF131 WILD-TYPE
  NO                16                400
  YES                4                 98
[1] 2 2
[1] FALSE
D66V9, continuous
[1] "Remove cluster labels:" "C9ORF131 MUTATED"      
clus
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-Z6-A8JD 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-Z6-A8JE 
"C9ORF131 WILD-TYPE" 
D66V10, continuous
[1] "Remove cluster labels:" "C9ORF131 MUTATED"      
clus
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A4OE 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-Z6-AAPN 
"C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" "C9ORF131 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF131 MUTATED       5                         2
  C9ORF131 WILD-TYPE   128                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF131 MUTATED                                           0    15
  C9ORF131 WILD-TYPE                                         1   342
D66V11, multiclass
                                           clus
vv                                          C9ORF131 MUTATED C9ORF131 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     2  15
  C9ORF131 WILD-TYPE   8 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      2   15
  C9ORF131 WILD-TYPE    8  383
                        clus
vv                       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               15                383
[1] 2 2
[1] FALSE

Clustering(67) Variable = MFRP MUTATION ANALYSIS
D67V1, survival
                sevent
clus2              0   1
  MFRP MUTATED    11   4
  MFRP WILD-TYPE 327 212
  MFRP MUTATED MFRP WILD-TYPE 
            15            539 
  MFRP MUTATED MFRP WILD-TYPE 
             4            212 
$`MFRP MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-JY-A93C TCGA-KH-A6WC TCGA-BR-6452 TCGA-BR-8081 
       19.99        21.99        23.18         6.28        34.68        32.25 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J4 TCGA-BR-A4QL 
       31.10         1.12        28.14        31.96         0.53        16.14 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5728 
        6.58         1.02        65.10 

$`MFRP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MFRP MUTATED MFRP WILD-TYPE 
          0.53           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
          65.1          122.3 
  MFRP MUTATED MFRP WILD-TYPE 
         21.99          13.51 
[1] "0.5 - 65.1 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D67V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFRP MUTATED         0        1        1        0         3         2
  MFRP WILD-TYPE      10       19       45       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFRP MUTATED           0          1          3          3        3         0
  MFRP WILD-TYPE        29         83         59         36       40         4
D67V3, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            3             59
  STAGE IIIC            3             36
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MFRP MUTATED       1   1   7   8
  MFRP WILD-TYPE    53 134 254  94
D67V4, multiclass
       clus
vv      MFRP MUTATED MFRP WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               7            254
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MFRP MUTATED     8   2   5   3
  MFRP WILD-TYPE 187 171  84  82
D67V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0            8            187
  N1            2            171
  N2            5             84
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                cls
clus               0   1
  MFRP MUTATED    14   3
  MFRP WILD-TYPE 468  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     14    3
  MFRP WILD-TYPE  468   35
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0           14            468
  1            3             35
[1] 2 2
[1] FALSE
D67V7, binary
                cls
clus               0   1
  MFRP MUTATED     9   9
  MFRP WILD-TYPE 163 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      9    9
  MFRP WILD-TYPE  163  397
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  FEMALE            9            163
  MALE              9            397
[1] 2 2
[1] FALSE
D67V8, binary
                cls
clus               0   1
  MFRP MUTATED    12   1
  MFRP WILD-TYPE 404 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     12    1
  MFRP WILD-TYPE  404  101
     clus
vv    MFRP MUTATED MFRP WILD-TYPE
  NO            12            404
  YES            1            101
[1] 2 2
[1] FALSE
D67V9, continuous
[1] "Remove cluster labels:" "MFRP MUTATED"          
clus
  MFRP MUTATED MFRP WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
D67V10, continuous
[1] "Remove cluster labels:" "MFRP MUTATED"          
clus
  MFRP MUTATED MFRP WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-L5-A43C     TCGA-L5-A43E 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" "MFRP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MFRP MUTATED       4                         0
  MFRP WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFRP MUTATED                                           0    11
  MFRP WILD-TYPE                                         1   346
D67V11, multiclass
                                           clus
vv                                          MFRP MUTATED MFRP WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                cls
clus               0   1
  MFRP MUTATED     0  13
  MFRP WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      0   13
  MFRP WILD-TYPE   10  385
                        clus
vv                       MFRP MUTATED MFRP WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(68) Variable = WASF3 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  WASF3 MUTATED    15   5
  WASF3 WILD-TYPE 323 211
  WASF3 MUTATED WASF3 WILD-TYPE 
             20             534 
  WASF3 MUTATED WASF3 WILD-TYPE 
              5             211 
$`WASF3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4ON TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 
        4.31        19.99        18.35        26.70        34.68        44.94 
TCGA-BR-7707 TCGA-BR-8682 TCGA-BR-A4CQ TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-A4YV 
       35.84        32.58        34.98         1.02        65.10         5.92 
TCGA-D7-A4YY TCGA-HF-7132 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-VQ-A8P2 
       13.78        77.29         6.51         6.58         2.10        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       37.22        22.19 

$`WASF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
       29.98         8.98         0.10        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PK 
        5.46        13.25        13.02        43.36        37.41        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  WASF3 MUTATED WASF3 WILD-TYPE 
           1.02            0.00 
  WASF3 MUTATED WASF3 WILD-TYPE 
          77.29          122.30 
  WASF3 MUTATED WASF3 WILD-TYPE 
         24.445          13.445 
[1] "1.0 - 77.3 (24.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D68V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WASF3 MUTATED         1        0        3        1         3         6
  WASF3 WILD-TYPE       9       20       43       30        81        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WASF3 MUTATED           0          3          2          2        1         0
  WASF3 WILD-TYPE        29         81         60         37       42         4
D68V3, multiclass
            clus
vv           WASF3 MUTATED WASF3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  WASF3 MUTATED       2   4  10   6
  WASF3 WILD-TYPE    52 131 251  96
D68V4, multiclass
       clus
vv      WASF3 MUTATED WASF3 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3               10             251
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  WASF3 MUTATED     9   8   1   4
  WASF3 WILD-TYPE 186 165  88  81
D68V5, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  N0             9             186
  N1             8             165
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                 cls
clus                0   1
  WASF3 MUTATED    17   1
  WASF3 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED     17    1
  WASF3 WILD-TYPE  465   37
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  WASF3 MUTATED     7  15
  WASF3 WILD-TYPE 165 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      7   15
  WASF3 WILD-TYPE  165  391
        clus
vv       WASF3 MUTATED WASF3 WILD-TYPE
  FEMALE             7             165
  MALE              15             391
[1] 2 2
[1] FALSE
D68V8, binary
                 cls
clus                0   1
  WASF3 MUTATED    13   4
  WASF3 WILD-TYPE 403  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED     13    4
  WASF3 WILD-TYPE  403   98
     clus
vv    WASF3 MUTATED WASF3 WILD-TYPE
  NO             13             403
  YES             4              98
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WASF3 MUTATED       4                         1
  WASF3 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WASF3 MUTATED                                           0    13
  WASF3 WILD-TYPE                                         1   344
D68V11, multiclass
                                           clus
vv                                          WASF3 MUTATED WASF3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                 cls
clus                0   1
  WASF3 MUTATED     0  12
  WASF3 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      0   12
  WASF3 WILD-TYPE   10  386
                        clus
vv                       WASF3 MUTATED WASF3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(69) Variable = ADAM30 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     8   9
  ADAM30 WILD-TYPE 330 207
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              17              537 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               9              207 
$`ADAM30 MUTATED`
TCGA-L5-A43M TCGA-L5-A8NM TCGA-VR-A8ER TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8059 
        8.94         7.76        12.43         6.97        30.90        14.43 
TCGA-BR-8284 TCGA-BR-8382 TCGA-CD-8525 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5734 
        8.05        25.05        12.59        12.62         1.02         7.99 
TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P2 
       14.47        30.51         6.51         6.58        38.14 

$`ADAM30 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       11.77        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            1.02             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           38.14           122.30 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           12.43            13.78 
[1] "1.0 - 38.1 (12.4)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.7"
D69V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAM30 MUTATED         0        0        2        0         1         2
  ADAM30 WILD-TYPE      10       20       44       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           2          4          0          3        2
  ADAM30 WILD-TYPE        27         80         62         36       41
                  vv
clus               STAGE IVA
  ADAM30 MUTATED           0
  ADAM30 WILD-TYPE         4
D69V3, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ADAM30 MUTATED       1   4   7   7
  ADAM30 WILD-TYPE    53 131 254  95
D69V4, multiclass
       clus
vv      ADAM30 MUTATED ADAM30 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 7              254
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ADAM30 MUTATED     3   8   3   3
  ADAM30 WILD-TYPE 192 165  86  82
D69V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0              3              192
  N1              8              165
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    16   1
  ADAM30 WILD-TYPE 466  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     16    1
  ADAM30 WILD-TYPE  466   37
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0             16              466
  1              1               37
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    10   9
  ADAM30 WILD-TYPE 162 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     10    9
  ADAM30 WILD-TYPE  162  397
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE             10              162
  MALE                9              397
[1] 2 2
[1] FALSE
D69V8, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    11   4
  ADAM30 WILD-TYPE 405  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     11    4
  ADAM30 WILD-TYPE  405   98
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO              11              405
  YES              4               98
[1] 2 2
[1] FALSE
D69V9, continuous
[1] "Remove cluster labels:" "ADAM30 MUTATED"        
clus
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
D69V10, continuous
[1] "Remove cluster labels:" "ADAM30 MUTATED"        
clus
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ADAM30 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ADAM30 MUTATED       4                         0
  ADAM30 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAM30 MUTATED                                           0    10
  ADAM30 WILD-TYPE                                         1   347
D69V11, multiclass
                                           clus
vv                                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     0  12
  ADAM30 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      0   12
  ADAM30 WILD-TYPE   10  386
                        clus
vv                       ADAM30 MUTATED ADAM30 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(70) Variable = HOXD8 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  HOXD8 MUTATED     9   4
  HOXD8 WILD-TYPE 329 212
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             13             541 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              4             212 
$`HOXD8 MUTATED`
TCGA-L5-A4OI TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8360 
       19.99        30.90        34.68        44.94        35.84         6.18 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-HU-A4GT TCGA-IN-8663 TCGA-MX-A5UJ 
        6.58         1.02         6.02         6.51         3.39        19.73 
TCGA-VQ-A8P2 
       38.14 

$`HOXD8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HOXD8 MUTATED HOXD8 WILD-TYPE 
           1.02            0.00 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
          44.94          122.30 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
          19.73           13.55 
[1] "1.0 - 44.9 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D70V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOXD8 MUTATED         0        0        1        0         5         1
  HOXD8 WILD-TYPE      10       20       45       31        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOXD8 MUTATED           0          3          0          1        2         0
  HOXD8 WILD-TYPE        29         81         62         38       41         4
D70V3, multiclass
            clus
vv           HOXD8 MUTATED HOXD8 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HOXD8 MUTATED       0   3   8   3
  HOXD8 WILD-TYPE    54 132 253  99
D70V4, multiclass
       clus
vv      HOXD8 MUTATED HOXD8 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                8             253
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HOXD8 MUTATED     7   2   3   1
  HOXD8 WILD-TYPE 188 171  86  84
D70V5, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  N0             7             188
  N1             2             171
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                 cls
clus                0   1
  HOXD8 MUTATED    12   1
  HOXD8 WILD-TYPE 470  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED     12    1
  HOXD8 WILD-TYPE  470   37
   clus
vv  HOXD8 MUTATED HOXD8 WILD-TYPE
  0            12             470
  1             1              37
[1] 2 2
[1] FALSE
D70V7, binary
                 cls
clus                0   1
  HOXD8 MUTATED     7   7
  HOXD8 WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      7    7
  HOXD8 WILD-TYPE  165  399
        clus
vv       HOXD8 MUTATED HOXD8 WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D70V8, binary
                 cls
clus                0   1
  HOXD8 MUTATED    11   1
  HOXD8 WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED     11    1
  HOXD8 WILD-TYPE  405  101
     clus
vv    HOXD8 MUTATED HOXD8 WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
[1] "Remove cluster labels:" "HOXD8 MUTATED"         
clus
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" "HOXD8 WILD-TYPE" 
     TCGA-Z6-AAPN 
"HOXD8 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOXD8 MUTATED       2                         0
  HOXD8 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOXD8 MUTATED                                           0    10
  HOXD8 WILD-TYPE                                         1   347
D70V11, multiclass
                                           clus
vv                                          HOXD8 MUTATED HOXD8 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                 cls
clus                0   1
  HOXD8 MUTATED     0  10
  HOXD8 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      0   10
  HOXD8 WILD-TYPE   10  388
                        clus
vv                       HOXD8 MUTATED HOXD8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(71) Variable = PAFAH1B1 MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  PAFAH1B1 MUTATED     9   3
  PAFAH1B1 WILD-TYPE 329 213
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                12                542 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                 3                213 
$`PAFAH1B1 MUTATED`
TCGA-L5-A8NS TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 
       13.41        34.68        12.16        31.27        31.96         1.02 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-IN-A7NR 
        6.02        11.08        22.32        29.98         0.10         6.51 

$`PAFAH1B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
               0.1                0.0 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
             34.68             122.30 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
            12.785             13.630 
[1] "0.1 - 34.7 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAFAH1B1 MUTATED         1        1        0        0         3         2
  PAFAH1B1 WILD-TYPE       9       19       46       31        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAFAH1B1 MUTATED           0          0          1          2        4
  PAFAH1B1 WILD-TYPE        29         84         61         37       39
                    vv
clus                 STAGE IVA
  PAFAH1B1 MUTATED           0
  PAFAH1B1 WILD-TYPE         4
D71V3, multiclass
            clus
vv           PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  4                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PAFAH1B1 MUTATED       3   1   6   5
  PAFAH1B1 WILD-TYPE    51 134 255  97
D71V4, multiclass
       clus
vv      PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  T0+T1                3                 51
  T2                   1                134
  T3                   6                255
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PAFAH1B1 MUTATED     5   3   3   3
  PAFAH1B1 WILD-TYPE 190 170  86  82
D71V5, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  N0                5                190
  N1                3                170
  N2                3                 86
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED    12   3
  PAFAH1B1 WILD-TYPE 470  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED     12    3
  PAFAH1B1 WILD-TYPE  470   35
   clus
vv  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  0               12                470
  1                3                 35
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     6  10
  PAFAH1B1 WILD-TYPE 166 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      6   10
  PAFAH1B1 WILD-TYPE  166  396
        clus
vv       PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  FEMALE                6                166
  MALE                 10                396
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED    10   3
  PAFAH1B1 WILD-TYPE 406  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED     10    3
  PAFAH1B1 WILD-TYPE  406   99
     clus
vv    PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  NO                10                406
  YES                3                 99
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
[1] "Remove cluster labels:" "PAFAH1B1 MUTATED"      
clus
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NW 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" "PAFAH1B1 WILD-TYPE" 
        TCGA-Z6-AAPN 
"PAFAH1B1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PAFAH1B1 MUTATED       5                         2
  PAFAH1B1 WILD-TYPE   128                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAFAH1B1 MUTATED                                           0     7
  PAFAH1B1 WILD-TYPE                                         1   350
D71V11, multiclass
                                           clus
vv                                          PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     0  13
  PAFAH1B1 WILD-TYPE  10 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      0   13
  PAFAH1B1 WILD-TYPE   10  385
                        clus
vv                       PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               13                385
[1] 2 2
[1] FALSE

Clustering(72) Variable = PAX2 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  PAX2 MUTATED     8   3
  PAX2 WILD-TYPE 330 213
  PAX2 MUTATED PAX2 WILD-TYPE 
            11            543 
  PAX2 MUTATED PAX2 WILD-TYPE 
             3            213 
$`PAX2 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8285 TCGA-BR-8372 
       26.70        19.56        34.68        44.94         0.56        31.27 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5723 TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        12.62       105.07         0.10         6.58 

$`PAX2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       19.73        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         8.05        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        12.20        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PAX2 MUTATED PAX2 WILD-TYPE 
           0.1            0.0 
  PAX2 MUTATED PAX2 WILD-TYPE 
        105.07         122.30 
  PAX2 MUTATED PAX2 WILD-TYPE 
         19.56          13.55 
[1] "0.1 - 105.1 (19.6)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D72V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX2 MUTATED         0        0        1        1         2         2
  PAX2 WILD-TYPE      10       20       45       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX2 MUTATED           0          2          0          4        0         0
  PAX2 WILD-TYPE        29         82         62         35       43         4
D72V3, multiclass
            clus
vv           PAX2 MUTATED PAX2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            4             35
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PAX2 MUTATED       0   2   4   6
  PAX2 WILD-TYPE    54 133 257  96
D72V4, multiclass
       clus
vv      PAX2 MUTATED PAX2 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PAX2 MUTATED     5   3   1   3
  PAX2 WILD-TYPE 190 170  88  82
D72V5, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  N0            5            190
  N1            3            170
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                cls
clus               0   1
  PAX2 MUTATED    12   0
  PAX2 WILD-TYPE 470  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED     12    0
  PAX2 WILD-TYPE  470   38
   clus
vv  PAX2 MUTATED PAX2 WILD-TYPE
  0           12            470
  1            0             38
[1] 2 2
[1] FALSE
D72V7, binary
                cls
clus               0   1
  PAX2 MUTATED     5   7
  PAX2 WILD-TYPE 167 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      5    7
  PAX2 WILD-TYPE  167  399
        clus
vv       PAX2 MUTATED PAX2 WILD-TYPE
  FEMALE            5            167
  MALE              7            399
[1] 2 2
[1] FALSE
D72V8, binary
                cls
clus               0   1
  PAX2 MUTATED    11   0
  PAX2 WILD-TYPE 405 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED     11    0
  PAX2 WILD-TYPE  405  102
     clus
vv    PAX2 MUTATED PAX2 WILD-TYPE
  NO            11            405
  YES            0            102
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PAX2 MUTATED       4                         0
  PAX2 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAX2 MUTATED                                           0     7
  PAX2 WILD-TYPE                                         1   350
D72V11, multiclass
                                           clus
vv                                          PAX2 MUTATED PAX2 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                cls
clus               0   1
  PAX2 MUTATED     0  11
  PAX2 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      0   11
  PAX2 WILD-TYPE   10  387
                        clus
vv                       PAX2 MUTATED PAX2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(73) Variable = INPPL1 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2                0   1
  INPPL1 MUTATED    16   5
  INPPL1 WILD-TYPE 322 211
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              21              533 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               5              211 
$`INPPL1 MUTATED`
TCGA-L5-A88V TCGA-V5-AASV TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 
        2.60        15.35        26.70         6.97        30.90         9.67 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 
        9.57        34.68        21.90        35.84        29.59        31.10 
TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-A448 
       12.43        15.95         1.02         6.02        65.10        21.27 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ 
        6.51         6.58        19.73 

$`INPPL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.34         6.18 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       44.94         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  INPPL1 MUTATED INPPL1 WILD-TYPE 
            1.02             0.00 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
            65.1            122.3 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
           15.95            13.51 
[1] "1.0 - 65.1 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D73V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INPPL1 MUTATED         0        0        3        3         2         5
  INPPL1 WILD-TYPE      10       20       43       28        82        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPPL1 MUTATED           1          2          1          1        4
  INPPL1 WILD-TYPE        28         82         61         38       39
                  vv
clus               STAGE IVA
  INPPL1 MUTATED           0
  INPPL1 WILD-TYPE         4
D73V3, multiclass
            clus
vv           INPPL1 MUTATED INPPL1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               2               82
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  INPPL1 MUTATED       0   6  12   6
  INPPL1 WILD-TYPE    54 129 249  96
D73V4, multiclass
       clus
vv      INPPL1 MUTATED INPPL1 WILD-TYPE
  T0+T1              0               54
  T2                 6              129
  T3                12              249
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  INPPL1 MUTATED    10   7   4   2
  INPPL1 WILD-TYPE 185 166  85  83
D73V5, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  N0             10              185
  N1              7              166
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    20   2
  INPPL1 WILD-TYPE 462  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     20    2
  INPPL1 WILD-TYPE  462   36
   clus
vv  INPPL1 MUTATED INPPL1 WILD-TYPE
  0             20              462
  1              2               36
[1] 2 2
[1] FALSE
D73V7, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    13  13
  INPPL1 WILD-TYPE 159 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     13   13
  INPPL1 WILD-TYPE  159  393
        clus
vv       INPPL1 MUTATED INPPL1 WILD-TYPE
  FEMALE             13              159
  MALE               13              393
[1] 2 2
[1] FALSE
D73V8, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    18   2
  INPPL1 WILD-TYPE 398 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     18    2
  INPPL1 WILD-TYPE  398  100
     clus
vv    INPPL1 MUTATED INPPL1 WILD-TYPE
  NO              18              398
  YES              2              100
[1] 2 2
[1] FALSE
D73V9, continuous
[1] "Remove cluster labels:" "INPPL1 MUTATED"        
clus
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
D73V10, continuous
[1] "Remove cluster labels:" "INPPL1 MUTATED"        
clus
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A893       TCGA-L5-A8NE 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" "INPPL1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INPPL1 MUTATED       3                         1
  INPPL1 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INPPL1 MUTATED                                           0    17
  INPPL1 WILD-TYPE                                         1   340
D73V11, multiclass
                                           clus
vv                                          INPPL1 MUTATED INPPL1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                  cls
clus                 0   1
  INPPL1 MUTATED     1  19
  INPPL1 WILD-TYPE   9 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED      1   19
  INPPL1 WILD-TYPE    9  379
                        clus
vv                       INPPL1 MUTATED INPPL1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             19              379
[1] 2 2
[1] FALSE

Clustering(74) Variable = MCM8 MUTATION ANALYSIS
D74V1, survival
                sevent
clus2              0   1
  MCM8 MUTATED    17   8
  MCM8 WILD-TYPE 321 208
  MCM8 MUTATED MCM8 WILD-TYPE 
            25            529 
  MCM8 MUTATED MCM8 WILD-TYPE 
             8            208 
$`MCM8 MUTATED`
TCGA-R6-A8WG TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
       12.69         9.67        34.68        14.43        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        8.05         6.18        31.96        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4437 TCGA-D7-8572 
       12.33        12.30        12.39        12.59         8.05        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A6EZ TCGA-FP-8209 TCGA-HF-7132 TCGA-HU-8243 
       17.19        14.66        20.32        59.54        77.29         5.92 
TCGA-VQ-A8P2 
       38.14 

$`MCM8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       29.56        33.21        37.25        11.44         0.69         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8527 TCGA-CD-8532 
       13.35        11.21        12.10        12.39         7.17        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 
       12.36        11.31        12.33        24.72        19.50        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        17.06         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MCM8 MUTATED MCM8 WILD-TYPE 
          5.92           0.00 
  MCM8 MUTATED MCM8 WILD-TYPE 
         77.29         122.30 
  MCM8 MUTATED MCM8 WILD-TYPE 
         12.76          13.58 
[1] "5.9 - 77.3 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D74V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MCM8 MUTATED         1        0        1        4         2         3
  MCM8 WILD-TYPE       9       20       45       27        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM8 MUTATED           1          7          1          2        2         0
  MCM8 WILD-TYPE        28         77         61         37       41         4
D74V3, multiclass
            clus
vv           MCM8 MUTATED MCM8 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              4             27
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            7             77
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MCM8 MUTATED       1   5   9   9
  MCM8 WILD-TYPE    53 130 252  93
D74V4, multiclass
       clus
vv      MCM8 MUTATED MCM8 WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               9            252
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MCM8 MUTATED     9   8   3   4
  MCM8 WILD-TYPE 186 165  86  81
D74V5, multiclass
    clus
vv   MCM8 MUTATED MCM8 WILD-TYPE
  N0            9            186
  N1            8            165
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                cls
clus               0   1
  MCM8 MUTATED    22   2
  MCM8 WILD-TYPE 460  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     22    2
  MCM8 WILD-TYPE  460   36
   clus
vv  MCM8 MUTATED MCM8 WILD-TYPE
  0           22            460
  1            2             36
[1] 2 2
[1] FALSE
D74V7, binary
                cls
clus               0   1
  MCM8 MUTATED    11  15
  MCM8 WILD-TYPE 161 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     11   15
  MCM8 WILD-TYPE  161  391
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  FEMALE           11            161
  MALE             15            391
[1] 2 2
[1] FALSE
D74V8, binary
                cls
clus               0   1
  MCM8 MUTATED    18   8
  MCM8 WILD-TYPE 398  94
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     18    8
  MCM8 WILD-TYPE  398   94
     clus
vv    MCM8 MUTATED MCM8 WILD-TYPE
  NO            18            398
  YES            8             94
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MCM8 MUTATED       9                         1
  MCM8 WILD-TYPE   124                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCM8 MUTATED                                           0    14
  MCM8 WILD-TYPE                                         1   343
D74V11, multiclass
                                           clus
vv                                          MCM8 MUTATED MCM8 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                cls
clus               0   1
  MCM8 MUTATED     1  22
  MCM8 WILD-TYPE   9 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED      1   22
  MCM8 WILD-TYPE    9  376
                        clus
vv                       MCM8 MUTATED MCM8 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           22            376
[1] 2 2
[1] FALSE

Clustering(75) Variable = NLK MUTATION ANALYSIS
D75V1, survival
               sevent
clus2             0   1
  NLK MUTATED     9   7
  NLK WILD-TYPE 329 209
  NLK MUTATED NLK WILD-TYPE 
           16           538 
  NLK MUTATED NLK WILD-TYPE 
            7           209 
$`NLK MUTATED`
TCGA-CG-4460 TCGA-IG-A5B8 TCGA-Q9-A6FW TCGA-V5-AASX TCGA-VR-A8EX TCGA-BR-4184 
       21.99         0.79         7.82         8.98        28.11         6.97 
TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 
       34.68        33.63         6.18         0.26         4.31        31.27 
TCGA-CD-A4MG TCGA-CG-5725 TCGA-HU-A4G8 TCGA-HU-A4GN 
        6.58        15.02        22.68        29.98 

$`NLK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NLK MUTATED NLK WILD-TYPE 
         0.26          0.00 
  NLK MUTATED NLK WILD-TYPE 
        34.68        122.30 
  NLK MUTATED NLK WILD-TYPE 
       12.000        13.565 
[1] "0.3 - 34.7 (12.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D75V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLK MUTATED         0        0        4        0         5         1
  NLK WILD-TYPE      10       20       42       31        79        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLK MUTATED           0          2          1          1        1         1
  NLK WILD-TYPE        29         82         61         38       42         3
D75V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             4            42
  STAGE II             0            31
  STAGE IIA            5            79
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           1            38
  STAGE IV             1            42
  STAGE IVA            1             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  NLK MUTATED       1   4   9   3
  NLK WILD-TYPE    53 131 252  99
D75V4, multiclass
       clus
vv      NLK MUTATED NLK WILD-TYPE
  T0+T1           1            53
  T2              4           131
  T3              9           252
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NLK MUTATED     9   5   1   1
  NLK WILD-TYPE 186 168  88  84
D75V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           9           186
  N1           5           168
  N2           1            88
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
               cls
clus              0   1
  NLK MUTATED    13   2
  NLK WILD-TYPE 469  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     13    2
  NLK WILD-TYPE  469   36
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0          13           469
  1           2            36
[1] 2 2
[1] FALSE
D75V7, binary
               cls
clus              0   1
  NLK MUTATED     7  11
  NLK WILD-TYPE 165 395
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      7   11
  NLK WILD-TYPE  165  395
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           7           165
  MALE            11           395
[1] 2 2
[1] FALSE
D75V8, binary
               cls
clus              0   1
  NLK MUTATED    15   0
  NLK WILD-TYPE 401 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     15    0
  NLK WILD-TYPE  401  102
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO           15           401
  YES           0           102
[1] 2 2
[1] FALSE
D75V9, continuous
[1] "Remove cluster labels:" "NLK MUTATED"           
clus
  NLK MUTATED NLK WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-V5-AASW    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EY    TCGA-VR-A8EZ 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" "NLK WILD-TYPE" 
   TCGA-Z6-A8JE 
"NLK WILD-TYPE" 
D75V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NLK MUTATED       3                         0
  NLK WILD-TYPE   130                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NLK MUTATED                                           0    12
  NLK WILD-TYPE                                         1   345
D75V11, multiclass
                                           clus
vv                                          NLK MUTATED NLK WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              12           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
               cls
clus              0   1
  NLK MUTATED     0  15
  NLK WILD-TYPE  10 383
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      0   15
  NLK WILD-TYPE   10  383
                        clus
vv                       NLK MUTATED NLK WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          15           383
[1] 2 2
[1] FALSE

Clustering(76) Variable = NFE2L2 MUTATION ANALYSIS
D76V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED    12   6
  NFE2L2 WILD-TYPE 326 210
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              18              536 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               6              210 
$`NFE2L2 MUTATED`
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A8O2 TCGA-L5-A88Z TCGA-LN-A49R 
       35.21         0.53        12.82         4.67         7.40        13.38 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.22         4.47        25.25        12.00        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-VR-A8ER TCGA-ZR-A9CJ TCGA-CG-5722 TCGA-VQ-AA64 
       13.38        13.18        12.43        19.73         0.99        18.41 

$`NFE2L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       15.52        11.54        12.33        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       12.03         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.53             0.00 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           35.21           122.30 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          13.000           13.905 
[1] "0.5 - 35.2 (13.0)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D76V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFE2L2 MUTATED         0        0        0        0         9         0
  NFE2L2 WILD-TYPE      10       20       46       31        75        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFE2L2 MUTATED           2          1          3          1        2
  NFE2L2 WILD-TYPE        27         83         59         38       41
                  vv
clus               STAGE IVA
  NFE2L2 MUTATED           0
  NFE2L2 WILD-TYPE         4
D76V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               9               75
  STAGE IIB               0               83
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NFE2L2 MUTATED       1   8   8   1
  NFE2L2 WILD-TYPE    53 127 253 101
D76V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T0+T1              1               53
  T2                 8              127
  T3                 8              253
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NFE2L2 MUTATED     8   5   4   1
  NFE2L2 WILD-TYPE 187 168  85  84
D76V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              8              187
  N1              5              168
  N2              4               85
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    15   2
  NFE2L2 WILD-TYPE 467  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     15    2
  NFE2L2 WILD-TYPE  467   36
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             15              467
  1              2               36
[1] 2 2
[1] FALSE
D76V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     3  15
  NFE2L2 WILD-TYPE 169 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      3   15
  NFE2L2 WILD-TYPE  169  391
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              3              169
  MALE               15              391
[1] 2 2
[1] FALSE
D76V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     9   5
  NFE2L2 WILD-TYPE 407  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      9    5
  NFE2L2 WILD-TYPE  407   97
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               9              407
  YES              5               97
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NFE2L2 MUTATED      12                         0
  NFE2L2 WILD-TYPE   121                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L2 MUTATED                                           0     4
  NFE2L2 WILD-TYPE                                         1   353
D76V11, multiclass
                                           clus
vv                                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                                 12              121
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  14
  NFE2L2 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   14
  NFE2L2 WILD-TYPE   10  384
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(77) Variable = NBN MUTATION ANALYSIS
D77V1, survival
               sevent
clus2             0   1
  NBN MUTATED    14   5
  NBN WILD-TYPE 324 211
  NBN MUTATED NBN WILD-TYPE 
           19           535 
  NBN MUTATED NBN WILD-TYPE 
            5           211 
$`NBN MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-JY-A93F TCGA-LN-A49P TCGA-VR-A8EP TCGA-B7-5816 
       19.99         7.69        24.03        12.33        27.09        26.70 
TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-6801 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C 
       19.56         9.34        40.21        12.43         6.31        11.61 
TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 
       11.44        77.29        22.68         0.10        20.25        14.07 
TCGA-IN-A6RI 
       18.38 

$`NBN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.66        19.73        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
       11.64        15.39        12.07        12.82        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NBN MUTATED NBN WILD-TYPE 
          0.1           0.0 
  NBN MUTATED NBN WILD-TYPE 
        77.29        122.30 
  NBN MUTATED NBN WILD-TYPE 
        18.38         13.51 
[1] "0.1 - 77.3 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D77V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NBN MUTATED         1        0        2        2         3         4
  NBN WILD-TYPE       9       20       44       29        81        79
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NBN MUTATED           0          0          2          4        0         0
  NBN WILD-TYPE        29         84         60         35       43         4
D77V3, multiclass
            clus
vv           NBN MUTATED NBN WILD-TYPE
  STAGE I              1             9
  STAGE IA             0            20
  STAGE IB             2            44
  STAGE II             2            29
  STAGE IIA            3            81
  STAGE IIB            4            79
  STAGE III            0            29
  STAGE IIIA           0            84
  STAGE IIIB           2            60
  STAGE IIIC           4            35
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  NBN MUTATED       4   2   9   4
  NBN WILD-TYPE    50 133 252  98
D77V4, multiclass
       clus
vv      NBN MUTATED NBN WILD-TYPE
  T0+T1           4            50
  T2              2           133
  T3              9           252
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NBN MUTATED     7   6   3   3
  NBN WILD-TYPE 188 167  86  82
D77V5, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  N0           7           188
  N1           6           167
  N2           3            86
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
               cls
clus              0   1
  NBN MUTATED    19   0
  NBN WILD-TYPE 463  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED     19    0
  NBN WILD-TYPE  463   38
   clus
vv  NBN MUTATED NBN WILD-TYPE
  0          19           463
  1           0            38
[1] 2 2
[1] FALSE
D77V7, binary
               cls
clus              0   1
  NBN MUTATED     7  13
  NBN WILD-TYPE 165 393
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      7   13
  NBN WILD-TYPE  165  393
        clus
vv       NBN MUTATED NBN WILD-TYPE
  FEMALE           7           165
  MALE            13           393
[1] 2 2
[1] FALSE
D77V8, binary
               cls
clus              0   1
  NBN MUTATED    17   2
  NBN WILD-TYPE 399 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED     17    2
  NBN WILD-TYPE  399  100
     clus
vv    NBN MUTATED NBN WILD-TYPE
  NO           17           399
  YES           2           100
[1] 2 2
[1] FALSE
D77V9, continuous
[1] "Remove cluster labels:" "NBN MUTATED"           
clus
  NBN MUTATED NBN WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EQ    TCGA-VR-A8ER    TCGA-VR-A8ET 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY    TCGA-VR-A8EZ 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" "NBN WILD-TYPE" 
   TCGA-Z6-A8JE 
"NBN WILD-TYPE" 
D77V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NBN MUTATED       8                         0
  NBN WILD-TYPE   125                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NBN MUTATED                                           0    11
  NBN WILD-TYPE                                         1   346
D77V11, multiclass
                                           clus
vv                                          NBN MUTATED NBN WILD-TYPE
  ASIAN                                               8           125
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              11           346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
               cls
clus              0   1
  NBN MUTATED     0  16
  NBN WILD-TYPE  10 382
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      0   16
  NBN WILD-TYPE   10  382
                        clus
vv                       NBN MUTATED NBN WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          16           382
[1] 2 2
[1] FALSE

Clustering(78) Variable = GLI1 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED    13   8
  GLI1 WILD-TYPE 325 208
  GLI1 MUTATED GLI1 WILD-TYPE 
            21            533 
  GLI1 MUTATED GLI1 WILD-TYPE 
             8            208 
$`GLI1 MUTATED`
TCGA-IG-A4P3 TCGA-JY-A6FG TCGA-L5-A4OJ TCGA-L5-A88Z TCGA-L5-A8NH TCGA-BR-4257 
       18.64        41.52        21.01         7.40        12.92         9.67 
TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5726 
       34.68        29.59        12.43         9.01       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 
       65.10        21.07        22.32        22.68         0.10        29.00 
TCGA-HU-A4H4 TCGA-IN-A6RJ TCGA-MX-A5UJ 
       23.84        12.46        19.73 

$`GLI1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.99        12.03        15.02         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GLI1 MUTATED GLI1 WILD-TYPE 
           0.1            0.0 
  GLI1 MUTATED GLI1 WILD-TYPE 
        105.07         122.30 
  GLI1 MUTATED GLI1 WILD-TYPE 
         21.07          13.48 
[1] "0.1 - 105.1 (21.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D78V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLI1 MUTATED         1        2        2        2         2         6
  GLI1 WILD-TYPE       9       18       44       29        82        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI1 MUTATED           1          2          0          2        3         0
  GLI1 WILD-TYPE        28         82         62         37       40         4
D78V3, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              2             44
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             6             77
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GLI1 MUTATED       5   6   5   7
  GLI1 WILD-TYPE    49 129 256  95
D78V4, multiclass
       clus
vv      GLI1 MUTATED GLI1 WILD-TYPE
  T0+T1            5             49
  T2               6            129
  T3               5            256
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GLI1 MUTATED    11   6   5   2
  GLI1 WILD-TYPE 184 167  84  83
D78V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0           11            184
  N1            6            167
  N2            5             84
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                cls
clus               0   1
  GLI1 MUTATED    23   2
  GLI1 WILD-TYPE 459  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     23    2
  GLI1 WILD-TYPE  459   36
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           23            459
  1            2             36
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus               0   1
  GLI1 MUTATED    15  10
  GLI1 WILD-TYPE 157 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     15   10
  GLI1 WILD-TYPE  157  396
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  FEMALE           15            157
  MALE             10            396
[1] 2 2
[1] FALSE
D78V8, binary
                cls
clus               0   1
  GLI1 MUTATED    16   1
  GLI1 WILD-TYPE 400 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     16    1
  GLI1 WILD-TYPE  400  101
     clus
vv    GLI1 MUTATED GLI1 WILD-TYPE
  NO            16            400
  YES            1            101
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, continuous
[1] "Remove cluster labels:" "GLI1 MUTATED"          
clus
  GLI1 MUTATED GLI1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" "GLI1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GLI1 MUTATED       6                         0
  GLI1 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLI1 MUTATED                                           0    13
  GLI1 WILD-TYPE                                         1   344
D78V11, multiclass
                                           clus
vv                                          GLI1 MUTATED GLI1 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                cls
clus               0   1
  GLI1 MUTATED     0  15
  GLI1 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED      0   15
  GLI1 WILD-TYPE   10  383
                        clus
vv                       GLI1 MUTATED GLI1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(79) Variable = FAM9A MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED     6   4
  FAM9A WILD-TYPE 332 212
  FAM9A MUTATED FAM9A WILD-TYPE 
             10             544 
  FAM9A MUTATED FAM9A WILD-TYPE 
              4             212 
$`FAM9A MUTATED`
TCGA-CG-4460 TCGA-RE-A7BO TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7715 TCGA-CD-A4MG 
       21.99         7.00         6.97        44.94        33.63         6.58 
TCGA-CG-5721 TCGA-D7-A4Z0 TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.02        14.76        19.04        38.14 

$`FAM9A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  FAM9A MUTATED FAM9A WILD-TYPE 
           6.02            0.00 
  FAM9A MUTATED FAM9A WILD-TYPE 
          44.94          122.30 
  FAM9A MUTATED FAM9A WILD-TYPE 
          16.90           13.53 
[1] "6.0 - 44.9 (16.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D79V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM9A MUTATED         1        0        1        0         3         2
  FAM9A WILD-TYPE       9       20       45       31        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM9A MUTATED           0          2          0          0        3         0
  FAM9A WILD-TYPE        29         82         62         39       40         4
D79V3, multiclass
            clus
vv           FAM9A MUTATED FAM9A WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FAM9A MUTATED       2   2   4   4
  FAM9A WILD-TYPE    52 133 257  98
D79V4, multiclass
       clus
vv      FAM9A MUTATED FAM9A WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                4             257
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FAM9A MUTATED     4   6   2   0
  FAM9A WILD-TYPE 191 167  87  85
D79V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  N0             4             191
  N1             6             167
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                 cls
clus                0   1
  FAM9A MUTATED    10   1
  FAM9A WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED     10    1
  FAM9A WILD-TYPE  472   37
   clus
vv  FAM9A MUTATED FAM9A WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus                0   1
  FAM9A MUTATED     7   6
  FAM9A WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      7    6
  FAM9A WILD-TYPE  165  400
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D79V8, binary
                 cls
clus                0   1
  FAM9A MUTATED     9   2
  FAM9A WILD-TYPE 407 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      9    2
  FAM9A WILD-TYPE  407  100
     clus
vv    FAM9A MUTATED FAM9A WILD-TYPE
  NO              9             407
  YES             2             100
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
[1] "Remove cluster labels:" "FAM9A MUTATED"         
clus
  FAM9A MUTATED FAM9A WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-V5-A7RB 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" "FAM9A WILD-TYPE" 
     TCGA-Z6-AAPN 
"FAM9A WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FAM9A MUTATED       1                         1
  FAM9A WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM9A MUTATED                                           0     9
  FAM9A WILD-TYPE                                         1   348
D79V11, multiclass
                                           clus
vv                                          FAM9A MUTATED FAM9A WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                 cls
clus                0   1
  FAM9A MUTATED     0  10
  FAM9A WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      0   10
  FAM9A WILD-TYPE   10  388
                        clus
vv                       FAM9A MUTATED FAM9A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(80) Variable = HDAC4 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  HDAC4 MUTATED    24  10
  HDAC4 WILD-TYPE 314 206
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             34             520 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             10             206 
$`HDAC4 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-L5-A4OH TCGA-LN-A49K 
        4.31        19.99        20.78        18.64        32.61         5.92 
TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4MR TCGA-LN-A9FP TCGA-R6-A8W5 TCGA-B7-5816 
       13.25        12.76        13.22        12.03        15.78        26.70 
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
       34.68        31.10         4.31        31.27         1.12        28.14 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5725 TCGA-CG-5733 TCGA-D7-A4YY TCGA-F1-6874 
       16.14         6.58        15.02        21.07        13.78        14.47 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ 
       77.29        26.47        22.32        24.20        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 
        6.51        20.25        29.00        38.14 

$`HDAC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        0.85         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        11.77        21.37         8.98         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HDAC4 MUTATED HDAC4 WILD-TYPE 
            0.1             0.0 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
          77.29          122.30 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
         19.315          13.410 
[1] "0.1 - 77.3 (19.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D80V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDAC4 MUTATED         2        1        5        1         8         4
  HDAC4 WILD-TYPE       8       19       41       30        76        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HDAC4 MUTATED           2          4          2          7        0         1
  HDAC4 WILD-TYPE        27         80         60         32       43         3
D80V3, multiclass
            clus
vv           HDAC4 MUTATED HDAC4 WILD-TYPE
  STAGE I                2               8
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               1              30
  STAGE IIA              8              76
  STAGE IIB              4              79
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             7              32
  STAGE IV               0              43
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HDAC4 MUTATED       3  11  12  11
  HDAC4 WILD-TYPE    51 124 249  91
D80V4, multiclass
       clus
vv      HDAC4 MUTATED HDAC4 WILD-TYPE
  T0+T1             3              51
  T2               11             124
  T3               12             249
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HDAC4 MUTATED    19   8   4   6
  HDAC4 WILD-TYPE 176 165  85  79
D80V5, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  N0            19             176
  N1             8             165
  N2             4              85
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                 cls
clus                0   1
  HDAC4 MUTATED    32   1
  HDAC4 WILD-TYPE 450  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     32    1
  HDAC4 WILD-TYPE  450   37
   clus
vv  HDAC4 MUTATED HDAC4 WILD-TYPE
  0            32             450
  1             1              37
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus                0   1
  HDAC4 MUTATED    15  22
  HDAC4 WILD-TYPE 157 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     15   22
  HDAC4 WILD-TYPE  157  384
        clus
vv       HDAC4 MUTATED HDAC4 WILD-TYPE
  FEMALE            15             157
  MALE              22             384
[1] 2 2
[1] FALSE
D80V8, binary
                 cls
clus                0   1
  HDAC4 MUTATED    26   7
  HDAC4 WILD-TYPE 390  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     26    7
  HDAC4 WILD-TYPE  390   95
     clus
vv    HDAC4 MUTATED HDAC4 WILD-TYPE
  NO             26             390
  YES             7              95
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HDAC4 MUTATED      13                         1
  HDAC4 WILD-TYPE   120                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HDAC4 MUTATED                                           0    19
  HDAC4 WILD-TYPE                                         1   338
D80V11, multiclass
                                           clus
vv                                          HDAC4 MUTATED HDAC4 WILD-TYPE
  ASIAN                                                13             120
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                 cls
clus                0   1
  HDAC4 MUTATED     0  28
  HDAC4 WILD-TYPE  10 370
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED      0   28
  HDAC4 WILD-TYPE   10  370
                        clus
vv                       HDAC4 MUTATED HDAC4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            28             370
[1] 2 2
[1] FALSE

Clustering(81) Variable = MOBKL1A MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  MOBKL1A MUTATED     6   0
  MOBKL1A WILD-TYPE 332 216
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                6               548 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                0               216 
$`MOBKL1A MUTATED`
TCGA-L5-A4OI TCGA-BR-6452 TCGA-CG-4305 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HU-A4GT 
       19.99        34.68        15.95       105.07        11.08         6.51 

$`MOBKL1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
             6.51              0.00 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
           105.07            122.30 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
            17.97             13.53 
[1] "6.5 - 105.1 (18.0)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9300000"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MOBKL1A MUTATED         0        0        0        2         3         0
  MOBKL1A WILD-TYPE      10       20       46       29        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOBKL1A MUTATED           0          0          0          1        1
  MOBKL1A WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  MOBKL1A MUTATED           0
  MOBKL1A WILD-TYPE         4
D81V3, multiclass
            clus
vv           MOBKL1A MUTATED MOBKL1A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 2                29
  STAGE IIA                3                81
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  MOBKL1A MUTATED       0   2   4   1
  MOBKL1A WILD-TYPE    54 133 257 101
D81V4, multiclass
       clus
vv      MOBKL1A MUTATED MOBKL1A WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  4               257
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  MOBKL1A MUTATED     3   2   1   1
  MOBKL1A WILD-TYPE 192 171  88  84
D81V5, multiclass
    clus
vv   MOBKL1A MUTATED MOBKL1A WILD-TYPE
  N0               3               192
  N1               2               171
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     6   0
  MOBKL1A WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      6    0
  MOBKL1A WILD-TYPE  476   38
   clus
vv  MOBKL1A MUTATED MOBKL1A WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     3   4
  MOBKL1A WILD-TYPE 169 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      3    4
  MOBKL1A WILD-TYPE  169  402
        clus
vv       MOBKL1A MUTATED MOBKL1A WILD-TYPE
  FEMALE               3               169
  MALE                 4               402
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     5   1
  MOBKL1A WILD-TYPE 411 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      5    1
  MOBKL1A WILD-TYPE  411  101
     clus
vv    MOBKL1A MUTATED MOBKL1A WILD-TYPE
  NO                5               411
  YES               1               101
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, continuous
[1] "Remove cluster labels:" "MOBKL1A MUTATED"       
clus
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" "MOBKL1A WILD-TYPE" 
       TCGA-Z6-AAPN 
"MOBKL1A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MOBKL1A MUTATED       1                         1
  MOBKL1A WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MOBKL1A MUTATED                                           0     3
  MOBKL1A WILD-TYPE                                         1   354
D81V11, multiclass
                                           clus
vv                                          MOBKL1A MUTATED MOBKL1A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     0   4
  MOBKL1A WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      0    4
  MOBKL1A WILD-TYPE   10  394
                        clus
vv                       MOBKL1A MUTATED MOBKL1A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(82) Variable = KIAA0664 MUTATION ANALYSIS
D82V1, survival
                    sevent
clus2                  0   1
  KIAA0664 MUTATED    16   7
  KIAA0664 WILD-TYPE 322 209
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                23                531 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 7                209 
$`KIAA0664 MUTATED`
TCGA-L5-A43M TCGA-L5-A4OI TCGA-JY-A6FH TCGA-L5-A8NK TCGA-BR-4184 TCGA-BR-4280 
        8.94        19.99        47.38        13.55         6.97         6.61 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5721 
       34.68        29.59         6.18         0.26         6.58         6.02 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A74A TCGA-HF-A5NB TCGA-HU-8602 
       12.03        28.96        65.10        19.96        30.51        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8DT TCGA-VQ-A8P2 
        0.10        20.25        19.73        48.79        38.14 

$`KIAA0664 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
               0.1                0.0 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
              65.1              122.3 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
             19.96              13.51 
[1] "0.1 - 65.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D82V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0664 MUTATED         1        1        2        0         4         3
  KIAA0664 WILD-TYPE       9       19       44       31        80        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0664 MUTATED           1          5          1          5        3
  KIAA0664 WILD-TYPE        28         79         61         34       40
                    vv
clus                 STAGE IVA
  KIAA0664 MUTATED           0
  KIAA0664 WILD-TYPE         4
D82V3, multiclass
            clus
vv           KIAA0664 MUTATED KIAA0664 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 4                 80
  STAGE IIB                 3                 80
  STAGE III                 1                 28
  STAGE IIIA                5                 79
  STAGE IIIB                1                 61
  STAGE IIIC                5                 34
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0664 MUTATED       2   4  11  10
  KIAA0664 WILD-TYPE    52 131 250  92
D82V4, multiclass
       clus
vv      KIAA0664 MUTATED KIAA0664 WILD-TYPE
  T0+T1                2                 52
  T2                   4                131
  T3                  11                250
  T4                  10                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0664 MUTATED    10   6   6   5
  KIAA0664 WILD-TYPE 185 167  83  80
D82V5, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  N0               10                185
  N1                6                167
  N2                6                 83
  N3                5                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    22   1
  KIAA0664 WILD-TYPE 460  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     22    1
  KIAA0664 WILD-TYPE  460   37
   clus
vv  KIAA0664 MUTATED KIAA0664 WILD-TYPE
  0               22                460
  1                1                 37
[1] 2 2
[1] FALSE
D82V7, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    15  12
  KIAA0664 WILD-TYPE 157 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     15   12
  KIAA0664 WILD-TYPE  157  394
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  FEMALE               15                157
  MALE                 12                394
[1] 2 2
[1] FALSE
D82V8, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    19   3
  KIAA0664 WILD-TYPE 397  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     19    3
  KIAA0664 WILD-TYPE  397   99
     clus
vv    KIAA0664 MUTATED KIAA0664 WILD-TYPE
  NO                19                397
  YES                3                 99
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0664 MUTATED       4                         1
  KIAA0664 WILD-TYPE   129                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0664 MUTATED                                           0    15
  KIAA0664 WILD-TYPE                                         1   342
D82V11, multiclass
                                           clus
vv                                          KIAA0664 MUTATED KIAA0664 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     0  16
  KIAA0664 WILD-TYPE  10 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      0   16
  KIAA0664 WILD-TYPE   10  382
                        clus
vv                       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               16                382
[1] 2 2
[1] FALSE

Clustering(83) Variable = CR2 MUTATION ANALYSIS
D83V1, survival
               sevent
clus2             0   1
  CR2 MUTATED    23   4
  CR2 WILD-TYPE 315 212
  CR2 MUTATED CR2 WILD-TYPE 
           27           527 
  CR2 MUTATED CR2 WILD-TYPE 
            4           212 
$`CR2 MUTATED`
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-LN-A49Y TCGA-LN-A9FO TCGA-B7-5816 TCGA-BR-4257 
        4.70        19.99        12.46         0.13        26.70         9.67 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 
       34.68        29.59        32.25         4.31        25.05        31.96 
TCGA-CG-5721 TCGA-CG-5723 TCGA-EQ-8122 TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 
        6.02       105.07         7.99        77.29        22.32        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       24.20        11.77         6.51         6.58        20.25         2.10 
TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A92D 
        0.92        38.14        66.81 

$`CR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        24.26         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         8.98         0.10         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        19.04         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        42.64        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CR2 MUTATED CR2 WILD-TYPE 
         0.13          0.00 
  CR2 MUTATED CR2 WILD-TYPE 
       105.07        122.30 
  CR2 MUTATED CR2 WILD-TYPE 
        20.25         13.51 
[1] "0.1 - 105.1 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D83V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR2 MUTATED         1        2        2        2         5         7
  CR2 WILD-TYPE       9       18       44       29        79        76
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CR2 MUTATED           0          1          0          4        2         0
  CR2 WILD-TYPE        29         83         62         35       41         4
D83V3, multiclass
            clus
vv           CR2 MUTATED CR2 WILD-TYPE
  STAGE I              1             9
  STAGE IA             2            18
  STAGE IB             2            44
  STAGE II             2            29
  STAGE IIA            5            79
  STAGE IIB            7            76
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           0            62
  STAGE IIIC           4            35
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CR2 MUTATED       3   5   8  10
  CR2 WILD-TYPE    51 130 253  92
D83V4, multiclass
       clus
vv      CR2 MUTATED CR2 WILD-TYPE
  T0+T1           3            51
  T2              5           130
  T3              8           253
  T4             10            92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CR2 MUTATED    14   7   2   3
  CR2 WILD-TYPE 181 166  87  82
D83V5, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  N0          14           181
  N1           7           166
  N2           2            87
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
               cls
clus              0   1
  CR2 MUTATED    24   1
  CR2 WILD-TYPE 458  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     24    1
  CR2 WILD-TYPE  458   37
   clus
vv  CR2 MUTATED CR2 WILD-TYPE
  0          24           458
  1           1            37
[1] 2 2
[1] FALSE
D83V7, binary
               cls
clus              0   1
  CR2 MUTATED    15  12
  CR2 WILD-TYPE 157 394
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     15   12
  CR2 WILD-TYPE  157  394
        clus
vv       CR2 MUTATED CR2 WILD-TYPE
  FEMALE          15           157
  MALE            12           394
[1] 2 2
[1] FALSE
D83V8, binary
               cls
clus              0   1
  CR2 MUTATED    24   3
  CR2 WILD-TYPE 392  99
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     24    3
  CR2 WILD-TYPE  392   99
     clus
vv    CR2 MUTATED CR2 WILD-TYPE
  NO           24           392
  YES           3            99
[1] 2 2
[1] FALSE
D83V9, continuous
[1] "Remove cluster labels:" "CR2 MUTATED"           
clus
  CR2 MUTATED CR2 WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" 
D83V10, continuous
[1] "Remove cluster labels:" "CR2 MUTATED"           
clus
  CR2 MUTATED CR2 WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A88T 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU    TCGA-IC-A6RE 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC    TCGA-IG-A4P3 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS    TCGA-IG-A8O2 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG    TCGA-JY-A6FH 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H    TCGA-L5-A4OH 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP    TCGA-L5-A4OQ 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX    TCGA-L5-A88S 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF    TCGA-L5-A8NK 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS    TCGA-L5-A8NW 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6    TCGA-LN-A4A9 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8    TCGA-Q9-A6FW 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" "CR2 WILD-TYPE" 
   TCGA-Z6-AAPN 
"CR2 WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CR2 MUTATED      11                         0
  CR2 WILD-TYPE   122                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR2 MUTATED                                           0    13
  CR2 WILD-TYPE                                         1   344
D83V11, multiclass
                                           clus
vv                                          CR2 MUTATED CR2 WILD-TYPE
  ASIAN                                              11           122
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              13           344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, binary
               cls
clus              0   1
  CR2 MUTATED     0  19
  CR2 WILD-TYPE  10 379
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED      0   19
  CR2 WILD-TYPE   10  379
                        clus
vv                       CR2 MUTATED CR2 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          19           379
[1] 2 2
[1] FALSE

Clustering(84) Variable = RTN2 MUTATION ANALYSIS
D84V1, survival
                sevent
clus2              0   1
  RTN2 MUTATED     9   5
  RTN2 WILD-TYPE 329 211
  RTN2 MUTATED RTN2 WILD-TYPE 
            14            540 
  RTN2 MUTATED RTN2 WILD-TYPE 
             5            211 
$`RTN2 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-LN-A8I0 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8360 
        4.31        35.97        13.38        34.68        32.25         6.18 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6526 
        6.58        15.95         6.02        28.96        21.07        17.19 
TCGA-D7-A4YV TCGA-VQ-A8E2 
        5.92        43.36 

$`RTN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RTN2 MUTATED RTN2 WILD-TYPE 
          4.31           0.00 
  RTN2 MUTATED RTN2 WILD-TYPE 
         43.36         122.30 
  RTN2 MUTATED RTN2 WILD-TYPE 
         16.57          13.53 
[1] "4.3 - 43.4 (16.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D84V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RTN2 MUTATED         1        1        0        1         4         4
  RTN2 WILD-TYPE       9       19       46       30        80        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTN2 MUTATED           1          3          1          0        1         0
  RTN2 WILD-TYPE        28         81         61         39       42         4
D84V3, multiclass
            clus
vv           RTN2 MUTATED RTN2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RTN2 MUTATED       2   3   8   4
  RTN2 WILD-TYPE    52 132 253  98
D84V4, multiclass
       clus
vv      RTN2 MUTATED RTN2 WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3               8            253
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RTN2 MUTATED     9   5   3   0
  RTN2 WILD-TYPE 186 168  86  85
D84V5, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  N0            9            186
  N1            5            168
  N2            3             86
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V6, binary
                cls
clus               0   1
  RTN2 MUTATED    16   0
  RTN2 WILD-TYPE 466  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED     16    0
  RTN2 WILD-TYPE  466   38
   clus
vv  RTN2 MUTATED RTN2 WILD-TYPE
  0           16            466
  1            0             38
[1] 2 2
[1] FALSE
D84V7, binary
                cls
clus               0   1
  RTN2 MUTATED     7  11
  RTN2 WILD-TYPE 165 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      7   11
  RTN2 WILD-TYPE  165  395
        clus
vv       RTN2 MUTATED RTN2 WILD-TYPE
  FEMALE            7            165
  MALE             11            395
[1] 2 2
[1] FALSE
D84V8, binary
                cls
clus               0   1
  RTN2 MUTATED    13   1
  RTN2 WILD-TYPE 403 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED     13    1
  RTN2 WILD-TYPE  403  101
     clus
vv    RTN2 MUTATED RTN2 WILD-TYPE
  NO            13            403
  YES            1            101
[1] 2 2
[1] FALSE
D84V9, continuous
D84V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RTN2 MUTATED       3                         1
  RTN2 WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RTN2 MUTATED                                           0    10
  RTN2 WILD-TYPE                                         1   347
D84V11, multiclass
                                           clus
vv                                          RTN2 MUTATED RTN2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, binary
                cls
clus               0   1
  RTN2 MUTATED     0  11
  RTN2 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      0   11
  RTN2 WILD-TYPE   10  387
                        clus
vv                       RTN2 MUTATED RTN2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(85) Variable = ABCC4 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    16   7
  ABCC4 WILD-TYPE 322 209
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             23             531 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              7             209 
$`ABCC4 MUTATED`
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-LN-A9FO TCGA-VR-A8EO TCGA-Z6-AAPN 
        7.76        21.37         8.71         0.13        25.81         2.66 
TCGA-B7-A5TJ TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8366 TCGA-BR-8368 
       11.01        44.94        14.43        32.25         0.95         4.31 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 
        1.12        31.96        15.95         1.02         9.01         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-A4YY 
      105.07        28.96        65.10         7.99        13.78 

$`ABCC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         5.49        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19        17.52        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 
       15.02         4.01        69.04        21.07        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           0.13            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         105.07          122.30 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
          11.01           13.58 
[1] "0.1 - 105.1 (11.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D85V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC4 MUTATED         0        1        2        2         7         3
  ABCC4 WILD-TYPE      10       19       44       29        77        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCC4 MUTATED           2          2          1          0        4         0
  ABCC4 WILD-TYPE        27         82         61         39       39         4
D85V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              7              77
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCC4 MUTATED       1   7  10   7
  ABCC4 WILD-TYPE    53 128 251  95
D85V4, multiclass
       clus
vv      ABCC4 MUTATED ABCC4 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3               10             251
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCC4 MUTATED    12   7   2   2
  ABCC4 WILD-TYPE 183 166  87  83
D85V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0            12             183
  N1             7             166
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V6, binary
                 cls
clus                0   1
  ABCC4 MUTATED    21   3
  ABCC4 WILD-TYPE 461  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     21    3
  ABCC4 WILD-TYPE  461   35
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            21             461
  1             3              35
[1] 2 2
[1] FALSE
D85V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED    10  15
  ABCC4 WILD-TYPE 162 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     10   15
  ABCC4 WILD-TYPE  162  391
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE            10             162
  MALE              15             391
[1] 2 2
[1] FALSE
D85V8, binary
                 cls
clus                0   1
  ABCC4 MUTATED    16   2
  ABCC4 WILD-TYPE 400 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     16    2
  ABCC4 WILD-TYPE  400  100
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO             16             400
  YES             2             100
[1] 2 2
[1] FALSE
D85V9, continuous
[1] "Remove cluster labels:" "ABCC4 MUTATED"         
clus
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EP 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" "ABCC4 WILD-TYPE" 
D85V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC4 MUTATED       2                         0
  ABCC4 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC4 MUTATED                                           0    14
  ABCC4 WILD-TYPE                                         1   343
D85V11, multiclass
                                           clus
vv                                          ABCC4 MUTATED ABCC4 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, binary
                 cls
clus                0   1
  ABCC4 MUTATED     0  13
  ABCC4 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      0   13
  ABCC4 WILD-TYPE   10  385
                        clus
vv                       ABCC4 MUTATED ABCC4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(86) Variable = ALDH2 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     9   5
  ALDH2 WILD-TYPE 329 211
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             14             540 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              5             211 
$`ALDH2 MUTATED`
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 
       13.55         7.76         6.97        36.16        35.84        29.59 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-8602 
       28.14        16.14         1.02         6.02        28.96        22.32 
TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.58        38.14 

$`ALDH2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
           1.02            0.00 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          38.14          122.30 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          19.23           13.51 
[1] "1.0 - 38.1 (19.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D86V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH2 MUTATED         0        2        1        0         1         4
  ALDH2 WILD-TYPE      10       18       45       31        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDH2 MUTATED           0          3          1          1        2         0
  ALDH2 WILD-TYPE        29         81         61         38       41         4
D86V3, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ALDH2 MUTATED       2   2   5   6
  ALDH2 WILD-TYPE    52 133 256  96
D86V4, multiclass
       clus
vv      ALDH2 MUTATED ALDH2 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                5             256
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ALDH2 MUTATED     7   5   1   2
  ALDH2 WILD-TYPE 188 168  88  83
D86V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             7             188
  N1             5             168
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                 cls
clus                0   1
  ALDH2 MUTATED    13   1
  ALDH2 WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED     13    1
  ALDH2 WILD-TYPE  469   37
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D86V7, binary
                 cls
clus                0   1
  ALDH2 MUTATED     7   8
  ALDH2 WILD-TYPE 165 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      7    8
  ALDH2 WILD-TYPE  165  398
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  FEMALE             7             165
  MALE               8             398
[1] 2 2
[1] FALSE
D86V8, binary
                 cls
clus                0   1
  ALDH2 MUTATED    10   1
  ALDH2 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED     10    1
  ALDH2 WILD-TYPE  406  101
     clus
vv    ALDH2 MUTATED ALDH2 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D86V9, continuous
D86V10, continuous
[1] "Remove cluster labels:" "ALDH2 MUTATED"         
clus
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" "ALDH2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ALDH2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALDH2 MUTATED       2                         0
  ALDH2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALDH2 MUTATED                                           0    10
  ALDH2 WILD-TYPE                                         1   347
D86V11, multiclass
                                           clus
vv                                          ALDH2 MUTATED ALDH2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, binary
                 cls
clus                0   1
  ALDH2 MUTATED     0   9
  ALDH2 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      0    9
  ALDH2 WILD-TYPE   10  389
                        clus
vv                       ALDH2 MUTATED ALDH2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(87) Variable = IWS1 MUTATION ANALYSIS
D87V1, survival
                sevent
clus2              0   1
  IWS1 MUTATED    12   3
  IWS1 WILD-TYPE 326 213
  IWS1 MUTATED IWS1 WILD-TYPE 
            15            539 
  IWS1 MUTATED IWS1 WILD-TYPE 
             3            213 
$`IWS1 MUTATED`
TCGA-JY-A6FD TCGA-R6-A6L6 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 
       68.02         7.04         6.97        34.68        29.59         6.18 
TCGA-BR-8487 TCGA-CD-8534 TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4YX TCGA-D7-A6EV 
        1.12        12.07         9.01       105.07        36.43        11.24 
TCGA-HF-A5NB TCGA-HU-A4GU TCGA-HU-A4H3 
       30.51         6.58        29.00 

$`IWS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        13.78        14.76        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  IWS1 MUTATED IWS1 WILD-TYPE 
          1.12           0.00 
  IWS1 MUTATED IWS1 WILD-TYPE 
        105.07         122.30 
  IWS1 MUTATED IWS1 WILD-TYPE 
         12.07          13.58 
[1] "1.1 - 105.1 (12.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.5"
D87V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IWS1 MUTATED         0        0        0        2         4         4
  IWS1 WILD-TYPE      10       20       46       29        80        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IWS1 MUTATED           0          2          0          2        1         0
  IWS1 WILD-TYPE        29         82         62         37       42         4
D87V3, multiclass
            clus
vv           IWS1 MUTATED IWS1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             4             80
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IWS1 MUTATED       0   2   8   5
  IWS1 WILD-TYPE    54 133 253  97
D87V4, multiclass
       clus
vv      IWS1 MUTATED IWS1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IWS1 MUTATED     7   4   1   3
  IWS1 WILD-TYPE 188 169  88  82
D87V5, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  N0            7            188
  N1            4            169
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                cls
clus               0   1
  IWS1 MUTATED    13   1
  IWS1 WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED     13    1
  IWS1 WILD-TYPE  469   37
   clus
vv  IWS1 MUTATED IWS1 WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D87V7, binary
                cls
clus               0   1
  IWS1 MUTATED     9   7
  IWS1 WILD-TYPE 163 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      9    7
  IWS1 WILD-TYPE  163  399
        clus
vv       IWS1 MUTATED IWS1 WILD-TYPE
  FEMALE            9            163
  MALE              7            399
[1] 2 2
[1] FALSE
D87V8, binary
                cls
clus               0   1
  IWS1 MUTATED    12   1
  IWS1 WILD-TYPE 404 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED     12    1
  IWS1 WILD-TYPE  404  101
     clus
vv    IWS1 MUTATED IWS1 WILD-TYPE
  NO            12            404
  YES            1            101
[1] 2 2
[1] FALSE
D87V9, continuous
D87V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IWS1 MUTATED       4                         0
  IWS1 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IWS1 MUTATED                                           0     9
  IWS1 WILD-TYPE                                         1   348
D87V11, multiclass
                                           clus
vv                                          IWS1 MUTATED IWS1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, binary
                cls
clus               0   1
  IWS1 MUTATED     0  12
  IWS1 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      0   12
  IWS1 WILD-TYPE   10  386
                        clus
vv                       IWS1 MUTATED IWS1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(88) Variable = SLC12A9 MUTATION ANALYSIS
D88V1, survival
                   sevent
clus2                 0   1
  SLC12A9 MUTATED     9   8
  SLC12A9 WILD-TYPE 329 208
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               17               537 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
                8               208 
$`SLC12A9 MUTATED`
TCGA-CG-4460 TCGA-V5-AASW TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8289 TCGA-BR-8368 
       21.99         9.27         6.97         9.34         2.66         4.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 
        6.58        11.77        12.62        15.95         6.02        65.10 
TCGA-D7-A4YV TCGA-HF-7132 TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-AA6I 
        5.92        77.29        20.25        38.14        16.14 

$`SLC12A9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.61        12.20        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
             2.66              0.00 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
            77.29            122.30 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
            11.77             13.68 
[1] "2.7 - 77.3 (11.8)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D88V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC12A9 MUTATED         1        0        3        2         1         2
  SLC12A9 WILD-TYPE       9       20       43       29        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A9 MUTATED           0          3          1          1        4
  SLC12A9 WILD-TYPE        29         81         61         38       39
                   vv
clus                STAGE IVA
  SLC12A9 MUTATED           0
  SLC12A9 WILD-TYPE         4
D88V3, multiclass
            clus
vv           SLC12A9 MUTATED SLC12A9 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 2                29
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 4                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC12A9 MUTATED       1   5   6   7
  SLC12A9 WILD-TYPE    53 130 255  95
D88V4, multiclass
       clus
vv      SLC12A9 MUTATED SLC12A9 WILD-TYPE
  T0+T1               1                53
  T2                  5               130
  T3                  6               255
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC12A9 MUTATED     5  10   2   2
  SLC12A9 WILD-TYPE 190 163  87  83
D88V5, multiclass
    clus
vv   SLC12A9 MUTATED SLC12A9 WILD-TYPE
  N0               5               190
  N1              10               163
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V6, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED    15   2
  SLC12A9 WILD-TYPE 467  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED     15    2
  SLC12A9 WILD-TYPE  467   36
   clus
vv  SLC12A9 MUTATED SLC12A9 WILD-TYPE
  0              15               467
  1               2                36
[1] 2 2
[1] FALSE
D88V7, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED     7  14
  SLC12A9 WILD-TYPE 165 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED      7   14
  SLC12A9 WILD-TYPE  165  392
        clus
vv       SLC12A9 MUTATED SLC12A9 WILD-TYPE
  FEMALE               7               165
  MALE                14               392
[1] 2 2
[1] FALSE
D88V8, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED    15   3
  SLC12A9 WILD-TYPE 401  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED     15    3
  SLC12A9 WILD-TYPE  401   99
     clus
vv    SLC12A9 MUTATED SLC12A9 WILD-TYPE
  NO               15               401
  YES               3                99
[1] 2 2
[1] FALSE
D88V9, continuous
[1] "Remove cluster labels:" "SLC12A9 MUTATED"       
clus
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" "SLC12A9 WILD-TYPE" 
D88V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC12A9 MUTATED       4                         1
  SLC12A9 WILD-TYPE   129                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC12A9 MUTATED                                           0    11
  SLC12A9 WILD-TYPE                                         1   346
D88V11, multiclass
                                           clus
vv                                          SLC12A9 MUTATED SLC12A9 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED     0  14
  SLC12A9 WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED      0   14
  SLC12A9 WILD-TYPE   10  384
                        clus
vv                       SLC12A9 MUTATED SLC12A9 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(89) Variable = IL2RG MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     8   3
  IL2RG WILD-TYPE 330 213
  IL2RG MUTATED IL2RG WILD-TYPE 
             11             543 
  IL2RG MUTATED IL2RG WILD-TYPE 
              3             213 
$`IL2RG MUTATED`
TCGA-L5-A43J TCGA-V5-A7RB TCGA-Z6-A8JD TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 
        4.31         5.29         3.42        34.68         6.18         1.12 
TCGA-BR-8680 TCGA-CG-5728 TCGA-HF-7132 TCGA-HJ-7597 TCGA-IN-A7NT 
       31.96        65.10        77.29        26.47        10.62 

$`IL2RG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IL2RG MUTATED IL2RG WILD-TYPE 
           1.12            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          77.29          122.30 
  IL2RG MUTATED IL2RG WILD-TYPE 
          10.62           13.58 
[1] "1.1 - 77.3 (10.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D89V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL2RG MUTATED         0        0        2        1         3         3
  IL2RG WILD-TYPE      10       20       44       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL2RG MUTATED           0          0          0          0        2         0
  IL2RG WILD-TYPE        29         84         62         39       41         4
D89V3, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IL2RG MUTATED       1   3   7   2
  IL2RG WILD-TYPE    53 132 254 100
D89V4, multiclass
       clus
vv      IL2RG MUTATED IL2RG WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IL2RG MUTATED     7   3   2   0
  IL2RG WILD-TYPE 188 170  87  85
D89V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             7             188
  N1             3             170
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V6, binary
                 cls
clus                0   1
  IL2RG MUTATED     8   1
  IL2RG WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      8    1
  IL2RG WILD-TYPE  474   37
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   6
  IL2RG WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    6
  IL2RG WILD-TYPE  165  400
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus                0   1
  IL2RG MUTATED     8   1
  IL2RG WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      8    1
  IL2RG WILD-TYPE  408  101
     clus
vv    IL2RG MUTATED IL2RG WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D89V9, continuous
[1] "Remove cluster labels:" "IL2RG MUTATED"         
clus
  IL2RG MUTATED IL2RG WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JE 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
D89V10, continuous
[1] "Remove cluster labels:" "IL2RG MUTATED"         
clus
  IL2RG MUTATED IL2RG WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RC 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" "IL2RG WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IL2RG MUTATED       1                         0
  IL2RG WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL2RG MUTATED                                           0     9
  IL2RG WILD-TYPE                                         1   348
D89V11, multiclass
                                           clus
vv                                          IL2RG MUTATED IL2RG WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, binary
                 cls
clus                0   1
  IL2RG MUTATED     1   9
  IL2RG WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      1    9
  IL2RG WILD-TYPE    9  389
                        clus
vv                       IL2RG MUTATED IL2RG WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(90) Variable = YY1 MUTATION ANALYSIS
D90V1, survival
               sevent
clus2             0   1
  YY1 MUTATED     8   2
  YY1 WILD-TYPE 330 214
  YY1 MUTATED YY1 WILD-TYPE 
           10           544 
  YY1 MUTATED YY1 WILD-TYPE 
            2           214 
$`YY1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A8O2 TCGA-L5-A8NM TCGA-LN-A8I0 TCGA-BR-7715 TCGA-BR-8078 
       19.99         4.67         7.76        13.38        33.63        29.59 
TCGA-BR-8591 TCGA-CD-8531 TCGA-SW-A7EA TCGA-VQ-A8P2 
       28.14        12.59        19.04        38.14 

$`YY1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  YY1 MUTATED YY1 WILD-TYPE 
         4.67          0.00 
  YY1 MUTATED YY1 WILD-TYPE 
        38.14        122.30 
  YY1 MUTATED YY1 WILD-TYPE 
       19.515        13.530 
[1] "4.7 - 38.1 (19.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D90V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YY1 MUTATED         0        0        1        0         2         2
  YY1 WILD-TYPE      10       20       45       31        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YY1 MUTATED           0          2          1          2        1         0
  YY1 WILD-TYPE        29         82         61         37       42         4
D90V3, multiclass
            clus
vv           YY1 MUTATED YY1 WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  YY1 MUTATED       1   3   4   4
  YY1 WILD-TYPE    53 132 257  98
D90V4, multiclass
       clus
vv      YY1 MUTATED YY1 WILD-TYPE
  T0+T1           1            53
  T2              3           132
  T3              4           257
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  YY1 MUTATED     4   3   2   2
  YY1 WILD-TYPE 191 170  87  83
D90V5, multiclass
    clus
vv   YY1 MUTATED YY1 WILD-TYPE
  N0           4           191
  N1           3           170
  N2           2            87
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
               cls
clus              0   1
  YY1 MUTATED    11   0
  YY1 WILD-TYPE 471  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED     11    0
  YY1 WILD-TYPE  471   38
   clus
vv  YY1 MUTATED YY1 WILD-TYPE
  0          11           471
  1           0            38
[1] 2 2
[1] FALSE
D90V7, binary
               cls
clus              0   1
  YY1 MUTATED     6   6
  YY1 WILD-TYPE 166 400
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      6    6
  YY1 WILD-TYPE  166  400
        clus
vv       YY1 MUTATED YY1 WILD-TYPE
  FEMALE           6           166
  MALE             6           400
[1] 2 2
[1] FALSE
D90V8, binary
               cls
clus              0   1
  YY1 MUTATED     7   2
  YY1 WILD-TYPE 409 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      7    2
  YY1 WILD-TYPE  409  100
     clus
vv    YY1 MUTATED YY1 WILD-TYPE
  NO            7           409
  YES           2           100
[1] 2 2
[1] FALSE
D90V9, continuous
D90V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  YY1 MUTATED       3                         0
  YY1 WILD-TYPE   130                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YY1 MUTATED                                           0     9
  YY1 WILD-TYPE                                         1   348
D90V11, multiclass
                                           clus
vv                                          YY1 MUTATED YY1 WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               9           348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, binary
               cls
clus              0   1
  YY1 MUTATED     0   9
  YY1 WILD-TYPE  10 389
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      0    9
  YY1 WILD-TYPE   10  389
                        clus
vv                       YY1 MUTATED YY1 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           9           389
[1] 2 2
[1] FALSE

Clustering(91) Variable = OPTN MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  OPTN MUTATED     8   4
  OPTN WILD-TYPE 330 212
  OPTN MUTATED OPTN WILD-TYPE 
            12            542 
  OPTN MUTATED OPTN WILD-TYPE 
             4            212 
$`OPTN MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-LN-A9FO TCGA-BR-4201 TCGA-BR-6452 
       19.99         7.69         0.79         0.13        30.90        34.68 
TCGA-BR-8060 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GU 
       11.44         1.12        12.30       105.07        28.96         6.58 

$`OPTN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  OPTN MUTATED OPTN WILD-TYPE 
          0.13           0.00 
  OPTN MUTATED OPTN WILD-TYPE 
        105.07         122.30 
  OPTN MUTATED OPTN WILD-TYPE 
         11.87          13.63 
[1] "0.1 - 105.1 (11.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D91V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPTN MUTATED         1        1        2        1         3         4
  OPTN WILD-TYPE       9       19       44       30        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OPTN MUTATED           0          1          0          1        1         0
  OPTN WILD-TYPE        29         83         62         38       42         4
D91V3, multiclass
            clus
vv           OPTN MUTATED OPTN WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  OPTN MUTATED       3   5   5   3
  OPTN WILD-TYPE    51 130 256  99
D91V4, multiclass
       clus
vv      OPTN MUTATED OPTN WILD-TYPE
  T0+T1            3             51
  T2               5            130
  T3               5            256
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  OPTN MUTATED     9   4   1   1
  OPTN WILD-TYPE 186 169  88  84
D91V5, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  N0            9            186
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V6, binary
                cls
clus               0   1
  OPTN MUTATED    13   1
  OPTN WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED     13    1
  OPTN WILD-TYPE  469   37
   clus
vv  OPTN MUTATED OPTN WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus               0   1
  OPTN MUTATED     5  11
  OPTN WILD-TYPE 167 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      5   11
  OPTN WILD-TYPE  167  395
        clus
vv       OPTN MUTATED OPTN WILD-TYPE
  FEMALE            5            167
  MALE             11            395
[1] 2 2
[1] FALSE
D91V8, binary
                cls
clus               0   1
  OPTN MUTATED    12   1
  OPTN WILD-TYPE 404 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED     12    1
  OPTN WILD-TYPE  404  101
     clus
vv    OPTN MUTATED OPTN WILD-TYPE
  NO            12            404
  YES            1            101
[1] 2 2
[1] FALSE
D91V9, continuous
D91V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  OPTN MUTATED       3                         1
  OPTN WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OPTN MUTATED                                           0     9
  OPTN WILD-TYPE                                         1   348
D91V11, multiclass
                                           clus
vv                                          OPTN MUTATED OPTN WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, binary
                cls
clus               0   1
  OPTN MUTATED     0  12
  OPTN WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      0   12
  OPTN WILD-TYPE   10  386
                        clus
vv                       OPTN MUTATED OPTN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(92) Variable = GRK4 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2              0   1
  GRK4 MUTATED     9   3
  GRK4 WILD-TYPE 329 213
  GRK4 MUTATED GRK4 WILD-TYPE 
            12            542 
  GRK4 MUTATED GRK4 WILD-TYPE 
             3            213 
$`GRK4 MUTATED`
TCGA-L5-A8NI TCGA-VR-AA7B TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8360 
       13.48        11.24        26.70         6.97        34.68         6.18 
TCGA-BR-8361 TCGA-BR-8487 TCGA-CG-5721 TCGA-FP-A4BE TCGA-VQ-A8P2 TCGA-VQ-AA64 
       31.10         1.12         6.02        11.08        38.14        18.41 

$`GRK4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GRK4 MUTATED GRK4 WILD-TYPE 
          1.12           0.00 
  GRK4 MUTATED GRK4 WILD-TYPE 
         38.14         122.30 
  GRK4 MUTATED GRK4 WILD-TYPE 
         12.36          13.63 
[1] "1.1 - 38.1 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D92V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GRK4 MUTATED         0        0        1        0         4         1
  GRK4 WILD-TYPE      10       20       45       31        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRK4 MUTATED           1          2          1          1        2         0
  GRK4 WILD-TYPE        28         82         61         38       41         4
D92V3, multiclass
            clus
vv           GRK4 MUTATED GRK4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GRK4 MUTATED       0   1   8   4
  GRK4 WILD-TYPE    54 134 253  98
D92V4, multiclass
       clus
vv      GRK4 MUTATED GRK4 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               8            253
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GRK4 MUTATED     6   4   2   1
  GRK4 WILD-TYPE 189 169  87  84
D92V5, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V6, binary
                cls
clus               0   1
  GRK4 MUTATED    11   1
  GRK4 WILD-TYPE 471  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED     11    1
  GRK4 WILD-TYPE  471   37
   clus
vv  GRK4 MUTATED GRK4 WILD-TYPE
  0           11            471
  1            1             37
[1] 2 2
[1] FALSE
D92V7, binary
                cls
clus               0   1
  GRK4 MUTATED     5   8
  GRK4 WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      5    8
  GRK4 WILD-TYPE  167  398
        clus
vv       GRK4 MUTATED GRK4 WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D92V8, binary
                cls
clus               0   1
  GRK4 MUTATED     9   3
  GRK4 WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      9    3
  GRK4 WILD-TYPE  407   99
     clus
vv    GRK4 MUTATED GRK4 WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D92V9, continuous
[1] "Remove cluster labels:" "GRK4 MUTATED"          
clus
  GRK4 MUTATED GRK4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GRK4 WILD-TYPE" "GRK4 WILD-TYPE" "GRK4 WILD-TYPE" 
D92V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GRK4 MUTATED       0                         1
  GRK4 WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GRK4 MUTATED                                           0    10
  GRK4 WILD-TYPE                                         1   347
D92V11, multiclass
                                           clus
vv                                          GRK4 MUTATED GRK4 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, binary
                cls
clus               0   1
  GRK4 MUTATED     0   7
  GRK4 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      0    7
  GRK4 WILD-TYPE   10  391
                        clus
vv                       GRK4 MUTATED GRK4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(93) Variable = CTCF MUTATION ANALYSIS
D93V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     9   6
  CTCF WILD-TYPE 329 210
  CTCF MUTATED CTCF WILD-TYPE 
            15            539 
  CTCF MUTATED CTCF WILD-TYPE 
             6            210 
$`CTCF MUTATED`
TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 
        9.34        35.84        18.15        29.59         0.26         1.12 
TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 
       12.79         6.28        31.96        16.14         6.02       105.07 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GT 
       30.51        26.47         6.51 

$`CTCF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       28.14         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CTCF MUTATED CTCF WILD-TYPE 
          0.26           0.00 
  CTCF MUTATED CTCF WILD-TYPE 
        105.07         122.30 
  CTCF MUTATED CTCF WILD-TYPE 
         16.14          13.55 
[1] "0.3 - 105.1 (16.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D93V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTCF MUTATED         0        0        3        1         2         3
  CTCF WILD-TYPE      10       20       43       30        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTCF MUTATED           0          0          2          1        3         0
  CTCF WILD-TYPE        29         84         60         38       40         4
D93V3, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTCF MUTATED       0   4   3   8
  CTCF WILD-TYPE    54 131 258  94
D93V4, multiclass
       clus
vv      CTCF MUTATED CTCF WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               3            258
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTCF MUTATED     8   5   1   2
  CTCF WILD-TYPE 187 168  88  83
D93V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            8            187
  N1            5            168
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V6, binary
                cls
clus               0   1
  CTCF MUTATED    14   1
  CTCF WILD-TYPE 468  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     14    1
  CTCF WILD-TYPE  468   37
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           14            468
  1            1             37
[1] 2 2
[1] FALSE
D93V7, binary
                cls
clus               0   1
  CTCF MUTATED    10   6
  CTCF WILD-TYPE 162 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     10    6
  CTCF WILD-TYPE  162  400
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE           10            162
  MALE              6            400
[1] 2 2
[1] FALSE
D93V8, binary
                cls
clus               0   1
  CTCF MUTATED    15   1
  CTCF WILD-TYPE 401 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    1
  CTCF WILD-TYPE  401  101
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            15            401
  YES            1            101
[1] 2 2
[1] FALSE
D93V9, continuous
D93V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTCF MUTATED       2                         0
  CTCF WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTCF MUTATED                                           0    11
  CTCF WILD-TYPE                                         1   346
D93V11, multiclass
                                           clus
vv                                          CTCF MUTATED CTCF WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V12, binary
                cls
clus               0   1
  CTCF MUTATED     0  13
  CTCF WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   13
  CTCF WILD-TYPE   10  385
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(94) Variable = EIF5B MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED    23   5
  EIF5B WILD-TYPE 315 211
  EIF5B MUTATED EIF5B WILD-TYPE 
             28             526 
  EIF5B MUTATED EIF5B WILD-TYPE 
              5             211 
$`EIF5B MUTATED`
TCGA-IG-A97H TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A8NS TCGA-Q9-A6FW TCGA-Z6-A8JE 
       14.50        24.03         0.30        13.41         7.82         2.10 
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 
        6.97        44.94        29.59        31.27         1.12        27.12 
TCGA-BR-8680 TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6525 
       31.96         7.99         6.02        28.96        65.10        13.35 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN 
       11.44        14.47        30.51        22.32        24.20        29.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.51        20.25        19.04        38.14 

$`EIF5B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        25.22         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26        33.11         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        0.99         0.99       105.07        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         0.10         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EIF5B MUTATED EIF5B WILD-TYPE 
            0.3             0.0 
  EIF5B MUTATED EIF5B WILD-TYPE 
           65.1           122.3 
  EIF5B MUTATED EIF5B WILD-TYPE 
         19.645          13.495 
[1] "0.3 - 65.1 (19.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.6"
D94V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF5B MUTATED         0        2        5        0         5         3
  EIF5B WILD-TYPE      10       18       41       31        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EIF5B MUTATED           1          4          3          3        2         0
  EIF5B WILD-TYPE        28         80         59         36       41         4
D94V3, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             3              59
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EIF5B MUTATED       3   7  10   9
  EIF5B WILD-TYPE    51 128 251  93
D94V4, multiclass
       clus
vv      EIF5B MUTATED EIF5B WILD-TYPE
  T0+T1             3              51
  T2                7             128
  T3               10             251
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EIF5B MUTATED    13   8   4   3
  EIF5B WILD-TYPE 182 165  85  82
D94V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0            13             182
  N1             8             165
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V6, binary
                 cls
clus                0   1
  EIF5B MUTATED    29   1
  EIF5B WILD-TYPE 453  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     29    1
  EIF5B WILD-TYPE  453   37
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            29             453
  1             1              37
[1] 2 2
[1] FALSE
D94V7, binary
                 cls
clus                0   1
  EIF5B MUTATED    15  16
  EIF5B WILD-TYPE 157 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     15   16
  EIF5B WILD-TYPE  157  390
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE            15             157
  MALE              16             390
[1] 2 2
[1] FALSE
D94V8, binary
                 cls
clus                0   1
  EIF5B MUTATED    22   3
  EIF5B WILD-TYPE 394  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     22    3
  EIF5B WILD-TYPE  394   99
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO             22             394
  YES             3              99
[1] 2 2
[1] FALSE
D94V9, continuous
[1] "Remove cluster labels:" "EIF5B MUTATED"         
clus
  EIF5B MUTATED EIF5B WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JD 
"EIF5B WILD-TYPE" "EIF5B WILD-TYPE" "EIF5B WILD-TYPE" 
D94V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EIF5B MUTATED       7                         0
  EIF5B WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF5B MUTATED                                           0    19
  EIF5B WILD-TYPE                                         1   338
D94V11, multiclass
                                           clus
vv                                          EIF5B MUTATED EIF5B WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, binary
                 cls
clus                0   1
  EIF5B MUTATED     0  22
  EIF5B WILD-TYPE  10 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      0   22
  EIF5B WILD-TYPE   10  376
                        clus
vv                       EIF5B MUTATED EIF5B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(95) Variable = RTKN2 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  RTKN2 MUTATED     8   5
  RTKN2 WILD-TYPE 330 211
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             13             541 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              5             211 
$`RTKN2 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NW TCGA-R6-A6XG TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 
        4.31        46.09        38.40        30.90        34.68        29.59 
TCGA-BR-8372 TCGA-BR-8590 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8602 
       31.27         9.34         6.02         5.92        30.51        22.32 
TCGA-R5-A7ZI 
       74.53 

$`RTKN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 
        9.21        20.22         1.12        12.79        27.12        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  RTKN2 MUTATED RTKN2 WILD-TYPE 
           4.31            0.00 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
          74.53          122.30 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
          30.51           13.51 
[1] "4.3 - 74.5 (30.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D95V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RTKN2 MUTATED         0        0        1        0         1         4
  RTKN2 WILD-TYPE      10       20       45       31        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTKN2 MUTATED           0          0          0          3        3         0
  RTKN2 WILD-TYPE        29         84         62         36       40         4
D95V3, multiclass
            clus
vv           RTKN2 MUTATED RTKN2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RTKN2 MUTATED       0   2   3   8
  RTKN2 WILD-TYPE    54 133 258  94
D95V4, multiclass
       clus
vv      RTKN2 MUTATED RTKN2 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                3             258
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RTKN2 MUTATED     4   4   2   2
  RTKN2 WILD-TYPE 191 169  87  83
D95V5, multiclass
    clus
vv   RTKN2 MUTATED RTKN2 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V6, binary
                 cls
clus                0   1
  RTKN2 MUTATED    11   1
  RTKN2 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED     11    1
  RTKN2 WILD-TYPE  471   37
   clus
vv  RTKN2 MUTATED RTKN2 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus                0   1
  RTKN2 MUTATED     8   6
  RTKN2 WILD-TYPE 164 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      8    6
  RTKN2 WILD-TYPE  164  400
        clus
vv       RTKN2 MUTATED RTKN2 WILD-TYPE
  FEMALE             8             164
  MALE               6             400
[1] 2 2
[1] FALSE
D95V8, binary
                 cls
clus                0   1
  RTKN2 MUTATED    11   1
  RTKN2 WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED     11    1
  RTKN2 WILD-TYPE  405  101
     clus
vv    RTKN2 MUTATED RTKN2 WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D95V9, continuous
D95V10, continuous
[1] "Remove cluster labels:" "RTKN2 MUTATED"         
clus
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-LN-A49O      TCGA-LN-A49P 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RTKN2 MUTATED       1                         0
  RTKN2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RTKN2 MUTATED                                           0    11
  RTKN2 WILD-TYPE                                         1   346
D95V11, multiclass
                                           clus
vv                                          RTKN2 MUTATED RTKN2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, binary
                 cls
clus                0   1
  RTKN2 MUTATED     1   9
  RTKN2 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      1    9
  RTKN2 WILD-TYPE    9  389
                        clus
vv                       RTKN2 MUTATED RTKN2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(96) Variable = ZNF48 MUTATION ANALYSIS
D96V1, survival
                 sevent
clus2               0   1
  ZNF48 MUTATED     9   2
  ZNF48 WILD-TYPE 329 214
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             11             543 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
              2             214 
$`ZNF48 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-CD-A48A 
       34.68        44.94        32.25         0.26         4.31        12.43 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-VQ-A8P2 
       22.32        22.68         0.10        19.73        38.14 

$`ZNF48 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZNF48 MUTATED ZNF48 WILD-TYPE 
            0.1             0.0 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
          44.94          122.30 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
          22.32           13.51 
[1] "0.1 - 44.9 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D96V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF48 MUTATED         0        0        3        0         3         3
  ZNF48 WILD-TYPE      10       20       43       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF48 MUTATED           0          2          0          1        0         0
  ZNF48 WILD-TYPE        29         82         62         38       43         4
D96V3, multiclass
            clus
vv           ZNF48 MUTATED ZNF48 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZNF48 MUTATED       1   3   5   4
  ZNF48 WILD-TYPE    53 132 256  98
D96V4, multiclass
       clus
vv      ZNF48 MUTATED ZNF48 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZNF48 MUTATED     8   2   2   0
  ZNF48 WILD-TYPE 187 171  87  85
D96V5, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  N0             8             187
  N1             2             171
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V6, binary
                 cls
clus                0   1
  ZNF48 MUTATED    13   0
  ZNF48 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED     13    0
  ZNF48 WILD-TYPE  469   38
   clus
vv  ZNF48 MUTATED ZNF48 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D96V7, binary
                 cls
clus                0   1
  ZNF48 MUTATED     9   4
  ZNF48 WILD-TYPE 163 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      9    4
  ZNF48 WILD-TYPE  163  402
        clus
vv       ZNF48 MUTATED ZNF48 WILD-TYPE
  FEMALE             9             163
  MALE               4             402
[1] 2 2
[1] FALSE
D96V8, binary
                 cls
clus                0   1
  ZNF48 MUTATED     9   2
  ZNF48 WILD-TYPE 407 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      9    2
  ZNF48 WILD-TYPE  407  100
     clus
vv    ZNF48 MUTATED ZNF48 WILD-TYPE
  NO              9             407
  YES             2             100
[1] 2 2
[1] FALSE
D96V9, continuous
D96V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF48 MUTATED       4                         0
  ZNF48 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF48 MUTATED                                           0     8
  ZNF48 WILD-TYPE                                         1   349
D96V11, multiclass
                                           clus
vv                                          ZNF48 MUTATED ZNF48 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, binary
                 cls
clus                0   1
  ZNF48 MUTATED     0  11
  ZNF48 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      0   11
  ZNF48 WILD-TYPE   10  387
                        clus
vv                       ZNF48 MUTATED ZNF48 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(97) Variable = INF2 MUTATION ANALYSIS
D97V1, survival
                sevent
clus2              0   1
  INF2 MUTATED    17   8
  INF2 WILD-TYPE 321 208
  INF2 MUTATED INF2 WILD-TYPE 
            25            529 
  INF2 MUTATED INF2 WILD-TYPE 
             8            208 
$`INF2 MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-CG-4460 TCGA-LN-A49W TCGA-LN-A8HZ 
       60.39        34.85         4.31        21.99        13.25        12.33 
TCGA-LN-A9FQ TCGA-Z6-AAPN TCGA-B7-5816 TCGA-BR-7901 TCGA-BR-8487 TCGA-CD-A4MG 
       12.85         2.66        26.70         3.45         1.12         6.58 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6EX TCGA-FP-A4BF 
        9.01         6.02       105.07        28.96        11.31         5.52 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H3 
       77.29        26.47        22.32        22.68         6.51        29.00 
TCGA-MX-A5UJ 
       19.73 

$`INF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        18.28         8.94        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       13.18        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 
       14.37         3.42         2.10         1.32        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        1.02         0.99         0.99        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56        11.08         6.21        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  INF2 MUTATED INF2 WILD-TYPE 
          1.12           0.00 
  INF2 MUTATED INF2 WILD-TYPE 
        105.07         122.30 
  INF2 MUTATED INF2 WILD-TYPE 
         13.25          13.58 
[1] "1.1 - 105.1 (13.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D97V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INF2 MUTATED         1        1        1        2         6         6
  INF2 WILD-TYPE       9       19       45       29        78        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INF2 MUTATED           1          4          0          1        3         0
  INF2 WILD-TYPE        28         80         62         38       40         4
D97V3, multiclass
            clus
vv           INF2 MUTATED INF2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             6             78
  STAGE IIB             6             77
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  INF2 MUTATED       2   4  13   7
  INF2 WILD-TYPE    52 131 248  95
D97V4, multiclass
       clus
vv      INF2 MUTATED INF2 WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3              13            248
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  INF2 MUTATED    14   7   3   2
  INF2 WILD-TYPE 181 166  86  83
D97V5, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  N0           14            181
  N1            7            166
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V6, binary
                cls
clus               0   1
  INF2 MUTATED    22   2
  INF2 WILD-TYPE 460  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     22    2
  INF2 WILD-TYPE  460   36
   clus
vv  INF2 MUTATED INF2 WILD-TYPE
  0           22            460
  1            2             36
[1] 2 2
[1] FALSE
D97V7, binary
                cls
clus               0   1
  INF2 MUTATED    12  14
  INF2 WILD-TYPE 160 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     12   14
  INF2 WILD-TYPE  160  392
        clus
vv       INF2 MUTATED INF2 WILD-TYPE
  FEMALE           12            160
  MALE             14            392
[1] 2 2
[1] FALSE
D97V8, binary
                cls
clus               0   1
  INF2 MUTATED    18   3
  INF2 WILD-TYPE 398  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     18    3
  INF2 WILD-TYPE  398   99
     clus
vv    INF2 MUTATED INF2 WILD-TYPE
  NO            18            398
  YES            3             99
[1] 2 2
[1] FALSE
D97V9, continuous
[1] "Remove cluster labels:" "INF2 MUTATED"          
clus
  INF2 MUTATED INF2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"INF2 WILD-TYPE" "INF2 WILD-TYPE" "INF2 WILD-TYPE" 
D97V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  INF2 MUTATED       8                         0
  INF2 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INF2 MUTATED                                           0    12
  INF2 WILD-TYPE                                         1   345
D97V11, multiclass
                                           clus
vv                                          INF2 MUTATED INF2 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, binary
                cls
clus               0   1
  INF2 MUTATED     0  16
  INF2 WILD-TYPE  10 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED      0   16
  INF2 WILD-TYPE   10  382
                        clus
vv                       INF2 MUTATED INF2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           16            382
[1] 2 2
[1] FALSE

Clustering(98) Variable = NAPEPLD MUTATION ANALYSIS
D98V1, survival
                   sevent
clus2                 0   1
  NAPEPLD MUTATED     7   5
  NAPEPLD WILD-TYPE 331 211
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               12               542 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
                5               211 
$`NAPEPLD MUTATED`
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-BR-6452 TCGA-BR-8080 TCGA-BR-8372 TCGA-CG-4436 
        7.76         5.49        34.68         9.60        31.27         7.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HJ-7597 TCGA-VQ-A8P2 
      105.07        28.96        11.44        14.47        26.47        38.14 

$`NAPEPLD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
             5.49              0.00 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
           105.07            122.30 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
            20.47             13.53 
[1] "5.5 - 105.1 (20.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D98V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAPEPLD MUTATED         0        1        3        1         1         1
  NAPEPLD WILD-TYPE      10       19       43       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAPEPLD MUTATED           1          1          1          2        0
  NAPEPLD WILD-TYPE        28         83         61         37       43
                   vv
clus                STAGE IVA
  NAPEPLD MUTATED           0
  NAPEPLD WILD-TYPE         4
D98V3, multiclass
            clus
vv           NAPEPLD MUTATED NAPEPLD WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  NAPEPLD MUTATED       1   5   3   3
  NAPEPLD WILD-TYPE    53 130 258  99
D98V4, multiclass
       clus
vv      NAPEPLD MUTATED NAPEPLD WILD-TYPE
  T0+T1               1                53
  T2                  5               130
  T3                  3               258
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  NAPEPLD MUTATED     5   4   0   3
  NAPEPLD WILD-TYPE 190 169  89  82
D98V5, multiclass
    clus
vv   NAPEPLD MUTATED NAPEPLD WILD-TYPE
  N0               5               190
  N1               4               169
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V6, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED    11   0
  NAPEPLD WILD-TYPE 471  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED     11    0
  NAPEPLD WILD-TYPE  471   38
   clus
vv  NAPEPLD MUTATED NAPEPLD WILD-TYPE
  0              11               471
  1               0                38
[1] 2 2
[1] FALSE
D98V7, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     5   7
  NAPEPLD WILD-TYPE 167 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      5    7
  NAPEPLD WILD-TYPE  167  399
        clus
vv       NAPEPLD MUTATED NAPEPLD WILD-TYPE
  FEMALE               5               167
  MALE                 7               399
[1] 2 2
[1] FALSE
D98V8, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED    10   1
  NAPEPLD WILD-TYPE 406 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED     10    1
  NAPEPLD WILD-TYPE  406  101
     clus
vv    NAPEPLD MUTATED NAPEPLD WILD-TYPE
  NO               10               406
  YES               1               101
[1] 2 2
[1] FALSE
D98V9, continuous
D98V10, continuous
[1] "Remove cluster labels:" "NAPEPLD MUTATED"       
clus
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NQ 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" "NAPEPLD WILD-TYPE" 
       TCGA-Z6-AAPN 
"NAPEPLD WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  NAPEPLD MUTATED       0                         0
  NAPEPLD WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAPEPLD MUTATED                                           0     9
  NAPEPLD WILD-TYPE                                         1   348
D98V11, multiclass
                                           clus
vv                                          NAPEPLD MUTATED NAPEPLD WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V12, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     0   6
  NAPEPLD WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      0    6
  NAPEPLD WILD-TYPE   10  392
                        clus
vv                       NAPEPLD MUTATED NAPEPLD WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(99) Variable = ELF3 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED     9   4
  ELF3 WILD-TYPE 329 212
  ELF3 MUTATED ELF3 WILD-TYPE 
            13            541 
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            212 
$`ELF3 MUTATED`
TCGA-L5-A4OH TCGA-B7-5816 TCGA-BR-6852 TCGA-CD-5813 TCGA-CG-4462 TCGA-CG-4469 
       32.61        26.70        44.94        12.39         0.00         7.07 
TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 
       30.97         6.02        21.07        13.78        14.47        21.27 
TCGA-HU-A4GT 
        6.51 

$`ELF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5718 
       19.07        12.03         9.01        18.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ELF3 MUTATED ELF3 WILD-TYPE 
           0.0            0.1 
  ELF3 MUTATED ELF3 WILD-TYPE 
         44.94         122.30 
  ELF3 MUTATED ELF3 WILD-TYPE 
         14.47          13.51 
[1] "0.0 - 44.9 (14.5)"  "0.1 - 122.3 (13.5)"
[1] "hr=" "1.3"
D99V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELF3 MUTATED         1        0        2        1         2         1
  ELF3 WILD-TYPE       9       20       44       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELF3 MUTATED           0          2          2          0        3         0
  ELF3 WILD-TYPE        29         82         60         39       40         4
D99V3, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ELF3 MUTATED       1   3   7   3
  ELF3 WILD-TYPE    53 132 254  99
D99V4, multiclass
       clus
vv      ELF3 MUTATED ELF3 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               7            254
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ELF3 MUTATED     8   1   1   4
  ELF3 WILD-TYPE 187 172  88  81
D99V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            8            187
  N1            1            172
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V6, binary
                cls
clus               0   1
  ELF3 MUTATED    13   1
  ELF3 WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     13    1
  ELF3 WILD-TYPE  469   37
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D99V7, binary
                cls
clus               0   1
  ELF3 MUTATED     7   7
  ELF3 WILD-TYPE 165 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      7    7
  ELF3 WILD-TYPE  165  399
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            7            165
  MALE              7            399
[1] 2 2
[1] FALSE
D99V8, binary
                cls
clus               0   1
  ELF3 MUTATED     8   3
  ELF3 WILD-TYPE 408  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      8    3
  ELF3 WILD-TYPE  408   99
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO             8            408
  YES            3             99
[1] 2 2
[1] FALSE
D99V9, continuous
D99V10, continuous
[1] "Remove cluster labels:" "ELF3 MUTATED"          
clus
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OM 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"ELF3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ELF3 MUTATED       2                         0
  ELF3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELF3 MUTATED                                           0     7
  ELF3 WILD-TYPE                                         1   350
D99V11, multiclass
                                           clus
vv                                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, binary
                cls
clus               0   1
  ELF3 MUTATED     1   7
  ELF3 WILD-TYPE   9 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      1    7
  ELF3 WILD-TYPE    9  391
                        clus
vv                       ELF3 MUTATED ELF3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(100) Variable = TTF1 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED    13   5
  TTF1 WILD-TYPE 325 211
  TTF1 MUTATED TTF1 WILD-TYPE 
            18            536 
  TTF1 MUTATED TTF1 WILD-TYPE 
             5            211 
$`TTF1 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-S8-A6BV TCGA-L5-A8NH TCGA-BR-4184 TCGA-BR-4201 
        4.31        35.97        20.02        12.92         6.97        30.90 
TCGA-BR-6452 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8382 
       34.68        21.90        35.84         6.18         4.31        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-4305 TCGA-D7-6822 TCGA-HU-A4GH 
        1.12        27.12        31.96        15.95        12.33        11.77 

$`TTF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       31.20        44.94         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TTF1 MUTATED TTF1 WILD-TYPE 
          1.12           0.00 
  TTF1 MUTATED TTF1 WILD-TYPE 
         35.97         122.30 
  TTF1 MUTATED TTF1 WILD-TYPE 
        17.985         13.530 
[1] "1.1 - 36.0 (18.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D100V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTF1 MUTATED         0        1        3        1         3         1
  TTF1 WILD-TYPE      10       19       43       30        81        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTF1 MUTATED           1          2          1          1        4         0
  TTF1 WILD-TYPE        28         82         61         38       39         4
D100V3, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TTF1 MUTATED       2   5   9   4
  TTF1 WILD-TYPE    52 130 252  98
D100V4, multiclass
       clus
vv      TTF1 MUTATED TTF1 WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3               9            252
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TTF1 MUTATED     9   5   2   2
  TTF1 WILD-TYPE 186 168  87  83
D100V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0            9            186
  N1            5            168
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V6, binary
                cls
clus               0   1
  TTF1 MUTATED    13   3
  TTF1 WILD-TYPE 469  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     13    3
  TTF1 WILD-TYPE  469   35
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0           13            469
  1            3             35
[1] 2 2
[1] FALSE
D100V7, binary
                cls
clus               0   1
  TTF1 MUTATED     7  13
  TTF1 WILD-TYPE 165 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      7   13
  TTF1 WILD-TYPE  165  393
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            7            165
  MALE             13            393
[1] 2 2
[1] FALSE
D100V8, binary
                cls
clus               0   1
  TTF1 MUTATED    16   0
  TTF1 WILD-TYPE 400 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     16    0
  TTF1 WILD-TYPE  400  102
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO            16            400
  YES            0            102
[1] 2 2
[1] FALSE
D100V9, continuous
D100V10, continuous
[1] "Remove cluster labels:" "TTF1 MUTATED"          
clus
  TTF1 MUTATED TTF1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NT 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL     TCGA-IG-A3Y9 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QT 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TTF1 MUTATED       2                         0
  TTF1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TTF1 MUTATED                                           0    17
  TTF1 WILD-TYPE                                         1   340
D100V11, multiclass
                                           clus
vv                                          TTF1 MUTATED TTF1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V12, binary
                cls
clus               0   1
  TTF1 MUTATED     0  16
  TTF1 WILD-TYPE  10 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      0   16
  TTF1 WILD-TYPE   10  382
                        clus
vv                       TTF1 MUTATED TTF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           16            382
[1] 2 2
[1] FALSE

Clustering(101) Variable = DDC MUTATION ANALYSIS
D101V1, survival
               sevent
clus2             0   1
  DDC MUTATED    10   2
  DDC WILD-TYPE 328 214
  DDC MUTATED DDC WILD-TYPE 
           12           542 
  DDC MUTATED DDC WILD-TYPE 
            2           214 
$`DDC MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NE TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8363 
       19.99        55.50         6.97        34.68        35.84         0.26 
TCGA-CD-8531 TCGA-CG-4305 TCGA-CG-4455 TCGA-CG-5721 TCGA-HU-A4GX TCGA-SW-A7EA 
       12.59        15.95        12.03         6.02        20.25        19.04 

$`DDC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DDC MUTATED DDC WILD-TYPE 
         0.26          0.00 
  DDC MUTATED DDC WILD-TYPE 
         55.5         122.3 
  DDC MUTATED DDC WILD-TYPE 
       17.495        13.530 
[1] "0.3 - 55.5 (17.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D101V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDC MUTATED         0        0        3        2         1         1
  DDC WILD-TYPE      10       20       43       29        83        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDC MUTATED           0          2          0          2        1         0
  DDC WILD-TYPE        29         82         62         37       42         4
D101V3, multiclass
            clus
vv           DDC MUTATED DDC WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             3            43
  STAGE II             2            29
  STAGE IIA            1            83
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           0            62
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  DDC MUTATED       0   6   4   2
  DDC WILD-TYPE    54 129 257 100
D101V4, multiclass
       clus
vv      DDC MUTATED DDC WILD-TYPE
  T0+T1           0            54
  T2              6           129
  T3              4           257
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DDC MUTATED     4   6   1   1
  DDC WILD-TYPE 191 167  88  84
D101V5, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  N0           4           191
  N1           6           167
  N2           1            88
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V6, binary
               cls
clus              0   1
  DDC MUTATED    10   0
  DDC WILD-TYPE 472  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED     10    0
  DDC WILD-TYPE  472   38
   clus
vv  DDC MUTATED DDC WILD-TYPE
  0          10           472
  1           0            38
[1] 2 2
[1] FALSE
D101V7, binary
               cls
clus              0   1
  DDC MUTATED     6   6
  DDC WILD-TYPE 166 400
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      6    6
  DDC WILD-TYPE  166  400
        clus
vv       DDC MUTATED DDC WILD-TYPE
  FEMALE           6           166
  MALE             6           400
[1] 2 2
[1] FALSE
D101V8, binary
               cls
clus              0   1
  DDC MUTATED    11   1
  DDC WILD-TYPE 405 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED     11    1
  DDC WILD-TYPE  405  101
     clus
vv    DDC MUTATED DDC WILD-TYPE
  NO           11           405
  YES           1           101
[1] 2 2
[1] FALSE
D101V9, continuous
D101V10, continuous
[1] "Remove cluster labels:" "DDC MUTATED"           
clus
  DDC MUTATED DDC WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NF    TCGA-L5-A8NK 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS    TCGA-L5-A8NW 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6    TCGA-LN-A4A9 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8    TCGA-Q9-A6FW 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" "DDC WILD-TYPE" 
   TCGA-Z6-AAPN 
"DDC WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DDC MUTATED       2                         0
  DDC WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDC MUTATED                                           0     7
  DDC WILD-TYPE                                         1   350
D101V11, multiclass
                                           clus
vv                                          DDC MUTATED DDC WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V12, binary
               cls
clus              0   1
  DDC MUTATED     0   7
  DDC WILD-TYPE  10 391
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      0    7
  DDC WILD-TYPE   10  391
                        clus
vv                       DDC MUTATED DDC WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           7           391
[1] 2 2
[1] FALSE

Clustering(102) Variable = KLHDC5 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  KLHDC5 MUTATED     6   5
  KLHDC5 WILD-TYPE 332 211
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
              11              543 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
               5              211 
$`KLHDC5 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GL TCGA-L5-A8NW TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 
       19.99         5.92        46.09        30.90        35.84        29.59 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5728 TCGA-HF-A5NB TCGA-IN-A6RL 
        6.58       105.07        65.10        30.51        13.35 

$`KLHDC5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
            5.92             0.00 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
          105.07           122.30 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
           30.51            13.51 
[1] "5.9 - 105.1 (30.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D102V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHDC5 MUTATED         1        0        3        1         1         1
  KLHDC5 WILD-TYPE       9       20       43       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC5 MUTATED           1          1          0          2        0
  KLHDC5 WILD-TYPE        28         83         62         37       43
                  vv
clus               STAGE IVA
  KLHDC5 MUTATED           0
  KLHDC5 WILD-TYPE         4
D102V3, multiclass
            clus
vv           KLHDC5 MUTATED KLHDC5 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KLHDC5 MUTATED       2   6   3   2
  KLHDC5 WILD-TYPE    52 129 258 100
D102V4, multiclass
       clus
vv      KLHDC5 MUTATED KLHDC5 WILD-TYPE
  T0+T1              2               52
  T2                 6              129
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KLHDC5 MUTATED     4   5   0   2
  KLHDC5 WILD-TYPE 191 168  89  83
D102V5, multiclass
    clus
vv   KLHDC5 MUTATED KLHDC5 WILD-TYPE
  N0              4              191
  N1              5              168
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V6, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED    11   0
  KLHDC5 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED     11    0
  KLHDC5 WILD-TYPE  471   38
   clus
vv  KLHDC5 MUTATED KLHDC5 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D102V7, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     6   7
  KLHDC5 WILD-TYPE 166 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      6    7
  KLHDC5 WILD-TYPE  166  399
        clus
vv       KLHDC5 MUTATED KLHDC5 WILD-TYPE
  FEMALE              6              166
  MALE                7              399
[1] 2 2
[1] FALSE
D102V8, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED    10   1
  KLHDC5 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED     10    1
  KLHDC5 WILD-TYPE  406  101
     clus
vv    KLHDC5 MUTATED KLHDC5 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D102V9, continuous
D102V10, continuous
[1] "Remove cluster labels:" "KLHDC5 MUTATED"        
clus
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-LN-A49O       TCGA-LN-A49P 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" "KLHDC5 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KLHDC5 MUTATED       1                         1
  KLHDC5 WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHDC5 MUTATED                                           0     7
  KLHDC5 WILD-TYPE                                         1   350
D102V11, multiclass
                                           clus
vv                                          KLHDC5 MUTATED KLHDC5 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V12, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     0   7
  KLHDC5 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      0    7
  KLHDC5 WILD-TYPE   10  391
                        clus
vv                       KLHDC5 MUTATED KLHDC5 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(103) Variable = FBXO21 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2                0   1
  FBXO21 MUTATED     8   7
  FBXO21 WILD-TYPE 330 209
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              15              539 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               7              209 
$`FBXO21 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NE TCGA-LN-A49R TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 
       21.99        55.50        13.38         6.97        30.90         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 
        9.67        34.68        14.43        31.10        31.27        28.14 
TCGA-D7-8579 TCGA-KB-A93J TCGA-VQ-A8PQ 
       20.91        36.95        15.65 

$`FBXO21 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
        7.43        18.35         4.08         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FBXO21 MUTATED FBXO21 WILD-TYPE 
            6.97             0.00 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
            55.5            122.3 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           21.99            13.48 
[1] "7.0 - 55.5 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D103V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO21 MUTATED         0        0        0        1         1         2
  FBXO21 WILD-TYPE      10       20       46       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO21 MUTATED           2          2          0          3        2
  FBXO21 WILD-TYPE        27         82         62         36       41
                  vv
clus               STAGE IVA
  FBXO21 MUTATED           0
  FBXO21 WILD-TYPE         4
D103V3, multiclass
            clus
vv           FBXO21 MUTATED FBXO21 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FBXO21 MUTATED       0   4   3   7
  FBXO21 WILD-TYPE    54 131 258  95
D103V4, multiclass
       clus
vv      FBXO21 MUTATED FBXO21 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 3              258
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FBXO21 MUTATED     2   9   2   2
  FBXO21 WILD-TYPE 193 164  87  83
D103V5, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  N0              2              193
  N1              9              164
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V6, binary
                  cls
clus                 0   1
  FBXO21 MUTATED    14   2
  FBXO21 WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED     14    2
  FBXO21 WILD-TYPE  468   36
   clus
vv  FBXO21 MUTATED FBXO21 WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D103V7, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     9   8
  FBXO21 WILD-TYPE 163 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      9    8
  FBXO21 WILD-TYPE  163  398
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  FEMALE              9              163
  MALE                8              398
[1] 2 2
[1] FALSE
D103V8, binary
                  cls
clus                 0   1
  FBXO21 MUTATED    12   3
  FBXO21 WILD-TYPE 404  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED     12    3
  FBXO21 WILD-TYPE  404   99
     clus
vv    FBXO21 MUTATED FBXO21 WILD-TYPE
  NO              12              404
  YES              3               99
[1] 2 2
[1] FALSE
D103V9, continuous
[1] "Remove cluster labels:" "FBXO21 MUTATED"        
clus
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
D103V10, continuous
[1] "Remove cluster labels:" "FBXO21 MUTATED"        
clus
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" "FBXO21 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO21 MUTATED       1                         0
  FBXO21 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO21 MUTATED                                           0    15
  FBXO21 WILD-TYPE                                         1   342
D103V11, multiclass
                                           clus
vv                                          FBXO21 MUTATED FBXO21 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V12, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     0  13
  FBXO21 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      0   13
  FBXO21 WILD-TYPE   10  385
                        clus
vv                       FBXO21 MUTATED FBXO21 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(104) Variable = IRF2 MUTATION ANALYSIS
D104V1, survival
                sevent
clus2              0   1
  IRF2 MUTATED     9   6
  IRF2 WILD-TYPE 329 210
  IRF2 MUTATED IRF2 WILD-TYPE 
            15            539 
  IRF2 MUTATED IRF2 WILD-TYPE 
             6            210 
$`IRF2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7715 
       26.70         6.97         9.67        34.68        44.94        33.63 
TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5726 TCGA-D7-A6EY TCGA-R5-A7ZI 
        0.56         6.18        31.96        28.96        11.44        74.53 
TCGA-RD-A8MV TCGA-VQ-A8DL TCGA-VQ-A8P2 
      122.30         0.92        38.14 

$`IRF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  IRF2 MUTATED IRF2 WILD-TYPE 
          0.56           0.00 
  IRF2 MUTATED IRF2 WILD-TYPE 
         122.3          122.1 
  IRF2 MUTATED IRF2 WILD-TYPE 
         28.96          13.51 
[1] "0.6 - 122.3 (29.0)" "0.0 - 122.1 (13.5)"
[1] "hr=" "1.5"
D104V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRF2 MUTATED         0        1        0        0         5         2
  IRF2 WILD-TYPE      10       19       46       31        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRF2 MUTATED           0          2          2          1        3         0
  IRF2 WILD-TYPE        29         82         60         38       40         4
D104V3, multiclass
            clus
vv           IRF2 MUTATED IRF2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IRF2 MUTATED       1   0   8   7
  IRF2 WILD-TYPE    53 135 253  95
D104V4, multiclass
       clus
vv      IRF2 MUTATED IRF2 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               8            253
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRF2 MUTATED     8   4   3   2
  IRF2 WILD-TYPE 187 169  86  83
D104V5, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  N0            8            187
  N1            4            169
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V6, binary
                cls
clus               0   1
  IRF2 MUTATED    16   2
  IRF2 WILD-TYPE 466  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     16    2
  IRF2 WILD-TYPE  466   36
   clus
vv  IRF2 MUTATED IRF2 WILD-TYPE
  0           16            466
  1            2             36
[1] 2 2
[1] FALSE
D104V7, binary
                cls
clus               0   1
  IRF2 MUTATED    11   8
  IRF2 WILD-TYPE 161 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     11    8
  IRF2 WILD-TYPE  161  398
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  FEMALE           11            161
  MALE              8            398
[1] 2 2
[1] FALSE
D104V8, binary
                cls
clus               0   1
  IRF2 MUTATED    13   2
  IRF2 WILD-TYPE 403 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     13    2
  IRF2 WILD-TYPE  403  100
     clus
vv    IRF2 MUTATED IRF2 WILD-TYPE
  NO            13            403
  YES            2            100
[1] 2 2
[1] FALSE
D104V9, continuous
D104V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRF2 MUTATED       1                         0
  IRF2 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRF2 MUTATED                                           0    17
  IRF2 WILD-TYPE                                         1   340
D104V11, multiclass
                                           clus
vv                                          IRF2 MUTATED IRF2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V12, binary
                cls
clus               0   1
  IRF2 MUTATED     1  15
  IRF2 WILD-TYPE   9 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      1   15
  IRF2 WILD-TYPE    9  383
                        clus
vv                       IRF2 MUTATED IRF2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(105) Variable = RHOQ MUTATION ANALYSIS
D105V1, survival
                sevent
clus2              0   1
  RHOQ MUTATED     3   1
  RHOQ WILD-TYPE 335 215
  RHOQ MUTATED RHOQ WILD-TYPE 
             4            550 
  RHOQ MUTATED RHOQ WILD-TYPE 
             1            215 
$`RHOQ MUTATED`
TCGA-BR-8487 TCGA-CG-4306 TCGA-HU-8602 TCGA-HU-A4H8 
        1.12         1.02        22.32        14.07 

$`RHOQ WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RHOQ MUTATED RHOQ WILD-TYPE 
          1.02           0.00 
  RHOQ MUTATED RHOQ WILD-TYPE 
         22.32         122.30 
  RHOQ MUTATED RHOQ WILD-TYPE 
         7.595         13.565 
[1] "1.0 - 22.3 (7.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D105V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOQ MUTATED         0        0        1        0         1         1
  RHOQ WILD-TYPE      10       20       45       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHOQ MUTATED           0          0          0          0        2         0
  RHOQ WILD-TYPE        29         84         62         39       41         4
D105V3, multiclass
            clus
vv           RHOQ MUTATED RHOQ WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RHOQ MUTATED       1   0   2   2
  RHOQ WILD-TYPE    53 135 259 100
D105V4, multiclass
       clus
vv      RHOQ MUTATED RHOQ WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RHOQ MUTATED     2   1   2   0
  RHOQ WILD-TYPE 193 172  87  85
D105V5, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  N0            2            193
  N1            1            172
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V6, binary
                cls
clus               0   1
  RHOQ MUTATED     4   1
  RHOQ WILD-TYPE 478  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      4    1
  RHOQ WILD-TYPE  478   37
   clus
vv  RHOQ MUTATED RHOQ WILD-TYPE
  0            4            478
  1            1             37
[1] 2 2
[1] FALSE
D105V7, binary
                cls
clus               0   1
  RHOQ MUTATED     3   2
  RHOQ WILD-TYPE 169 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      3    2
  RHOQ WILD-TYPE  169  404
        clus
vv       RHOQ MUTATED RHOQ WILD-TYPE
  FEMALE            3            169
  MALE              2            404
[1] 2 2
[1] FALSE
D105V8, binary
                cls
clus               0   1
  RHOQ MUTATED     3   0
  RHOQ WILD-TYPE 413 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      3    0
  RHOQ WILD-TYPE  413  102
     clus
vv    RHOQ MUTATED RHOQ WILD-TYPE
  NO             3            413
  YES            0            102
[1] 2 2
[1] FALSE
D105V9, continuous
D105V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RHOQ MUTATED       2                         0
  RHOQ WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHOQ MUTATED                                           0     2
  RHOQ WILD-TYPE                                         1   355
D105V11, multiclass
                                           clus
vv                                          RHOQ MUTATED RHOQ WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V12, binary
                cls
clus               0   1
  RHOQ MUTATED     0   4
  RHOQ WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      0    4
  RHOQ WILD-TYPE   10  394
                        clus
vv                       RHOQ MUTATED RHOQ WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(106) Variable = GRINA MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  GRINA MUTATED     7   1
  GRINA WILD-TYPE 331 215
  GRINA MUTATED GRINA WILD-TYPE 
              8             546 
  GRINA MUTATED GRINA WILD-TYPE 
              1             215 
$`GRINA MUTATED`
TCGA-LN-A9FP TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5728 TCGA-HF-7132 
       12.03        28.14         6.58         6.02        65.10        77.29 
TCGA-HU-A4GX TCGA-SW-A7EA 
       20.25        19.04 

$`GRINA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GRINA MUTATED GRINA WILD-TYPE 
           6.02            0.00 
  GRINA MUTATED GRINA WILD-TYPE 
          77.29          122.30 
  GRINA MUTATED GRINA WILD-TYPE 
         19.645          13.530 
[1] "6.0 - 77.3 (19.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.6"
D106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GRINA MUTATED         1        0        3        1         2         0
  GRINA WILD-TYPE       9       20       43       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRINA MUTATED           0          0          0          2        1         0
  GRINA WILD-TYPE        29         84         62         37       42         4
D106V3, multiclass
            clus
vv           GRINA MUTATED GRINA WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GRINA MUTATED       1   5   1   3
  GRINA WILD-TYPE    53 130 260  99
D106V4, multiclass
       clus
vv      GRINA MUTATED GRINA WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                1             260
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GRINA MUTATED     5   3   1   1
  GRINA WILD-TYPE 190 170  88  84
D106V5, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  N0             5             190
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V6, binary
                 cls
clus                0   1
  GRINA MUTATED     9   0
  GRINA WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      9    0
  GRINA WILD-TYPE  473   38
   clus
vv  GRINA MUTATED GRINA WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus                0   1
  GRINA MUTATED     4   6
  GRINA WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    6
  GRINA WILD-TYPE  168  400
        clus
vv       GRINA MUTATED GRINA WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D106V8, binary
                 cls
clus                0   1
  GRINA MUTATED     6   2
  GRINA WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      6    2
  GRINA WILD-TYPE  410  100
     clus
vv    GRINA MUTATED GRINA WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D106V9, continuous
D106V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GRINA MUTATED       3                         1
  GRINA WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GRINA MUTATED                                           0     2
  GRINA WILD-TYPE                                         1   355
D106V11, multiclass
                                           clus
vv                                          GRINA MUTATED GRINA WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V12, binary
                 cls
clus                0   1
  GRINA MUTATED     0   6
  GRINA WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      0    6
  GRINA WILD-TYPE   10  392
                        clus
vv                       GRINA MUTATED GRINA WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(107) Variable = EPHX1 MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2               0   1
  EPHX1 MUTATED     6   5
  EPHX1 WILD-TYPE 332 211
  EPHX1 MUTATED EPHX1 WILD-TYPE 
             11             543 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              5             211 
$`EPHX1 MUTATED`
TCGA-IG-A5B8 TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 
        0.79         7.76         6.97         9.67        34.68         6.18 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-R5-A7ZI 
        6.58       105.07        14.47        22.68        74.53 

$`EPHX1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  EPHX1 MUTATED EPHX1 WILD-TYPE 
           0.79            0.00 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
         105.07          122.30 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
           9.67           13.58 
[1] "0.8 - 105.1 (9.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D107V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHX1 MUTATED         0        0        2        1         3         2
  EPHX1 WILD-TYPE      10       20       44       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHX1 MUTATED           0          1          0          0        1         0
  EPHX1 WILD-TYPE        29         83         62         39       42         4
D107V3, multiclass
            clus
vv           EPHX1 MUTATED EPHX1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPHX1 MUTATED       1   3   6   1
  EPHX1 WILD-TYPE    53 132 255 101
D107V4, multiclass
       clus
vv      EPHX1 MUTATED EPHX1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPHX1 MUTATED     5   5   0   0
  EPHX1 WILD-TYPE 190 168  89  85
D107V5, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  N0             5             190
  N1             5             168
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V6, binary
                 cls
clus                0   1
  EPHX1 MUTATED    10   1
  EPHX1 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED     10    1
  EPHX1 WILD-TYPE  472   37
   clus
vv  EPHX1 MUTATED EPHX1 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D107V7, binary
                 cls
clus                0   1
  EPHX1 MUTATED     6   6
  EPHX1 WILD-TYPE 166 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      6    6
  EPHX1 WILD-TYPE  166  400
        clus
vv       EPHX1 MUTATED EPHX1 WILD-TYPE
  FEMALE             6             166
  MALE               6             400
[1] 2 2
[1] FALSE
D107V8, binary
                 cls
clus                0   1
  EPHX1 MUTATED    11   0
  EPHX1 WILD-TYPE 405 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED     11    0
  EPHX1 WILD-TYPE  405  102
     clus
vv    EPHX1 MUTATED EPHX1 WILD-TYPE
  NO             11             405
  YES             0             102
[1] 2 2
[1] FALSE
D107V9, continuous
D107V10, continuous
[1] "Remove cluster labels:" "EPHX1 MUTATED"         
clus
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A6QS 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EPHX1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHX1 MUTATED       2                         0
  EPHX1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHX1 MUTATED                                           0     9
  EPHX1 WILD-TYPE                                         1   348
D107V11, multiclass
                                           clus
vv                                          EPHX1 MUTATED EPHX1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V12, binary
                 cls
clus                0   1
  EPHX1 MUTATED     1   9
  EPHX1 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      1    9
  EPHX1 WILD-TYPE    9  389
                        clus
vv                       EPHX1 MUTATED EPHX1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(108) Variable = C13ORF33 MUTATION ANALYSIS
D108V1, survival
                    sevent
clus2                  0   1
  C13ORF33 MUTATED     5   3
  C13ORF33 WILD-TYPE 333 213
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 8                546 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 3                213 
$`C13ORF33 MUTATED`
TCGA-L5-A8NM TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL 
        7.76        29.59        31.10        31.27        28.14        16.14 
TCGA-HU-A4GQ TCGA-HU-A4H3 
        0.10        29.00 

$`C13ORF33 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
               0.1                0.0 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             31.27             122.30 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             28.57              13.51 
[1] "0.1 - 31.3 (28.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D108V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C13ORF33 MUTATED         0        0        0        0         0         2
  C13ORF33 WILD-TYPE      10       20       46       31        84        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF33 MUTATED           0          0          1          5        0
  C13ORF33 WILD-TYPE        29         84         61         34       43
                    vv
clus                 STAGE IVA
  C13ORF33 MUTATED           0
  C13ORF33 WILD-TYPE         4
D108V3, multiclass
            clus
vv           C13ORF33 MUTATED C13ORF33 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                5                 34
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C13ORF33 MUTATED       0   1   1   6
  C13ORF33 WILD-TYPE    54 134 260  96
D108V4, multiclass
       clus
vv      C13ORF33 MUTATED C13ORF33 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   1                260
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C13ORF33 MUTATED     1   1   2   4
  C13ORF33 WILD-TYPE 194 172  87  81
D108V5, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  N0                1                194
  N1                1                172
  N2                2                 87
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V6, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     8   0
  C13ORF33 WILD-TYPE 474  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      8    0
  C13ORF33 WILD-TYPE  474   38
   clus
vv  C13ORF33 MUTATED C13ORF33 WILD-TYPE
  0                8                474
  1                0                 38
[1] 2 2
[1] FALSE
D108V7, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     5   3
  C13ORF33 WILD-TYPE 167 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      5    3
  C13ORF33 WILD-TYPE  167  403
        clus
vv       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  FEMALE                5                167
  MALE                  3                403
[1] 2 2
[1] FALSE
D108V8, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     7   0
  C13ORF33 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      7    0
  C13ORF33 WILD-TYPE  409  102
     clus
vv    C13ORF33 MUTATED C13ORF33 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D108V9, continuous
D108V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C13ORF33 MUTATED       2                         0
  C13ORF33 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C13ORF33 MUTATED                                           0     6
  C13ORF33 WILD-TYPE                                         1   351
D108V11, multiclass
                                           clus
vv                                          C13ORF33 MUTATED C13ORF33 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V12, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     0   7
  C13ORF33 WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      0    7
  C13ORF33 WILD-TYPE   10  391
                        clus
vv                       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(109) Variable = C19ORF40 MUTATION ANALYSIS
D109V1, survival
                    sevent
clus2                  0   1
  C19ORF40 MUTATED     4   2
  C19ORF40 WILD-TYPE 334 214
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 6                548 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 2                214 
$`C19ORF40 MUTATED`
TCGA-CG-4444 TCGA-BR-4184 TCGA-CD-8536 TCGA-CG-5721 TCGA-HU-A4GX TCGA-RD-A7BT 
       47.05         6.97        12.43         6.02        20.25         8.61 

$`C19ORF40 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
              6.02               0.00 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
             47.05             122.30 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
             10.52              13.63 
[1] "6.0 - 47.0 (10.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D109V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF40 MUTATED         0        0        0        1         0         0
  C19ORF40 WILD-TYPE      10       20       46       30        84        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF40 MUTATED           0          2          0          1        2
  C19ORF40 WILD-TYPE        29         82         62         38       41
                    vv
clus                 STAGE IVA
  C19ORF40 MUTATED           0
  C19ORF40 WILD-TYPE         4
D109V3, multiclass
            clus
vv           C19ORF40 MUTATED C19ORF40 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 0                 84
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C19ORF40 MUTATED       0   1   3   2
  C19ORF40 WILD-TYPE    54 134 258 100
D109V4, multiclass
       clus
vv      C19ORF40 MUTATED C19ORF40 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   3                258
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C19ORF40 MUTATED     1   2   2   1
  C19ORF40 WILD-TYPE 194 171  87  84
D109V5, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  N0                1                194
  N1                2                171
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V6, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     6   0
  C19ORF40 WILD-TYPE 476  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      6    0
  C19ORF40 WILD-TYPE  476   38
   clus
vv  C19ORF40 MUTATED C19ORF40 WILD-TYPE
  0                6                476
  1                0                 38
[1] 2 2
[1] FALSE
D109V7, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     2   5
  C19ORF40 WILD-TYPE 170 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      2    5
  C19ORF40 WILD-TYPE  170  401
        clus
vv       C19ORF40 MUTATED C19ORF40 WILD-TYPE
  FEMALE                2                170
  MALE                  5                401
[1] 2 2
[1] FALSE
D109V8, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     5   1
  C19ORF40 WILD-TYPE 411 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      5    1
  C19ORF40 WILD-TYPE  411  101
     clus
vv    C19ORF40 MUTATED C19ORF40 WILD-TYPE
  NO                 5                411
  YES                1                101
[1] 2 2
[1] FALSE
D109V9, continuous
D109V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF40 MUTATED       2                         0
  C19ORF40 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF40 MUTATED                                           1     2
  C19ORF40 WILD-TYPE                                         0   355
D109V11, multiclass
                                           clus
vv                                          C19ORF40 MUTATED C19ORF40 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                    2                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V12, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     0   5
  C19ORF40 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      0    5
  C19ORF40 WILD-TYPE   10  393
                        clus
vv                       C19ORF40 MUTATED C19ORF40 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(110) Variable = MRE11A MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2                0   1
  MRE11A MUTATED     5   3
  MRE11A WILD-TYPE 333 213
  MRE11A MUTATED MRE11A WILD-TYPE 
               8              546 
  MRE11A MUTATED MRE11A WILD-TYPE 
               3              213 
$`MRE11A MUTATED`
TCGA-L5-A891 TCGA-Z6-A8JD TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 
        3.75         3.42        11.01         6.97        34.68         0.26 
TCGA-D7-A4YV TCGA-HU-A4GX 
        5.92        20.25 

$`MRE11A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        19.56         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MRE11A MUTATED MRE11A WILD-TYPE 
            0.26             0.00 
  MRE11A MUTATED MRE11A WILD-TYPE 
           34.68           122.30 
  MRE11A MUTATED MRE11A WILD-TYPE 
           6.445           13.730 
[1] "0.3 - 34.7 (6.4)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.7"
D110V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRE11A MUTATED         0        0        2        0         1         3
  MRE11A WILD-TYPE      10       20       44       31        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRE11A MUTATED           0          1          0          1        0
  MRE11A WILD-TYPE        29         83         62         38       43
                  vv
clus               STAGE IVA
  MRE11A MUTATED           0
  MRE11A WILD-TYPE         4
D110V3, multiclass
            clus
vv           MRE11A MUTATED MRE11A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MRE11A MUTATED       0   2   5   2
  MRE11A WILD-TYPE    54 133 256 100
D110V4, multiclass
       clus
vv      MRE11A MUTATED MRE11A WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MRE11A MUTATED     4   3   1   0
  MRE11A WILD-TYPE 191 170  88  85
D110V5, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  N0              4              191
  N1              3              170
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V6, binary
                  cls
clus                 0   1
  MRE11A MUTATED     8   0
  MRE11A WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      8    0
  MRE11A WILD-TYPE  474   38
   clus
vv  MRE11A MUTATED MRE11A WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                 0   1
  MRE11A MUTATED     4   5
  MRE11A WILD-TYPE 168 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      4    5
  MRE11A WILD-TYPE  168  401
        clus
vv       MRE11A MUTATED MRE11A WILD-TYPE
  FEMALE              4              168
  MALE                5              401
[1] 2 2
[1] FALSE
D110V8, binary
                  cls
clus                 0   1
  MRE11A MUTATED     7   0
  MRE11A WILD-TYPE 409 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      7    0
  MRE11A WILD-TYPE  409  102
     clus
vv    MRE11A MUTATED MRE11A WILD-TYPE
  NO               7              409
  YES              0              102
[1] 2 2
[1] FALSE
D110V9, continuous
[1] "Remove cluster labels:" "MRE11A MUTATED"        
clus
  MRE11A MUTATED MRE11A WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JE 
"MRE11A WILD-TYPE" "MRE11A WILD-TYPE" "MRE11A WILD-TYPE" 
D110V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MRE11A MUTATED       1                         0
  MRE11A WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRE11A MUTATED                                           0     7
  MRE11A WILD-TYPE                                         1   350
D110V11, multiclass
                                           clus
vv                                          MRE11A MUTATED MRE11A WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V12, binary
                  cls
clus                 0   1
  MRE11A MUTATED     0   7
  MRE11A WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      0    7
  MRE11A WILD-TYPE   10  391
                        clus
vv                       MRE11A MUTATED MRE11A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(111) Variable = ERF MUTATION ANALYSIS
D111V1, survival
               sevent
clus2             0   1
  ERF MUTATED    10   6
  ERF WILD-TYPE 328 210
  ERF MUTATED ERF WILD-TYPE 
           16           538 
  ERF MUTATED ERF WILD-TYPE 
            6           210 
$`ERF MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8361 
       19.99         7.76        34.68         9.21        39.78        31.10 
TCGA-BR-8382 TCGA-CD-5813 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 
       25.05        12.39        12.62         1.02         6.02        65.10 
TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HJ-7597 TCGA-SW-A7EA 
       11.44        30.51        26.47        19.04 

$`ERF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       21.90        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 
        5.52         6.21        77.29        63.06        52.21         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ERF MUTATED ERF WILD-TYPE 
         1.02          0.00 
  ERF MUTATED ERF WILD-TYPE 
         65.1         122.3 
  ERF MUTATED ERF WILD-TYPE 
       19.515        13.530 
[1] "1.0 - 65.1 (19.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D111V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERF MUTATED         0        0        4        2         1         2
  ERF WILD-TYPE      10       20       42       29        83        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERF MUTATED           0          0          1          4        2         0
  ERF WILD-TYPE        29         84         61         35       41         4
D111V3, multiclass
            clus
vv           ERF MUTATED ERF WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             4            42
  STAGE II             2            29
  STAGE IIA            1            83
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           0            84
  STAGE IIIB           1            61
  STAGE IIIC           4            35
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  ERF MUTATED       1   5   7   4
  ERF WILD-TYPE    53 130 254  98
D111V4, multiclass
       clus
vv      ERF MUTATED ERF WILD-TYPE
  T0+T1           1            53
  T2              5           130
  T3              7           254
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ERF MUTATED     7   3   2   4
  ERF WILD-TYPE 188 170  87  81
D111V5, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  N0           7           188
  N1           3           170
  N2           2            87
  N3           4            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V6, binary
               cls
clus              0   1
  ERF MUTATED    15   1
  ERF WILD-TYPE 467  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     15    1
  ERF WILD-TYPE  467   37
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0          15           467
  1           1            37
[1] 2 2
[1] FALSE
D111V7, binary
               cls
clus              0   1
  ERF MUTATED    12   6
  ERF WILD-TYPE 160 400
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     12    6
  ERF WILD-TYPE  160  400
        clus
vv       ERF MUTATED ERF WILD-TYPE
  FEMALE          12           160
  MALE             6           400
[1] 2 2
[1] FALSE
D111V8, binary
               cls
clus              0   1
  ERF MUTATED    13   1
  ERF WILD-TYPE 403 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     13    1
  ERF WILD-TYPE  403  101
     clus
vv    ERF MUTATED ERF WILD-TYPE
  NO           13           403
  YES           1           101
[1] 2 2
[1] FALSE
D111V9, continuous
D111V10, continuous
[1] "Remove cluster labels:" "ERF MUTATED"           
clus
  ERF MUTATED ERF WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" "ERF WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"ERF WILD-TYPE" "ERF WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  ERF MUTATED       2                         0
  ERF WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERF MUTATED                                           0    12
  ERF WILD-TYPE                                         1   345
D111V11, multiclass
                                           clus
vv                                          ERF MUTATED ERF WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              12           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V12, binary
               cls
clus              0   1
  ERF MUTATED     0  12
  ERF WILD-TYPE  10 386
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      0   12
  ERF WILD-TYPE   10  386
                        clus
vv                       ERF MUTATED ERF WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          12           386
[1] 2 2
[1] FALSE

Clustering(112) Variable = GYLTL1B MUTATION ANALYSIS
D112V1, survival
                   sevent
clus2                 0   1
  GYLTL1B MUTATED    14   4
  GYLTL1B WILD-TYPE 324 212
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               18               536 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
                4               212 
$`GYLTL1B MUTATED`
TCGA-L5-A8NM TCGA-LN-A49N TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8078 
        7.76        12.43         6.97        34.68        32.78        29.59 
TCGA-BR-8487 TCGA-BR-A453 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
        1.12         6.08        12.62         1.02         6.02       105.07 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.08        30.51        24.20        14.07        19.73        38.14 

$`GYLTL1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
             1.02              0.00 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
           105.07            122.30 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
           13.345            13.565 
[1] "1.0 - 105.1 (13.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D112V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GYLTL1B MUTATED         0        1        2        1         4         4
  GYLTL1B WILD-TYPE      10       19       44       30        80        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GYLTL1B MUTATED           0          3          0          1        3
  GYLTL1B WILD-TYPE        29         81         62         38       40
                   vv
clus                STAGE IVA
  GYLTL1B MUTATED           0
  GYLTL1B WILD-TYPE         4
D112V3, multiclass
            clus
vv           GYLTL1B MUTATED GYLTL1B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                4                80
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GYLTL1B MUTATED       2   4   7   6
  GYLTL1B WILD-TYPE    52 131 254  96
D112V4, multiclass
       clus
vv      GYLTL1B MUTATED GYLTL1B WILD-TYPE
  T0+T1               2                52
  T2                  4               131
  T3                  7               254
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GYLTL1B MUTATED     8   7   2   2
  GYLTL1B WILD-TYPE 187 166  87  83
D112V5, multiclass
    clus
vv   GYLTL1B MUTATED GYLTL1B WILD-TYPE
  N0               8               187
  N1               7               166
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V6, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED    16   2
  GYLTL1B WILD-TYPE 466  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED     16    2
  GYLTL1B WILD-TYPE  466   36
   clus
vv  GYLTL1B MUTATED GYLTL1B WILD-TYPE
  0              16               466
  1               2                36
[1] 2 2
[1] FALSE
D112V7, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED     8  11
  GYLTL1B WILD-TYPE 164 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED      8   11
  GYLTL1B WILD-TYPE  164  395
        clus
vv       GYLTL1B MUTATED GYLTL1B WILD-TYPE
  FEMALE               8               164
  MALE                11               395
[1] 2 2
[1] FALSE
D112V8, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED    15   3
  GYLTL1B WILD-TYPE 401  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED     15    3
  GYLTL1B WILD-TYPE  401   99
     clus
vv    GYLTL1B MUTATED GYLTL1B WILD-TYPE
  NO               15               401
  YES               3                99
[1] 2 2
[1] FALSE
D112V9, continuous
[1] "Remove cluster labels:" "GYLTL1B MUTATED"       
clus
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" "GYLTL1B WILD-TYPE" 
D112V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GYLTL1B MUTATED       5                         1
  GYLTL1B WILD-TYPE   128                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GYLTL1B MUTATED                                           0     9
  GYLTL1B WILD-TYPE                                         1   348
D112V11, multiclass
                                           clus
vv                                          GYLTL1B MUTATED GYLTL1B WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V12, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED     0  13
  GYLTL1B WILD-TYPE  10 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED      0   13
  GYLTL1B WILD-TYPE   10  385
                        clus
vv                       GYLTL1B MUTATED GYLTL1B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              13               385
[1] 2 2
[1] FALSE

Clustering(113) Variable = POLM MUTATION ANALYSIS
D113V1, survival
                sevent
clus2              0   1
  POLM MUTATED     8   2
  POLM WILD-TYPE 330 214
  POLM MUTATED POLM WILD-TYPE 
            10            544 
  POLM MUTATED POLM WILD-TYPE 
             2            214 
$`POLM MUTATED`
TCGA-LN-A9FP TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-A4MJ TCGA-CG-5723 
       12.03        34.68         0.26         1.12        12.62       105.07 
TCGA-F1-6875 TCGA-HU-A4G9 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       72.23        24.20        19.73        38.14 

$`POLM WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  POLM MUTATED POLM WILD-TYPE 
          0.26           0.00 
  POLM MUTATED POLM WILD-TYPE 
        105.07         122.30 
  POLM MUTATED POLM WILD-TYPE 
        21.965         13.530 
[1] "0.3 - 105.1 (22.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3"  
D113V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POLM MUTATED         1        2        3        1         3         1
  POLM WILD-TYPE       9       18       43       30        81        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLM MUTATED           0          2          0          0        0         0
  POLM WILD-TYPE        29         82         62         39       43         4
D113V3, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  POLM MUTATED       2   6   3   2
  POLM WILD-TYPE    52 129 258 100
D113V4, multiclass
       clus
vv      POLM MUTATED POLM WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  POLM MUTATED     9   3   1   0
  POLM WILD-TYPE 186 170  88  85
D113V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            9            186
  N1            3            170
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V6, binary
                cls
clus               0   1
  POLM MUTATED    13   0
  POLM WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED     13    0
  POLM WILD-TYPE  469   38
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D113V7, binary
                cls
clus               0   1
  POLM MUTATED     7   7
  POLM WILD-TYPE 165 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      7    7
  POLM WILD-TYPE  165  399
        clus
vv       POLM MUTATED POLM WILD-TYPE
  FEMALE            7            165
  MALE              7            399
[1] 2 2
[1] FALSE
D113V8, binary
                cls
clus               0   1
  POLM MUTATED    10   2
  POLM WILD-TYPE 406 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED     10    2
  POLM WILD-TYPE  406  100
     clus
vv    POLM MUTATED POLM WILD-TYPE
  NO            10            406
  YES            2            100
[1] 2 2
[1] FALSE
D113V9, continuous
D113V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  POLM MUTATED       3                         2
  POLM WILD-TYPE   130                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POLM MUTATED                                           0     7
  POLM WILD-TYPE                                         1   350
D113V11, multiclass
                                           clus
vv                                          POLM MUTATED POLM WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V12, binary
                cls
clus               0   1
  POLM MUTATED     0  11
  POLM WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      0   11
  POLM WILD-TYPE   10  387
                        clus
vv                       POLM MUTATED POLM WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(114) Variable = HLA-A MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    12   5
  HLA-A WILD-TYPE 326 211
  HLA-A MUTATED HLA-A WILD-TYPE 
             17             537 
  HLA-A MUTATED HLA-A WILD-TYPE 
              5             211 
$`HLA-A MUTATED`
TCGA-L5-A88W TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8372 
       25.12         9.67        44.94        29.59        32.25        31.27 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4438 TCGA-CG-5718 TCGA-D7-A6EZ TCGA-F1-6874 
       12.43         6.58        54.08        36.00        20.32        14.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-R5-A7ZI TCGA-VQ-A8P2 
       22.32        22.68         6.51        74.53        38.14 

$`HLA-A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HLA-A MUTATED HLA-A WILD-TYPE 
           6.51            0.00 
  HLA-A MUTATED HLA-A WILD-TYPE 
          74.53          122.30 
  HLA-A MUTATED HLA-A WILD-TYPE 
          25.12           13.41 
[1] "6.5 - 74.5 (25.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D114V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-A MUTATED         0        0        1        2         4         4
  HLA-A WILD-TYPE      10       20       45       29        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-A MUTATED           0          3          0          1        2         0
  HLA-A WILD-TYPE        29         81         62         38       41         4
D114V3, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HLA-A MUTATED       0   2   7   8
  HLA-A WILD-TYPE    54 133 254  94
D114V4, multiclass
       clus
vv      HLA-A MUTATED HLA-A WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                7             254
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HLA-A MUTATED    10   5   2   1
  HLA-A WILD-TYPE 185 168  87  84
D114V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0            10             185
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    18   1
  HLA-A WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     18    1
  HLA-A WILD-TYPE  464   37
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D114V7, binary
                 cls
clus                0   1
  HLA-A MUTATED    12   8
  HLA-A WILD-TYPE 160 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     12    8
  HLA-A WILD-TYPE  160  398
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE            12             160
  MALE               8             398
[1] 2 2
[1] FALSE
D114V8, binary
                 cls
clus                0   1
  HLA-A MUTATED    14   2
  HLA-A WILD-TYPE 402 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     14    2
  HLA-A WILD-TYPE  402  100
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO             14             402
  YES             2             100
[1] 2 2
[1] FALSE
D114V9, continuous
D114V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HLA-A MUTATED       5                         0
  HLA-A WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-A MUTATED                                           0    13
  HLA-A WILD-TYPE                                         1   344
D114V11, multiclass
                                           clus
vv                                          HLA-A MUTATED HLA-A WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V12, binary
                 cls
clus                0   1
  HLA-A MUTATED     1  15
  HLA-A WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1   15
  HLA-A WILD-TYPE    9  383
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(115) Variable = EIF4G3 MUTATION ANALYSIS
D115V1, survival
                  sevent
clus2                0   1
  EIF4G3 MUTATED    14  10
  EIF4G3 WILD-TYPE 324 206
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              24              530 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              10              206 
$`EIF4G3 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-L5-A8NS TCGA-R6-A8WG TCGA-B7-5818 
       21.99         4.21        33.27        13.41        12.69        11.70 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8487 
       34.68        29.59         2.66         0.26        31.27         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-D7-A6EY 
       28.14        31.96        16.14         6.58         9.01        11.44 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       21.27        11.08        13.35        19.73        74.53        38.14 

$`EIF4G3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
            0.26             0.00 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
           74.53           122.30 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
          14.775           13.565 
[1] "0.3 - 74.5 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D115V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4G3 MUTATED         0        0        2        0         5         2
  EIF4G3 WILD-TYPE      10       20       44       31        79        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G3 MUTATED           1          3          3          2        5
  EIF4G3 WILD-TYPE        28         81         59         37       38
                  vv
clus               STAGE IVA
  EIF4G3 MUTATED           0
  EIF4G3 WILD-TYPE         4
D115V3, multiclass
            clus
vv           EIF4G3 MUTATED EIF4G3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              3               59
  STAGE IIIC              2               37
  STAGE IV                5               38
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  EIF4G3 MUTATED       0   3  11   9
  EIF4G3 WILD-TYPE    54 132 250  93
D115V4, multiclass
       clus
vv      EIF4G3 MUTATED EIF4G3 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                11              250
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  EIF4G3 MUTATED     9   5   2   7
  EIF4G3 WILD-TYPE 186 168  87  78
D115V5, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  N0              9              186
  N1              5              168
  N2              2               87
  N3              7               78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V6, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    18   5
  EIF4G3 WILD-TYPE 464  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     18    5
  EIF4G3 WILD-TYPE  464   33
   clus
vv  EIF4G3 MUTATED EIF4G3 WILD-TYPE
  0             18              464
  1              5               33
[1] 2 2
[1] FALSE
D115V7, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    11  13
  EIF4G3 WILD-TYPE 161 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     11   13
  EIF4G3 WILD-TYPE  161  393
        clus
vv       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  FEMALE             11              161
  MALE               13              393
[1] 2 2
[1] FALSE
D115V8, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    19   4
  EIF4G3 WILD-TYPE 397  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     19    4
  EIF4G3 WILD-TYPE  397   98
     clus
vv    EIF4G3 MUTATED EIF4G3 WILD-TYPE
  NO              19              397
  YES              4               98
[1] 2 2
[1] FALSE
D115V9, continuous
[1] "Remove cluster labels:" "EIF4G3 MUTATED"        
clus
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
               1               67 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YB 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
D115V10, continuous
[1] "Remove cluster labels:" "EIF4G3 MUTATED"        
clus
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" "EIF4G3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"EIF4G3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EIF4G3 MUTATED       2                         1
  EIF4G3 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4G3 MUTATED                                           0    18
  EIF4G3 WILD-TYPE                                         1   339
D115V11, multiclass
                                           clus
vv                                          EIF4G3 MUTATED EIF4G3 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V12, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     3  16
  EIF4G3 WILD-TYPE   7 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      3   16
  EIF4G3 WILD-TYPE    7  382
                        clus
vv                       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  HISPANIC OR LATINO                  3                7
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(116) Variable = CTNNB1 MUTATION ANALYSIS
D116V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    24   9
  CTNNB1 WILD-TYPE 314 207
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              33              521 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              207 
$`CTNNB1 MUTATED`
TCGA-CG-5727 TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-L5-A8NR TCGA-LN-A7HX TCGA-R6-A6XQ 
       79.07        21.01         7.76         8.71        12.23         6.35 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-VR-AA4G TCGA-B7-5816 TCGA-BR-4188 
       15.78        12.69         5.29        18.05        26.70         7.43 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J5 
       34.68        32.78        35.84        27.12        31.96        28.34 
TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-6524 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-A4YX 
        7.07         6.02        17.85        12.33        19.50        36.43 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A747 TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4G6 
       11.31        20.32         8.38        52.21        22.32        24.26 
TCGA-HU-A4H5 TCGA-VQ-A8P2 TCGA-VQ-AA69 
       23.80        38.14        28.41 

$`CTNNB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        22.29        15.65         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        18.41        43.66        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            5.29             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           79.07           122.30 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           20.32            13.41 
[1] "5.3 - 79.1 (20.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D116V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNNB1 MUTATED         1        2        3        2         4         5
  CTNNB1 WILD-TYPE       9       18       43       29        80        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED           1          6          1          0        3
  CTNNB1 WILD-TYPE        28         78         61         39       40
                  vv
clus               STAGE IVA
  CTNNB1 MUTATED           1
  CTNNB1 WILD-TYPE         3
D116V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                2               18
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              6               78
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CTNNB1 MUTATED       4   7  12   7
  CTNNB1 WILD-TYPE    50 128 249  95
D116V4, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T0+T1              4               50
  T2                 7              128
  T3                12              249
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CTNNB1 MUTATED    13  12   5   1
  CTNNB1 WILD-TYPE 182 161  84  84
D116V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             13              182
  N1             12              161
  N2              5               84
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    28   2
  CTNNB1 WILD-TYPE 454  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     28    2
  CTNNB1 WILD-TYPE  454   36
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             28              454
  1              2               36
[1] 2 2
[1] FALSE
D116V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    11  22
  CTNNB1 WILD-TYPE 161 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     11   22
  CTNNB1 WILD-TYPE  161  384
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             11              161
  MALE               22              384
[1] 2 2
[1] FALSE
D116V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    29   3
  CTNNB1 WILD-TYPE 387  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     29    3
  CTNNB1 WILD-TYPE  387   99
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              29              387
  YES              3               99
[1] 2 2
[1] FALSE
D116V9, continuous
D116V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNNB1 MUTATED       6                         0
  CTNNB1 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNB1 MUTATED                                           0    21
  CTNNB1 WILD-TYPE                                         1   336
D116V11, multiclass
                                           clus
vv                                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 21              336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V12, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     2  21
  CTNNB1 WILD-TYPE   8 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      2   21
  CTNNB1 WILD-TYPE    8  377
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(117) Variable = TMEM41A MUTATION ANALYSIS
D117V1, survival
                   sevent
clus2                 0   1
  TMEM41A MUTATED     5   3
  TMEM41A WILD-TYPE 333 213
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                8               546 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                3               213 
$`TMEM41A MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5726 
       34.68        29.59         1.12         6.58        11.77        28.96 
TCGA-HF-A5NB TCGA-VQ-A8P2 
       30.51        38.14 

$`TMEM41A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TMEM41A MUTATED TMEM41A WILD-TYPE 
             1.12              0.00 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
            38.14            122.30 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
           29.275            13.530 
[1] "1.1 - 38.1 (29.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D117V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM41A MUTATED         0        1        0        0         3         1
  TMEM41A WILD-TYPE      10       19       46       31        81        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41A MUTATED           0          3          0          1        0
  TMEM41A WILD-TYPE        29         81         62         38       43
                   vv
clus                STAGE IVA
  TMEM41A MUTATED           0
  TMEM41A WILD-TYPE         4
D117V3, multiclass
            clus
vv           TMEM41A MUTATED TMEM41A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM41A MUTATED       1   0   4   4
  TMEM41A WILD-TYPE    53 135 257  98
D117V4, multiclass
       clus
vv      TMEM41A MUTATED TMEM41A WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  4               257
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM41A MUTATED     6   2   0   1
  TMEM41A WILD-TYPE 189 171  89  84
D117V5, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  N0               6               189
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V6, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     9   0
  TMEM41A WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      9    0
  TMEM41A WILD-TYPE  473   38
   clus
vv  TMEM41A MUTATED TMEM41A WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D117V7, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     5   4
  TMEM41A WILD-TYPE 167 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      5    4
  TMEM41A WILD-TYPE  167  402
        clus
vv       TMEM41A MUTATED TMEM41A WILD-TYPE
  FEMALE               5               167
  MALE                 4               402
[1] 2 2
[1] FALSE
D117V8, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     5   2
  TMEM41A WILD-TYPE 411 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      5    2
  TMEM41A WILD-TYPE  411  100
     clus
vv    TMEM41A MUTATED TMEM41A WILD-TYPE
  NO                5               411
  YES               2               100
[1] 2 2
[1] FALSE
D117V9, continuous
D117V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM41A MUTATED       2                         0
  TMEM41A WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM41A MUTATED                                           0     5
  TMEM41A WILD-TYPE                                         1   352
D117V11, multiclass
                                           clus
vv                                          TMEM41A MUTATED TMEM41A WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V12, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     0   6
  TMEM41A WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      0    6
  TMEM41A WILD-TYPE   10  392
                        clus
vv                       TMEM41A MUTATED TMEM41A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(118) Variable = VPS13B MUTATION ANALYSIS
D118V1, survival
                  sevent
clus2                0   1
  VPS13B MUTATED    35  23
  VPS13B WILD-TYPE 303 193
  VPS13B MUTATED VPS13B WILD-TYPE 
              58              496 
  VPS13B MUTATED VPS13B WILD-TYPE 
              23              193 
$`VPS13B MUTATED`
TCGA-CG-4460 TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A93D TCGA-L5-A4OH 
       21.99         0.79         4.67       122.10        31.56        32.61 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A4A4 TCGA-LN-A9FQ TCGA-VR-A8EO 
       12.92        13.55        13.22        12.59        12.85        25.81 
TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 
       22.82        19.73        26.70         6.97        30.90         9.34 
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8289 
       34.68        44.94        35.84        14.43        29.59         2.66 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
        6.18         0.26        25.05         1.12        28.14        31.96 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
       12.30        15.39        15.95         1.02         6.02       105.07 
TCGA-CG-5726 TCGA-D7-6525 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-7134 
       28.96        13.35        11.31        11.44        21.27        52.21 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       26.47        22.68        24.20         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZI 
       20.25         2.10        29.00        36.95        19.73        74.53 
TCGA-RD-A7C1 TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PM 
       16.67        13.25        38.14         1.87 

$`VPS13B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50         2.66        13.48        16.47         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        8.98        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5818 
       14.37         3.42         2.10         1.32         2.66        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       31.20        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       29.56        33.21        37.25        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.78        14.76        26.43        11.24        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        8.98         0.26        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A666 
       13.51         2.53         5.56        63.62         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ 
       43.36        37.41        37.22        22.19        17.85        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  VPS13B MUTATED VPS13B WILD-TYPE 
             0.1              0.0 
  VPS13B MUTATED VPS13B WILD-TYPE 
           122.1            122.3 
  VPS13B MUTATED VPS13B WILD-TYPE 
           18.20            13.41 
[1] "0.1 - 122.1 (18.2)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.2"
D118V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS13B MUTATED         2        4        7        4         8         4
  VPS13B WILD-TYPE       8       16       39       27        76        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13B MUTATED           4          6          3          8        9
  VPS13B WILD-TYPE        25         78         59         31       34
                  vv
clus               STAGE IVA
  VPS13B MUTATED           0
  VPS13B WILD-TYPE         4
D118V3, multiclass
            clus
vv           VPS13B MUTATED VPS13B WILD-TYPE
  STAGE I                 2                8
  STAGE IA                4               16
  STAGE IB                7               39
  STAGE II                4               27
  STAGE IIA               8               76
  STAGE IIB               4               79
  STAGE III               4               25
  STAGE IIIA              6               78
  STAGE IIIB              3               59
  STAGE IIIC              8               31
  STAGE IV                9               34
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  VPS13B MUTATED       7  12  23  18
  VPS13B WILD-TYPE    47 123 238  84
D118V4, multiclass
       clus
vv      VPS13B MUTATED VPS13B WILD-TYPE
  T0+T1              7               47
  T2                12              123
  T3                23              238
  T4                18               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  VPS13B MUTATED    27  16   8  10
  VPS13B WILD-TYPE 168 157  81  75
D118V5, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  N0             27              168
  N1             16              157
  N2              8               81
  N3             10               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V6, binary
                  cls
clus                 0   1
  VPS13B MUTATED    52   7
  VPS13B WILD-TYPE 430  31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     52    7
  VPS13B WILD-TYPE  430   31
   clus
vv  VPS13B MUTATED VPS13B WILD-TYPE
  0             52              430
  1              7               31
[1] 2 2
[1] FALSE
D118V7, binary
                  cls
clus                 0   1
  VPS13B MUTATED    23  39
  VPS13B WILD-TYPE 149 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     23   39
  VPS13B WILD-TYPE  149  367
        clus
vv       VPS13B MUTATED VPS13B WILD-TYPE
  FEMALE             23              149
  MALE               39              367
[1] 2 2
[1] FALSE
D118V8, binary
                  cls
clus                 0   1
  VPS13B MUTATED    43   9
  VPS13B WILD-TYPE 373  93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     43    9
  VPS13B WILD-TYPE  373   93
     clus
vv    VPS13B MUTATED VPS13B WILD-TYPE
  NO              43              373
  YES              9               93
[1] 2 2
[1] FALSE
D118V9, continuous
D118V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  VPS13B MUTATED      15                         0
  VPS13B WILD-TYPE   118                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS13B MUTATED                                           0    39
  VPS13B WILD-TYPE                                         1   318
D118V11, multiclass
                                           clus
vv                                          VPS13B MUTATED VPS13B WILD-TYPE
  ASIAN                                                 15              118
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 39              318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V12, binary
                  cls
clus                 0   1
  VPS13B MUTATED     2  40
  VPS13B WILD-TYPE   8 358
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED      2   40
  VPS13B WILD-TYPE    8  358
                        clus
vv                       VPS13B MUTATED VPS13B WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             40              358
[1] 2 2
[1] FALSE

Clustering(119) Variable = PBRM1 MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    21   9
  PBRM1 WILD-TYPE 317 207
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             30             524 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              9             207 
$`PBRM1 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-2H-A9GG TCGA-IG-A50L TCGA-L5-A88Z TCGA-L5-A8NM 
       34.85        19.99        20.05         0.53         7.40         7.76 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-8284 
       18.21         3.42        26.70        19.56        34.68         8.05 
TCGA-BR-8382 TCGA-BR-8589 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8536 TCGA-CD-A4MG 
       25.05        27.12        13.18        12.39        12.43         6.58 
TCGA-CG-4438 TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-8602 
       54.08         6.02        65.10        21.07        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-IN-AB1X TCGA-VQ-A8DL TCGA-VQ-A8P2 
       22.68        20.25        23.84        13.51         0.92        38.14 

$`PBRM1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
       14.37         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44         8.94        35.61        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.53            0.00 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
           65.1           122.3 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         20.020          13.445 
[1] "0.5 - 65.1 (20.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D119V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PBRM1 MUTATED         0        1        1        2         5         8
  PBRM1 WILD-TYPE      10       19       45       29        79        75
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PBRM1 MUTATED           1          4          1          6        3         0
  PBRM1 WILD-TYPE        28         80         61         33       40         4
D119V3, multiclass
            clus
vv           PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              5              79
  STAGE IIB              8              75
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             6              33
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PBRM1 MUTATED       4   4  13  13
  PBRM1 WILD-TYPE    50 131 248  89
D119V4, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  T0+T1             4              50
  T2                4             131
  T3               13             248
  T4               13              89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PBRM1 MUTATED    13  10   5   5
  PBRM1 WILD-TYPE 182 163  84  80
D119V5, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  N0            13             182
  N1            10             163
  N2             5              84
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED    32   0
  PBRM1 WILD-TYPE 450  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     32    0
  PBRM1 WILD-TYPE  450   38
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0            32             450
  1             0              38
[1] 2 2
[1] FALSE
D119V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    17  17
  PBRM1 WILD-TYPE 155 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     17   17
  PBRM1 WILD-TYPE  155  389
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            17             155
  MALE              17             389
[1] 2 2
[1] FALSE
D119V8, binary
                 cls
clus                0   1
  PBRM1 MUTATED    26   3
  PBRM1 WILD-TYPE 390  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     26    3
  PBRM1 WILD-TYPE  390   99
     clus
vv    PBRM1 MUTATED PBRM1 WILD-TYPE
  NO             26             390
  YES             3              99
[1] 2 2
[1] FALSE
D119V9, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JE 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
D119V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PBRM1 MUTATED      10                         0
  PBRM1 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PBRM1 MUTATED                                           0    18
  PBRM1 WILD-TYPE                                         1   339
D119V11, multiclass
                                           clus
vv                                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V12, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0  22
  PBRM1 WILD-TYPE  10 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0   22
  PBRM1 WILD-TYPE   10  376
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(120) Variable = ALPK2 MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    19   8
  ALPK2 WILD-TYPE 319 208
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             27             527 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              8             208 
$`ALPK2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A3QL TCGA-IG-A4P3 TCGA-L5-A4OJ TCGA-LN-A9FQ 
       19.99        21.99        35.21        18.64        21.01        12.85 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 
        6.97         9.34         6.61        34.68        44.94        35.84 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A453 TCGA-CD-A4MG 
       25.05         1.12        28.14        31.96         6.08         6.58 
TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GT 
        6.02        21.27        22.32        24.20        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-VQ-A8P2 
       20.25        14.07        38.14 

$`ALPK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         4.08         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           1.12            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          44.94          122.30 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          21.01           13.41 
[1] "1.1 - 44.9 (21.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D120V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALPK2 MUTATED         1        1        2        0         8         2
  ALPK2 WILD-TYPE       9       19       44       31        76        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALPK2 MUTATED           1          2          1          4        4         0
  ALPK2 WILD-TYPE        28         82         61         35       39         4
D120V3, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              8              76
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ALPK2 MUTATED       4   5   9   9
  ALPK2 WILD-TYPE    50 130 252  93
D120V4, multiclass
       clus
vv      ALPK2 MUTATED ALPK2 WILD-TYPE
  T0+T1             4              50
  T2                5             130
  T3                9             252
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ALPK2 MUTATED    11   9   2   5
  ALPK2 WILD-TYPE 184 164  87  80
D120V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0            11             184
  N1             9             164
  N2             2              87
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V6, binary
                 cls
clus                0   1
  ALPK2 MUTATED    24   3
  ALPK2 WILD-TYPE 458  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     24    3
  ALPK2 WILD-TYPE  458   35
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            24             458
  1             3              35
[1] 2 2
[1] FALSE
D120V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    14  15
  ALPK2 WILD-TYPE 158 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     14   15
  ALPK2 WILD-TYPE  158  391
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            14             158
  MALE              15             391
[1] 2 2
[1] FALSE
D120V8, binary
                 cls
clus                0   1
  ALPK2 MUTATED    24   3
  ALPK2 WILD-TYPE 392  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     24    3
  ALPK2 WILD-TYPE  392   99
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             24             392
  YES             3              99
[1] 2 2
[1] FALSE
D120V9, continuous
[1] "Remove cluster labels:" "ALPK2 MUTATED"         
clus
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" "ALPK2 WILD-TYPE" 
D120V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALPK2 MUTATED      10                         0
  ALPK2 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALPK2 MUTATED                                           0    17
  ALPK2 WILD-TYPE                                         1   340
D120V11, multiclass
                                           clus
vv                                          ALPK2 MUTATED ALPK2 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V12, binary
                 cls
clus                0   1
  ALPK2 MUTATED     1  23
  ALPK2 WILD-TYPE   9 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      1   23
  ALPK2 WILD-TYPE    9  375
                        clus
vv                       ALPK2 MUTATED ALPK2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            23             375
[1] 2 2
[1] FALSE

Clustering(121) Variable = MED15 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2               0   1
  MED15 MUTATED    15   6
  MED15 WILD-TYPE 323 210
  MED15 MUTATED MED15 WILD-TYPE 
             21             533 
  MED15 MUTATED MED15 WILD-TYPE 
              6             210 
$`MED15 MUTATED`
TCGA-L5-A43H TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-V5-A7RB TCGA-BR-4201 TCGA-BR-6802 
        0.30        13.18        12.26         5.29        30.90        30.90 
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8589 TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-A6EY 
       44.94        29.59        27.12        11.77        65.10        11.44 
TCGA-F1-A72C TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UG 
       11.38        77.29        30.51        29.98        20.25         3.72 
TCGA-SW-A7EA TCGA-VQ-AA6J TCGA-ZA-A8F6 
       19.04        27.55        17.26 

$`MED15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.38         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        12.43 

  MED15 MUTATED MED15 WILD-TYPE 
            0.3             0.0 
  MED15 MUTATED MED15 WILD-TYPE 
          77.29          122.30 
  MED15 MUTATED MED15 WILD-TYPE 
          20.25           13.51 
[1] "0.3 - 77.3 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D121V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MED15 MUTATED         1        0        3        1         4         2
  MED15 WILD-TYPE       9       20       43       30        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED15 MUTATED           1          3          3          2        0         0
  MED15 WILD-TYPE        28         81         59         37       43         4
D121V3, multiclass
            clus
vv           MED15 MUTATED MED15 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MED15 MUTATED       2   8   7   5
  MED15 WILD-TYPE    52 127 254  97
D121V4, multiclass
       clus
vv      MED15 MUTATED MED15 WILD-TYPE
  T0+T1             2              52
  T2                8             127
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MED15 MUTATED     7   9   3   2
  MED15 WILD-TYPE 188 164  86  83
D121V5, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  N0             7             188
  N1             9             164
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V6, binary
                 cls
clus                0   1
  MED15 MUTATED    19   0
  MED15 WILD-TYPE 463  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED     19    0
  MED15 WILD-TYPE  463   38
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0            19             463
  1             0              38
[1] 2 2
[1] FALSE
D121V7, binary
                 cls
clus                0   1
  MED15 MUTATED     9  13
  MED15 WILD-TYPE 163 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      9   13
  MED15 WILD-TYPE  163  393
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  FEMALE             9             163
  MALE              13             393
[1] 2 2
[1] FALSE
D121V8, binary
                 cls
clus                0   1
  MED15 MUTATED    17   4
  MED15 WILD-TYPE 399  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED     17    4
  MED15 WILD-TYPE  399   98
     clus
vv    MED15 MUTATED MED15 WILD-TYPE
  NO             17             399
  YES             4              98
[1] 2 2
[1] FALSE
D121V9, continuous
[1] "Remove cluster labels:" "MED15 MUTATED"         
clus
  MED15 MUTATED MED15 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
D121V10, continuous
[1] "Remove cluster labels:" "MED15 MUTATED"         
clus
  MED15 MUTATED MED15 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RC 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" "MED15 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MED15 MUTATED       7                         2
  MED15 WILD-TYPE   126                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MED15 MUTATED                                           0     9
  MED15 WILD-TYPE                                         1   348
D121V11, multiclass
                                           clus
vv                                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V12, binary
                 cls
clus                0   1
  MED15 MUTATED     1  16
  MED15 WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      1   16
  MED15 WILD-TYPE    9  382
                        clus
vv                       MED15 MUTATED MED15 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(122) Variable = TBC1D10C MUTATION ANALYSIS
D122V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     6   2
  TBC1D10C WILD-TYPE 332 214
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 8                546 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 2                214 
$`TBC1D10C MUTATED`
TCGA-2H-A9GJ TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-HU-8602 
       58.55        44.94         1.12        28.14         6.58        22.32 
TCGA-HU-A4G9 TCGA-VQ-A8P2 
       24.20        38.14 

$`TBC1D10C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.12               0.00 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             58.55             122.30 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             26.17              13.51 
[1] "1.1 - 58.5 (26.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D122V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D10C MUTATED         1        1        0        0         3         2
  TBC1D10C WILD-TYPE       9       19       46       31        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D10C MUTATED           0          1          0          1        0
  TBC1D10C WILD-TYPE        29         83         62         38       43
                    vv
clus                 STAGE IVA
  TBC1D10C MUTATED           0
  TBC1D10C WILD-TYPE         4
D122V3, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TBC1D10C MUTATED       2   0   3   4
  TBC1D10C WILD-TYPE    52 135 258  98
D122V4, multiclass
       clus
vv      TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T0+T1                2                 52
  T2                   0                135
  T3                   3                258
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TBC1D10C MUTATED     7   2   0   1
  TBC1D10C WILD-TYPE 188 171  89  84
D122V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                7                188
  N1                2                171
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V6, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED    10   0
  TBC1D10C WILD-TYPE 472  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED     10    0
  TBC1D10C WILD-TYPE  472   38
   clus
vv  TBC1D10C MUTATED TBC1D10C WILD-TYPE
  0               10                472
  1                0                 38
[1] 2 2
[1] FALSE
D122V7, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     5   5
  TBC1D10C WILD-TYPE 167 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      5    5
  TBC1D10C WILD-TYPE  167  401
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                5                167
  MALE                  5                401
[1] 2 2
[1] FALSE
D122V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     8   1
  TBC1D10C WILD-TYPE 408 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      8    1
  TBC1D10C WILD-TYPE  408  101
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  NO                 8                408
  YES                1                101
[1] 2 2
[1] FALSE
D122V9, continuous
D122V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D10C MUTATED       3                         0
  TBC1D10C WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D10C MUTATED                                           0     6
  TBC1D10C WILD-TYPE                                         1   351
D122V11, multiclass
                                           clus
vv                                          TBC1D10C MUTATED TBC1D10C WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V12, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     0   8
  TBC1D10C WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      0    8
  TBC1D10C WILD-TYPE   10  390
                        clus
vv                       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(123) Variable = CDH16 MUTATION ANALYSIS
D123V1, survival
                 sevent
clus2               0   1
  CDH16 MUTATED    11   5
  CDH16 WILD-TYPE 327 211
  CDH16 MUTATED CDH16 WILD-TYPE 
             16             538 
  CDH16 MUTATED CDH16 WILD-TYPE 
              5             211 
$`CDH16 MUTATED`
TCGA-VR-AA4G TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8372 
       18.05        30.90        44.94         6.18         4.31        31.27 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 TCGA-D7-6815 TCGA-FP-7998 TCGA-HJ-7597 
       31.96        16.14         1.02        15.98        22.29        26.47 
TCGA-HU-A4G9 TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-AA64 
       24.20        29.00        38.14        18.41 

$`CDH16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CDH16 MUTATED CDH16 WILD-TYPE 
           1.02            0.00 
  CDH16 MUTATED CDH16 WILD-TYPE 
          44.94          122.30 
  CDH16 MUTATED CDH16 WILD-TYPE 
         23.245          13.410 
[1] "1.0 - 44.9 (23.2)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D123V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH16 MUTATED         0        2        2        0         2         1
  CDH16 WILD-TYPE      10       18       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH16 MUTATED           0          2          2          3        2         0
  CDH16 WILD-TYPE        29         82         60         36       41         4
D123V3, multiclass
            clus
vv           CDH16 MUTATED CDH16 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CDH16 MUTATED       2   5   5   5
  CDH16 WILD-TYPE    52 130 256  97
D123V4, multiclass
       clus
vv      CDH16 MUTATED CDH16 WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CDH16 MUTATED     6   1   5   4
  CDH16 WILD-TYPE 189 172  84  81
D123V5, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  N0             6             189
  N1             1             172
  N2             5              84
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V6, binary
                 cls
clus                0   1
  CDH16 MUTATED    13   2
  CDH16 WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED     13    2
  CDH16 WILD-TYPE  469   36
   clus
vv  CDH16 MUTATED CDH16 WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D123V7, binary
                 cls
clus                0   1
  CDH16 MUTATED     9   8
  CDH16 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      9    8
  CDH16 WILD-TYPE  163  398
        clus
vv       CDH16 MUTATED CDH16 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D123V8, binary
                 cls
clus                0   1
  CDH16 MUTATED    12   3
  CDH16 WILD-TYPE 404  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED     12    3
  CDH16 WILD-TYPE  404   99
     clus
vv    CDH16 MUTATED CDH16 WILD-TYPE
  NO             12             404
  YES             3              99
[1] 2 2
[1] FALSE
D123V9, continuous
[1] "Remove cluster labels:" "CDH16 MUTATED"         
clus
  CDH16 MUTATED CDH16 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
D123V10, continuous
[1] "Remove cluster labels:" "CDH16 MUTATED"         
clus
  CDH16 MUTATED CDH16 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CDH16 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDH16 MUTATED       4                         0
  CDH16 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH16 MUTATED                                           0    12
  CDH16 WILD-TYPE                                         1   345
D123V11, multiclass
                                           clus
vv                                          CDH16 MUTATED CDH16 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V12, binary
                 cls
clus                0   1
  CDH16 MUTATED     1  12
  CDH16 WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      1   12
  CDH16 WILD-TYPE    9  386
                        clus
vv                       CDH16 MUTATED CDH16 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(124) Variable = ANAPC1 MUTATION ANALYSIS
D124V1, survival
                  sevent
clus2                0   1
  ANAPC1 MUTATED    14   4
  ANAPC1 WILD-TYPE 324 212
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              18              536 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               4              212 
$`ANAPC1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A3YC TCGA-JY-A6FD TCGA-L5-A4OJ TCGA-L5-A8NM 
       19.99        21.99        20.12        68.02        21.01         7.76 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8680 
       29.59         6.18         0.26         7.36        25.05        31.96 
TCGA-CG-5723 TCGA-CG-5728 TCGA-HF-A5NB TCGA-HU-A4GU TCGA-SW-A7EA TCGA-VQ-A8P2 
      105.07        65.10        30.51         6.58        19.04        38.14 

$`ANAPC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8384 
       14.04         3.32        11.80        31.27        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
            0.26             0.00 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
          105.07           122.30 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
          21.500           13.445 
[1] "0.3 - 105.1 (21.5)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2.6"
D124V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANAPC1 MUTATED         2        0        4        1         2         4
  ANAPC1 WILD-TYPE       8       20       42       30        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC1 MUTATED           0          3          0          3        2
  ANAPC1 WILD-TYPE        29         81         62         36       41
                  vv
clus               STAGE IVA
  ANAPC1 MUTATED           0
  ANAPC1 WILD-TYPE         4
D124V3, multiclass
            clus
vv           ANAPC1 MUTATED ANAPC1 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ANAPC1 MUTATED       2   6   6   7
  ANAPC1 WILD-TYPE    52 129 255  95
D124V4, multiclass
       clus
vv      ANAPC1 MUTATED ANAPC1 WILD-TYPE
  T0+T1              2               52
  T2                 6              129
  T3                 6              255
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ANAPC1 MUTATED     9   8   1   3
  ANAPC1 WILD-TYPE 186 165  88  82
D124V5, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  N0              9              186
  N1              8              165
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V6, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED    17   2
  ANAPC1 WILD-TYPE 465  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED     17    2
  ANAPC1 WILD-TYPE  465   36
   clus
vv  ANAPC1 MUTATED ANAPC1 WILD-TYPE
  0             17              465
  1              2               36
[1] 2 2
[1] FALSE
D124V7, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED    11  10
  ANAPC1 WILD-TYPE 161 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED     11   10
  ANAPC1 WILD-TYPE  161  396
        clus
vv       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  FEMALE             11              161
  MALE               10              396
[1] 2 2
[1] FALSE
D124V8, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED    16   2
  ANAPC1 WILD-TYPE 400 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED     16    2
  ANAPC1 WILD-TYPE  400  100
     clus
vv    ANAPC1 MUTATED ANAPC1 WILD-TYPE
  NO              16              400
  YES              2              100
[1] 2 2
[1] FALSE
D124V9, continuous
[1] "Remove cluster labels:" "ANAPC1 MUTATED"        
clus
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
D124V10, continuous
[1] "Remove cluster labels:" "ANAPC1 MUTATED"        
clus
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A4P3       TCGA-IG-A4QT 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS       TCGA-IG-A8O2 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" "ANAPC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ANAPC1 MUTATED       3                         1
  ANAPC1 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANAPC1 MUTATED                                           0    12
  ANAPC1 WILD-TYPE                                         1   345
D124V11, multiclass
                                           clus
vv                                          ANAPC1 MUTATED ANAPC1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V12, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     0  11
  ANAPC1 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      0   11
  ANAPC1 WILD-TYPE   10  387
                        clus
vv                       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(125) Variable = SLC9A11 MUTATION ANALYSIS
D125V1, survival
                   sevent
clus2                 0   1
  SLC9A11 MUTATED    17  11
  SLC9A11 WILD-TYPE 321 205
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               28               526 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               11               205 
$`SLC9A11 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-JY-A6F8 TCGA-M9-A5M8 
        4.31        21.99        33.27        35.21       122.10        33.11 
TCGA-VR-A8EU TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7715 
       18.31        26.70        30.90         9.34        34.68        33.63 
TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8528 
        2.66        31.10        31.96        16.14        13.18        12.33 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6528 TCGA-HU-A4GN 
       15.95         6.02        28.96        21.07        15.22        29.98 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-IN-A6RI TCGA-VQ-A8PQ 
        6.58        29.00        18.38        15.65 

$`SLC9A11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56        29.42        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
             2.66              0.00 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            122.1             122.3 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           21.530            13.395 
[1] "2.7 - 122.1 (21.5)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D125V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A11 MUTATED         2        1        1        1         6         3
  SLC9A11 WILD-TYPE       8       19       45       30        78        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A11 MUTATED           0          4          1          2        6
  SLC9A11 WILD-TYPE        29         80         61         37       37
                   vv
clus                STAGE IVA
  SLC9A11 MUTATED           0
  SLC9A11 WILD-TYPE         4
D125V3, multiclass
            clus
vv           SLC9A11 MUTATED SLC9A11 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                6                78
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 6                37
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC9A11 MUTATED       4   6   8  10
  SLC9A11 WILD-TYPE    50 129 253  92
D125V4, multiclass
       clus
vv      SLC9A11 MUTATED SLC9A11 WILD-TYPE
  T0+T1               4                50
  T2                  6               129
  T3                  8               253
  T4                 10                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC9A11 MUTATED    13   9   3   3
  SLC9A11 WILD-TYPE 182 164  86  82
D125V5, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  N0              13               182
  N1               9               164
  N2               3                86
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V6, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    24   5
  SLC9A11 WILD-TYPE 458  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     24    5
  SLC9A11 WILD-TYPE  458   33
   clus
vv  SLC9A11 MUTATED SLC9A11 WILD-TYPE
  0              24               458
  1               5                33
[1] 2 2
[1] FALSE
D125V7, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    14  16
  SLC9A11 WILD-TYPE 158 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     14   16
  SLC9A11 WILD-TYPE  158  390
        clus
vv       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  FEMALE              14               158
  MALE                16               390
[1] 2 2
[1] FALSE
D125V8, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    23   2
  SLC9A11 WILD-TYPE 393 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     23    2
  SLC9A11 WILD-TYPE  393  100
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO               23               393
  YES               2               100
[1] 2 2
[1] FALSE
D125V9, continuous
D125V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A11 MUTATED       6                         0
  SLC9A11 WILD-TYPE   127                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A11 MUTATED                                           0    18
  SLC9A11 WILD-TYPE                                         1   339
D125V11, multiclass
                                           clus
vv                                          SLC9A11 MUTATED SLC9A11 WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V12, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED     0  20
  SLC9A11 WILD-TYPE  10 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      0   20
  SLC9A11 WILD-TYPE   10  378
                        clus
vv                       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              20               378
[1] 2 2
[1] FALSE

Clustering(126) Variable = C22ORF30 MUTATION ANALYSIS
D126V1, survival
                    sevent
clus2                  0   1
  C22ORF30 MUTATED     6   4
  C22ORF30 WILD-TYPE 332 212
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                10                544 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 4                212 
$`C22ORF30 MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NM TCGA-L5-A8NV TCGA-R6-A6KZ TCGA-VR-AA7B TCGA-B7-5816 
       24.00         7.76        52.57         5.06        11.24        26.70 
TCGA-BR-6452 TCGA-CG-5723 TCGA-HU-A4G8 TCGA-SW-A7EA 
       34.68       105.07        22.68        19.04 

$`C22ORF30 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
              5.06               0.00 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
            105.07             122.30 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
             23.34              13.51 
[1] "5.1 - 105.1 (23.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D126V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C22ORF30 MUTATED         0        0        1        1         2         3
  C22ORF30 WILD-TYPE      10       20       45       30        82        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C22ORF30 MUTATED           0          1          1          0        1
  C22ORF30 WILD-TYPE        29         83         61         39       42
                    vv
clus                 STAGE IVA
  C22ORF30 MUTATED           0
  C22ORF30 WILD-TYPE         4
D126V3, multiclass
            clus
vv           C22ORF30 MUTATED C22ORF30 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 2                 82
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C22ORF30 MUTATED       0   3   5   2
  C22ORF30 WILD-TYPE    54 132 256 100
D126V4, multiclass
       clus
vv      C22ORF30 MUTATED C22ORF30 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   5                256
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C22ORF30 MUTATED     5   3   1   1
  C22ORF30 WILD-TYPE 190 170  88  84
D126V5, multiclass
    clus
vv   C22ORF30 MUTATED C22ORF30 WILD-TYPE
  N0                5                190
  N1                3                170
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V6, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     8   1
  C22ORF30 WILD-TYPE 474  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      8    1
  C22ORF30 WILD-TYPE  474   37
   clus
vv  C22ORF30 MUTATED C22ORF30 WILD-TYPE
  0                8                474
  1                1                 37
[1] 2 2
[1] FALSE
D126V7, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     7   4
  C22ORF30 WILD-TYPE 165 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      7    4
  C22ORF30 WILD-TYPE  165  402
        clus
vv       C22ORF30 MUTATED C22ORF30 WILD-TYPE
  FEMALE                7                165
  MALE                  4                402
[1] 2 2
[1] FALSE
D126V8, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED    10   0
  C22ORF30 WILD-TYPE 406 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED     10    0
  C22ORF30 WILD-TYPE  406  102
     clus
vv    C22ORF30 MUTATED C22ORF30 WILD-TYPE
  NO                10                406
  YES                0                102
[1] 2 2
[1] FALSE
D126V9, continuous
[1] "Remove cluster labels:" "C22ORF30 MUTATED"      
clus
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-Z6-A8JE 
"C22ORF30 WILD-TYPE" 
D126V10, continuous
[1] "Remove cluster labels:" "C22ORF30 MUTATED"      
clus
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" "C22ORF30 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C22ORF30 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C22ORF30 MUTATED       1                         0
  C22ORF30 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C22ORF30 MUTATED                                           0     9
  C22ORF30 WILD-TYPE                                         1   348
D126V11, multiclass
                                           clus
vv                                          C22ORF30 MUTATED C22ORF30 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V12, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     0   6
  C22ORF30 WILD-TYPE  10 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      0    6
  C22ORF30 WILD-TYPE   10  392
                        clus
vv                       C22ORF30 MUTATED C22ORF30 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                6                392
[1] 2 2
[1] FALSE

Clustering(127) Variable = ANKRD34A MUTATION ANALYSIS
D127V1, survival
                    sevent
clus2                  0   1
  ANKRD34A MUTATED     5   4
  ANKRD34A WILD-TYPE 333 212
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                 9                545 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                 4                212 
$`ANKRD34A MUTATED`
TCGA-CG-4460 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5723 TCGA-HJ-7597 TCGA-HU-A4G8 
       21.99         1.12         6.58       105.07        26.47        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-VQ-A8P2 
       29.98         0.10        38.14 

$`ANKRD34A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
               0.1                0.0 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
            105.07             122.30 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
             22.68              13.51 
[1] "0.1 - 105.1 (22.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D127V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD34A MUTATED         0        0        1        1         3         1
  ANKRD34A WILD-TYPE      10       20       45       30        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD34A MUTATED           0          1          0          2        2
  ANKRD34A WILD-TYPE        29         83         62         37       41
                    vv
clus                 STAGE IVA
  ANKRD34A MUTATED           0
  ANKRD34A WILD-TYPE         4
D127V3, multiclass
            clus
vv           ANKRD34A MUTATED ANKRD34A WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ANKRD34A MUTATED       0   3   3   5
  ANKRD34A WILD-TYPE    54 132 258  97
D127V4, multiclass
       clus
vv      ANKRD34A MUTATED ANKRD34A WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   3                258
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ANKRD34A MUTATED     3   5   2   1
  ANKRD34A WILD-TYPE 192 168  87  84
D127V5, multiclass
    clus
vv   ANKRD34A MUTATED ANKRD34A WILD-TYPE
  N0                3                192
  N1                5                168
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V6, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     9   1
  ANKRD34A WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      9    1
  ANKRD34A WILD-TYPE  473   37
   clus
vv  ANKRD34A MUTATED ANKRD34A WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D127V7, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     6   5
  ANKRD34A WILD-TYPE 166 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      6    5
  ANKRD34A WILD-TYPE  166  401
        clus
vv       ANKRD34A MUTATED ANKRD34A WILD-TYPE
  FEMALE                6                166
  MALE                  5                401
[1] 2 2
[1] FALSE
D127V8, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     9   1
  ANKRD34A WILD-TYPE 407 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      9    1
  ANKRD34A WILD-TYPE  407  101
     clus
vv    ANKRD34A MUTATED ANKRD34A WILD-TYPE
  NO                 9                407
  YES                1                101
[1] 2 2
[1] FALSE
D127V9, continuous
D127V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD34A MUTATED       4                         0
  ANKRD34A WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD34A MUTATED                                           0     5
  ANKRD34A WILD-TYPE                                         1   352
D127V11, multiclass
                                           clus
vv                                          ANKRD34A MUTATED ANKRD34A WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V12, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     0   8
  ANKRD34A WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      0    8
  ANKRD34A WILD-TYPE   10  390
                        clus
vv                       ANKRD34A MUTATED ANKRD34A WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(128) Variable = WNK4 MUTATION ANALYSIS
D128V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    13   9
  WNK4 WILD-TYPE 325 207
  WNK4 MUTATED WNK4 WILD-TYPE 
            22            532 
  WNK4 MUTATED WNK4 WILD-TYPE 
             9            207 
$`WNK4 MUTATED`
TCGA-CG-4460 TCGA-JY-A6FA TCGA-M9-A5M8 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 
       21.99        44.75        33.11         6.97        34.68        35.84 
TCGA-BR-7723 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-8533 TCGA-CG-5721 
       28.73         1.12        16.14         7.17        15.39         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YV TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 
      105.07        28.96         5.92        77.29        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H3 
       22.68        29.98         0.10        29.00 

$`WNK4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  WNK4 MUTATED WNK4 WILD-TYPE 
           0.1            0.0 
  WNK4 MUTATED WNK4 WILD-TYPE 
        105.07         122.30 
  WNK4 MUTATED WNK4 WILD-TYPE 
        25.705         13.410 
[1] "0.1 - 105.1 (25.7)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D128V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNK4 MUTATED         0        1        1        4         4         5
  WNK4 WILD-TYPE      10       19       45       27        80        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK4 MUTATED           0          2          2          3        2         0
  WNK4 WILD-TYPE        29         82         60         36       41         4
D128V3, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              4             27
  STAGE IIA             4             80
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WNK4 MUTATED       1   6  10   8
  WNK4 WILD-TYPE    53 129 251  94
D128V4, multiclass
       clus
vv      WNK4 MUTATED WNK4 WILD-TYPE
  T0+T1            1             53
  T2               6            129
  T3              10            251
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WNK4 MUTATED     9  10   1   4
  WNK4 WILD-TYPE 186 163  88  81
D128V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0            9            186
  N1           10            163
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V6, binary
                cls
clus               0   1
  WNK4 MUTATED    23   1
  WNK4 WILD-TYPE 459  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     23    1
  WNK4 WILD-TYPE  459   37
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           23            459
  1            1             37
[1] 2 2
[1] FALSE
D128V7, binary
                cls
clus               0   1
  WNK4 MUTATED    14  12
  WNK4 WILD-TYPE 158 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     14   12
  WNK4 WILD-TYPE  158  394
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  FEMALE           14            158
  MALE             12            394
[1] 2 2
[1] FALSE
D128V8, binary
                cls
clus               0   1
  WNK4 MUTATED    19   2
  WNK4 WILD-TYPE 397 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     19    2
  WNK4 WILD-TYPE  397  100
     clus
vv    WNK4 MUTATED WNK4 WILD-TYPE
  NO            19            397
  YES            2            100
[1] 2 2
[1] FALSE
D128V9, continuous
D128V10, continuous
[1] "Remove cluster labels:" "WNK4 MUTATED"          
clus
  WNK4 MUTATED WNK4 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FE 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" "WNK4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WNK4 MUTATED       8                         0
  WNK4 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNK4 MUTATED                                           0    11
  WNK4 WILD-TYPE                                         1   346
D128V11, multiclass
                                           clus
vv                                          WNK4 MUTATED WNK4 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V12, binary
                cls
clus               0   1
  WNK4 MUTATED     0  18
  WNK4 WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      0   18
  WNK4 WILD-TYPE   10  380
                        clus
vv                       WNK4 MUTATED WNK4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(129) Variable = PLA2G1B MUTATION ANALYSIS
D129V1, survival
                   sevent
clus2                 0   1
  PLA2G1B MUTATED     5   1
  PLA2G1B WILD-TYPE 333 215
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               548 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                1               215 
$`PLA2G1B MUTATED`
TCGA-BR-8371 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8531 TCGA-D7-8573 TCGA-FP-8211 
       11.80        12.76        12.59        12.59        19.50        13.58 

$`PLA2G1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
        0.95        26.33         4.31        14.04         3.32        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
             11.8               0.0 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
             19.5             122.3 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
           12.675            13.730 
[1] "11.8 - 19.5 (12.7)" "0.0 - 122.3 (13.7)"
[1] "hr=" "1.9"
D129V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G1B MUTATED         0        0        0        1         1         1
  PLA2G1B WILD-TYPE      10       20       46       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G1B MUTATED           0          2          1          0        0
  PLA2G1B WILD-TYPE        29         82         61         39       43
                   vv
clus                STAGE IVA
  PLA2G1B MUTATED           0
  PLA2G1B WILD-TYPE         4
D129V3, multiclass
            clus
vv           PLA2G1B MUTATED PLA2G1B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PLA2G1B MUTATED       0   0   6   0
  PLA2G1B WILD-TYPE    54 135 255 102
D129V4, multiclass
       clus
vv      PLA2G1B MUTATED PLA2G1B WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  6               255
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PLA2G1B MUTATED     2   3   0   1
  PLA2G1B WILD-TYPE 193 170  89  84
D129V5, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  N0               2               193
  N1               3               170
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V6, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     5   0
  PLA2G1B WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      5    0
  PLA2G1B WILD-TYPE  477   38
   clus
vv  PLA2G1B MUTATED PLA2G1B WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D129V7, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     3   3
  PLA2G1B WILD-TYPE 169 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      3    3
  PLA2G1B WILD-TYPE  169  403
        clus
vv       PLA2G1B MUTATED PLA2G1B WILD-TYPE
  FEMALE               3               169
  MALE                 3               403
[1] 2 2
[1] FALSE
D129V8, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     3   3
  PLA2G1B WILD-TYPE 413  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      3    3
  PLA2G1B WILD-TYPE  413   99
     clus
vv    PLA2G1B MUTATED PLA2G1B WILD-TYPE
  NO                3               413
  YES               3                99
[1] 2 2
[1] FALSE
D129V9, continuous
D129V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLA2G1B MUTATED       3                         0
  PLA2G1B WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLA2G1B MUTATED                                           0     3
  PLA2G1B WILD-TYPE                                         1   354
D129V11, multiclass
                                           clus
vv                                          PLA2G1B MUTATED PLA2G1B WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V12, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     0   6
  PLA2G1B WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      0    6
  PLA2G1B WILD-TYPE   10  392
                        clus
vv                       PLA2G1B MUTATED PLA2G1B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(130) Variable = ORC3L MUTATION ANALYSIS
D130V1, survival
                 sevent
clus2               0   1
  ORC3L MUTATED     8   3
  ORC3L WILD-TYPE 330 213
  ORC3L MUTATED ORC3L WILD-TYPE 
             11             543 
  ORC3L MUTATED ORC3L WILD-TYPE 
              3             213 
$`ORC3L MUTATED`
TCGA-L5-A8NJ TCGA-L5-A8NV TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8058 
       16.47        52.57         6.97         9.34        34.68        37.25 
TCGA-BR-8360 TCGA-BR-8591 TCGA-HU-8238 TCGA-HU-A4GP TCGA-VQ-A8P2 
        6.18        28.14         1.51         8.98        38.14 

$`ORC3L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ORC3L MUTATED ORC3L WILD-TYPE 
           1.51            0.00 
  ORC3L MUTATED ORC3L WILD-TYPE 
          52.57          122.30 
  ORC3L MUTATED ORC3L WILD-TYPE 
          16.47           13.55 
[1] "1.5 - 52.6 (16.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D130V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ORC3L MUTATED         0        0        1        0         4         0
  ORC3L WILD-TYPE      10       20       45       31        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ORC3L MUTATED           1          2          1          1        0         0
  ORC3L WILD-TYPE        28         82         61         38       43         4
D130V3, multiclass
            clus
vv           ORC3L MUTATED ORC3L WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ORC3L MUTATED       0   2   7   3
  ORC3L WILD-TYPE    54 133 254  99
D130V4, multiclass
       clus
vv      ORC3L MUTATED ORC3L WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ORC3L MUTATED     4   6   2   1
  ORC3L WILD-TYPE 191 167  87  84
D130V5, multiclass
    clus
vv   ORC3L MUTATED ORC3L WILD-TYPE
  N0             4             191
  N1             6             167
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V6, binary
                 cls
clus                0   1
  ORC3L MUTATED    12   0
  ORC3L WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED     12    0
  ORC3L WILD-TYPE  470   38
   clus
vv  ORC3L MUTATED ORC3L WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D130V7, binary
                 cls
clus                0   1
  ORC3L MUTATED     5   9
  ORC3L WILD-TYPE 167 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED      5    9
  ORC3L WILD-TYPE  167  397
        clus
vv       ORC3L MUTATED ORC3L WILD-TYPE
  FEMALE             5             167
  MALE               9             397
[1] 2 2
[1] FALSE
D130V8, binary
                 cls
clus                0   1
  ORC3L MUTATED    10   1
  ORC3L WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED     10    1
  ORC3L WILD-TYPE  406  101
     clus
vv    ORC3L MUTATED ORC3L WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D130V9, continuous
D130V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ORC3L MUTATED       2                         0
  ORC3L WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ORC3L MUTATED                                           0    11
  ORC3L WILD-TYPE                                         1   346
D130V11, multiclass
                                           clus
vv                                          ORC3L MUTATED ORC3L WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V12, binary
                 cls
clus                0   1
  ORC3L MUTATED     0  10
  ORC3L WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED      0   10
  ORC3L WILD-TYPE   10  388
                        clus
vv                       ORC3L MUTATED ORC3L WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(131) Variable = SLC9A10 MUTATION ANALYSIS
D131V1, survival
                   sevent
clus2                 0   1
  SLC9A10 MUTATED    13   6
  SLC9A10 WILD-TYPE 325 210
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               19               535 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
                6               210 
$`SLC9A10 MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-L5-A893 TCGA-L5-A8NM TCGA-L5-A8NQ 
       19.99         7.69         0.79         3.02         7.76        21.37 
TCGA-L5-A8NS TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8680 
       13.41        34.68        29.59         6.18         0.26        31.96 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-8602 TCGA-MX-A5UJ TCGA-RD-A7BT 
        6.02       105.07        11.44        22.32        19.73         8.61 
TCGA-VQ-A8P2 
       38.14 

$`SLC9A10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.55        13.22         5.49         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 
        2.66        19.96         2.20         7.40        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
             0.26              0.00 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           105.07            122.30 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
            13.41             13.58 
[1] "0.3 - 105.1 (13.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D131V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A10 MUTATED         2        0        2        1         3         5
  SLC9A10 WILD-TYPE       8       20       44       30        81        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A10 MUTATED           0          2          1          1        3
  SLC9A10 WILD-TYPE        29         82         61         38       40
                   vv
clus                STAGE IVA
  SLC9A10 MUTATED           0
  SLC9A10 WILD-TYPE         4
D131V3, multiclass
            clus
vv           SLC9A10 MUTATED SLC9A10 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                5                78
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC9A10 MUTATED       3   4   8   5
  SLC9A10 WILD-TYPE    51 131 253  97
D131V4, multiclass
       clus
vv      SLC9A10 MUTATED SLC9A10 WILD-TYPE
  T0+T1               3                51
  T2                  4               131
  T3                  8               253
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC9A10 MUTATED     9   6   2   3
  SLC9A10 WILD-TYPE 186 167  87  82
D131V5, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  N0               9               186
  N1               6               167
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V6, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    17   1
  SLC9A10 WILD-TYPE 465  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     17    1
  SLC9A10 WILD-TYPE  465   37
   clus
vv  SLC9A10 MUTATED SLC9A10 WILD-TYPE
  0              17               465
  1               1                37
[1] 2 2
[1] FALSE
D131V7, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED     8  12
  SLC9A10 WILD-TYPE 164 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED      8   12
  SLC9A10 WILD-TYPE  164  394
        clus
vv       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  FEMALE               8               164
  MALE                12               394
[1] 2 2
[1] FALSE
D131V8, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    18   2
  SLC9A10 WILD-TYPE 398 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     18    2
  SLC9A10 WILD-TYPE  398  100
     clus
vv    SLC9A10 MUTATED SLC9A10 WILD-TYPE
  NO               18               398
  YES               2               100
[1] 2 2
[1] FALSE
D131V9, continuous
D131V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A10 MUTATED       2                         1
  SLC9A10 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A10 MUTATED                                           1    14
  SLC9A10 WILD-TYPE                                         0   343
D131V11, multiclass
                                           clus
vv                                          SLC9A10 MUTATED SLC9A10 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  14               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V12, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED     0  12
  SLC9A10 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED      0   12
  SLC9A10 WILD-TYPE   10  386
                        clus
vv                       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(132) Variable = ADAMDEC1 MUTATION ANALYSIS
D132V1, survival
                    sevent
clus2                  0   1
  ADAMDEC1 MUTATED    10   3
  ADAMDEC1 WILD-TYPE 328 213
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                13                541 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                 3                213 
$`ADAMDEC1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A4OW TCGA-L5-A891 TCGA-BR-8368 TCGA-BR-8487 
       19.99        21.99         7.13         3.75         4.31         1.12 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-A448 TCGA-HU-8602 
       31.96        11.77         6.02        65.10        21.27        22.32 
TCGA-VQ-A8P2 
       38.14 

$`ADAMDEC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
              1.12               0.00 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
              65.1              122.3 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
             19.99              13.55 
[1] "1.1 - 65.1 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D132V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAMDEC1 MUTATED         0        0        2        0         1         2
  ADAMDEC1 WILD-TYPE      10       20       44       31        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMDEC1 MUTATED           0          3          1          1        3
  ADAMDEC1 WILD-TYPE        29         81         61         38       40
                    vv
clus                 STAGE IVA
  ADAMDEC1 MUTATED           0
  ADAMDEC1 WILD-TYPE         4
D132V3, multiclass
            clus
vv           ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ADAMDEC1 MUTATED       1   3   5   6
  ADAMDEC1 WILD-TYPE    53 132 256  96
D132V4, multiclass
       clus
vv      ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                   5                256
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ADAMDEC1 MUTATED     5   6   1   2
  ADAMDEC1 WILD-TYPE 190 167  88  83
D132V5, multiclass
    clus
vv   ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  N0                5                190
  N1                6                167
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V6, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED    12   2
  ADAMDEC1 WILD-TYPE 470  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED     12    2
  ADAMDEC1 WILD-TYPE  470   36
   clus
vv  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  0               12                470
  1                2                 36
[1] 2 2
[1] FALSE
D132V7, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     8   7
  ADAMDEC1 WILD-TYPE 164 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      8    7
  ADAMDEC1 WILD-TYPE  164  399
        clus
vv       ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  FEMALE                8                164
  MALE                  7                399
[1] 2 2
[1] FALSE
D132V8, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     9   2
  ADAMDEC1 WILD-TYPE 407 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      9    2
  ADAMDEC1 WILD-TYPE  407  100
     clus
vv    ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  NO                 9                407
  YES                2                100
[1] 2 2
[1] FALSE
D132V9, continuous
D132V10, continuous
[1] "Remove cluster labels:" "ADAMDEC1 MUTATED"      
clus
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OX 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" "ADAMDEC1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ADAMDEC1 MUTATED       3                         0
  ADAMDEC1 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAMDEC1 MUTATED                                           0     8
  ADAMDEC1 WILD-TYPE                                         1   349
D132V11, multiclass
                                           clus
vv                                          ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V12, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     1   7
  ADAMDEC1 WILD-TYPE   9 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      1    7
  ADAMDEC1 WILD-TYPE    9  391
                        clus
vv                       ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(133) Variable = ASAP2 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  ASAP2 MUTATED    10   8
  ASAP2 WILD-TYPE 328 208
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             18             536 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
              8             208 
$`ASAP2 MUTATED`
TCGA-L5-A43J TCGA-EQ-A4SO TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A8NI TCGA-L5-A8NK 
        4.31        16.24         0.30         3.32        13.48        13.55 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8589 TCGA-CD-8533 TCGA-CG-5728 
        6.97        34.68        31.27        27.12        15.39        65.10 
TCGA-CG-5733 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-RD-A7C1 
       21.07        11.31        11.44         0.10        23.84        16.67 

$`ASAP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        12.92        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.24        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ASAP2 MUTATED ASAP2 WILD-TYPE 
            0.1             0.0 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
           65.1           122.3 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
         14.470          13.545 
[1] "0.1 - 65.1 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D133V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASAP2 MUTATED         0        0        2        1         2         3
  ASAP2 WILD-TYPE      10       20       44       30        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASAP2 MUTATED           2          3          3          3        1         0
  ASAP2 WILD-TYPE        27         81         59         36       42         4
D133V3, multiclass
            clus
vv           ASAP2 MUTATED ASAP2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ASAP2 MUTATED       0   4  10   6
  ASAP2 WILD-TYPE    54 131 251  96
D133V4, multiclass
       clus
vv      ASAP2 MUTATED ASAP2 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3               10             251
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASAP2 MUTATED     7   6   5   3
  ASAP2 WILD-TYPE 188 167  84  82
D133V5, multiclass
    clus
vv   ASAP2 MUTATED ASAP2 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             5              84
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V6, binary
                 cls
clus                0   1
  ASAP2 MUTATED    18   0
  ASAP2 WILD-TYPE 464  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED     18    0
  ASAP2 WILD-TYPE  464   38
   clus
vv  ASAP2 MUTATED ASAP2 WILD-TYPE
  0            18             464
  1             0              38
[1] 2 2
[1] FALSE
D133V7, binary
                 cls
clus                0   1
  ASAP2 MUTATED     9  12
  ASAP2 WILD-TYPE 163 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED      9   12
  ASAP2 WILD-TYPE  163  394
        clus
vv       ASAP2 MUTATED ASAP2 WILD-TYPE
  FEMALE             9             163
  MALE              12             394
[1] 2 2
[1] FALSE
D133V8, binary
                 cls
clus                0   1
  ASAP2 MUTATED    14   1
  ASAP2 WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED     14    1
  ASAP2 WILD-TYPE  402  101
     clus
vv    ASAP2 MUTATED ASAP2 WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D133V9, continuous
D133V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASAP2 MUTATED       3                         0
  ASAP2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASAP2 MUTATED                                           0    16
  ASAP2 WILD-TYPE                                         1   341
D133V11, multiclass
                                           clus
vv                                          ASAP2 MUTATED ASAP2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V12, binary
                 cls
clus                0   1
  ASAP2 MUTATED     0  14
  ASAP2 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED      0   14
  ASAP2 WILD-TYPE   10  384
                        clus
vv                       ASAP2 MUTATED ASAP2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(134) Variable = BCORL1 MUTATION ANALYSIS
D134V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    17   7
  BCORL1 WILD-TYPE 321 209
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              24              530 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               7              209 
$`BCORL1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-B7-A5TI TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 
       19.99        21.99        19.56         6.61        34.68        32.25 
TCGA-BR-8284 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5723 
        8.05         0.26        31.27         1.12        16.14       105.07 
TCGA-D7-5577 TCGA-D7-6528 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 
       25.71        15.22        14.47        30.51        26.47        22.68 
TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       29.00        19.73        14.04        74.53        38.14        38.93 

$`BCORL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        52.21         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       36.95         3.72        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            0.26             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          105.07           122.30 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          22.335           13.380 
[1] "0.3 - 105.1 (22.3)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D134V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCORL1 MUTATED         0        0        4        1         3         3
  BCORL1 WILD-TYPE      10       20       42       30        81        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          4          1          7        2
  BCORL1 WILD-TYPE        28         80         61         32       41
                  vv
clus               STAGE IVA
  BCORL1 MUTATED           0
  BCORL1 WILD-TYPE         4
D134V3, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              7               32
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  BCORL1 MUTATED       0   8   6  12
  BCORL1 WILD-TYPE    54 127 255  90
D134V4, multiclass
       clus
vv      BCORL1 MUTATED BCORL1 WILD-TYPE
  T0+T1              0               54
  T2                 8              127
  T3                 6              255
  T4                12               90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BCORL1 MUTATED     9   7   1   9
  BCORL1 WILD-TYPE 186 166  88  76
D134V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0              9              186
  N1              7              166
  N2              1               88
  N3              9               76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V6, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    22   2
  BCORL1 WILD-TYPE 460  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     22    2
  BCORL1 WILD-TYPE  460   36
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             22              460
  1              2               36
[1] 2 2
[1] FALSE
D134V7, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    18   9
  BCORL1 WILD-TYPE 154 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     18    9
  BCORL1 WILD-TYPE  154  397
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  FEMALE             18              154
  MALE                9              397
[1] 2 2
[1] FALSE
D134V8, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    21   3
  BCORL1 WILD-TYPE 395  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     21    3
  BCORL1 WILD-TYPE  395   99
     clus
vv    BCORL1 MUTATED BCORL1 WILD-TYPE
  NO              21              395
  YES              3               99
[1] 2 2
[1] FALSE
D134V9, continuous
D134V10, continuous
[1] "Remove cluster labels:" "BCORL1 MUTATED"        
clus
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" "BCORL1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"BCORL1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCORL1 MUTATED       2                         0
  BCORL1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCORL1 MUTATED                                           0    22
  BCORL1 WILD-TYPE                                         1   335
D134V11, multiclass
                                           clus
vv                                          BCORL1 MUTATED BCORL1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V12, binary
                  cls
clus                 0   1
  BCORL1 MUTATED     1  20
  BCORL1 WILD-TYPE   9 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED      1   20
  BCORL1 WILD-TYPE    9  378
                        clus
vv                       BCORL1 MUTATED BCORL1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             20              378
[1] 2 2
[1] FALSE

Clustering(135) Variable = KCNJ10 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  KCNJ10 MUTATED     8   4
  KCNJ10 WILD-TYPE 330 212
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              12              542 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
               4              212 
$`KCNJ10 MUTATED`
TCGA-L5-A4OI TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8487 
       19.99        26.70         6.97        34.68        36.16         1.12 
TCGA-CD-A4MG TCGA-CG-5733 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.58        21.07        11.44        22.32         6.51        38.14 

$`KCNJ10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
            1.12             0.00 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
           38.14           122.30 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
           20.53            13.53 
[1] "1.1 - 38.1 (20.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D135V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNJ10 MUTATED         1        1        0        0         4         2
  KCNJ10 WILD-TYPE       9       19       46       31        80        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNJ10 MUTATED           0          4          1          1        0
  KCNJ10 WILD-TYPE        29         80         61         38       43
                  vv
clus               STAGE IVA
  KCNJ10 MUTATED           0
  KCNJ10 WILD-TYPE         4
D135V3, multiclass
            clus
vv           KCNJ10 MUTATED KCNJ10 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KCNJ10 MUTATED       2   1   7   4
  KCNJ10 WILD-TYPE    52 134 254  98
D135V4, multiclass
       clus
vv      KCNJ10 MUTATED KCNJ10 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 7              254
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KCNJ10 MUTATED     8   4   1   2
  KCNJ10 WILD-TYPE 187 169  88  83
D135V5, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  N0              8              187
  N1              4              169
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V6, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED    12   0
  KCNJ10 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED     12    0
  KCNJ10 WILD-TYPE  470   38
   clus
vv  KCNJ10 MUTATED KCNJ10 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D135V7, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     9   6
  KCNJ10 WILD-TYPE 163 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      9    6
  KCNJ10 WILD-TYPE  163  400
        clus
vv       KCNJ10 MUTATED KCNJ10 WILD-TYPE
  FEMALE              9              163
  MALE                6              400
[1] 2 2
[1] FALSE
D135V8, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED    12   1
  KCNJ10 WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED     12    1
  KCNJ10 WILD-TYPE  404  101
     clus
vv    KCNJ10 MUTATED KCNJ10 WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D135V9, continuous
D135V10, continuous
[1] "Remove cluster labels:" "KCNJ10 MUTATED"        
clus
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" "KCNJ10 WILD-TYPE" 
      TCGA-Z6-AAPN 
"KCNJ10 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KCNJ10 MUTATED       3                         1
  KCNJ10 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNJ10 MUTATED                                           0    10
  KCNJ10 WILD-TYPE                                         1   347
D135V11, multiclass
                                           clus
vv                                          KCNJ10 MUTATED KCNJ10 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V12, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     0  12
  KCNJ10 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      0   12
  KCNJ10 WILD-TYPE   10  386
                        clus
vv                       KCNJ10 MUTATED KCNJ10 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(136) Variable = WNT16 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED    10   2
  WNT16 WILD-TYPE 328 214
  WNT16 MUTATED WNT16 WILD-TYPE 
             12             542 
  WNT16 MUTATED WNT16 WILD-TYPE 
              2             214 
$`WNT16 MUTATED`
TCGA-L5-A4OI TCGA-JY-A93E TCGA-BR-8081 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ 
       19.99        25.22        32.25        28.14        16.14        12.62 
TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.02        11.44        22.68        29.98        19.73        74.53 

$`WNT16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  WNT16 MUTATED WNT16 WILD-TYPE 
           6.02            0.00 
  WNT16 MUTATED WNT16 WILD-TYPE 
          74.53          122.30 
  WNT16 MUTATED WNT16 WILD-TYPE 
         21.335          13.495 
[1] "6.0 - 74.5 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D136V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT16 MUTATED         0        0        2        0         1         2
  WNT16 WILD-TYPE      10       20       44       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNT16 MUTATED           0          2          2          2        2         0
  WNT16 WILD-TYPE        29         82         60         37       41         4
D136V3, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  WNT16 MUTATED       0   3   6   4
  WNT16 WILD-TYPE    54 132 255  98
D136V4, multiclass
       clus
vv      WNT16 MUTATED WNT16 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                6             255
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  WNT16 MUTATED     3   6   1   4
  WNT16 WILD-TYPE 192 167  88  81
D136V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             3             192
  N1             6             167
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V6, binary
                 cls
clus                0   1
  WNT16 MUTATED    12   1
  WNT16 WILD-TYPE 470  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED     12    1
  WNT16 WILD-TYPE  470   37
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0            12             470
  1             1              37
[1] 2 2
[1] FALSE
D136V7, binary
                 cls
clus                0   1
  WNT16 MUTATED     7   7
  WNT16 WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      7    7
  WNT16 WILD-TYPE  165  399
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D136V8, binary
                 cls
clus                0   1
  WNT16 MUTATED    12   0
  WNT16 WILD-TYPE 404 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED     12    0
  WNT16 WILD-TYPE  404  102
     clus
vv    WNT16 MUTATED WNT16 WILD-TYPE
  NO             12             404
  YES             0             102
[1] 2 2
[1] FALSE
D136V9, continuous
D136V10, continuous
[1] "Remove cluster labels:" "WNT16 MUTATED"         
clus
  WNT16 MUTATED WNT16 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" "WNT16 WILD-TYPE" 
     TCGA-Z6-AAPN 
"WNT16 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WNT16 MUTATED       3                         0
  WNT16 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNT16 MUTATED                                           0     9
  WNT16 WILD-TYPE                                         1   348
D136V11, multiclass
                                           clus
vv                                          WNT16 MUTATED WNT16 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V12, binary
                 cls
clus                0   1
  WNT16 MUTATED     1   9
  WNT16 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      1    9
  WNT16 WILD-TYPE    9  389
                        clus
vv                       WNT16 MUTATED WNT16 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(137) Variable = JARID2 MUTATION ANALYSIS
D137V1, survival
                  sevent
clus2                0   1
  JARID2 MUTATED    30  10
  JARID2 WILD-TYPE 308 206
  JARID2 MUTATED JARID2 WILD-TYPE 
              40              514 
  JARID2 MUTATED JARID2 WILD-TYPE 
              10              206 
$`JARID2 MUTATED`
TCGA-2H-A9GM TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A8NM 
       13.94        25.22         3.16        29.00         2.60         7.76 
TCGA-VR-AA4D TCGA-XP-A8T8 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 
       46.19        14.37         9.67        34.68        44.94        14.43 
TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       29.59         4.31        25.05         1.12        28.14        31.96 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5723 
       12.43         6.58        12.62         1.02        12.03       105.07 
TCGA-CG-5726 TCGA-D7-5578 TCGA-D7-A74A TCGA-F1-6874 TCGA-FP-A9TM TCGA-HU-A4G8 
       28.96        12.66        19.96        14.47         6.21        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.98         0.10         6.51         2.10        29.00        14.07 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.73        74.53        19.04        38.14 

$`JARID2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       20.32        22.29        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56        11.08         5.52        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        21.37         8.98         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  JARID2 MUTATED JARID2 WILD-TYPE 
             0.1              0.0 
  JARID2 MUTATED JARID2 WILD-TYPE 
          105.07           122.30 
  JARID2 MUTATED JARID2 WILD-TYPE 
          14.450           13.445 
[1] "0.1 - 105.1 (14.4)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D137V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JARID2 MUTATED         0        1        6        3         7         6
  JARID2 WILD-TYPE      10       19       40       28        77        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JARID2 MUTATED           2          6          0          5        3
  JARID2 WILD-TYPE        27         78         62         34       40
                  vv
clus               STAGE IVA
  JARID2 MUTATED           0
  JARID2 WILD-TYPE         4
D137V3, multiclass
            clus
vv           JARID2 MUTATED JARID2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                6               40
  STAGE II                3               28
  STAGE IIA               7               77
  STAGE IIB               6               77
  STAGE III               2               27
  STAGE IIIA              6               78
  STAGE IIIB              0               62
  STAGE IIIC              5               34
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  JARID2 MUTATED       7   9  15  11
  JARID2 WILD-TYPE    47 126 246  91
D137V4, multiclass
       clus
vv      JARID2 MUTATED JARID2 WILD-TYPE
  T0+T1              7               47
  T2                 9              126
  T3                15              246
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  JARID2 MUTATED    15  15   6   4
  JARID2 WILD-TYPE 180 158  83  81
D137V5, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  N0             15              180
  N1             15              158
  N2              6               83
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V6, binary
                  cls
clus                 0   1
  JARID2 MUTATED    38   3
  JARID2 WILD-TYPE 444  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     38    3
  JARID2 WILD-TYPE  444   35
   clus
vv  JARID2 MUTATED JARID2 WILD-TYPE
  0             38              444
  1              3               35
[1] 2 2
[1] FALSE
D137V7, binary
                  cls
clus                 0   1
  JARID2 MUTATED    18  26
  JARID2 WILD-TYPE 154 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     18   26
  JARID2 WILD-TYPE  154  380
        clus
vv       JARID2 MUTATED JARID2 WILD-TYPE
  FEMALE             18              154
  MALE               26              380
[1] 2 2
[1] FALSE
D137V8, binary
                  cls
clus                 0   1
  JARID2 MUTATED    33   4
  JARID2 WILD-TYPE 383  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     33    4
  JARID2 WILD-TYPE  383   98
     clus
vv    JARID2 MUTATED JARID2 WILD-TYPE
  NO              33              383
  YES              4               98
[1] 2 2
[1] FALSE
D137V9, continuous
[1] "Remove cluster labels:" "JARID2 MUTATED"        
clus
  JARID2 MUTATED JARID2 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7B 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"JARID2 WILD-TYPE" "JARID2 WILD-TYPE" 
D137V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  JARID2 MUTATED      11                         1
  JARID2 WILD-TYPE   122                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JARID2 MUTATED                                           0    26
  JARID2 WILD-TYPE                                         1   331
D137V11, multiclass
                                           clus
vv                                          JARID2 MUTATED JARID2 WILD-TYPE
  ASIAN                                                 11              122
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 26              331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V12, binary
                  cls
clus                 0   1
  JARID2 MUTATED     2  29
  JARID2 WILD-TYPE   8 369
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED      2   29
  JARID2 WILD-TYPE    8  369
                        clus
vv                       JARID2 MUTATED JARID2 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             29              369
[1] 2 2
[1] FALSE

Clustering(138) Variable = SLC27A3 MUTATION ANALYSIS
D138V1, survival
                   sevent
clus2                 0   1
  SLC27A3 MUTATED     3   5
  SLC27A3 WILD-TYPE 335 211
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                8               546 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                5               211 
$`SLC27A3 MUTATED`
TCGA-L5-A4OI TCGA-LN-A5U7 TCGA-BR-8059 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MG 
       19.99        25.25        14.43        25.05        16.14         6.58 
TCGA-HF-7132 TCGA-HJ-7597 
       77.29        26.47 

$`SLC27A3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
             6.58              0.00 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            77.29            122.30 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
           22.520            13.495 
[1] "6.6 - 77.3 (22.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D138V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC27A3 MUTATED         1        0        2        1         2         0
  SLC27A3 WILD-TYPE       9       20       44       30        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A3 MUTATED           1          0          1          2        0
  SLC27A3 WILD-TYPE        28         84         61         37       43
                   vv
clus                STAGE IVA
  SLC27A3 MUTATED           0
  SLC27A3 WILD-TYPE         4
D138V3, multiclass
            clus
vv           SLC27A3 MUTATED SLC27A3 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC27A3 MUTATED       2   4   3   2
  SLC27A3 WILD-TYPE    52 131 258 100
D138V4, multiclass
       clus
vv      SLC27A3 MUTATED SLC27A3 WILD-TYPE
  T0+T1               2                52
  T2                  4               131
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC27A3 MUTATED     4   3   0   3
  SLC27A3 WILD-TYPE 191 170  89  82
D138V5, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V6, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     8   0
  SLC27A3 WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      8    0
  SLC27A3 WILD-TYPE  474   38
   clus
vv  SLC27A3 MUTATED SLC27A3 WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D138V7, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     4   7
  SLC27A3 WILD-TYPE 168 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      4    7
  SLC27A3 WILD-TYPE  168  399
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  FEMALE               4               168
  MALE                 7               399
[1] 2 2
[1] FALSE
D138V8, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     8   1
  SLC27A3 WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      8    1
  SLC27A3 WILD-TYPE  408  101
     clus
vv    SLC27A3 MUTATED SLC27A3 WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D138V9, continuous
[1] "Remove cluster labels:" "SLC27A3 MUTATED"       
clus
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A7HV 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
D138V10, continuous
[1] "Remove cluster labels:" "SLC27A3 MUTATED"       
clus
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A7HV        TCGA-LN-A7HW 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" "SLC27A3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC27A3 MUTATED       2                         1
  SLC27A3 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC27A3 MUTATED                                           0     6
  SLC27A3 WILD-TYPE                                         1   351
D138V11, multiclass
                                           clus
vv                                          SLC27A3 MUTATED SLC27A3 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V12, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     0   8
  SLC27A3 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      0    8
  SLC27A3 WILD-TYPE   10  390
                        clus
vv                       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(139) Variable = MICALCL MUTATION ANALYSIS
D139V1, survival
                   sevent
clus2                 0   1
  MICALCL MUTATED    12   6
  MICALCL WILD-TYPE 326 210
  MICALCL MUTATED MICALCL WILD-TYPE 
               18               536 
  MICALCL MUTATED MICALCL WILD-TYPE 
                6               210 
$`MICALCL MUTATED`
TCGA-L5-A8NS TCGA-Q9-A6FW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-BR-4257 TCGA-BR-4280 
       13.41         7.82         8.98        22.82         9.67         6.61 
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-5804 
       34.68        32.25         2.66         6.18        31.96        12.10 
TCGA-CD-8533 TCGA-D7-8573 TCGA-D7-8574 TCGA-F1-6874 TCGA-FP-8209 TCGA-VQ-A8DV 
       15.39        19.50        17.19        14.47        59.54        13.25 

$`MICALCL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       16.44        15.35         9.27        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
       29.42        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        17.06         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MICALCL MUTATED MICALCL WILD-TYPE 
             2.66              0.00 
  MICALCL MUTATED MICALCL WILD-TYPE 
            59.54            122.30 
  MICALCL MUTATED MICALCL WILD-TYPE 
           13.940            13.565 
[1] "2.7 - 59.5 (13.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D139V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MICALCL MUTATED         0        0        3        1         3         2
  MICALCL WILD-TYPE      10       20       43       30        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICALCL MUTATED           2          1          1          0        2
  MICALCL WILD-TYPE        27         83         61         39       41
                   vv
clus                STAGE IVA
  MICALCL MUTATED           0
  MICALCL WILD-TYPE         4
D139V3, multiclass
            clus
vv           MICALCL MUTATED MICALCL WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                2                27
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  MICALCL MUTATED       0   5   9   3
  MICALCL WILD-TYPE    54 130 252  99
D139V4, multiclass
       clus
vv      MICALCL MUTATED MICALCL WILD-TYPE
  T0+T1               0                54
  T2                  5               130
  T3                  9               252
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  MICALCL MUTATED     9   3   2   2
  MICALCL WILD-TYPE 186 170  87  83
D139V5, multiclass
    clus
vv   MICALCL MUTATED MICALCL WILD-TYPE
  N0               9               186
  N1               3               170
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V6, binary
                   cls
clus                  0   1
  MICALCL MUTATED    15   2
  MICALCL WILD-TYPE 467  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED     15    2
  MICALCL WILD-TYPE  467   36
   clus
vv  MICALCL MUTATED MICALCL WILD-TYPE
  0              15               467
  1               2                36
[1] 2 2
[1] FALSE
D139V7, binary
                   cls
clus                  0   1
  MICALCL MUTATED     5  14
  MICALCL WILD-TYPE 167 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      5   14
  MICALCL WILD-TYPE  167  392
        clus
vv       MICALCL MUTATED MICALCL WILD-TYPE
  FEMALE               5               167
  MALE                14               392
[1] 2 2
[1] FALSE
D139V8, binary
                   cls
clus                  0   1
  MICALCL MUTATED    14   3
  MICALCL WILD-TYPE 402  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED     14    3
  MICALCL WILD-TYPE  402   99
     clus
vv    MICALCL MUTATED MICALCL WILD-TYPE
  NO               14               402
  YES               3                99
[1] 2 2
[1] FALSE
D139V9, continuous
[1] "Remove cluster labels:" "MICALCL MUTATED"       
clus
  MICALCL MUTATED MICALCL WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-VR-A8EO        TCGA-VR-A8EP 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
D139V10, continuous
[1] "Remove cluster labels:" "MICALCL MUTATED"       
clus
  MICALCL MUTATED MICALCL WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NW        TCGA-LN-A49O 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-R6-A6DN        TCGA-R6-A6L4 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MICALCL MUTATED       3                         0
  MICALCL WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MICALCL MUTATED                                           0    16
  MICALCL WILD-TYPE                                         1   341
D139V11, multiclass
                                           clus
vv                                          MICALCL MUTATED MICALCL WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  16               341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V12, binary
                   cls
clus                  0   1
  MICALCL MUTATED     0  16
  MICALCL WILD-TYPE  10 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      0   16
  MICALCL WILD-TYPE   10  382
                        clus
vv                       MICALCL MUTATED MICALCL WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              16               382
[1] 2 2
[1] FALSE

Clustering(140) Variable = KLHDC8B MUTATION ANALYSIS
D140V1, survival
                   sevent
clus2                 0   1
  KLHDC8B MUTATED     6   4
  KLHDC8B WILD-TYPE 332 212
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
               10               544 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                4               212 
$`KLHDC8B MUTATED`
TCGA-L5-A43J TCGA-B7-A5TI TCGA-BR-8081 TCGA-BR-8363 TCGA-CD-8536 TCGA-CD-A4MI 
        4.31        19.56        32.25         0.26        12.43        11.77 
TCGA-CG-5728 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GU 
       65.10        30.51        26.47         6.58 

$`KLHDC8B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 
        5.52         6.21        77.29        63.06        52.21         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
             0.26              0.00 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
             65.1             122.3 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
           15.995            13.565 
[1] "0.3 - 65.1 (16.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D140V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHDC8B MUTATED         0        0        3        1         0         3
  KLHDC8B WILD-TYPE      10       20       43       30        84        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC8B MUTATED           0          1          0          2        0
  KLHDC8B WILD-TYPE        29         83         62         37       43
                   vv
clus                STAGE IVA
  KLHDC8B MUTATED           0
  KLHDC8B WILD-TYPE         4
D140V3, multiclass
            clus
vv           KLHDC8B MUTATED KLHDC8B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  KLHDC8B MUTATED       0   3   4   3
  KLHDC8B WILD-TYPE    54 132 257  99
D140V4, multiclass
       clus
vv      KLHDC8B MUTATED KLHDC8B WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  4               257
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  KLHDC8B MUTATED     6   2   0   2
  KLHDC8B WILD-TYPE 189 171  89  83
D140V5, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  N0               6               189
  N1               2               171
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V6, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     9   0
  KLHDC8B WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      9    0
  KLHDC8B WILD-TYPE  473   38
   clus
vv  KLHDC8B MUTATED KLHDC8B WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D140V7, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     5   6
  KLHDC8B WILD-TYPE 167 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      5    6
  KLHDC8B WILD-TYPE  167  400
        clus
vv       KLHDC8B MUTATED KLHDC8B WILD-TYPE
  FEMALE               5               167
  MALE                 6               400
[1] 2 2
[1] FALSE
D140V8, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     7   1
  KLHDC8B WILD-TYPE 409 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      7    1
  KLHDC8B WILD-TYPE  409  101
     clus
vv    KLHDC8B MUTATED KLHDC8B WILD-TYPE
  NO                7               409
  YES               1               101
[1] 2 2
[1] FALSE
D140V9, continuous
D140V10, continuous
[1] "Remove cluster labels:" "KLHDC8B MUTATED"       
clus
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" "KLHDC8B WILD-TYPE" 
       TCGA-Z6-AAPN 
"KLHDC8B WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  KLHDC8B MUTATED       3                         0
  KLHDC8B WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHDC8B MUTATED                                           0     6
  KLHDC8B WILD-TYPE                                         1   351
D140V11, multiclass
                                           clus
vv                                          KLHDC8B MUTATED KLHDC8B WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V12, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     0   8
  KLHDC8B WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      0    8
  KLHDC8B WILD-TYPE   10  390
                        clus
vv                       KLHDC8B MUTATED KLHDC8B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(141) Variable = B3GNT5 MUTATION ANALYSIS
D141V1, survival
                  sevent
clus2                0   1
  B3GNT5 MUTATED     9   1
  B3GNT5 WILD-TYPE 329 215
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              10              544 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               1              215 
$`B3GNT5 MUTATED`
TCGA-LN-A4MR TCGA-BR-4257 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
       13.22         9.67         4.31         1.12        31.96         6.02 
TCGA-CG-5723 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-VQ-A8P2 
      105.07         6.58        20.25        38.14 

$`B3GNT5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
            1.12             0.00 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
          105.07           122.30 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
          11.445           13.630 
[1] "1.1 - 105.1 (11.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "4.4"
D141V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B3GNT5 MUTATED         0        0        1        1         2         2
  B3GNT5 WILD-TYPE      10       20       45       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B3GNT5 MUTATED           0          1          0          1        3
  B3GNT5 WILD-TYPE        29         83         62         38       40
                  vv
clus               STAGE IVA
  B3GNT5 MUTATED           0
  B3GNT5 WILD-TYPE         4
D141V3, multiclass
            clus
vv           B3GNT5 MUTATED B3GNT5 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  B3GNT5 MUTATED       0   3   2   6
  B3GNT5 WILD-TYPE    54 132 259  96
D141V4, multiclass
       clus
vv      B3GNT5 MUTATED B3GNT5 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 2              259
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  B3GNT5 MUTATED     4   4   3   0
  B3GNT5 WILD-TYPE 191 169  86  85
D141V5, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V6, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED    11   1
  B3GNT5 WILD-TYPE 471  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED     11    1
  B3GNT5 WILD-TYPE  471   37
   clus
vv  B3GNT5 MUTATED B3GNT5 WILD-TYPE
  0             11              471
  1              1               37
[1] 2 2
[1] FALSE
D141V7, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     5   7
  B3GNT5 WILD-TYPE 167 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      5    7
  B3GNT5 WILD-TYPE  167  399
        clus
vv       B3GNT5 MUTATED B3GNT5 WILD-TYPE
  FEMALE              5              167
  MALE                7              399
[1] 2 2
[1] FALSE
D141V8, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED    10   1
  B3GNT5 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED     10    1
  B3GNT5 WILD-TYPE  406  101
     clus
vv    B3GNT5 MUTATED B3GNT5 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D141V9, continuous
[1] "Remove cluster labels:" "B3GNT5 MUTATED"        
clus
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" "B3GNT5 WILD-TYPE" 
D141V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  B3GNT5 MUTATED       4                         0
  B3GNT5 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B3GNT5 MUTATED                                           0     6
  B3GNT5 WILD-TYPE                                         1   351
D141V11, multiclass
                                           clus
vv                                          B3GNT5 MUTATED B3GNT5 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V12, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     0   9
  B3GNT5 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      0    9
  B3GNT5 WILD-TYPE   10  389
                        clus
vv                       B3GNT5 MUTATED B3GNT5 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(142) Variable = SPTY2D1 MUTATION ANALYSIS
D142V1, survival
                   sevent
clus2                 0   1
  SPTY2D1 MUTATED    13   5
  SPTY2D1 WILD-TYPE 325 211
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               18               536 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
                5               211 
$`SPTY2D1 MUTATED`
TCGA-IC-A6RE TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 
        7.69        20.38         6.97        31.10         4.31        31.27 
TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 
       13.15        12.59         6.58         6.02        28.96        65.10 
TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8602 TCGA-MX-A5UJ TCGA-VQ-A8P2 
        5.92        30.51         5.92        22.32        19.73        38.14 

$`SPTY2D1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        15.02         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             4.31              0.00 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             65.1             122.3 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
           16.440            13.565 
[1] "4.3 - 65.1 (16.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D142V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTY2D1 MUTATED         0        1        3        1         1         4
  SPTY2D1 WILD-TYPE      10       19       43       30        83        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPTY2D1 MUTATED           0          4          0          4        1
  SPTY2D1 WILD-TYPE        29         80         62         35       42
                   vv
clus                STAGE IVA
  SPTY2D1 MUTATED           0
  SPTY2D1 WILD-TYPE         4
D142V3, multiclass
            clus
vv           SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               0                62
  STAGE IIIC               4                35
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SPTY2D1 MUTATED       3   3   6   8
  SPTY2D1 WILD-TYPE    51 132 255  94
D142V4, multiclass
       clus
vv      SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  T0+T1               3                51
  T2                  3               132
  T3                  6               255
  T4                  8                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SPTY2D1 MUTATED     8   7   2   3
  SPTY2D1 WILD-TYPE 187 166  87  82
D142V5, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  N0               8               187
  N1               7               166
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V6, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    19   0
  SPTY2D1 WILD-TYPE 463  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     19    0
  SPTY2D1 WILD-TYPE  463   38
   clus
vv  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  0              19               463
  1               0                38
[1] 2 2
[1] FALSE
D142V7, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    11  10
  SPTY2D1 WILD-TYPE 161 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     11   10
  SPTY2D1 WILD-TYPE  161  396
        clus
vv       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  FEMALE              11               161
  MALE                10               396
[1] 2 2
[1] FALSE
D142V8, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    14   3
  SPTY2D1 WILD-TYPE 402  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     14    3
  SPTY2D1 WILD-TYPE  402   99
     clus
vv    SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  NO               14               402
  YES               3                99
[1] 2 2
[1] FALSE
D142V9, continuous
D142V10, continuous
[1] "Remove cluster labels:" "SPTY2D1 MUTATED"       
clus
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IG-A3QL 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" "SPTY2D1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SPTY2D1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPTY2D1 MUTATED       5                         0
  SPTY2D1 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPTY2D1 MUTATED                                           0    12
  SPTY2D1 WILD-TYPE                                         1   345
D142V11, multiclass
                                           clus
vv                                          SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V12, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     0  16
  SPTY2D1 WILD-TYPE  10 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      0   16
  SPTY2D1 WILD-TYPE   10  382
                        clus
vv                       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              16               382
[1] 2 2
[1] FALSE

Clustering(143) Variable = TP53BP2 MUTATION ANALYSIS
D143V1, survival
                   sevent
clus2                 0   1
  TP53BP2 MUTATED    13   4
  TP53BP2 WILD-TYPE 325 212
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               17               537 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
                4               212 
$`TP53BP2 MUTATED`
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-BR-6452 TCGA-BR-7715 
       52.57         5.92        13.38        12.03        34.68        33.63 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-A4YX 
        4.31        25.05        31.96        15.95        65.10        36.43 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GU TCGA-HU-A4GX 
       11.44        11.08        30.51         6.58        20.25 

$`TP53BP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
             4.31              0.00 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
             65.1             122.3 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
            20.25             13.51 
[1] "4.3 - 65.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D143V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP2 MUTATED         0        0        2        1         7         2
  TP53BP2 WILD-TYPE      10       20       44       30        77        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP2 MUTATED           0          1          1          3        1
  TP53BP2 WILD-TYPE        29         83         61         36       42
                   vv
clus                STAGE IVA
  TP53BP2 MUTATED           0
  TP53BP2 WILD-TYPE         4
D143V3, multiclass
            clus
vv           TP53BP2 MUTATED TP53BP2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                7                77
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TP53BP2 MUTATED       0   5   8   5
  TP53BP2 WILD-TYPE    54 130 253  97
D143V4, multiclass
       clus
vv      TP53BP2 MUTATED TP53BP2 WILD-TYPE
  T0+T1               0                54
  T2                  5               130
  T3                  8               253
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TP53BP2 MUTATED    10   3   2   3
  TP53BP2 WILD-TYPE 185 170  87  82
D143V5, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  N0              10               185
  N1               3               170
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V6, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED    17   1
  TP53BP2 WILD-TYPE 465  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED     17    1
  TP53BP2 WILD-TYPE  465   37
   clus
vv  TP53BP2 MUTATED TP53BP2 WILD-TYPE
  0              17               465
  1               1                37
[1] 2 2
[1] FALSE
D143V7, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     9   9
  TP53BP2 WILD-TYPE 163 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      9    9
  TP53BP2 WILD-TYPE  163  397
        clus
vv       TP53BP2 MUTATED TP53BP2 WILD-TYPE
  FEMALE               9               163
  MALE                 9               397
[1] 2 2
[1] FALSE
D143V8, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED    13   3
  TP53BP2 WILD-TYPE 403  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED     13    3
  TP53BP2 WILD-TYPE  403   99
     clus
vv    TP53BP2 MUTATED TP53BP2 WILD-TYPE
  NO               13               403
  YES               3                99
[1] 2 2
[1] FALSE
D143V9, continuous
[1] "Remove cluster labels:" "TP53BP2 MUTATED"       
clus
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49L        TCGA-LN-A49M 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
D143V10, continuous
[1] "Remove cluster labels:" "TP53BP2 MUTATED"       
clus
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" "TP53BP2 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TP53BP2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TP53BP2 MUTATED       6                         1
  TP53BP2 WILD-TYPE   127                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53BP2 MUTATED                                           0     8
  TP53BP2 WILD-TYPE                                         1   349
D143V11, multiclass
                                           clus
vv                                          TP53BP2 MUTATED TP53BP2 WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V12, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     0  14
  TP53BP2 WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      0   14
  TP53BP2 WILD-TYPE   10  384
                        clus
vv                       TP53BP2 MUTATED TP53BP2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(144) Variable = HDLBP MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2               0   1
  HDLBP MUTATED    26  11
  HDLBP WILD-TYPE 312 205
  HDLBP MUTATED HDLBP WILD-TYPE 
             37             517 
  HDLBP MUTATED HDLBP WILD-TYPE 
             11             205 
$`HDLBP MUTATED`
TCGA-IC-A6RF TCGA-L5-A4OI TCGA-CG-4460 TCGA-IC-A6RE TCGA-JY-A6FG TCGA-JY-A93F 
       15.68        19.99        21.99         7.69        41.52        24.03 
TCGA-L5-A4OW TCGA-L5-A8NM TCGA-L7-A6VZ TCGA-LN-A9FP TCGA-B7-5816 TCGA-B7-A5TI 
        7.13         7.76        10.36        12.03        26.70        19.56 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8363 
        9.34         9.67        44.94        35.24        29.59         0.26 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-8530 TCGA-CG-4305 TCGA-CG-5721 
        4.31        25.05        16.14        12.39        15.95         6.02 
TCGA-CG-5726 TCGA-D7-6518 TCGA-D7-A4YT TCGA-D7-A74A TCGA-FP-A4BE TCGA-HF-A5NB 
       28.96        19.13        14.27        19.96        11.08        30.51 
TCGA-HU-8604 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-RD-A7C1 
       22.82        29.98         6.51         6.58        23.84        16.67 
TCGA-VQ-A8P2 
       38.14 

$`HDLBP WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32         2.66        19.73        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        20.91        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37         8.98         0.10        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HDLBP MUTATED HDLBP WILD-TYPE 
           0.26            0.00 
  HDLBP MUTATED HDLBP WILD-TYPE 
          44.94          122.30 
  HDLBP MUTATED HDLBP WILD-TYPE 
          16.67           13.41 
[1] "0.3 - 44.9 (16.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D144V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDLBP MUTATED         0        2        5        3         6         7
  HDLBP WILD-TYPE      10       18       41       28        78        76
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HDLBP MUTATED           1          6          1          5        2         0
  HDLBP WILD-TYPE        28         78         61         34       41         4
D144V3, multiclass
            clus
vv           HDLBP MUTATED HDLBP WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               3              28
  STAGE IIA              6              78
  STAGE IIB              7              76
  STAGE III              1              28
  STAGE IIIA             6              78
  STAGE IIIB             1              61
  STAGE IIIC             5              34
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HDLBP MUTATED       3  13  13   9
  HDLBP WILD-TYPE    51 122 248  93
D144V4, multiclass
       clus
vv      HDLBP MUTATED HDLBP WILD-TYPE
  T0+T1             3              51
  T2               13             122
  T3               13             248
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HDLBP MUTATED    17  12   2   8
  HDLBP WILD-TYPE 178 161  87  77
D144V5, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  N0            17             178
  N1            12             161
  N2             2              87
  N3             8              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V6, binary
                 cls
clus                0   1
  HDLBP MUTATED    37   1
  HDLBP WILD-TYPE 445  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     37    1
  HDLBP WILD-TYPE  445   37
   clus
vv  HDLBP MUTATED HDLBP WILD-TYPE
  0            37             445
  1             1              37
[1] 2 2
[1] FALSE
D144V7, binary
                 cls
clus                0   1
  HDLBP MUTATED    21  19
  HDLBP WILD-TYPE 151 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     21   19
  HDLBP WILD-TYPE  151  387
        clus
vv       HDLBP MUTATED HDLBP WILD-TYPE
  FEMALE            21             151
  MALE              19             387
[1] 2 2
[1] FALSE
D144V8, binary
                 cls
clus                0   1
  HDLBP MUTATED    30   7
  HDLBP WILD-TYPE 386  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     30    7
  HDLBP WILD-TYPE  386   95
     clus
vv    HDLBP MUTATED HDLBP WILD-TYPE
  NO             30             386
  YES             7              95
[1] 2 2
[1] FALSE
D144V9, continuous
D144V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HDLBP MUTATED       7                         1
  HDLBP WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HDLBP MUTATED                                           0    24
  HDLBP WILD-TYPE                                         1   333
D144V11, multiclass
                                           clus
vv                                          HDLBP MUTATED HDLBP WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                24             333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V12, binary
                 cls
clus                0   1
  HDLBP MUTATED     0  27
  HDLBP WILD-TYPE  10 371
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      0   27
  HDLBP WILD-TYPE   10  371
                        clus
vv                       HDLBP MUTATED HDLBP WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            27             371
[1] 2 2
[1] FALSE

Clustering(145) Variable = SYNJ1 MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2               0   1
  SYNJ1 MUTATED    10   5
  SYNJ1 WILD-TYPE 328 211
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             15             539 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              5             211 
$`SYNJ1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A6QS TCGA-L5-A8NN TCGA-LN-A49M TCGA-LN-A4A6 TCGA-LN-A9FP 
       19.99         9.96         5.49        12.66        12.85        12.03 
TCGA-XP-A8T6 TCGA-BR-8360 TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CG-5718 
       25.08         6.18        31.96         1.48        16.14        36.00 
TCGA-HF-A5NB TCGA-HU-A4GH TCGA-HU-A4GT 
       30.51        11.77         6.51 

$`SYNJ1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           1.48            0.00 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           36.0           122.3 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          12.66           13.68 
[1] "1.5 - 36.0 (12.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D145V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYNJ1 MUTATED         0        1        1        2         4         3
  SYNJ1 WILD-TYPE      10       19       45       29        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNJ1 MUTATED           1          0          1          3        1         0
  SYNJ1 WILD-TYPE        28         84         61         36       42         4
D145V3, multiclass
            clus
vv           SYNJ1 MUTATED SYNJ1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SYNJ1 MUTATED       1   7   5   4
  SYNJ1 WILD-TYPE    53 128 256  98
D145V4, multiclass
       clus
vv      SYNJ1 MUTATED SYNJ1 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SYNJ1 MUTATED     8   4   1   4
  SYNJ1 WILD-TYPE 187 169  88  81
D145V5, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  N0             8             187
  N1             4             169
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V6, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    16   1
  SYNJ1 WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     16    1
  SYNJ1 WILD-TYPE  466   37
   clus
vv  SYNJ1 MUTATED SYNJ1 WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D145V7, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     6  12
  SYNJ1 WILD-TYPE 166 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      6   12
  SYNJ1 WILD-TYPE  166  394
        clus
vv       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  FEMALE             6             166
  MALE              12             394
[1] 2 2
[1] FALSE
D145V8, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    13   3
  SYNJ1 WILD-TYPE 403  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     13    3
  SYNJ1 WILD-TYPE  403   99
     clus
vv    SYNJ1 MUTATED SYNJ1 WILD-TYPE
  NO             13             403
  YES             3              99
[1] 2 2
[1] FALSE
D145V9, continuous
D145V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SYNJ1 MUTATED       6                         1
  SYNJ1 WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYNJ1 MUTATED                                           0     8
  SYNJ1 WILD-TYPE                                         1   349
D145V11, multiclass
                                           clus
vv                                          SYNJ1 MUTATED SYNJ1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V12, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     1  12
  SYNJ1 WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      1   12
  SYNJ1 WILD-TYPE    9  386
                        clus
vv                       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(146) Variable = PIGT MUTATION ANALYSIS
D146V1, survival
                sevent
clus2              0   1
  PIGT MUTATED     9   6
  PIGT WILD-TYPE 329 210
  PIGT MUTATED PIGT WILD-TYPE 
            15            539 
  PIGT MUTATED PIGT WILD-TYPE 
             6            210 
$`PIGT MUTATED`
TCGA-2H-A9GH TCGA-IG-A8O2 TCGA-L5-A8NM TCGA-LN-A7HW TCGA-BR-8059 TCGA-BR-8487 
       31.27         4.67         7.76        12.00        14.43         1.12 
TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 
       28.14         6.58       105.07        28.96        65.10        14.47 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       30.51        22.68        29.98 

$`PIGT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        0.99         6.02         0.99        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PIGT MUTATED PIGT WILD-TYPE 
          1.12           0.00 
  PIGT MUTATED PIGT WILD-TYPE 
        105.07         122.30 
  PIGT MUTATED PIGT WILD-TYPE 
         22.68          13.51 
[1] "1.1 - 105.1 (22.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D146V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGT MUTATED         0        1        2        1         4         3
  PIGT WILD-TYPE      10       19       44       30        80        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGT MUTATED           1          0          1          2        0         0
  PIGT WILD-TYPE        28         84         61         37       43         4
D146V3, multiclass
            clus
vv           PIGT MUTATED PIGT WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PIGT MUTATED       2   6   4   3
  PIGT WILD-TYPE    52 129 257  99
D146V4, multiclass
       clus
vv      PIGT MUTATED PIGT WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PIGT MUTATED     6   6   1   2
  PIGT WILD-TYPE 189 167  88  83
D146V5, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  N0            6            189
  N1            6            167
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V6, binary
                cls
clus               0   1
  PIGT MUTATED    15   0
  PIGT WILD-TYPE 467  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED     15    0
  PIGT WILD-TYPE  467   38
   clus
vv  PIGT MUTATED PIGT WILD-TYPE
  0           15            467
  1            0             38
[1] 2 2
[1] FALSE
D146V7, binary
                cls
clus               0   1
  PIGT MUTATED     5  10
  PIGT WILD-TYPE 167 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      5   10
  PIGT WILD-TYPE  167  396
        clus
vv       PIGT MUTATED PIGT WILD-TYPE
  FEMALE            5            167
  MALE             10            396
[1] 2 2
[1] FALSE
D146V8, binary
                cls
clus               0   1
  PIGT MUTATED    11   1
  PIGT WILD-TYPE 405 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED     11    1
  PIGT WILD-TYPE  405  101
     clus
vv    PIGT MUTATED PIGT WILD-TYPE
  NO            11            405
  YES            1            101
[1] 2 2
[1] FALSE
D146V9, continuous
[1] "Remove cluster labels:" "PIGT MUTATED"          
clus
  PIGT MUTATED PIGT WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
D146V10, continuous
[1] "Remove cluster labels:" "PIGT MUTATED"          
clus
  PIGT MUTATED PIGT WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" "PIGT WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGT MUTATED       5                         0
  PIGT WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGT MUTATED                                           0     5
  PIGT WILD-TYPE                                         1   352
D146V11, multiclass
                                           clus
vv                                          PIGT MUTATED PIGT WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V12, binary
                cls
clus               0   1
  PIGT MUTATED     0   9
  PIGT WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      0    9
  PIGT WILD-TYPE   10  389
                        clus
vv                       PIGT MUTATED PIGT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(147) Variable = TRIP4 MUTATION ANALYSIS
D147V1, survival
                 sevent
clus2               0   1
  TRIP4 MUTATED     8   5
  TRIP4 WILD-TYPE 330 211
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             13             541 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
              5             211 
$`TRIP4 MUTATED`
TCGA-CG-4460 TCGA-LN-A4A6 TCGA-VR-AA7D TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 
       21.99        12.85         9.17        14.43        32.25         8.05 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5723 
       25.05         1.12        31.96        15.95         8.05       105.07 
TCGA-HF-7132 
       77.29 

$`TRIP4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TRIP4 MUTATED TRIP4 WILD-TYPE 
           1.12            0.00 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
         105.07          122.30 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
          15.95           13.51 
[1] "1.1 - 105.1 (15.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D147V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP4 MUTATED         0        0        0        5         1         1
  TRIP4 WILD-TYPE      10       20       46       26        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIP4 MUTATED           1          0          0          3        2         0
  TRIP4 WILD-TYPE        28         84         62         36       41         4
D147V3, multiclass
            clus
vv           TRIP4 MUTATED TRIP4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               5              26
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TRIP4 MUTATED       1   5   2   6
  TRIP4 WILD-TYPE    53 130 259  96
D147V4, multiclass
       clus
vv      TRIP4 MUTATED TRIP4 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                2             259
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TRIP4 MUTATED     3   6   1   3
  TRIP4 WILD-TYPE 192 167  88  82
D147V5, multiclass
    clus
vv   TRIP4 MUTATED TRIP4 WILD-TYPE
  N0             3             192
  N1             6             167
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V6, binary
                 cls
clus                0   1
  TRIP4 MUTATED    12   2
  TRIP4 WILD-TYPE 470  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED     12    2
  TRIP4 WILD-TYPE  470   36
   clus
vv  TRIP4 MUTATED TRIP4 WILD-TYPE
  0            12             470
  1             2              36
[1] 2 2
[1] FALSE
D147V7, binary
                 cls
clus                0   1
  TRIP4 MUTATED     6   8
  TRIP4 WILD-TYPE 166 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED      6    8
  TRIP4 WILD-TYPE  166  398
        clus
vv       TRIP4 MUTATED TRIP4 WILD-TYPE
  FEMALE             6             166
  MALE               8             398
[1] 2 2
[1] FALSE
D147V8, binary
                 cls
clus                0   1
  TRIP4 MUTATED    11   2
  TRIP4 WILD-TYPE 405 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED     11    2
  TRIP4 WILD-TYPE  405  100
     clus
vv    TRIP4 MUTATED TRIP4 WILD-TYPE
  NO             11             405
  YES             2             100
[1] 2 2
[1] FALSE
D147V9, continuous
[1] "Remove cluster labels:" "TRIP4 MUTATED"         
clus
  TRIP4 MUTATED TRIP4 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
D147V10, continuous
[1] "Remove cluster labels:" "TRIP4 MUTATED"         
clus
  TRIP4 MUTATED TRIP4 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7I      TCGA-X8-AAAR 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" "TRIP4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRIP4 MUTATED       2                         0
  TRIP4 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP4 MUTATED                                           0     6
  TRIP4 WILD-TYPE                                         1   351
D147V11, multiclass
                                           clus
vv                                          TRIP4 MUTATED TRIP4 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V12, binary
                 cls
clus                0   1
  TRIP4 MUTATED     0   8
  TRIP4 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED      0    8
  TRIP4 WILD-TYPE   10  390
                        clus
vv                       TRIP4 MUTATED TRIP4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(148) Variable = SGOL2 MUTATION ANALYSIS
D148V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED    10   5
  SGOL2 WILD-TYPE 328 211
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             15             539 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              5             211 
$`SGOL2 MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NI TCGA-LN-A9FR TCGA-V5-A7RE TCGA-BR-6452 TCGA-BR-7703 
       24.00        13.48        12.26        16.44        34.68        36.16 
TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-4306 TCGA-CG-5728 
        0.26        28.14        31.96        13.18         1.02        65.10 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-MX-A5UJ 
       20.25        29.00        19.73 

$`SGOL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.26            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
           65.1           122.3 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          20.25           13.51 
[1] "0.3 - 65.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D148V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGOL2 MUTATED         0        1        4        0         1         1
  SGOL2 WILD-TYPE      10       19       42       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGOL2 MUTATED           1          2          1          3        2         0
  SGOL2 WILD-TYPE        28         82         61         36       41         4
D148V3, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SGOL2 MUTATED       2   4   6   4
  SGOL2 WILD-TYPE    52 131 255  98
D148V4, multiclass
       clus
vv      SGOL2 MUTATED SGOL2 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                6             255
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SGOL2 MUTATED     6   4   5   2
  SGOL2 WILD-TYPE 189 169  84  83
D148V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             5              84
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V6, binary
                 cls
clus                0   1
  SGOL2 MUTATED    14   2
  SGOL2 WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     14    2
  SGOL2 WILD-TYPE  468   36
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D148V7, binary
                 cls
clus                0   1
  SGOL2 MUTATED     7  10
  SGOL2 WILD-TYPE 165 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      7   10
  SGOL2 WILD-TYPE  165  396
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             7             165
  MALE              10             396
[1] 2 2
[1] FALSE
D148V8, binary
                 cls
clus                0   1
  SGOL2 MUTATED    10   2
  SGOL2 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     10    2
  SGOL2 WILD-TYPE  406  100
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D148V9, continuous
[1] "Remove cluster labels:" "SGOL2 MUTATED"         
clus
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
D148V10, continuous
[1] "Remove cluster labels:" "SGOL2 MUTATED"         
clus
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OG 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SGOL2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SGOL2 MUTATED       5                         0
  SGOL2 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGOL2 MUTATED                                           0     9
  SGOL2 WILD-TYPE                                         1   348
D148V11, multiclass
                                           clus
vv                                          SGOL2 MUTATED SGOL2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V12, binary
                 cls
clus                0   1
  SGOL2 MUTATED     0  12
  SGOL2 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      0   12
  SGOL2 WILD-TYPE   10  386
                        clus
vv                       SGOL2 MUTATED SGOL2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(149) Variable = ARID2 MUTATION ANALYSIS
D149V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    20   9
  ARID2 WILD-TYPE 318 207
  ARID2 MUTATED ARID2 WILD-TYPE 
             29             525 
  ARID2 MUTATED ARID2 WILD-TYPE 
              9             207 
$`ARID2 MUTATED`
TCGA-L5-A8NN TCGA-LN-A49O TCGA-LN-A7HX TCGA-VR-A8EU TCGA-BR-4184 TCGA-BR-6452 
        5.49        13.41        12.23        18.31         6.97        34.68 
TCGA-BR-6455 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8588 
       13.87        30.90        44.94        35.24        29.59        12.79 
TCGA-BR-A4J6 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-A4YV 
        0.66         6.58       105.07        21.07        13.35         5.92 
TCGA-F1-A72C TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 
       11.38        11.08        77.29        22.32         0.10        14.07 
TCGA-IN-A6RL TCGA-IN-A7NU TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.35        11.70        74.53        38.14        37.22 

$`ARID2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        15.95        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        5.39        25.18         9.21        20.22         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.41        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ARID2 MUTATED ARID2 WILD-TYPE 
            0.1             0.0 
  ARID2 MUTATED ARID2 WILD-TYPE 
         105.07          122.30 
  ARID2 MUTATED ARID2 WILD-TYPE 
          13.87           13.55 
[1] "0.1 - 105.1 (13.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D149V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID2 MUTATED         0        0        1        3         8         5
  ARID2 WILD-TYPE      10       20       45       28        76        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID2 MUTATED           1          7          1          1        3         0
  ARID2 WILD-TYPE        28         77         61         38       40         4
D149V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              8              76
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             7              77
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ARID2 MUTATED       3   6  15   8
  ARID2 WILD-TYPE    51 129 246  94
D149V4, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  T0+T1             3              51
  T2                6             129
  T3               15             246
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ARID2 MUTATED    12  12   5   1
  ARID2 WILD-TYPE 183 161  84  84
D149V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            12             183
  N1            12             161
  N2             5              84
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    28   3
  ARID2 WILD-TYPE 454  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     28    3
  ARID2 WILD-TYPE  454   35
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            28             454
  1             3              35
[1] 2 2
[1] FALSE
D149V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    14  19
  ARID2 WILD-TYPE 158 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     14   19
  ARID2 WILD-TYPE  158  387
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            14             158
  MALE              19             387
[1] 2 2
[1] FALSE
D149V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    22   7
  ARID2 WILD-TYPE 394  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     22    7
  ARID2 WILD-TYPE  394   95
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             22             394
  YES             7              95
[1] 2 2
[1] FALSE
D149V9, continuous
D149V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ARID2 MUTATED       7                         1
  ARID2 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID2 MUTATED                                           0    21
  ARID2 WILD-TYPE                                         1   336
D149V11, multiclass
                                           clus
vv                                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V12, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  24
  ARID2 WILD-TYPE   9 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   24
  ARID2 WILD-TYPE    9  374
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            24             374
[1] 2 2
[1] FALSE

Clustering(150) Variable = MTMR9 MUTATION ANALYSIS
D150V1, survival
                 sevent
clus2               0   1
  MTMR9 MUTATED     9   5
  MTMR9 WILD-TYPE 329 211
  MTMR9 MUTATED MTMR9 WILD-TYPE 
             14             540 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
              5             211 
$`MTMR9 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GN TCGA-LN-A7HV TCGA-R6-A6DQ TCGA-VR-A8EY TCGA-BR-6452 
       19.99         8.94        10.52         7.59        33.70        34.68 
TCGA-BR-7704 TCGA-BR-8360 TCGA-CG-4305 TCGA-CG-4465 TCGA-D7-A4YV TCGA-HU-8602 
       35.24         6.18        15.95         9.01         5.92        22.32 
TCGA-HU-A4GQ TCGA-VQ-A8P2 
        0.10        38.14 

$`MTMR9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MTMR9 MUTATED MTMR9 WILD-TYPE 
            0.1             0.0 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
          38.14          122.30 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
         13.235          13.565 
[1] "0.1 - 38.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D150V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTMR9 MUTATED         0        0        1        2         4         2
  MTMR9 WILD-TYPE      10       20       45       29        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTMR9 MUTATED           1          1          0          2        1         0
  MTMR9 WILD-TYPE        28         83         62         37       42         4
D150V3, multiclass
            clus
vv           MTMR9 MUTATED MTMR9 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MTMR9 MUTATED       1   3   8   4
  MTMR9 WILD-TYPE    53 132 253  98
D150V4, multiclass
       clus
vv      MTMR9 MUTATED MTMR9 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MTMR9 MUTATED     7   5   1   2
  MTMR9 WILD-TYPE 188 168  88  83
D150V5, multiclass
    clus
vv   MTMR9 MUTATED MTMR9 WILD-TYPE
  N0             7             188
  N1             5             168
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V6, binary
                 cls
clus                0   1
  MTMR9 MUTATED    14   1
  MTMR9 WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED     14    1
  MTMR9 WILD-TYPE  468   37
   clus
vv  MTMR9 MUTATED MTMR9 WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D150V7, binary
                 cls
clus                0   1
  MTMR9 MUTATED    10   8
  MTMR9 WILD-TYPE 162 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED     10    8
  MTMR9 WILD-TYPE  162  398
        clus
vv       MTMR9 MUTATED MTMR9 WILD-TYPE
  FEMALE            10             162
  MALE               8             398
[1] 2 2
[1] FALSE
D150V8, binary
                 cls
clus                0   1
  MTMR9 MUTATED    10   2
  MTMR9 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED     10    2
  MTMR9 WILD-TYPE  406  100
     clus
vv    MTMR9 MUTATED MTMR9 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D150V9, continuous
[1] "Remove cluster labels:" "MTMR9 MUTATED"         
clus
  MTMR9 MUTATED MTMR9 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
D150V10, continuous
[1] "Remove cluster labels:" "MTMR9 MUTATED"         
clus
  MTMR9 MUTATED MTMR9 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HW 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" "MTMR9 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTMR9 MUTATED       3                         0
  MTMR9 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTMR9 MUTATED                                           0    11
  MTMR9 WILD-TYPE                                         1   346
D150V11, multiclass
                                           clus
vv                                          MTMR9 MUTATED MTMR9 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V12, binary
                 cls
clus                0   1
  MTMR9 MUTATED     0  11
  MTMR9 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED      0   11
  MTMR9 WILD-TYPE   10  387
                        clus
vv                       MTMR9 MUTATED MTMR9 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(151) Variable = CR1L MUTATION ANALYSIS
D151V1, survival
                sevent
clus2              0   1
  CR1L MUTATED     9   6
  CR1L WILD-TYPE 329 210
  CR1L MUTATED CR1L WILD-TYPE 
            15            539 
  CR1L MUTATED CR1L WILD-TYPE 
             6            210 
$`CR1L MUTATED`
TCGA-LN-A4A1 TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-8363 TCGA-CD-A4MI TCGA-CG-4306 
       12.59        26.70         9.67         0.26        11.77         1.02 
TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GH 
        8.05         6.02       105.07        11.44        24.20        11.77 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-RD-A8MW 
        6.58         0.26        37.91 

$`CR1L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CR1L MUTATED CR1L WILD-TYPE 
          0.26           0.00 
  CR1L MUTATED CR1L WILD-TYPE 
        105.07         122.30 
  CR1L MUTATED CR1L WILD-TYPE 
         11.44          13.87 
[1] "0.3 - 105.1 (11.4)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D151V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1L MUTATED         1        3        1        2         1         2
  CR1L WILD-TYPE       9       17       45       29        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CR1L MUTATED           0          2          2          0        2         0
  CR1L WILD-TYPE        29         82         60         39       41         4
D151V3, multiclass
            clus
vv           CR1L MUTATED CR1L WILD-TYPE
  STAGE I               1              9
  STAGE IA              3             17
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CR1L MUTATED       4   3   6   3
  CR1L WILD-TYPE    50 132 255  99
D151V4, multiclass
       clus
vv      CR1L MUTATED CR1L WILD-TYPE
  T0+T1            4             50
  T2               3            132
  T3               6            255
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CR1L MUTATED     6   7   2   1
  CR1L WILD-TYPE 189 166  87  84
D151V5, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  N0            6            189
  N1            7            166
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V6, binary
                cls
clus               0   1
  CR1L MUTATED    15   1
  CR1L WILD-TYPE 467  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED     15    1
  CR1L WILD-TYPE  467   37
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0           15            467
  1            1             37
[1] 2 2
[1] FALSE
D151V7, binary
                cls
clus               0   1
  CR1L MUTATED     6  11
  CR1L WILD-TYPE 166 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      6   11
  CR1L WILD-TYPE  166  395
        clus
vv       CR1L MUTATED CR1L WILD-TYPE
  FEMALE            6            166
  MALE             11            395
[1] 2 2
[1] FALSE
D151V8, binary
                cls
clus               0   1
  CR1L MUTATED    14   2
  CR1L WILD-TYPE 402 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED     14    2
  CR1L WILD-TYPE  402  100
     clus
vv    CR1L MUTATED CR1L WILD-TYPE
  NO            14            402
  YES            2            100
[1] 2 2
[1] FALSE
D151V9, continuous
[1] "Remove cluster labels:" "CR1L MUTATED"          
clus
  CR1L MUTATED CR1L WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A2 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
D151V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CR1L MUTATED       7                         1
  CR1L WILD-TYPE   126                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR1L MUTATED                                           0     5
  CR1L WILD-TYPE                                         1   352
D151V11, multiclass
                                           clus
vv                                          CR1L MUTATED CR1L WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V12, binary
                cls
clus               0   1
  CR1L MUTATED     0  13
  CR1L WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      0   13
  CR1L WILD-TYPE   10  385
                        clus
vv                       CR1L MUTATED CR1L WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(152) Variable = YIPF2 MUTATION ANALYSIS
D152V1, survival
                 sevent
clus2               0   1
  YIPF2 MUTATED     8   2
  YIPF2 WILD-TYPE 330 214
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             10             544 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              2             214 
$`YIPF2 MUTATED`
TCGA-L5-A893 TCGA-LN-A7HY TCGA-LN-A9FP TCGA-BR-4184 TCGA-BR-8059 TCGA-CG-4305 
        3.02        12.03        12.03         6.97        14.43        15.95 
TCGA-HF-A5NB TCGA-HU-A4GP TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       30.51         8.98        37.41        38.14 

$`YIPF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  YIPF2 MUTATED YIPF2 WILD-TYPE 
           3.02            0.00 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
          38.14          122.30 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
         13.230          13.565 
[1] "3.0 - 38.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D152V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YIPF2 MUTATED         1        0        0        1         2         0
  YIPF2 WILD-TYPE       9       20       46       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YIPF2 MUTATED           2          2          0          1        1         0
  YIPF2 WILD-TYPE        27         82         62         38       42         4
D152V3, multiclass
            clus
vv           YIPF2 MUTATED YIPF2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  YIPF2 MUTATED       1   3   3   3
  YIPF2 WILD-TYPE    53 132 258  99
D152V4, multiclass
       clus
vv      YIPF2 MUTATED YIPF2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  YIPF2 MUTATED     2   7   0   1
  YIPF2 WILD-TYPE 193 166  89  84
D152V5, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  N0             2             193
  N1             7             166
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V6, binary
                 cls
clus                0   1
  YIPF2 MUTATED     8   1
  YIPF2 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      8    1
  YIPF2 WILD-TYPE  474   37
   clus
vv  YIPF2 MUTATED YIPF2 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D152V7, binary
                 cls
clus                0   1
  YIPF2 MUTATED     4   6
  YIPF2 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      4    6
  YIPF2 WILD-TYPE  168  400
        clus
vv       YIPF2 MUTATED YIPF2 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D152V8, binary
                 cls
clus                0   1
  YIPF2 MUTATED     7   3
  YIPF2 WILD-TYPE 409  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      7    3
  YIPF2 WILD-TYPE  409   99
     clus
vv    YIPF2 MUTATED YIPF2 WILD-TYPE
  NO              7             409
  YES             3              99
[1] 2 2
[1] FALSE
D152V9, continuous
[1] "Remove cluster labels:" "YIPF2 MUTATED"         
clus
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
D152V10, continuous
[1] "Remove cluster labels:" "YIPF2 MUTATED"         
clus
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A8NE 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"YIPF2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YIPF2 MUTATED       3                         0
  YIPF2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YIPF2 MUTATED                                           0     5
  YIPF2 WILD-TYPE                                         1   352
D152V11, multiclass
                                           clus
vv                                          YIPF2 MUTATED YIPF2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V12, binary
                 cls
clus                0   1
  YIPF2 MUTATED     0   5
  YIPF2 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      0    5
  YIPF2 WILD-TYPE   10  393
                        clus
vv                       YIPF2 MUTATED YIPF2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(153) Variable = ITGA6 MUTATION ANALYSIS
D153V1, survival
                 sevent
clus2               0   1
  ITGA6 MUTATED     9   5
  ITGA6 WILD-TYPE 329 211
  ITGA6 MUTATED ITGA6 WILD-TYPE 
             14             540 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              5             211 
$`ITGA6 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NT TCGA-2H-A9GI TCGA-L5-A8NM TCGA-LN-A49P TCGA-LN-A5U6 
        4.31        27.12        14.30         7.76        12.33        12.33 
TCGA-LN-A7HX TCGA-B7-A5TI TCGA-BR-4280 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-8573 
       12.23        19.56         6.61         6.58       105.07        19.50 
TCGA-HU-8602 TCGA-VQ-A8P2 
       22.32        38.14 

$`ITGA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ITGA6 MUTATED ITGA6 WILD-TYPE 
           4.31            0.00 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
         105.07          122.30 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
         13.315          13.565 
[1] "4.3 - 105.1 (13.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D153V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGA6 MUTATED         0        0        1        1         4         5
  ITGA6 WILD-TYPE      10       20       45       30        80        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA6 MUTATED           2          1          0          1        0         0
  ITGA6 WILD-TYPE        27         83         62         38       43         4
D153V3, multiclass
            clus
vv           ITGA6 MUTATED ITGA6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              5              78
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGA6 MUTATED       0   6   6   3
  ITGA6 WILD-TYPE    54 129 255  99
D153V4, multiclass
       clus
vv      ITGA6 MUTATED ITGA6 WILD-TYPE
  T0+T1             0              54
  T2                6             129
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGA6 MUTATED     8   7   0   1
  ITGA6 WILD-TYPE 187 166  89  84
D153V5, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  N0             8             187
  N1             7             166
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V6, binary
                 cls
clus                0   1
  ITGA6 MUTATED    15   0
  ITGA6 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED     15    0
  ITGA6 WILD-TYPE  467   38
   clus
vv  ITGA6 MUTATED ITGA6 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D153V7, binary
                 cls
clus                0   1
  ITGA6 MUTATED     4  12
  ITGA6 WILD-TYPE 168 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      4   12
  ITGA6 WILD-TYPE  168  394
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  FEMALE             4             168
  MALE              12             394
[1] 2 2
[1] FALSE
D153V8, binary
                 cls
clus                0   1
  ITGA6 MUTATED     8   5
  ITGA6 WILD-TYPE 408  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      8    5
  ITGA6 WILD-TYPE  408   97
     clus
vv    ITGA6 MUTATED ITGA6 WILD-TYPE
  NO              8             408
  YES             5              97
[1] 2 2
[1] FALSE
D153V9, continuous
D153V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGA6 MUTATED       5                         0
  ITGA6 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGA6 MUTATED                                           0     8
  ITGA6 WILD-TYPE                                         1   349
D153V11, multiclass
                                           clus
vv                                          ITGA6 MUTATED ITGA6 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V12, binary
                 cls
clus                0   1
  ITGA6 MUTATED     0   9
  ITGA6 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    9
  ITGA6 WILD-TYPE   10  389
                        clus
vv                       ITGA6 MUTATED ITGA6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(154) Variable = ATP6V1B1 MUTATION ANALYSIS
D154V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED     9  11
  ATP6V1B1 WILD-TYPE 329 205
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                20                534 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                11                205 
$`ATP6V1B1 MUTATED`
TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-7707 TCGA-BR-8078 
        7.76        26.70         6.97        18.35        35.84        29.59 
TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 
       32.25        31.96        16.14         6.58         1.02         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HU-A4GN TCGA-HU-A4GQ 
       28.96        21.07         5.92        11.44        29.98         0.10 
TCGA-HU-A4H4 TCGA-HU-A4H8 
       23.84        14.07 

$`ATP6V1B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44         0.69         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
               0.1                0.0 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             35.84             122.30 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
            17.245             13.510 
[1] "0.1 - 35.8 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D154V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1B1 MUTATED         0        1        2        0         2         6
  ATP6V1B1 WILD-TYPE      10       19       44       31        82        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          2          2          1        3
  ATP6V1B1 WILD-TYPE        29         82         60         38       40
                    vv
clus                 STAGE IVA
  ATP6V1B1 MUTATED           0
  ATP6V1B1 WILD-TYPE         4
D154V3, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 6                 77
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ATP6V1B1 MUTATED       2   5   6   6
  ATP6V1B1 WILD-TYPE    52 130 255  96
D154V4, multiclass
       clus
vv      ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T0+T1                2                 52
  T2                   5                130
  T3                   6                255
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ATP6V1B1 MUTATED     6   8   5   2
  ATP6V1B1 WILD-TYPE 189 165  84  83
D154V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0                6                189
  N1                8                165
  N2                5                 84
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V6, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    19   2
  ATP6V1B1 WILD-TYPE 463  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     19    2
  ATP6V1B1 WILD-TYPE  463   36
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               19                463
  1                2                 36
[1] 2 2
[1] FALSE
D154V7, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    12  10
  ATP6V1B1 WILD-TYPE 160 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     12   10
  ATP6V1B1 WILD-TYPE  160  396
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  FEMALE               12                160
  MALE                 10                396
[1] 2 2
[1] FALSE
D154V8, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    18   0
  ATP6V1B1 WILD-TYPE 398 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     18    0
  ATP6V1B1 WILD-TYPE  398  102
     clus
vv    ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  NO                18                398
  YES                0                102
[1] 2 2
[1] FALSE
D154V9, continuous
D154V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1B1 MUTATED       6                         0
  ATP6V1B1 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1B1 MUTATED                                           0    12
  ATP6V1B1 WILD-TYPE                                         1   345
D154V11, multiclass
                                           clus
vv                                          ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V12, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED     0  17
  ATP6V1B1 WILD-TYPE  10 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED      0   17
  ATP6V1B1 WILD-TYPE   10  381
                        clus
vv                       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               17                381
[1] 2 2
[1] FALSE

Clustering(155) Variable = GXYLT1 MUTATION ANALYSIS
D155V1, survival
                  sevent
clus2                0   1
  GXYLT1 MUTATED     9   5
  GXYLT1 WILD-TYPE 329 211
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              14              540 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               5              211 
$`GXYLT1 MUTATED`
TCGA-L5-A4OI TCGA-B7-5816 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 
       19.99        26.70        30.90        31.10         0.26        31.27 
TCGA-BR-8382 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5733 
       25.05        12.30         6.58        11.77        12.62        21.07 
TCGA-F1-6874 TCGA-VQ-A8P2 
       14.47        38.14 

$`GXYLT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 
        2.66        19.96         2.20         7.40         6.18        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
            0.26             0.00 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           38.14           122.30 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           20.53            13.51 
[1] "0.3 - 38.1 (20.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D155V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GXYLT1 MUTATED         0        0        3        0         1         1
  GXYLT1 WILD-TYPE      10       20       43       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GXYLT1 MUTATED           0          4          0          4        1
  GXYLT1 WILD-TYPE        29         80         62         35       42
                  vv
clus               STAGE IVA
  GXYLT1 MUTATED           0
  GXYLT1 WILD-TYPE         4
D155V3, multiclass
            clus
vv           GXYLT1 MUTATED GXYLT1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              4               35
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GXYLT1 MUTATED       1   4   4   6
  GXYLT1 WILD-TYPE    53 131 257  96
D155V4, multiclass
       clus
vv      GXYLT1 MUTATED GXYLT1 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 4              257
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GXYLT1 MUTATED     6   2   3   3
  GXYLT1 WILD-TYPE 189 171  86  82
D155V5, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  N0              6              189
  N1              2              171
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V6, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED    13   1
  GXYLT1 WILD-TYPE 469  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED     13    1
  GXYLT1 WILD-TYPE  469   37
   clus
vv  GXYLT1 MUTATED GXYLT1 WILD-TYPE
  0             13              469
  1              1               37
[1] 2 2
[1] FALSE
D155V7, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     6   9
  GXYLT1 WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      6    9
  GXYLT1 WILD-TYPE  166  397
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D155V8, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED    12   2
  GXYLT1 WILD-TYPE 404 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED     12    2
  GXYLT1 WILD-TYPE  404  100
     clus
vv    GXYLT1 MUTATED GXYLT1 WILD-TYPE
  NO              12              404
  YES              2              100
[1] 2 2
[1] FALSE
D155V9, continuous
D155V10, continuous
[1] "Remove cluster labels:" "GXYLT1 MUTATED"        
clus
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" "GXYLT1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"GXYLT1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GXYLT1 MUTATED       4                         0
  GXYLT1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GXYLT1 MUTATED                                           0    10
  GXYLT1 WILD-TYPE                                         1   347
D155V11, multiclass
                                           clus
vv                                          GXYLT1 MUTATED GXYLT1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V12, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     0  12
  GXYLT1 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      0   12
  GXYLT1 WILD-TYPE   10  386
                        clus
vv                       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(156) Variable = DOCK5 MUTATION ANALYSIS
D156V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED    21   6
  DOCK5 WILD-TYPE 317 210
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             27             527 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6             210 
$`DOCK5 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-KH-A6WC TCGA-LN-A4A4 TCGA-R6-A8W8 TCGA-R6-A8WG 
       19.99        21.99         6.28        12.59         2.89        12.69 
TCGA-VR-A8EP TCGA-XP-A8T7 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8285 
       27.09        41.23         6.97        34.68        29.59         0.56 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8531 TCGA-CD-8536 
       31.27         1.12        28.14        31.96        12.59        12.43 
TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GN 
       21.07        30.51        22.32         0.76        22.68        29.98 
TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8P2 
       20.25        19.73        38.14 

$`DOCK5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
       53.95         9.30        15.78         2.30         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.39        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.56            0.00 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          41.23          122.30 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          21.07           13.48 
[1] "0.6 - 41.2 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D156V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOCK5 MUTATED         1        2        1        1         4         4
  DOCK5 WILD-TYPE       9       18       45       30        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK5 MUTATED           1          5          1          6        2         0
  DOCK5 WILD-TYPE        28         79         61         33       41         4
D156V3, multiclass
            clus
vv           DOCK5 MUTATED DOCK5 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             1              61
  STAGE IIIC             6              33
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DOCK5 MUTATED       3   4  11  11
  DOCK5 WILD-TYPE    51 131 250  91
D156V4, multiclass
       clus
vv      DOCK5 MUTATED DOCK5 WILD-TYPE
  T0+T1             3              51
  T2                4             131
  T3               11             250
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DOCK5 MUTATED    10   9   5   5
  DOCK5 WILD-TYPE 185 164  84  80
D156V5, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  N0            10             185
  N1             9             164
  N2             5              84
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V6, binary
                 cls
clus                0   1
  DOCK5 MUTATED    24   2
  DOCK5 WILD-TYPE 458  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     24    2
  DOCK5 WILD-TYPE  458   36
   clus
vv  DOCK5 MUTATED DOCK5 WILD-TYPE
  0            24             458
  1             2              36
[1] 2 2
[1] FALSE
D156V7, binary
                 cls
clus                0   1
  DOCK5 MUTATED    15  17
  DOCK5 WILD-TYPE 157 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     15   17
  DOCK5 WILD-TYPE  157  389
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  FEMALE            15             157
  MALE              17             389
[1] 2 2
[1] FALSE
D156V8, binary
                 cls
clus                0   1
  DOCK5 MUTATED    24   5
  DOCK5 WILD-TYPE 392  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     24    5
  DOCK5 WILD-TYPE  392   97
     clus
vv    DOCK5 MUTATED DOCK5 WILD-TYPE
  NO             24             392
  YES             5              97
[1] 2 2
[1] FALSE
D156V9, continuous
D156V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DOCK5 MUTATED       9                         1
  DOCK5 WILD-TYPE   124                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOCK5 MUTATED                                           0    18
  DOCK5 WILD-TYPE                                         1   339
D156V11, multiclass
                                           clus
vv                                          DOCK5 MUTATED DOCK5 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V12, binary
                 cls
clus                0   1
  DOCK5 MUTATED     2  23
  DOCK5 WILD-TYPE   8 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      2   23
  DOCK5 WILD-TYPE    8  375
                        clus
vv                       DOCK5 MUTATED DOCK5 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            23             375
[1] 2 2
[1] FALSE

Clustering(157) Variable = ARHGAP5 MUTATION ANALYSIS
D157V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    17  10
  ARHGAP5 WILD-TYPE 321 206
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               27               527 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               10               206 
$`ARHGAP5 MUTATED`
TCGA-L5-A8NT TCGA-IG-A50L TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A891 TCGA-L7-A6VZ 
       27.12         0.53         0.30        26.33         3.75        10.36 
TCGA-LN-A4MQ TCGA-V5-AASX TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8081 
       12.33         8.98         9.34        34.68        14.43        32.25 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-A4J5 TCGA-CD-8529 TCGA-CD-A4MG 
        4.31         1.12        27.12        28.34        12.30         6.58 
TCGA-CG-4305 TCGA-CG-4465 TCGA-D7-A6EZ TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN 
       15.95         9.01        20.32        26.47        22.68        29.98 
TCGA-HU-A4GQ TCGA-RD-A7C1 TCGA-VQ-A8P2 
        0.10        16.67        38.14 

$`ARHGAP5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       30.25        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
              0.1               0.0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            38.14            122.30 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            14.43             13.55 
[1] "0.1 - 38.1 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D157V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGAP5 MUTATED         0        0        5        1         4         5
  ARHGAP5 WILD-TYPE      10       20       41       30        80        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           3          4          1          2        2
  ARHGAP5 WILD-TYPE        26         80         61         37       41
                   vv
clus                STAGE IVA
  ARHGAP5 MUTATED           0
  ARHGAP5 WILD-TYPE         4
D157V3, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 5                41
  STAGE II                 1                30
  STAGE IIA                4                80
  STAGE IIB                5                78
  STAGE III                3                26
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ARHGAP5 MUTATED       1   7  11   9
  ARHGAP5 WILD-TYPE    53 128 250  93
D157V4, multiclass
       clus
vv      ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T0+T1               1                53
  T2                  7               128
  T3                 11               250
  T4                  9                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ARHGAP5 MUTATED    12  13   2   2
  ARHGAP5 WILD-TYPE 183 160  87  83
D157V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              12               183
  N1              13               160
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V6, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    24   2
  ARHGAP5 WILD-TYPE 458  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     24    2
  ARHGAP5 WILD-TYPE  458   36
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              24               458
  1               2                36
[1] 2 2
[1] FALSE
D157V7, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     8  22
  ARHGAP5 WILD-TYPE 164 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      8   22
  ARHGAP5 WILD-TYPE  164  384
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  FEMALE               8               164
  MALE                22               384
[1] 2 2
[1] FALSE
D157V8, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    21   4
  ARHGAP5 WILD-TYPE 395  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     21    4
  ARHGAP5 WILD-TYPE  395   98
     clus
vv    ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  NO               21               395
  YES               4                98
[1] 2 2
[1] FALSE
D157V9, continuous
[1] "Remove cluster labels:" "ARHGAP5 MUTATED"       
clus
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MR 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ARHGAP5 WILD-TYPE" "ARHGAP5 WILD-TYPE" 
D157V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ARHGAP5 MUTATED       8                         0
  ARHGAP5 WILD-TYPE   125                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP5 MUTATED                                           0    19
  ARHGAP5 WILD-TYPE                                         1   338
D157V11, multiclass
                                           clus
vv                                          ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  ASIAN                                                   8               125
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  19               338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V12, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     0  22
  ARHGAP5 WILD-TYPE  10 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      0   22
  ARHGAP5 WILD-TYPE   10  376
                        clus
vv                       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              22               376
[1] 2 2
[1] FALSE

Clustering(158) Variable = BTBD7 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  BTBD7 MUTATED    14   7
  BTBD7 WILD-TYPE 324 209
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             21             533 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
              7             209 
$`BTBD7 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A8NU TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 
       21.01        83.24         6.97        30.90        34.68        35.84 
TCGA-BR-8078 TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-4469 TCGA-CG-5726 TCGA-F1-6874 
       29.59        31.27        11.77         7.07        28.96        14.47 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 
       77.29        26.47        22.32         6.58        20.25        23.84 
TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.73        19.04        38.14 

$`BTBD7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  BTBD7 MUTATED BTBD7 WILD-TYPE 
           6.58            0.00 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          83.24          122.30 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          23.84           13.41 
[1] "6.6 - 83.2 (23.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D158V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD7 MUTATED         1        1        4        1         2         4
  BTBD7 WILD-TYPE       9       19       42       30        82        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTBD7 MUTATED           0          5          0          2        1         0
  BTBD7 WILD-TYPE        29         79         62         37       42         4
D158V3, multiclass
            clus
vv           BTBD7 MUTATED BTBD7 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BTBD7 MUTATED       2   8   6   6
  BTBD7 WILD-TYPE    52 127 255  96
D158V4, multiclass
       clus
vv      BTBD7 MUTATED BTBD7 WILD-TYPE
  T0+T1             2              52
  T2                8             127
  T3                6             255
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BTBD7 MUTATED    11   5   3   2
  BTBD7 WILD-TYPE 184 168  86  83
D158V5, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  N0            11             184
  N1             5             168
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V6, binary
                 cls
clus                0   1
  BTBD7 MUTATED    20   0
  BTBD7 WILD-TYPE 462  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     20    0
  BTBD7 WILD-TYPE  462   38
   clus
vv  BTBD7 MUTATED BTBD7 WILD-TYPE
  0            20             462
  1             0              38
[1] 2 2
[1] FALSE
D158V7, binary
                 cls
clus                0   1
  BTBD7 MUTATED    12  10
  BTBD7 WILD-TYPE 160 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     12   10
  BTBD7 WILD-TYPE  160  396
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  FEMALE            12             160
  MALE              10             396
[1] 2 2
[1] FALSE
D158V8, binary
                 cls
clus                0   1
  BTBD7 MUTATED    16   2
  BTBD7 WILD-TYPE 400 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     16    2
  BTBD7 WILD-TYPE  400  100
     clus
vv    BTBD7 MUTATED BTBD7 WILD-TYPE
  NO             16             400
  YES             2             100
[1] 2 2
[1] FALSE
D158V9, continuous
D158V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BTBD7 MUTATED       5                         0
  BTBD7 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD7 MUTATED                                           0    14
  BTBD7 WILD-TYPE                                         1   343
D158V11, multiclass
                                           clus
vv                                          BTBD7 MUTATED BTBD7 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V12, binary
                 cls
clus                0   1
  BTBD7 MUTATED     0  16
  BTBD7 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      0   16
  BTBD7 WILD-TYPE   10  382
                        clus
vv                       BTBD7 MUTATED BTBD7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(159) Variable = GANAB MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2               0   1
  GANAB MUTATED    13   7
  GANAB WILD-TYPE 325 209
  GANAB MUTATED GANAB WILD-TYPE 
             20             534 
  GANAB MUTATED GANAB WILD-TYPE 
              7             209 
$`GANAB MUTATED`
TCGA-JY-A6FB TCGA-LN-A49K TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8284 
       60.39         5.92        26.70         9.34        34.68         8.05 
TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-8534 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 
       31.27        31.96        12.07         6.58        11.77         6.02 
TCGA-D7-8573 TCGA-D7-A4YY TCGA-F1-A448 TCGA-FP-7735 TCGA-HU-8243 TCGA-HU-8602 
       19.50        13.78        21.27         3.48         5.92        22.32 
TCGA-HU-A4GN TCGA-HU-A4GP 
       29.98         8.98 

$`GANAB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GANAB MUTATED GANAB WILD-TYPE 
           3.48            0.00 
  GANAB MUTATED GANAB WILD-TYPE 
          60.39          122.30 
  GANAB MUTATED GANAB WILD-TYPE 
         12.925          13.565 
[1] "3.5 - 60.4 (12.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D159V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GANAB MUTATED         1        0        1        1         6         2
  GANAB WILD-TYPE       9       20       45       30        78        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GANAB MUTATED           0          1          2          3        2         0
  GANAB WILD-TYPE        29         83         60         36       41         4
D159V3, multiclass
            clus
vv           GANAB MUTATED GANAB WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              6              78
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GANAB MUTATED       1   3   8   7
  GANAB WILD-TYPE    53 132 253  95
D159V4, multiclass
       clus
vv      GANAB MUTATED GANAB WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                8             253
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GANAB MUTATED     9   5   1   5
  GANAB WILD-TYPE 186 168  88  80
D159V5, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  N0             9             186
  N1             5             168
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V6, binary
                 cls
clus                0   1
  GANAB MUTATED    18   1
  GANAB WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     18    1
  GANAB WILD-TYPE  464   37
   clus
vv  GANAB MUTATED GANAB WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus                0   1
  GANAB MUTATED     5  15
  GANAB WILD-TYPE 167 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      5   15
  GANAB WILD-TYPE  167  391
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  FEMALE             5             167
  MALE              15             391
[1] 2 2
[1] FALSE
D159V8, binary
                 cls
clus                0   1
  GANAB MUTATED    18   2
  GANAB WILD-TYPE 398 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     18    2
  GANAB WILD-TYPE  398  100
     clus
vv    GANAB MUTATED GANAB WILD-TYPE
  NO             18             398
  YES             2             100
[1] 2 2
[1] FALSE
D159V9, continuous
[1] "Remove cluster labels:" "GANAB MUTATED"         
clus
  GANAB MUTATED GANAB WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49M 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"GANAB WILD-TYPE" "GANAB WILD-TYPE" "GANAB WILD-TYPE" 
D159V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GANAB MUTATED       9                         1
  GANAB WILD-TYPE   124                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GANAB MUTATED                                           0     9
  GANAB WILD-TYPE                                         1   348
D159V11, multiclass
                                           clus
vv                                          GANAB MUTATED GANAB WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V12, binary
                 cls
clus                0   1
  GANAB MUTATED     1  17
  GANAB WILD-TYPE   9 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      1   17
  GANAB WILD-TYPE    9  381
                        clus
vv                       GANAB MUTATED GANAB WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(160) Variable = MLL3 MUTATION ANALYSIS
D160V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    43  21
  MLL3 WILD-TYPE 295 195
  MLL3 MUTATED MLL3 WILD-TYPE 
            64            490 
  MLL3 MUTATED MLL3 WILD-TYPE 
            21            195 
$`MLL3 MUTATED`
TCGA-L5-A4OG TCGA-L5-A8NG TCGA-CG-4460 TCGA-EQ-A4SO TCGA-2H-A9GH TCGA-2H-A9GL 
        4.70        35.97        21.99        16.24        31.27         5.92 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OQ TCGA-L5-A8NK 
       35.21         0.85        47.38         3.16         1.38        13.55 
TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-R6-A6Y0 TCGA-VR-A8Q7 TCGA-VR-AA7D 
       11.54        10.52        13.18        53.95        52.27         9.17 
TCGA-XP-A8T7 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 
       41.23         6.97         9.34         9.67        34.68        35.84 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 
       31.10         0.26        31.27        25.05        28.14         7.53 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MG 
       31.96        16.14        12.30        12.59        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4449 
       11.77        12.62        15.95         1.02         7.99        19.07 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5721 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-FP-7916 
        9.01        30.97         6.02        14.27        16.44        14.07 
TCGA-FP-A9TM TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4H3 
        6.21        22.68        24.20         8.98         6.51        29.00 
TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NU TCGA-R5-A7O7 TCGA-R5-A7ZI 
       14.07        13.35        12.59        11.70        45.67        74.53 
TCGA-R5-A805 TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA6K 
        9.24        19.04        38.14        12.43 

$`MLL3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        47.05        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        9.86        25.78        20.05        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05        11.24        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        4.08         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       12.79        27.12         9.34         6.28        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 
       12.59        12.53         7.17        12.33        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        12.20        20.02         3.02        27.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        0.00        18.97         7.07         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       14.04        18.21         8.52         6.08         4.60        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  MLL3 MUTATED MLL3 WILD-TYPE 
          0.26           0.00 
  MLL3 MUTATED MLL3 WILD-TYPE 
         74.53         122.30 
  MLL3 MUTATED MLL3 WILD-TYPE 
         13.45          13.63 
[1] "0.3 - 74.5 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D160V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL3 MUTATED         2        2        7        3        10         3
  MLL3 WILD-TYPE       8       18       39       28        74        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL3 MUTATED           2          9          6          8        9         0
  MLL3 WILD-TYPE        27         75         56         31       34         4
D160V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               2              8
  STAGE IA              2             18
  STAGE IB              7             39
  STAGE II              3             28
  STAGE IIA            10             74
  STAGE IIB             3             80
  STAGE III             2             27
  STAGE IIIA            9             75
  STAGE IIIB            6             56
  STAGE IIIC            8             31
  STAGE IV              9             34
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLL3 MUTATED       8  18  21  17
  MLL3 WILD-TYPE    46 117 240  85
D160V4, multiclass
       clus
vv      MLL3 MUTATED MLL3 WILD-TYPE
  T0+T1            8             46
  T2              18            117
  T3              21            240
  T4              17             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLL3 MUTATED    21  23   6  13
  MLL3 WILD-TYPE 174 150  83  72
D160V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           21            174
  N1           23            150
  N2            6             83
  N3           13             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V6, binary
                cls
clus               0   1
  MLL3 MUTATED    54   7
  MLL3 WILD-TYPE 428  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     54    7
  MLL3 WILD-TYPE  428   31
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           54            428
  1            7             31
[1] 2 2
[1] FALSE
D160V7, binary
                cls
clus               0   1
  MLL3 MUTATED    24  45
  MLL3 WILD-TYPE 148 361
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     24   45
  MLL3 WILD-TYPE  148  361
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           24            148
  MALE             45            361
[1] 2 2
[1] FALSE
D160V8, binary
                cls
clus               0   1
  MLL3 MUTATED    51   9
  MLL3 WILD-TYPE 365  93
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     51    9
  MLL3 WILD-TYPE  365   93
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            51            365
  YES            9             93
[1] 2 2
[1] FALSE
D160V9, continuous
D160V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL3 MUTATED      17                         1
  MLL3 WILD-TYPE   116                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL3 MUTATED                                           0    40
  MLL3 WILD-TYPE                                         1   317
D160V11, multiclass
                                           clus
vv                                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                               17            116
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               40            317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V12, binary
                cls
clus               0   1
  MLL3 MUTATED     3  46
  MLL3 WILD-TYPE   7 352
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      3   46
  MLL3 WILD-TYPE    7  352
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                3              7
  NOT HISPANIC OR LATINO           46            352
[1] 2 2
[1] FALSE

Clustering(161) Variable = CLDN6 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  CLDN6 MUTATED     5   4
  CLDN6 WILD-TYPE 333 212
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              9             545 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              4             212 
$`CLDN6 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NM TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4QL 
       21.99         7.76        35.84         4.31        31.96        16.14 
TCGA-D7-A4YV TCGA-HU-A4GT TCGA-MX-A5UJ 
        5.92         6.51        19.73 

$`CLDN6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CLDN6 MUTATED CLDN6 WILD-TYPE 
           4.31            0.00 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
          35.84          122.30 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
          16.14           13.55 
[1] "4.3 - 35.8 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLDN6 MUTATED         0        0        2        0         1         2
  CLDN6 WILD-TYPE      10       20       44       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLDN6 MUTATED           0          2          1          0        2         0
  CLDN6 WILD-TYPE        29         82         61         39       41         4
D161V3, multiclass
            clus
vv           CLDN6 MUTATED CLDN6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CLDN6 MUTATED       0   3   4   3
  CLDN6 WILD-TYPE    54 132 257  99
D161V4, multiclass
       clus
vv      CLDN6 MUTATED CLDN6 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CLDN6 MUTATED     4   3   2   1
  CLDN6 WILD-TYPE 191 170  87  84
D161V5, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V6, binary
                 cls
clus                0   1
  CLDN6 MUTATED     8   2
  CLDN6 WILD-TYPE 474  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      8    2
  CLDN6 WILD-TYPE  474   36
   clus
vv  CLDN6 MUTATED CLDN6 WILD-TYPE
  0             8             474
  1             2              36
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus                0   1
  CLDN6 MUTATED     9   1
  CLDN6 WILD-TYPE 163 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      9    1
  CLDN6 WILD-TYPE  163  405
        clus
vv       CLDN6 MUTATED CLDN6 WILD-TYPE
  FEMALE             9             163
  MALE               1             405
[1] 2 2
[1] FALSE
D161V8, binary
                 cls
clus                0   1
  CLDN6 MUTATED     9   0
  CLDN6 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      9    0
  CLDN6 WILD-TYPE  407  102
     clus
vv    CLDN6 MUTATED CLDN6 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D161V9, continuous
D161V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CLDN6 MUTATED       2                         0
  CLDN6 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLDN6 MUTATED                                           0     7
  CLDN6 WILD-TYPE                                         1   350
D161V11, multiclass
                                           clus
vv                                          CLDN6 MUTATED CLDN6 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V12, binary
                 cls
clus                0   1
  CLDN6 MUTATED     0   8
  CLDN6 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      0    8
  CLDN6 WILD-TYPE   10  390
                        clus
vv                       CLDN6 MUTATED CLDN6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(162) Variable = SAMD9L MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    24   8
  SAMD9L WILD-TYPE 314 208
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              32              522 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               8              208 
$`SAMD9L MUTATED`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-CG-4460 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-IG-A3QL 
       15.68        18.28        21.99        31.27        14.30        35.21 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A8NJ TCGA-LN-A7HX TCGA-R6-A6Y2 
       14.50        68.02        21.70        16.47        12.23         9.30 
TCGA-VR-AA4D TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8370 
       46.19        26.70        11.70        34.68         0.26         3.32 
TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-8602 
       31.96        12.62         8.05         6.02        65.10        22.32 
TCGA-HU-8604 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H5 TCGA-IN-8663 
       22.82         6.51         6.58        20.25        23.80         3.39 
TCGA-IN-A7NT TCGA-VQ-A8P3 
       10.62        37.22 

$`SAMD9L WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15         9.86        25.78        20.05        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
      122.10        44.75         3.68        41.52        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       28.96        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         8.98         0.10         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        38.14        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            0.26             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
           68.02           122.30 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          17.375           13.445 
[1] "0.3 - 68.0 (17.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D162V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAMD9L MUTATED         0        1        5        1         7         8
  SAMD9L WILD-TYPE      10       19       41       30        77        75
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           2          3          1          1        4
  SAMD9L WILD-TYPE        27         81         61         38       39
                  vv
clus               STAGE IVA
  SAMD9L MUTATED           0
  SAMD9L WILD-TYPE         4
D162V3, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                5               41
  STAGE II                1               30
  STAGE IIA               7               77
  STAGE IIB               8               75
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SAMD9L MUTATED       4   9  11   9
  SAMD9L WILD-TYPE    50 126 250  93
D162V4, multiclass
       clus
vv      SAMD9L MUTATED SAMD9L WILD-TYPE
  T0+T1              4               50
  T2                 9              126
  T3                11              250
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SAMD9L MUTATED    15  12   4   1
  SAMD9L WILD-TYPE 180 161  85  84
D162V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             15              180
  N1             12              161
  N2              4               85
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V6, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    30   2
  SAMD9L WILD-TYPE 452  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     30    2
  SAMD9L WILD-TYPE  452   36
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             30              452
  1              2               36
[1] 2 2
[1] FALSE
D162V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    14  20
  SAMD9L WILD-TYPE 158 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     14   20
  SAMD9L WILD-TYPE  158  386
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  FEMALE             14              158
  MALE               20              386
[1] 2 2
[1] FALSE
D162V8, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    26   4
  SAMD9L WILD-TYPE 390  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     26    4
  SAMD9L WILD-TYPE  390   98
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO              26              390
  YES              4               98
[1] 2 2
[1] FALSE
D162V9, continuous
D162V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SAMD9L MUTATED      11                         0
  SAMD9L WILD-TYPE   122                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SAMD9L MUTATED                                           0    17
  SAMD9L WILD-TYPE                                         1   340
D162V11, multiclass
                                           clus
vv                                          SAMD9L MUTATED SAMD9L WILD-TYPE
  ASIAN                                                 11              122
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V12, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     1  21
  SAMD9L WILD-TYPE   9 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      1   21
  SAMD9L WILD-TYPE    9  377
                        clus
vv                       SAMD9L MUTATED SAMD9L WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(163) Variable = FAM133A MUTATION ANALYSIS
D163V1, survival
                   sevent
clus2                 0   1
  FAM133A MUTATED     7   5
  FAM133A WILD-TYPE 331 211
  FAM133A MUTATED FAM133A WILD-TYPE 
               12               542 
  FAM133A MUTATED FAM133A WILD-TYPE 
                5               211 
$`FAM133A MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A4P3 TCGA-L5-A893 TCGA-BR-4201 TCGA-BR-6458 
       19.99        21.99        18.64         3.02        30.90        19.33 
TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-HU-A4H3 TCGA-VQ-A8P2 
       35.84        29.59         6.58        12.62        29.00        38.14 

$`FAM133A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM133A MUTATED FAM133A WILD-TYPE 
             3.02              0.00 
  FAM133A MUTATED FAM133A WILD-TYPE 
            38.14            122.30 
  FAM133A MUTATED FAM133A WILD-TYPE 
           20.990            13.495 
[1] "3.0 - 38.1 (21.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D163V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM133A MUTATED         1        0        2        0         1         3
  FAM133A WILD-TYPE       9       20       44       31        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133A MUTATED           0          1          0          2        1
  FAM133A WILD-TYPE        29         83         62         37       42
                   vv
clus                STAGE IVA
  FAM133A MUTATED           0
  FAM133A WILD-TYPE         4
D163V3, multiclass
            clus
vv           FAM133A MUTATED FAM133A WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM133A MUTATED       1   4   3   4
  FAM133A WILD-TYPE    53 131 258  98
D163V4, multiclass
       clus
vv      FAM133A MUTATED FAM133A WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  3               258
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM133A MUTATED     5   4   0   2
  FAM133A WILD-TYPE 190 169  89  83
D163V5, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  N0               5               190
  N1               4               169
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V6, binary
                   cls
clus                  0   1
  FAM133A MUTATED    10   1
  FAM133A WILD-TYPE 472  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED     10    1
  FAM133A WILD-TYPE  472   37
   clus
vv  FAM133A MUTATED FAM133A WILD-TYPE
  0              10               472
  1               1                37
[1] 2 2
[1] FALSE
D163V7, binary
                   cls
clus                  0   1
  FAM133A MUTATED     7   5
  FAM133A WILD-TYPE 165 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      7    5
  FAM133A WILD-TYPE  165  401
        clus
vv       FAM133A MUTATED FAM133A WILD-TYPE
  FEMALE               7               165
  MALE                 5               401
[1] 2 2
[1] FALSE
D163V8, binary
                   cls
clus                  0   1
  FAM133A MUTATED     9   2
  FAM133A WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      9    2
  FAM133A WILD-TYPE  407  100
     clus
vv    FAM133A MUTATED FAM133A WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D163V9, continuous
D163V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM133A MUTATED       3                         0
  FAM133A WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM133A MUTATED                                           0     8
  FAM133A WILD-TYPE                                         1   349
D163V11, multiclass
                                           clus
vv                                          FAM133A MUTATED FAM133A WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V12, binary
                   cls
clus                  0   1
  FAM133A MUTATED     0   8
  FAM133A WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      0    8
  FAM133A WILD-TYPE   10  390
                        clus
vv                       FAM133A MUTATED FAM133A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(164) Variable = MTIF2 MUTATION ANALYSIS
D164V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED    16   8
  MTIF2 WILD-TYPE 322 208
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             24             530 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              8             208 
$`MTIF2 MUTATED`
TCGA-2H-A9GF TCGA-JY-A6FA TCGA-L5-A4OH TCGA-L5-A8NM TCGA-LN-A49R TCGA-LN-A49U 
       25.78        44.75        32.61         7.76        13.38        15.35 
TCGA-VR-A8Q7 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8363 TCGA-BR-8487 
       52.27         6.97        44.94        36.16         0.26         1.12 
TCGA-BR-8589 TCGA-BR-A4J4 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 
       27.12         0.53         6.58        11.77         1.02         6.02 
TCGA-CG-5728 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-KB-A6F7 
       65.10        77.29        30.51        22.68        23.84        63.62 

$`MTIF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
           0.26            0.00 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          77.29          122.30 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          23.26           13.51 
[1] "0.3 - 77.3 (23.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D164V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTIF2 MUTATED         1        1        3        1         4         4
  MTIF2 WILD-TYPE       9       19       43       30        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTIF2 MUTATED           2          4          2          1        2         0
  MTIF2 WILD-TYPE        27         80         60         38       41         4
D164V3, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MTIF2 MUTATED       3   6  11   5
  MTIF2 WILD-TYPE    51 129 250  97
D164V4, multiclass
       clus
vv      MTIF2 MUTATED MTIF2 WILD-TYPE
  T0+T1             3              51
  T2                6             129
  T3               11             250
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MTIF2 MUTATED     9  12   3   1
  MTIF2 WILD-TYPE 186 161  86  84
D164V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             9             186
  N1            12             161
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V6, binary
                 cls
clus                0   1
  MTIF2 MUTATED    23   1
  MTIF2 WILD-TYPE 459  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     23    1
  MTIF2 WILD-TYPE  459   37
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0            23             459
  1             1              37
[1] 2 2
[1] FALSE
D164V7, binary
                 cls
clus                0   1
  MTIF2 MUTATED    10  15
  MTIF2 WILD-TYPE 162 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     10   15
  MTIF2 WILD-TYPE  162  391
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  FEMALE            10             162
  MALE              15             391
[1] 2 2
[1] FALSE
D164V8, binary
                 cls
clus                0   1
  MTIF2 MUTATED    16   5
  MTIF2 WILD-TYPE 400  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     16    5
  MTIF2 WILD-TYPE  400   97
     clus
vv    MTIF2 MUTATED MTIF2 WILD-TYPE
  NO             16             400
  YES             5              97
[1] 2 2
[1] FALSE
D164V9, continuous
D164V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTIF2 MUTATED       8                         0
  MTIF2 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTIF2 MUTATED                                           0    10
  MTIF2 WILD-TYPE                                         1   347
D164V11, multiclass
                                           clus
vv                                          MTIF2 MUTATED MTIF2 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V12, binary
                 cls
clus                0   1
  MTIF2 MUTATED     0  14
  MTIF2 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      0   14
  MTIF2 WILD-TYPE   10  384
                        clus
vv                       MTIF2 MUTATED MTIF2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(165) Variable = CR1 MUTATION ANALYSIS
D165V1, survival
               sevent
clus2             0   1
  CR1 MUTATED    19  11
  CR1 WILD-TYPE 319 205
  CR1 MUTATED CR1 WILD-TYPE 
           30           524 
  CR1 MUTATED CR1 WILD-TYPE 
           11           205 
$`CR1 MUTATED`
TCGA-2H-A9GK TCGA-L5-A4OW TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 
        7.63         7.13         9.34         9.67         6.61        34.68 
TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 
       30.90        35.84        29.59        32.25         0.26        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-A4MG 
        1.12        27.12         6.28        12.33        12.30         6.58 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YU 
       12.62        15.95         7.99         6.02        65.10        16.44 
TCGA-D7-A4YY TCGA-HF-7132 TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-A6RL TCGA-VQ-AA64 
       13.78        77.29        20.25        29.00        13.35        18.41 

$`CR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        4.08         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        28.14 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.53         7.17        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CR1 MUTATED CR1 WILD-TYPE 
         0.26          0.00 
  CR1 MUTATED CR1 WILD-TYPE 
        77.29        122.30 
  CR1 MUTATED CR1 WILD-TYPE 
       13.565        13.565 
[1] "0.3 - 77.3 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D165V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1 MUTATED         0        0        6        2         3         4
  CR1 WILD-TYPE      10       20       40       29        81        79
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CR1 MUTATED           2          3          5          3        2         0
  CR1 WILD-TYPE        27         81         57         36       41         4
D165V3, multiclass
            clus
vv           CR1 MUTATED CR1 WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             6            40
  STAGE II             2            29
  STAGE IIA            3            81
  STAGE IIB            4            79
  STAGE III            2            27
  STAGE IIIA           3            81
  STAGE IIIB           5            57
  STAGE IIIC           3            36
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CR1 MUTATED       0  11   8  11
  CR1 WILD-TYPE    54 124 253  91
D165V4, multiclass
       clus
vv      CR1 MUTATED CR1 WILD-TYPE
  T0+T1           0            54
  T2             11           124
  T3              8           253
  T4             11            91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CR1 MUTATED    14  10   3   4
  CR1 WILD-TYPE 181 163  86  81
D165V5, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  N0          14           181
  N1          10           163
  N2           3            86
  N3           4            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V6, binary
               cls
clus              0   1
  CR1 MUTATED    31   1
  CR1 WILD-TYPE 451  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     31    1
  CR1 WILD-TYPE  451   37
   clus
vv  CR1 MUTATED CR1 WILD-TYPE
  0          31           451
  1           1            37
[1] 2 2
[1] FALSE
D165V7, binary
               cls
clus              0   1
  CR1 MUTATED    15  17
  CR1 WILD-TYPE 157 389
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     15   17
  CR1 WILD-TYPE  157  389
        clus
vv       CR1 MUTATED CR1 WILD-TYPE
  FEMALE          15           157
  MALE            17           389
[1] 2 2
[1] FALSE
D165V8, binary
               cls
clus              0   1
  CR1 MUTATED    24   5
  CR1 WILD-TYPE 392  97
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     24    5
  CR1 WILD-TYPE  392   97
     clus
vv    CR1 MUTATED CR1 WILD-TYPE
  NO           24           392
  YES           5            97
[1] 2 2
[1] FALSE
D165V9, continuous
D165V10, continuous
[1] "Remove cluster labels:" "CR1 MUTATED"           
clus
  CR1 MUTATED CR1 WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OX 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" "CR1 WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"CR1 WILD-TYPE" "CR1 WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CR1 MUTATED       6                         0
  CR1 WILD-TYPE   127                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR1 MUTATED                                           0    18
  CR1 WILD-TYPE                                         1   339
D165V11, multiclass
                                           clus
vv                                          CR1 MUTATED CR1 WILD-TYPE
  ASIAN                                               6           127
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              18           339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V12, binary
               cls
clus              0   1
  CR1 MUTATED     0  23
  CR1 WILD-TYPE  10 375
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      0   23
  CR1 WILD-TYPE   10  375
                        clus
vv                       CR1 MUTATED CR1 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          23           375
[1] 2 2
[1] FALSE

Clustering(166) Variable = SERPINI1 MUTATION ANALYSIS
D166V1, survival
                    sevent
clus2                  0   1
  SERPINI1 MUTATED     6   2
  SERPINI1 WILD-TYPE 332 214
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 8                546 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 2                214 
$`SERPINI1 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8589 TCGA-CG-4306 
       21.99        26.70         6.18        31.27        27.12         1.02 
TCGA-HU-8602 TCGA-HU-A4H4 
       22.32        23.84 

$`SERPINI1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
              1.02               0.00 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
             31.27             122.30 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
             23.08              13.51 
[1] "1.0 - 31.3 (23.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D166V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINI1 MUTATED         0        0        0        0         1         3
  SERPINI1 WILD-TYPE      10       20       46       31        83        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINI1 MUTATED           0          0          1          1        2
  SERPINI1 WILD-TYPE        29         84         61         38       41
                    vv
clus                 STAGE IVA
  SERPINI1 MUTATED           0
  SERPINI1 WILD-TYPE         4
D166V3, multiclass
            clus
vv           SERPINI1 MUTATED SERPINI1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SERPINI1 MUTATED       1   1   2   5
  SERPINI1 WILD-TYPE    53 134 259  97
D166V4, multiclass
       clus
vv      SERPINI1 MUTATED SERPINI1 WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   2                259
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SERPINI1 MUTATED     3   2   2   1
  SERPINI1 WILD-TYPE 192 171  87  84
D166V5, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V6, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     7   2
  SERPINI1 WILD-TYPE 475  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      7    2
  SERPINI1 WILD-TYPE  475   36
   clus
vv  SERPINI1 MUTATED SERPINI1 WILD-TYPE
  0                7                475
  1                2                 36
[1] 2 2
[1] FALSE
D166V7, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     5   4
  SERPINI1 WILD-TYPE 167 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      5    4
  SERPINI1 WILD-TYPE  167  402
        clus
vv       SERPINI1 MUTATED SERPINI1 WILD-TYPE
  FEMALE                5                167
  MALE                  4                402
[1] 2 2
[1] FALSE
D166V8, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     7   0
  SERPINI1 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      7    0
  SERPINI1 WILD-TYPE  409  102
     clus
vv    SERPINI1 MUTATED SERPINI1 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D166V9, continuous
D166V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINI1 MUTATED       2                         0
  SERPINI1 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINI1 MUTATED                                           0     5
  SERPINI1 WILD-TYPE                                         1   352
D166V11, multiclass
                                           clus
vv                                          SERPINI1 MUTATED SERPINI1 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V12, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     0   7
  SERPINI1 WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      0    7
  SERPINI1 WILD-TYPE   10  391
                        clus
vv                       SERPINI1 MUTATED SERPINI1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(167) Variable = KIAA0195 MUTATION ANALYSIS
D167V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    14   5
  KIAA0195 WILD-TYPE 324 211
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                19                535 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 5                211 
$`KIAA0195 MUTATED`
TCGA-L5-A4OW TCGA-L5-A8NK TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8372 
        7.13        13.55        26.70        34.68         4.31        31.27 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-FP-A4BE TCGA-HF-A5NB 
        1.12        16.14        12.43         6.58        11.08        30.51 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8DT 
       26.47        22.32         0.10         6.51         6.58        48.79 
TCGA-VQ-A8P2 
       38.14 

$`KIAA0195 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       52.21         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
               0.1                0.0 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             48.79             122.30 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             13.55              13.58 
[1] "0.1 - 48.8 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D167V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0195 MUTATED         1        0        2        1         6         4
  KIAA0195 WILD-TYPE       9       20       44       30        78        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           0          2          2          3        0
  KIAA0195 WILD-TYPE        29         82         60         36       43
                    vv
clus                 STAGE IVA
  KIAA0195 MUTATED           0
  KIAA0195 WILD-TYPE         4
D167V3, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 6                 78
  STAGE IIB                 4                 79
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                2                 60
  STAGE IIIC                3                 36
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0195 MUTATED       1   3  10   7
  KIAA0195 WILD-TYPE    53 132 251  95
D167V4, multiclass
       clus
vv      KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                  10                251
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0195 MUTATED    12   4   1   4
  KIAA0195 WILD-TYPE 183 169  88  81
D167V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               12                183
  N1                4                169
  N2                1                 88
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V6, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    20   0
  KIAA0195 WILD-TYPE 462  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     20    0
  KIAA0195 WILD-TYPE  462   38
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               20                462
  1                0                 38
[1] 2 2
[1] FALSE
D167V7, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    13   9
  KIAA0195 WILD-TYPE 159 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     13    9
  KIAA0195 WILD-TYPE  159  397
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  FEMALE               13                159
  MALE                  9                397
[1] 2 2
[1] FALSE
D167V8, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    15   4
  KIAA0195 WILD-TYPE 401  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     15    4
  KIAA0195 WILD-TYPE  401   98
     clus
vv    KIAA0195 MUTATED KIAA0195 WILD-TYPE
  NO                15                401
  YES                4                 98
[1] 2 2
[1] FALSE
D167V9, continuous
D167V10, continuous
[1] "Remove cluster labels:" "KIAA0195 MUTATED"      
clus
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" "KIAA0195 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0195 MUTATED       6                         2
  KIAA0195 WILD-TYPE   127                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0195 MUTATED                                           0    11
  KIAA0195 WILD-TYPE                                         1   346
D167V11, multiclass
                                           clus
vv                                          KIAA0195 MUTATED KIAA0195 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V12, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     0  17
  KIAA0195 WILD-TYPE  10 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      0   17
  KIAA0195 WILD-TYPE   10  381
                        clus
vv                       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               17                381
[1] 2 2
[1] FALSE

Clustering(168) Variable = PPIG MUTATION ANALYSIS
D168V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    12   5
  PPIG WILD-TYPE 326 211
  PPIG MUTATED PPIG WILD-TYPE 
            17            537 
  PPIG MUTATED PPIG WILD-TYPE 
             5            211 
$`PPIG MUTATED`
TCGA-L5-A8NM TCGA-VR-A8EU TCGA-B7-5818 TCGA-BR-4256 TCGA-BR-8361 TCGA-BR-8368 
        7.76        18.31        11.70         9.34        31.10         4.31 
TCGA-BR-8372 TCGA-BR-8486 TCGA-CD-A4MI TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-A4GT 
       31.27        20.22        11.77       105.07        14.47         6.51 
TCGA-HU-A4GU TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-R5-A804 TCGA-VQ-A8P2 
        6.58        63.62        19.73         4.60        38.14 

$`PPIG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J 
       11.70        15.75        13.51         2.53         5.56        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PPIG MUTATED PPIG WILD-TYPE 
          4.31           0.00 
  PPIG MUTATED PPIG WILD-TYPE 
        105.07         122.30 
  PPIG MUTATED PPIG WILD-TYPE 
         14.47          13.55 
[1] "4.3 - 105.1 (14.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D168V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPIG MUTATED         1        1        5        1         1         2
  PPIG WILD-TYPE       9       19       41       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPIG MUTATED           0          3          0          2        3         0
  PPIG WILD-TYPE        29         81         62         37       40         4
D168V3, multiclass
            clus
vv           PPIG MUTATED PPIG WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              5             41
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PPIG MUTATED       4   6   5   4
  PPIG WILD-TYPE    50 129 256  98
D168V4, multiclass
       clus
vv      PPIG MUTATED PPIG WILD-TYPE
  T0+T1            4             50
  T2               6            129
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PPIG MUTATED     6   9   4   1
  PPIG WILD-TYPE 189 164  85  84
D168V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  N0            6            189
  N1            9            164
  N2            4             85
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V6, binary
                cls
clus               0   1
  PPIG MUTATED    17   2
  PPIG WILD-TYPE 465  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     17    2
  PPIG WILD-TYPE  465   36
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0           17            465
  1            2             36
[1] 2 2
[1] FALSE
D168V7, binary
                cls
clus               0   1
  PPIG MUTATED     8  12
  PPIG WILD-TYPE 164 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      8   12
  PPIG WILD-TYPE  164  394
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            8            164
  MALE             12            394
[1] 2 2
[1] FALSE
D168V8, binary
                cls
clus               0   1
  PPIG MUTATED    15   3
  PPIG WILD-TYPE 401  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     15    3
  PPIG WILD-TYPE  401   99
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO            15            401
  YES            3             99
[1] 2 2
[1] FALSE
D168V9, continuous
[1] "Remove cluster labels:" "PPIG MUTATED"          
clus
  PPIG MUTATED PPIG WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
D168V10, continuous
[1] "Remove cluster labels:" "PPIG MUTATED"          
clus
  PPIG MUTATED PPIG WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-Z6-AAPN 
"PPIG WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PPIG MUTATED       3                         2
  PPIG WILD-TYPE   130                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIG MUTATED                                           0    12
  PPIG WILD-TYPE                                         1   345
D168V11, multiclass
                                           clus
vv                                          PPIG MUTATED PPIG WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V12, binary
                cls
clus               0   1
  PPIG MUTATED     0  14
  PPIG WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      0   14
  PPIG WILD-TYPE   10  384
                        clus
vv                       PPIG MUTATED PPIG WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(169) Variable = HTR7 MUTATION ANALYSIS
D169V1, survival
                sevent
clus2              0   1
  HTR7 MUTATED     9   6
  HTR7 WILD-TYPE 329 210
  HTR7 MUTATED HTR7 WILD-TYPE 
            15            539 
  HTR7 MUTATED HTR7 WILD-TYPE 
             6            210 
$`HTR7 MUTATED`
TCGA-L5-A8NF TCGA-R6-A6XG TCGA-X8-AAAR TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 
        2.66        38.40        18.21         6.61        34.68        35.84 
TCGA-BR-8360 TCGA-BR-8589 TCGA-CD-A4MI TCGA-CG-4465 TCGA-D7-6527 TCGA-FP-A9TM 
        6.18        27.12        11.77         9.01        10.26         6.21 
TCGA-HU-8602 TCGA-HU-A4H3 TCGA-R5-A7ZE 
       22.32        29.00        18.21 

$`HTR7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  HTR7 MUTATED HTR7 WILD-TYPE 
          2.66           0.00 
  HTR7 MUTATED HTR7 WILD-TYPE 
          38.4          122.3 
  HTR7 MUTATED HTR7 WILD-TYPE 
         18.21          13.55 
[1] "2.7 - 38.4 (18.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D169V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTR7 MUTATED         0        0        1        1         2         2
  HTR7 WILD-TYPE      10       20       45       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR7 MUTATED           1          2          1          1        1         1
  HTR7 WILD-TYPE        28         82         61         38       42         3
D169V3, multiclass
            clus
vv           HTR7 MUTATED HTR7 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HTR7 MUTATED       3   3   4   5
  HTR7 WILD-TYPE    51 132 257  97
D169V4, multiclass
       clus
vv      HTR7 MUTATED HTR7 WILD-TYPE
  T0+T1            3             51
  T2               3            132
  T3               4            257
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HTR7 MUTATED     6   7   1   2
  HTR7 WILD-TYPE 189 166  88  83
D169V5, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  N0            6            189
  N1            7            166
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V6, binary
                cls
clus               0   1
  HTR7 MUTATED    13   2
  HTR7 WILD-TYPE 469  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED     13    2
  HTR7 WILD-TYPE  469   36
   clus
vv  HTR7 MUTATED HTR7 WILD-TYPE
  0           13            469
  1            2             36
[1] 2 2
[1] FALSE
D169V7, binary
                cls
clus               0   1
  HTR7 MUTATED     8   9
  HTR7 WILD-TYPE 164 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      8    9
  HTR7 WILD-TYPE  164  397
        clus
vv       HTR7 MUTATED HTR7 WILD-TYPE
  FEMALE            8            164
  MALE              9            397
[1] 2 2
[1] FALSE
D169V8, binary
                cls
clus               0   1
  HTR7 MUTATED    12   2
  HTR7 WILD-TYPE 404 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED     12    2
  HTR7 WILD-TYPE  404  100
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO            12            404
  YES            2            100
[1] 2 2
[1] FALSE
D169V9, continuous
D169V10, continuous
[1] "Remove cluster labels:" "HTR7 MUTATED"          
clus
  HTR7 MUTATED HTR7 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" "HTR7 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HTR7 MUTATED       3                         0
  HTR7 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTR7 MUTATED                                           0    13
  HTR7 WILD-TYPE                                         1   344
D169V11, multiclass
                                           clus
vv                                          HTR7 MUTATED HTR7 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V12, binary
                cls
clus               0   1
  HTR7 MUTATED     0  15
  HTR7 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      0   15
  HTR7 WILD-TYPE   10  383
                        clus
vv                       HTR7 MUTATED HTR7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(170) Variable = PIGB MUTATION ANALYSIS
D170V1, survival
                sevent
clus2              0   1
  PIGB MUTATED     6   2
  PIGB WILD-TYPE 332 214
  PIGB MUTATED PIGB WILD-TYPE 
             8            546 
  PIGB MUTATED PIGB WILD-TYPE 
             2            214 
$`PIGB MUTATED`
TCGA-VR-AA7D TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-5721 
        9.17        26.70        35.84         1.12        27.12         6.02 
TCGA-HF-7132 TCGA-HU-A4GQ 
       77.29         0.10 

$`PIGB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PIGB MUTATED PIGB WILD-TYPE 
           0.1            0.0 
  PIGB MUTATED PIGB WILD-TYPE 
         77.29         122.30 
  PIGB MUTATED PIGB WILD-TYPE 
        17.935         13.565 
[1] "0.1 - 77.3 (17.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D170V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGB MUTATED         0        0        2        1         1         1
  PIGB WILD-TYPE      10       20       44       30        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGB MUTATED           0          0          1          2        1         0
  PIGB WILD-TYPE        29         84         61         37       42         4
D170V3, multiclass
            clus
vv           PIGB MUTATED PIGB WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PIGB MUTATED       1   3   2   4
  PIGB WILD-TYPE    53 132 259  98
D170V4, multiclass
       clus
vv      PIGB MUTATED PIGB WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PIGB MUTATED     4   3   1   1
  PIGB WILD-TYPE 191 170  88  84
D170V5, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  N0            4            191
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V6, binary
                cls
clus               0   1
  PIGB MUTATED    11   0
  PIGB WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED     11    0
  PIGB WILD-TYPE  471   38
   clus
vv  PIGB MUTATED PIGB WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D170V7, binary
                cls
clus               0   1
  PIGB MUTATED     5   6
  PIGB WILD-TYPE 167 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      5    6
  PIGB WILD-TYPE  167  400
        clus
vv       PIGB MUTATED PIGB WILD-TYPE
  FEMALE            5            167
  MALE              6            400
[1] 2 2
[1] FALSE
D170V8, binary
                cls
clus               0   1
  PIGB MUTATED     6   2
  PIGB WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      6    2
  PIGB WILD-TYPE  410  100
     clus
vv    PIGB MUTATED PIGB WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D170V9, continuous
[1] "Remove cluster labels:" "PIGB MUTATED"          
clus
  PIGB MUTATED PIGB WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
D170V10, continuous
[1] "Remove cluster labels:" "PIGB MUTATED"          
clus
  PIGB MUTATED PIGB WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7I 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" "PIGB WILD-TYPE" 
    TCGA-Z6-AAPN 
"PIGB WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGB MUTATED       1                         0
  PIGB WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGB MUTATED                                           0     6
  PIGB WILD-TYPE                                         1   351
D170V11, multiclass
                                           clus
vv                                          PIGB MUTATED PIGB WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V12, binary
                cls
clus               0   1
  PIGB MUTATED     0   7
  PIGB WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      0    7
  PIGB WILD-TYPE   10  391
                        clus
vv                       PIGB MUTATED PIGB WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(171) Variable = EEF2K MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2               0   1
  EEF2K MUTATED     7   4
  EEF2K WILD-TYPE 331 212
  EEF2K MUTATED EEF2K WILD-TYPE 
             11             543 
  EEF2K MUTATED EEF2K WILD-TYPE 
              4             212 
$`EEF2K MUTATED`
TCGA-JY-A93F TCGA-L5-A8NH TCGA-L5-A8NM TCGA-LN-A8HZ TCGA-B7-A5TI TCGA-BR-4184 
       24.03        12.92         7.76        12.33        19.56         6.97 
TCGA-CG-4305 TCGA-CG-5721 TCGA-FP-7735 TCGA-FP-A4BE TCGA-HU-8602 
       15.95         6.02         3.48        11.08        22.32 

$`EEF2K WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        25.22         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  EEF2K MUTATED EEF2K WILD-TYPE 
           3.48            0.00 
  EEF2K MUTATED EEF2K WILD-TYPE 
          24.03          122.30 
  EEF2K MUTATED EEF2K WILD-TYPE 
          12.33           13.68 
[1] "3.5 - 24.0 (12.3)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EEF2K MUTATED         0        0        2        1         2         2
  EEF2K WILD-TYPE      10       20       44       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EEF2K MUTATED           0          3          0          1        3         0
  EEF2K WILD-TYPE        29         81         62         38       40         4
D171V3, multiclass
            clus
vv           EEF2K MUTATED EEF2K WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EEF2K MUTATED       1   5   3   5
  EEF2K WILD-TYPE    53 130 258  97
D171V4, multiclass
       clus
vv      EEF2K MUTATED EEF2K WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                3             258
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EEF2K MUTATED     7   5   1   1
  EEF2K WILD-TYPE 188 168  88  84
D171V5, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  N0             7             188
  N1             5             168
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V6, binary
                 cls
clus                0   1
  EEF2K MUTATED    11   1
  EEF2K WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED     11    1
  EEF2K WILD-TYPE  471   37
   clus
vv  EEF2K MUTATED EEF2K WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus                0   1
  EEF2K MUTATED     5   9
  EEF2K WILD-TYPE 167 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      5    9
  EEF2K WILD-TYPE  167  397
        clus
vv       EEF2K MUTATED EEF2K WILD-TYPE
  FEMALE             5             167
  MALE               9             397
[1] 2 2
[1] FALSE
D171V8, binary
                 cls
clus                0   1
  EEF2K MUTATED     8   3
  EEF2K WILD-TYPE 408  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      8    3
  EEF2K WILD-TYPE  408   99
     clus
vv    EEF2K MUTATED EEF2K WILD-TYPE
  NO              8             408
  YES             3              99
[1] 2 2
[1] FALSE
D171V9, continuous
D171V10, continuous
[1] "Remove cluster labels:" "EEF2K MUTATED"         
clus
  EEF2K MUTATED EEF2K WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" "EEF2K WILD-TYPE" 
     TCGA-Z6-AAPN 
"EEF2K WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EEF2K MUTATED       2                         2
  EEF2K WILD-TYPE   131                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EEF2K MUTATED                                           0     7
  EEF2K WILD-TYPE                                         1   350
D171V11, multiclass
                                           clus
vv                                          EEF2K MUTATED EEF2K WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V12, binary
                 cls
clus                0   1
  EEF2K MUTATED     0   8
  EEF2K WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      0    8
  EEF2K WILD-TYPE   10  390
                        clus
vv                       EEF2K MUTATED EEF2K WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(172) Variable = SNRNP35 MUTATION ANALYSIS
D172V1, survival
                   sevent
clus2                 0   1
  SNRNP35 MUTATED     5   2
  SNRNP35 WILD-TYPE 333 214
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                7               547 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                2               214 
$`SNRNP35 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4305 TCGA-HU-A4G9 
       19.99        21.99         1.12         6.58        15.95        24.20 
TCGA-HU-A4GT 
        6.51 

$`SNRNP35 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
             1.12              0.00 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
             24.2             122.3 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
            15.95             13.55 
[1] "1.1 - 24.2 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D172V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNRNP35 MUTATED         0        1        0        1         3         0
  SNRNP35 WILD-TYPE      10       19       46       30        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNRNP35 MUTATED           0          0          0          1        1
  SNRNP35 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  SNRNP35 MUTATED           0
  SNRNP35 WILD-TYPE         4
D172V3, multiclass
            clus
vv           SNRNP35 MUTATED SNRNP35 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SNRNP35 MUTATED       1   1   4   1
  SNRNP35 WILD-TYPE    53 134 257 101
D172V4, multiclass
       clus
vv      SNRNP35 MUTATED SNRNP35 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  4               257
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SNRNP35 MUTATED     4   2   0   1
  SNRNP35 WILD-TYPE 191 171  89  84
D172V5, multiclass
    clus
vv   SNRNP35 MUTATED SNRNP35 WILD-TYPE
  N0               4               191
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V6, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     5   1
  SNRNP35 WILD-TYPE 477  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      5    1
  SNRNP35 WILD-TYPE  477   37
   clus
vv  SNRNP35 MUTATED SNRNP35 WILD-TYPE
  0               5               477
  1               1                37
[1] 2 2
[1] FALSE
D172V7, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     4   3
  SNRNP35 WILD-TYPE 168 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      4    3
  SNRNP35 WILD-TYPE  168  403
        clus
vv       SNRNP35 MUTATED SNRNP35 WILD-TYPE
  FEMALE               4               168
  MALE                 3               403
[1] 2 2
[1] FALSE
D172V8, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     7   0
  SNRNP35 WILD-TYPE 409 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      7    0
  SNRNP35 WILD-TYPE  409  102
     clus
vv    SNRNP35 MUTATED SNRNP35 WILD-TYPE
  NO                7               409
  YES               0               102
[1] 2 2
[1] FALSE
D172V9, continuous
D172V10, continuous
[1] "Remove cluster labels:" "SNRNP35 MUTATED"       
clus
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" "SNRNP35 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SNRNP35 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SNRNP35 MUTATED       3                         0
  SNRNP35 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNRNP35 MUTATED                                           0     2
  SNRNP35 WILD-TYPE                                         1   355
D172V11, multiclass
                                           clus
vv                                          SNRNP35 MUTATED SNRNP35 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V12, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     0   4
  SNRNP35 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      0    4
  SNRNP35 WILD-TYPE   10  394
                        clus
vv                       SNRNP35 MUTATED SNRNP35 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(173) Variable = ZKSCAN5 MUTATION ANALYSIS
D173V1, survival
                   sevent
clus2                 0   1
  ZKSCAN5 MUTATED    10   2
  ZKSCAN5 WILD-TYPE 328 214
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               12               542 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                2               214 
$`ZKSCAN5 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 
       21.01         7.76        26.70         9.67        34.68        29.59 
TCGA-CD-8529 TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-VQ-A8P2 
       12.30         6.02        14.47        20.25        14.07        38.14 

$`ZKSCAN5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
             6.02              0.00 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
            38.14            122.30 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
            17.36             13.51 
[1] "6.0 - 38.1 (17.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D173V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZKSCAN5 MUTATED         1        0        2        0         1         4
  ZKSCAN5 WILD-TYPE       9       20       44       31        83        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN5 MUTATED           0          1          0          1        2
  ZKSCAN5 WILD-TYPE        29         83         62         38       41
                   vv
clus                STAGE IVA
  ZKSCAN5 MUTATED           0
  ZKSCAN5 WILD-TYPE         4
D173V3, multiclass
            clus
vv           ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZKSCAN5 MUTATED       2   2   1   7
  ZKSCAN5 WILD-TYPE    52 133 260  95
D173V4, multiclass
       clus
vv      ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  1               260
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZKSCAN5 MUTATED     7   4   1   0
  ZKSCAN5 WILD-TYPE 188 169  88  85
D173V5, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  N0               7               188
  N1               4               169
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V6, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED    12   1
  ZKSCAN5 WILD-TYPE 470  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED     12    1
  ZKSCAN5 WILD-TYPE  470   37
   clus
vv  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  0              12               470
  1               1                37
[1] 2 2
[1] FALSE
D173V7, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     7   6
  ZKSCAN5 WILD-TYPE 165 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      7    6
  ZKSCAN5 WILD-TYPE  165  400
        clus
vv       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  FEMALE               7               165
  MALE                 6               400
[1] 2 2
[1] FALSE
D173V8, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED    11   2
  ZKSCAN5 WILD-TYPE 405 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED     11    2
  ZKSCAN5 WILD-TYPE  405  100
     clus
vv    ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  NO               11               405
  YES               2               100
[1] 2 2
[1] FALSE
D173V9, continuous
D173V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZKSCAN5 MUTATED       3                         0
  ZKSCAN5 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZKSCAN5 MUTATED                                           0     9
  ZKSCAN5 WILD-TYPE                                         1   348
D173V11, multiclass
                                           clus
vv                                          ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V12, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     0   9
  ZKSCAN5 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      0    9
  ZKSCAN5 WILD-TYPE   10  389
                        clus
vv                       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(174) Variable = CELSR1 MUTATION ANALYSIS
D174V1, survival
                  sevent
clus2                0   1
  CELSR1 MUTATED    21  18
  CELSR1 WILD-TYPE 317 198
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              39              515 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              18              198 
$`CELSR1 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NV TCGA-LN-A4A3 
        4.31        21.99         2.66        12.92        52.57        12.76 
TCGA-R6-A6DN TCGA-V5-AASW TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-7703 
        8.02         9.27        19.73        26.70        34.68        36.16 
TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8368 
       35.84        14.43        29.59         8.05         7.40         4.31 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-A4MG TCGA-CD-A4MI 
        1.12        27.12         8.22        20.65         6.58        11.77 
TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        1.02         9.01         6.02       105.07        28.96        65.10 
TCGA-CG-5733 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4G9 
       21.07        11.44        77.29        26.47        22.82        24.20 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-MX-A5UJ 
        6.58        20.25        19.73 

$`CELSR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI 
       25.12         7.40         3.75         3.02        55.50        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        83.24        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10         1.32         2.66        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
        0.99         0.99        12.03        15.02         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CELSR1 MUTATED CELSR1 WILD-TYPE 
            1.02             0.00 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          105.07           122.30 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
           19.73            13.51 
[1] "1.0 - 105.1 (19.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D174V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CELSR1 MUTATED         1        3        5        2         5         6
  CELSR1 WILD-TYPE       9       17       41       29        79        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CELSR1 MUTATED           2          4          2          5        5
  CELSR1 WILD-TYPE        27         80         60         34       38
                  vv
clus               STAGE IVA
  CELSR1 MUTATED           1
  CELSR1 WILD-TYPE         3
D174V3, multiclass
            clus
vv           CELSR1 MUTATED CELSR1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                3               17
  STAGE IB                5               41
  STAGE II                2               29
  STAGE IIA               5               79
  STAGE IIB               6               77
  STAGE III               2               27
  STAGE IIIA              4               80
  STAGE IIIB              2               60
  STAGE IIIC              5               34
  STAGE IV                5               38
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CELSR1 MUTATED       7   8  13  14
  CELSR1 WILD-TYPE    47 127 248  88
D174V4, multiclass
       clus
vv      CELSR1 MUTATED CELSR1 WILD-TYPE
  T0+T1              7               47
  T2                 8              127
  T3                13              248
  T4                14               88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CELSR1 MUTATED    21  10   5   5
  CELSR1 WILD-TYPE 174 163  84  80
D174V5, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  N0             21              174
  N1             10              163
  N2              5               84
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V6, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    34   5
  CELSR1 WILD-TYPE 448  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     34    5
  CELSR1 WILD-TYPE  448   33
   clus
vv  CELSR1 MUTATED CELSR1 WILD-TYPE
  0             34              448
  1              5               33
[1] 2 2
[1] FALSE
D174V7, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    22  23
  CELSR1 WILD-TYPE 150 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     22   23
  CELSR1 WILD-TYPE  150  383
        clus
vv       CELSR1 MUTATED CELSR1 WILD-TYPE
  FEMALE             22              150
  MALE               23              383
[1] 2 2
[1] FALSE
D174V8, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    31   3
  CELSR1 WILD-TYPE 385  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     31    3
  CELSR1 WILD-TYPE  385   99
     clus
vv    CELSR1 MUTATED CELSR1 WILD-TYPE
  NO              31              385
  YES              3               99
[1] 2 2
[1] FALSE
D174V9, continuous
[1] "Remove cluster labels:" "CELSR1 MUTATED"        
clus
  CELSR1 MUTATED CELSR1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CELSR1 WILD-TYPE" "CELSR1 WILD-TYPE" 
D174V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CELSR1 MUTATED       7                         1
  CELSR1 WILD-TYPE   126                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CELSR1 MUTATED                                           0    27
  CELSR1 WILD-TYPE                                         1   330
D174V11, multiclass
                                           clus
vv                                          CELSR1 MUTATED CELSR1 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 27              330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V12, binary
                  cls
clus                 0   1
  CELSR1 MUTATED     0  31
  CELSR1 WILD-TYPE  10 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED      0   31
  CELSR1 WILD-TYPE   10  367
                        clus
vv                       CELSR1 MUTATED CELSR1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             31              367
[1] 2 2
[1] FALSE

Clustering(175) Variable = CBLL1 MUTATION ANALYSIS
D175V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     3   4
  CBLL1 WILD-TYPE 335 212
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              7             547 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             212 
$`CBLL1 MUTATED`
TCGA-BR-4256 TCGA-BR-7703 TCGA-BR-8289 TCGA-BR-8686 TCGA-CG-4305 TCGA-D7-A6EY 
        9.34        36.16         2.66        20.88        15.95        11.44 
TCGA-MX-A5UJ 
       19.73 

$`CBLL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           2.66            0.00 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          36.16          122.30 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          15.95           13.55 
[1] "2.7 - 36.2 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D175V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBLL1 MUTATED         1        1        0        1         0         0
  CBLL1 WILD-TYPE       9       19       46       30        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBLL1 MUTATED           0          1          2          0        1         0
  CBLL1 WILD-TYPE        29         83         60         39       42         4
D175V3, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CBLL1 MUTATED       2   1   2   2
  CBLL1 WILD-TYPE    52 134 259 100
D175V4, multiclass
       clus
vv      CBLL1 MUTATED CBLL1 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CBLL1 MUTATED     1   4   1   2
  CBLL1 WILD-TYPE 194 169  88  83
D175V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             1             194
  N1             4             169
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V6, binary
                 cls
clus                0   1
  CBLL1 MUTATED     6   1
  CBLL1 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      6    1
  CBLL1 WILD-TYPE  476   37
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D175V7, binary
                 cls
clus                0   1
  CBLL1 MUTATED     2   6
  CBLL1 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      2    6
  CBLL1 WILD-TYPE  170  400
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D175V8, binary
                 cls
clus                0   1
  CBLL1 MUTATED     8   0
  CBLL1 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      8    0
  CBLL1 WILD-TYPE  408  102
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D175V9, continuous
D175V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBLL1 MUTATED       1                         1
  CBLL1 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBLL1 MUTATED                                           0     5
  CBLL1 WILD-TYPE                                         1   352
D175V11, multiclass
                                           clus
vv                                          CBLL1 MUTATED CBLL1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V12, binary
                 cls
clus                0   1
  CBLL1 MUTATED     0   7
  CBLL1 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    7
  CBLL1 WILD-TYPE   10  391
                        clus
vv                       CBLL1 MUTATED CBLL1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(176) Variable = NPHP1 MUTATION ANALYSIS
D176V1, survival
                 sevent
clus2               0   1
  NPHP1 MUTATED     8   3
  NPHP1 WILD-TYPE 330 213
  NPHP1 MUTATED NPHP1 WILD-TYPE 
             11             543 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
              3             213 
$`NPHP1 MUTATED`
TCGA-L5-A4OI TCGA-LN-A4A4 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8487 
       19.99        12.59         6.97        30.90        29.59         1.12 
TCGA-BR-8591 TCGA-CG-4306 TCGA-HU-A4G6 TCGA-IN-A6RS TCGA-R5-A7ZI 
       28.14         1.02        24.26        12.59        74.53 

$`NPHP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  NPHP1 MUTATED NPHP1 WILD-TYPE 
           1.02            0.00 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
          74.53          122.30 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
          19.99           13.55 
[1] "1.0 - 74.5 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D176V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NPHP1 MUTATED         0        2        0        0         1         1
  NPHP1 WILD-TYPE      10       18       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NPHP1 MUTATED           1          2          0          2        2         0
  NPHP1 WILD-TYPE        28         82         62         37       41         4
D176V3, multiclass
            clus
vv           NPHP1 MUTATED NPHP1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NPHP1 MUTATED       2   1   5   4
  NPHP1 WILD-TYPE    52 134 256  98
D176V4, multiclass
       clus
vv      NPHP1 MUTATED NPHP1 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NPHP1 MUTATED     5   3   1   2
  NPHP1 WILD-TYPE 190 170  88  83
D176V5, multiclass
    clus
vv   NPHP1 MUTATED NPHP1 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V6, binary
                 cls
clus                0   1
  NPHP1 MUTATED     8   2
  NPHP1 WILD-TYPE 474  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      8    2
  NPHP1 WILD-TYPE  474   36
   clus
vv  NPHP1 MUTATED NPHP1 WILD-TYPE
  0             8             474
  1             2              36
[1] 2 2
[1] FALSE
D176V7, binary
                 cls
clus                0   1
  NPHP1 MUTATED     5   7
  NPHP1 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      5    7
  NPHP1 WILD-TYPE  167  399
        clus
vv       NPHP1 MUTATED NPHP1 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D176V8, binary
                 cls
clus                0   1
  NPHP1 MUTATED     9   1
  NPHP1 WILD-TYPE 407 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      9    1
  NPHP1 WILD-TYPE  407  101
     clus
vv    NPHP1 MUTATED NPHP1 WILD-TYPE
  NO              9             407
  YES             1             101
[1] 2 2
[1] FALSE
D176V9, continuous
[1] "Remove cluster labels:" "NPHP1 MUTATED"         
clus
  NPHP1 MUTATED NPHP1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A5      TCGA-LN-A4A6 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
D176V10, continuous
[1] "Remove cluster labels:" "NPHP1 MUTATED"         
clus
  NPHP1 MUTATED NPHP1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" "NPHP1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"NPHP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NPHP1 MUTATED       2                         0
  NPHP1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPHP1 MUTATED                                           0     9
  NPHP1 WILD-TYPE                                         1   348
D176V11, multiclass
                                           clus
vv                                          NPHP1 MUTATED NPHP1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V12, binary
                 cls
clus                0   1
  NPHP1 MUTATED     1   9
  NPHP1 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      1    9
  NPHP1 WILD-TYPE    9  389
                        clus
vv                       NPHP1 MUTATED NPHP1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(177) Variable = CCDC88A MUTATION ANALYSIS
D177V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    16  11
  CCDC88A WILD-TYPE 322 205
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               27               527 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               11               205 
$`CCDC88A MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-JY-A93F TCGA-L5-A4OF TCGA-L5-A4OU TCGA-L5-A8NS 
        0.85         0.53        24.03        26.33        29.00        13.41 
TCGA-LN-A49K TCGA-R6-A6L4 TCGA-VR-A8EZ TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 
        5.92        16.31        18.18        26.70        30.90        34.68 
TCGA-BR-6707 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4306 
       19.89         0.26        25.05         1.12        31.96         1.02 
TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-6528 TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4G8 
        8.05         6.02        15.22        14.47        11.08        22.68 
TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-VQ-A8P2 
        0.10        29.00        38.14 

$`CCDC88A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
              0.1               0.0 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            38.14            122.30 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            16.31             13.51 
[1] "0.1 - 38.1 (16.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D177V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC88A MUTATED         0        0        5        1         6         4
  CCDC88A WILD-TYPE      10       20       41       30        78        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           0          4          0          4        4
  CCDC88A WILD-TYPE        29         80         62         35       39
                   vv
clus                STAGE IVA
  CCDC88A MUTATED           0
  CCDC88A WILD-TYPE         4
D177V3, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 5                41
  STAGE II                 1                30
  STAGE IIA                6                78
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               0                62
  STAGE IIIC               4                35
  STAGE IV                 4                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC88A MUTATED       1   7  11  10
  CCDC88A WILD-TYPE    53 128 250  92
D177V4, multiclass
       clus
vv      CCDC88A MUTATED CCDC88A WILD-TYPE
  T0+T1               1                53
  T2                  7               128
  T3                 11               250
  T4                 10                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC88A MUTATED    15   6   4   3
  CCDC88A WILD-TYPE 180 167  85  82
D177V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              15               180
  N1               6               167
  N2               4                85
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V6, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    27   2
  CCDC88A WILD-TYPE 455  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     27    2
  CCDC88A WILD-TYPE  455   36
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              27               455
  1               2                36
[1] 2 2
[1] FALSE
D177V7, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    13  18
  CCDC88A WILD-TYPE 159 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     13   18
  CCDC88A WILD-TYPE  159  388
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE              13               159
  MALE                18               388
[1] 2 2
[1] FALSE
D177V8, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    21   3
  CCDC88A WILD-TYPE 395  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     21    3
  CCDC88A WILD-TYPE  395   99
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO               21               395
  YES               3                99
[1] 2 2
[1] FALSE
D177V9, continuous
D177V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC88A MUTATED       6                         1
  CCDC88A WILD-TYPE   127                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC88A MUTATED                                           0    20
  CCDC88A WILD-TYPE                                         1   337
D177V11, multiclass
                                           clus
vv                                          CCDC88A MUTATED CCDC88A WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  20               337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V12, binary
                   cls
clus                  0   1
  CCDC88A MUTATED     0  21
  CCDC88A WILD-TYPE  10 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      0   21
  CCDC88A WILD-TYPE   10  377
                        clus
vv                       CCDC88A MUTATED CCDC88A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              21               377
[1] 2 2
[1] FALSE

Clustering(178) Variable = DTX3 MUTATION ANALYSIS
D178V1, survival
                sevent
clus2              0   1
  DTX3 MUTATED     5   2
  DTX3 WILD-TYPE 333 214
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            547 
  DTX3 MUTATED DTX3 WILD-TYPE 
             2            214 
$`DTX3 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-CG-5728 TCGA-D7-A6F0 TCGA-FP-A4BE TCGA-HU-A4GT 
       30.90        29.59        65.10        22.29        11.08         6.51 
TCGA-RD-A7C1 
       16.67 

$`DTX3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DTX3 MUTATED DTX3 WILD-TYPE 
          6.51           0.00 
  DTX3 MUTATED DTX3 WILD-TYPE 
          65.1          122.3 
  DTX3 MUTATED DTX3 WILD-TYPE 
         22.29          13.51 
[1] "6.5 - 65.1 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D178V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DTX3 MUTATED         0        0        3        0         2         1
  DTX3 WILD-TYPE      10       20       43       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DTX3 MUTATED           0          0          0          0        0         0
  DTX3 WILD-TYPE        29         84         62         39       43         4
D178V3, multiclass
            clus
vv           DTX3 MUTATED DTX3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DTX3 MUTATED       0   4   2   1
  DTX3 WILD-TYPE    54 131 259 101
D178V4, multiclass
       clus
vv      DTX3 MUTATED DTX3 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DTX3 MUTATED     6   0   0   0
  DTX3 WILD-TYPE 189 173  89  85
D178V5, multiclass
    clus
vv   DTX3 MUTATED DTX3 WILD-TYPE
  N0            6            189
  N1            0            173
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V6, binary
                cls
clus               0   1
  DTX3 MUTATED     7   0
  DTX3 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      7    0
  DTX3 WILD-TYPE  475   38
   clus
vv  DTX3 MUTATED DTX3 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D178V7, binary
                cls
clus               0   1
  DTX3 MUTATED     5   2
  DTX3 WILD-TYPE 167 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      5    2
  DTX3 WILD-TYPE  167  404
        clus
vv       DTX3 MUTATED DTX3 WILD-TYPE
  FEMALE            5            167
  MALE              2            404
[1] 2 2
[1] FALSE
D178V8, binary
                cls
clus               0   1
  DTX3 MUTATED     5   1
  DTX3 WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      5    1
  DTX3 WILD-TYPE  411  101
     clus
vv    DTX3 MUTATED DTX3 WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D178V9, continuous
D178V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DTX3 MUTATED       1                         1
  DTX3 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DTX3 MUTATED                                           0     4
  DTX3 WILD-TYPE                                         1   353
D178V11, multiclass
                                           clus
vv                                          DTX3 MUTATED DTX3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V12, binary
                cls
clus               0   1
  DTX3 MUTATED     0   6
  DTX3 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      0    6
  DTX3 WILD-TYPE   10  392
                        clus
vv                       DTX3 MUTATED DTX3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(179) Variable = ZNF43 MUTATION ANALYSIS
D179V1, survival
                 sevent
clus2               0   1
  ZNF43 MUTATED    22   6
  ZNF43 WILD-TYPE 316 210
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             28             526 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              6             210 
$`ZNF43 MUTATED`
TCGA-KB-A93G TCGA-2H-A9GM TCGA-IG-A3QL TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A8NR 
       20.15        13.94        35.21        18.35         4.90         8.71 
TCGA-L7-A6VZ TCGA-BR-4183 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-6566 
       10.36         6.61        34.68        15.95        19.33        32.78 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8589 TCGA-BR-8680 
       44.94         9.21        35.84        32.25        27.12        31.96 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5578 TCGA-D7-A4Z0 
        6.58        15.95         6.02        65.10        12.66        14.76 
TCGA-HU-A4GU TCGA-IN-A7NR TCGA-VQ-A8P2 TCGA-VQ-AA6J 
        6.58         6.51        38.14        27.55 

$`ZNF43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24         0.23         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       30.90        31.20        21.90        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44         6.74        12.59        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        17.26 

  ZNF43 MUTATED ZNF43 WILD-TYPE 
            4.9             0.0 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
           65.1           122.3 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
         17.150          13.445 
[1] "4.9 - 65.1 (17.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D179V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF43 MUTATED         1        0        3        2         6         6
  ZNF43 WILD-TYPE       9       20       43       29        78        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF43 MUTATED           1          4          2          1        4         0
  ZNF43 WILD-TYPE        28         80         60         38       39         4
D179V3, multiclass
            clus
vv           ZNF43 MUTATED ZNF43 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZNF43 MUTATED       3   7  13   7
  ZNF43 WILD-TYPE    51 128 248  95
D179V4, multiclass
       clus
vv      ZNF43 MUTATED ZNF43 WILD-TYPE
  T0+T1             3              51
  T2                7             128
  T3               13             248
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZNF43 MUTATED    11  14   4   2
  ZNF43 WILD-TYPE 184 159  85  83
D179V5, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  N0            11             184
  N1            14             159
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V6, binary
                 cls
clus                0   1
  ZNF43 MUTATED    25   3
  ZNF43 WILD-TYPE 457  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     25    3
  ZNF43 WILD-TYPE  457   35
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0            25             457
  1             3              35
[1] 2 2
[1] FALSE
D179V7, binary
                 cls
clus                0   1
  ZNF43 MUTATED    13  18
  ZNF43 WILD-TYPE 159 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     13   18
  ZNF43 WILD-TYPE  159  388
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  FEMALE            13             159
  MALE              18             388
[1] 2 2
[1] FALSE
D179V8, binary
                 cls
clus                0   1
  ZNF43 MUTATED    24   3
  ZNF43 WILD-TYPE 392  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     24    3
  ZNF43 WILD-TYPE  392   99
     clus
vv    ZNF43 MUTATED ZNF43 WILD-TYPE
  NO             24             392
  YES             3              99
[1] 2 2
[1] FALSE
D179V9, continuous
[1] "Remove cluster labels:" "ZNF43 MUTATED"         
clus
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
D179V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF43 MUTATED       3                         2
  ZNF43 WILD-TYPE   130                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF43 MUTATED                                           0    21
  ZNF43 WILD-TYPE                                         1   336
D179V11, multiclass
                                           clus
vv                                          ZNF43 MUTATED ZNF43 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V12, binary
                 cls
clus                0   1
  ZNF43 MUTATED     0  21
  ZNF43 WILD-TYPE  10 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      0   21
  ZNF43 WILD-TYPE   10  377
                        clus
vv                       ZNF43 MUTATED ZNF43 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            21             377
[1] 2 2
[1] FALSE

Clustering(180) Variable = GLT6D1 MUTATION ANALYSIS
D180V1, survival
                  sevent
clus2                0   1
  GLT6D1 MUTATED    10   4
  GLT6D1 WILD-TYPE 328 212
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              14              540 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
               4              212 
$`GLT6D1 MUTATED`
TCGA-L5-A4OH TCGA-B7-A5TK TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8366 TCGA-BR-A44U 
       32.61         9.47        29.59         8.05         0.95        13.87 
TCGA-BR-A4J2 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8534 TCGA-CG-5725 TCGA-FP-8209 
       14.17        12.59        12.33        12.07        15.02        59.54 
TCGA-FP-8211 TCGA-HU-A4GP 
       13.58         8.98 

$`GLT6D1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98         0.72         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       14.07        22.29        17.06         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
            0.95             0.00 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
           59.54           122.30 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
          13.085           13.615 
[1] "0.9 - 59.5 (13.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D180V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLT6D1 MUTATED         1        0        2        1         2         3
  GLT6D1 WILD-TYPE       9       20       44       30        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT6D1 MUTATED           0          4          1          1        0
  GLT6D1 WILD-TYPE        29         80         61         38       43
                  vv
clus               STAGE IVA
  GLT6D1 MUTATED           0
  GLT6D1 WILD-TYPE         4
D180V3, multiclass
            clus
vv           GLT6D1 MUTATED GLT6D1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GLT6D1 MUTATED       1   3   5   6
  GLT6D1 WILD-TYPE    53 132 256  96
D180V4, multiclass
       clus
vv      GLT6D1 MUTATED GLT6D1 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 5              256
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GLT6D1 MUTATED     9   3   0   2
  GLT6D1 WILD-TYPE 186 170  89  83
D180V5, multiclass
    clus
vv   GLT6D1 MUTATED GLT6D1 WILD-TYPE
  N0              9              186
  N1              3              170
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V6, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED    14   0
  GLT6D1 WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED     14    0
  GLT6D1 WILD-TYPE  468   38
   clus
vv  GLT6D1 MUTATED GLT6D1 WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D180V7, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED     7   8
  GLT6D1 WILD-TYPE 165 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED      7    8
  GLT6D1 WILD-TYPE  165  398
        clus
vv       GLT6D1 MUTATED GLT6D1 WILD-TYPE
  FEMALE              7              165
  MALE                8              398
[1] 2 2
[1] FALSE
D180V8, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED    10   4
  GLT6D1 WILD-TYPE 406  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED     10    4
  GLT6D1 WILD-TYPE  406   98
     clus
vv    GLT6D1 MUTATED GLT6D1 WILD-TYPE
  NO              10              406
  YES              4               98
[1] 2 2
[1] FALSE
D180V9, continuous
D180V10, continuous
[1] "Remove cluster labels:" "GLT6D1 MUTATED"        
clus
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OM 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" "GLT6D1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"GLT6D1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLT6D1 MUTATED       5                         0
  GLT6D1 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLT6D1 MUTATED                                           0     9
  GLT6D1 WILD-TYPE                                         1   348
D180V11, multiclass
                                           clus
vv                                          GLT6D1 MUTATED GLT6D1 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V12, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED     0  13
  GLT6D1 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED      0   13
  GLT6D1 WILD-TYPE   10  385
                        clus
vv                       GLT6D1 MUTATED GLT6D1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(181) Variable = TAC4 MUTATION ANALYSIS
D181V1, survival
                sevent
clus2              0   1
  TAC4 MUTATED     4   0
  TAC4 WILD-TYPE 334 216
  TAC4 MUTATED TAC4 WILD-TYPE 
             4            550 
  TAC4 MUTATED TAC4 WILD-TYPE 
             0            216 
$`TAC4 MUTATED`
TCGA-L5-A4OI TCGA-BR-7707 TCGA-CG-5723 TCGA-HU-8238 
       19.99        35.84       105.07         1.51 

$`TAC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       77.29        63.06        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TAC4 MUTATED TAC4 WILD-TYPE 
          1.51           0.00 
  TAC4 MUTATED TAC4 WILD-TYPE 
        105.07         122.30 
  TAC4 MUTATED TAC4 WILD-TYPE 
        27.915         13.530 
[1] "1.5 - 105.1 (27.9)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9300000"
D181V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAC4 MUTATED         0        0        1        1         0         0
  TAC4 WILD-TYPE      10       20       45       30        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAC4 MUTATED           0          0          0          1        0         0
  TAC4 WILD-TYPE        29         84         62         38       43         4
D181V3, multiclass
            clus
vv           TAC4 MUTATED TAC4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TAC4 MUTATED       0   2   2   0
  TAC4 WILD-TYPE    54 133 259 102
D181V4, multiclass
       clus
vv      TAC4 MUTATED TAC4 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               2            259
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TAC4 MUTATED     1   1   1   1
  TAC4 WILD-TYPE 194 172  88  84
D181V5, multiclass
    clus
vv   TAC4 MUTATED TAC4 WILD-TYPE
  N0            1            194
  N1            1            172
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V6, binary
                cls
clus               0   1
  TAC4 MUTATED     3   0
  TAC4 WILD-TYPE 479  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      3    0
  TAC4 WILD-TYPE  479   38
   clus
vv  TAC4 MUTATED TAC4 WILD-TYPE
  0            3            479
  1            0             38
[1] 2 2
[1] FALSE
D181V7, binary
                cls
clus               0   1
  TAC4 MUTATED     1   3
  TAC4 WILD-TYPE 171 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      1    3
  TAC4 WILD-TYPE  171  403
        clus
vv       TAC4 MUTATED TAC4 WILD-TYPE
  FEMALE            1            171
  MALE              3            403
[1] 2 2
[1] FALSE
D181V8, binary
                cls
clus               0   1
  TAC4 MUTATED     4   0
  TAC4 WILD-TYPE 412 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      4    0
  TAC4 WILD-TYPE  412  102
     clus
vv    TAC4 MUTATED TAC4 WILD-TYPE
  NO             4            412
  YES            0            102
[1] 2 2
[1] FALSE
D181V9, continuous
D181V10, continuous
[1] "Remove cluster labels:" "TAC4 MUTATED"          
clus
  TAC4 MUTATED TAC4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" "TAC4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"TAC4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TAC4 MUTATED       1                         0
  TAC4 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAC4 MUTATED                                           0     2
  TAC4 WILD-TYPE                                         1   355
D181V11, multiclass
                                           clus
vv                                          TAC4 MUTATED TAC4 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V12, binary
                cls
clus               0   1
  TAC4 MUTATED     0   2
  TAC4 WILD-TYPE  10 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAC4 MUTATED      0    2
  TAC4 WILD-TYPE   10  396
                        clus
vv                       TAC4 MUTATED TAC4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            2            396
[1] 2 2
[1] FALSE

Clustering(182) Variable = CCDC108 MUTATION ANALYSIS
D182V1, survival
                   sevent
clus2                 0   1
  CCDC108 MUTATED    20   7
  CCDC108 WILD-TYPE 318 209
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               27               527 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                7               209 
$`CCDC108 MUTATED`
TCGA-L5-A4OM TCGA-L5-A8NM TCGA-Z6-AAPN TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 
       47.93         7.76         2.66        11.70         6.97        30.90 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 
       34.68        29.59         4.31        25.05         1.12        31.96 
TCGA-BR-A4PE TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A487 TCGA-CG-4465 
       20.42         7.17        12.30        12.43        12.30         9.01 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GN 
        6.02        11.08        77.29        52.21        22.32        29.98 
TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-VQ-A8P2 
        6.51        14.07        38.14 

$`CCDC108 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        3.42         2.10         1.32        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59        12.53        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
       11.64        15.39        12.07        12.82         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CCDC108 MUTATED CCDC108 WILD-TYPE 
             1.12              0.00 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            77.29            122.30 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            12.43             13.58 
[1] "1.1 - 77.3 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D182V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC108 MUTATED         0        2        5        3         6         4
  CCDC108 WILD-TYPE      10       18       41       28        78        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC108 MUTATED           0          2          0          1        4
  CCDC108 WILD-TYPE        29         82         62         38       39
                   vv
clus                STAGE IVA
  CCDC108 MUTATED           0
  CCDC108 WILD-TYPE         4
D182V3, multiclass
            clus
vv           CCDC108 MUTATED CCDC108 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                18
  STAGE IB                 5                41
  STAGE II                 3                28
  STAGE IIA                6                78
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 4                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC108 MUTATED       4   9   8   8
  CCDC108 WILD-TYPE    50 126 253  94
D182V4, multiclass
       clus
vv      CCDC108 MUTATED CCDC108 WILD-TYPE
  T0+T1               4                50
  T2                  9               126
  T3                  8               253
  T4                  8                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC108 MUTATED    15   9   1   2
  CCDC108 WILD-TYPE 180 164  88  83
D182V5, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  N0              15               180
  N1               9               164
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V6, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    24   3
  CCDC108 WILD-TYPE 458  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     24    3
  CCDC108 WILD-TYPE  458   35
   clus
vv  CCDC108 MUTATED CCDC108 WILD-TYPE
  0              24               458
  1               3                35
[1] 2 2
[1] FALSE
D182V7, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    14  15
  CCDC108 WILD-TYPE 158 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     14   15
  CCDC108 WILD-TYPE  158  391
        clus
vv       CCDC108 MUTATED CCDC108 WILD-TYPE
  FEMALE              14               158
  MALE                15               391
[1] 2 2
[1] FALSE
D182V8, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    22   4
  CCDC108 WILD-TYPE 394  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     22    4
  CCDC108 WILD-TYPE  394   98
     clus
vv    CCDC108 MUTATED CCDC108 WILD-TYPE
  NO               22               394
  YES               4                98
[1] 2 2
[1] FALSE
D182V9, continuous
D182V10, continuous
[1] "Remove cluster labels:" "CCDC108 MUTATED"       
clus
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC108 MUTATED       9                         1
  CCDC108 WILD-TYPE   124                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC108 MUTATED                                           0    14
  CCDC108 WILD-TYPE                                         1   343
D182V11, multiclass
                                           clus
vv                                          CCDC108 MUTATED CCDC108 WILD-TYPE
  ASIAN                                                   9               124
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V12, binary
                   cls
clus                  0   1
  CCDC108 MUTATED     0  21
  CCDC108 WILD-TYPE  10 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      0   21
  CCDC108 WILD-TYPE   10  377
                        clus
vv                       CCDC108 MUTATED CCDC108 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              21               377
[1] 2 2
[1] FALSE

Clustering(183) Variable = TNRC6C MUTATION ANALYSIS
D183V1, survival
                  sevent
clus2                0   1
  TNRC6C MUTATED    12   6
  TNRC6C WILD-TYPE 326 210
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              536 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              210 
$`TNRC6C MUTATED`
TCGA-L5-A4OI TCGA-CG-4444 TCGA-IG-A4P3 TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NQ 
       19.99        47.05        18.64         7.40         2.66        21.37 
TCGA-Q9-A6FW TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CG-4465 
        7.82        34.68        44.94        35.84        16.14         9.01 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4G9 TCGA-HU-A4H8 
        6.02        11.08        26.47        22.82        24.20        14.07 

$`TNRC6C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        55.50        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
            2.66             0.00 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           47.05           122.30 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
          19.315           13.495 
[1] "2.7 - 47.0 (19.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D183V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNRC6C MUTATED         1        1        4        0         6         1
  TNRC6C WILD-TYPE       9       19       42       31        78        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6C MUTATED           0          1          2          1        2
  TNRC6C WILD-TYPE        29         83         60         38       41
                  vv
clus               STAGE IVA
  TNRC6C MUTATED           1
  TNRC6C WILD-TYPE         3
D183V3, multiclass
            clus
vv           TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                4               42
  STAGE II                0               31
  STAGE IIA               6               78
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TNRC6C MUTATED       5   6   7   2
  TNRC6C WILD-TYPE    49 129 254 100
D183V4, multiclass
       clus
vv      TNRC6C MUTATED TNRC6C WILD-TYPE
  T0+T1              5               49
  T2                 6              129
  T3                 7              254
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TNRC6C MUTATED    10   6   2   3
  TNRC6C WILD-TYPE 185 167  87  82
D183V5, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  N0             10              185
  N1              6              167
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V6, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    16   2
  TNRC6C WILD-TYPE 466  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     16    2
  TNRC6C WILD-TYPE  466   36
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0             16              466
  1              2               36
[1] 2 2
[1] FALSE
D183V7, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    10  11
  TNRC6C WILD-TYPE 162 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     10   11
  TNRC6C WILD-TYPE  162  395
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE             10              162
  MALE               11              395
[1] 2 2
[1] FALSE
D183V8, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    15   3
  TNRC6C WILD-TYPE 401  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     15    3
  TNRC6C WILD-TYPE  401   99
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO              15              401
  YES              3               99
[1] 2 2
[1] FALSE
D183V9, continuous
D183V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TNRC6C MUTATED       3                         2
  TNRC6C WILD-TYPE   130                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNRC6C MUTATED                                           0    12
  TNRC6C WILD-TYPE                                         1   345
D183V11, multiclass
                                           clus
vv                                          TNRC6C MUTATED TNRC6C WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V12, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     0  13
  TNRC6C WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      0   13
  TNRC6C WILD-TYPE   10  385
                        clus
vv                       TNRC6C MUTATED TNRC6C WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(184) Variable = TATDN1 MUTATION ANALYSIS
D184V1, survival
                  sevent
clus2                0   1
  TATDN1 MUTATED     4   2
  TATDN1 WILD-TYPE 334 214
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              548 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               2              214 
$`TATDN1 MUTATED`
TCGA-BR-8078 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4G9 
       29.59        11.77        12.62         6.02        11.44        24.20 

$`TATDN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TATDN1 MUTATED TATDN1 WILD-TYPE 
            6.02             0.00 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
           29.59           122.30 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
          12.195           13.630 
[1] "6.0 - 29.6 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D184V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TATDN1 MUTATED         0        1        1        0         0         1
  TATDN1 WILD-TYPE      10       19       45       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TATDN1 MUTATED           0          1          1          0        1
  TATDN1 WILD-TYPE        29         83         61         39       42
                  vv
clus               STAGE IVA
  TATDN1 MUTATED           0
  TATDN1 WILD-TYPE         4
D184V3, multiclass
            clus
vv           TATDN1 MUTATED TATDN1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TATDN1 MUTATED       1   1   2   2
  TATDN1 WILD-TYPE    53 134 259 100
D184V4, multiclass
       clus
vv      TATDN1 MUTATED TATDN1 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 2              259
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TATDN1 MUTATED     3   2   0   1
  TATDN1 WILD-TYPE 192 171  89  84
D184V5, multiclass
    clus
vv   TATDN1 MUTATED TATDN1 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V6, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     6   0
  TATDN1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      6    0
  TATDN1 WILD-TYPE  476   38
   clus
vv  TATDN1 MUTATED TATDN1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D184V7, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     3   3
  TATDN1 WILD-TYPE 169 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      3    3
  TATDN1 WILD-TYPE  169  403
        clus
vv       TATDN1 MUTATED TATDN1 WILD-TYPE
  FEMALE              3              169
  MALE                3              403
[1] 2 2
[1] FALSE
D184V8, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     6   0
  TATDN1 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      6    0
  TATDN1 WILD-TYPE  410  102
     clus
vv    TATDN1 MUTATED TATDN1 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D184V9, continuous
D184V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TATDN1 MUTATED       3                         0
  TATDN1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TATDN1 MUTATED                                           0     2
  TATDN1 WILD-TYPE                                         1   355
D184V11, multiclass
                                           clus
vv                                          TATDN1 MUTATED TATDN1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V12, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     0   5
  TATDN1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      0    5
  TATDN1 WILD-TYPE   10  393
                        clus
vv                       TATDN1 MUTATED TATDN1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(185) Variable = INO80D MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2                0   1
  INO80D MUTATED    14   6
  INO80D WILD-TYPE 324 210
  INO80D MUTATED INO80D WILD-TYPE 
              20              534 
  INO80D MUTATED INO80D WILD-TYPE 
               6              210 
$`INO80D MUTATED`
TCGA-L5-A4OI TCGA-IG-A7DP TCGA-JY-A6FH TCGA-L5-A4OR TCGA-L5-A891 TCGA-LN-A4A2 
       19.99        14.86        47.38         3.16         3.75        12.49 
TCGA-LN-A9FR TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7901 TCGA-BR-8680 TCGA-BR-A4QL 
       12.26        30.90        44.94         3.45        31.96        16.14 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5723 TCGA-HF-7132 
       12.82        12.43         1.02         9.01       105.07        77.29 
TCGA-HU-A4H0 TCGA-VQ-A8P2 
        2.10        38.14 

$`INO80D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  INO80D MUTATED INO80D WILD-TYPE 
            1.02             0.00 
  INO80D MUTATED INO80D WILD-TYPE 
          105.07           122.30 
  INO80D MUTATED INO80D WILD-TYPE 
          13.840           13.565 
[1] "1.0 - 105.1 (13.8)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D185V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INO80D MUTATED         0        1        0        3         2         3
  INO80D WILD-TYPE      10       19       46       28        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INO80D MUTATED           0          4          1          2        3
  INO80D WILD-TYPE        29         80         61         37       40
                  vv
clus               STAGE IVA
  INO80D MUTATED           0
  INO80D WILD-TYPE         4
D185V3, multiclass
            clus
vv           INO80D MUTATED INO80D WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                3               28
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  INO80D MUTATED       2   5   9   6
  INO80D WILD-TYPE    52 130 252  96
D185V4, multiclass
       clus
vv      INO80D MUTATED INO80D WILD-TYPE
  T0+T1              2               52
  T2                 5              130
  T3                 9              252
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  INO80D MUTATED     5   9   2   4
  INO80D WILD-TYPE 190 164  87  81
D185V5, multiclass
    clus
vv   INO80D MUTATED INO80D WILD-TYPE
  N0              5              190
  N1              9              164
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V6, binary
                  cls
clus                 0   1
  INO80D MUTATED    17   3
  INO80D WILD-TYPE 465  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED     17    3
  INO80D WILD-TYPE  465   35
   clus
vv  INO80D MUTATED INO80D WILD-TYPE
  0             17              465
  1              3               35
[1] 2 2
[1] FALSE
D185V7, binary
                  cls
clus                 0   1
  INO80D MUTATED     8  15
  INO80D WILD-TYPE 164 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED      8   15
  INO80D WILD-TYPE  164  391
        clus
vv       INO80D MUTATED INO80D WILD-TYPE
  FEMALE              8              164
  MALE               15              391
[1] 2 2
[1] FALSE
D185V8, binary
                  cls
clus                 0   1
  INO80D MUTATED    13   4
  INO80D WILD-TYPE 403  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED     13    4
  INO80D WILD-TYPE  403   98
     clus
vv    INO80D MUTATED INO80D WILD-TYPE
  NO              13              403
  YES              4               98
[1] 2 2
[1] FALSE
D185V9, continuous
[1] "Remove cluster labels:" "INO80D MUTATED"        
clus
  INO80D MUTATED INO80D WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A3 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" 
D185V10, continuous
[1] "Remove cluster labels:" "INO80D MUTATED"        
clus
  INO80D MUTATED INO80D WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" "INO80D WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INO80D MUTATED       6                         0
  INO80D WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INO80D MUTATED                                           0    13
  INO80D WILD-TYPE                                         1   344
D185V11, multiclass
                                           clus
vv                                          INO80D MUTATED INO80D WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V12, binary
                  cls
clus                 0   1
  INO80D MUTATED     0  14
  INO80D WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED      0   14
  INO80D WILD-TYPE   10  384
                        clus
vv                       INO80D MUTATED INO80D WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(186) Variable = WDR7 MUTATION ANALYSIS
D186V1, survival
                sevent
clus2              0   1
  WDR7 MUTATED    14   9
  WDR7 WILD-TYPE 324 207
  WDR7 MUTATED WDR7 WILD-TYPE 
            23            531 
  WDR7 MUTATED WDR7 WILD-TYPE 
             9            207 
$`WDR7 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GH TCGA-2H-A9GM TCGA-IG-A5B8 TCGA-JY-A6F8 
        4.31        19.99        31.27        13.94         0.79       122.10 
TCGA-R6-A8W8 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8372 
        2.89         9.34        34.68        44.94        36.16        31.27 
TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 
       11.77         6.02       105.07        65.10        21.07        21.27 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4GX TCGA-R5-A7ZR 
       11.08        30.51         6.51        20.25         6.08 

$`WDR7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       14.04        45.67        18.21         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  WDR7 MUTATED WDR7 WILD-TYPE 
          0.79           0.00 
  WDR7 MUTATED WDR7 WILD-TYPE 
         122.1          122.3 
  WDR7 MUTATED WDR7 WILD-TYPE 
         20.25          13.51 
[1] "0.8 - 122.1 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D186V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR7 MUTATED         2        1        3        1         4         4
  WDR7 WILD-TYPE       8       19       43       30        80        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR7 MUTATED           1          3          1          4        2         0
  WDR7 WILD-TYPE        28         81         61         35       41         4
D186V3, multiclass
            clus
vv           WDR7 MUTATED WDR7 WILD-TYPE
  STAGE I               2              8
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            4             35
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WDR7 MUTATED       6   4  10   7
  WDR7 WILD-TYPE    48 131 251  95
D186V4, multiclass
       clus
vv      WDR7 MUTATED WDR7 WILD-TYPE
  T0+T1            6             48
  T2               4            131
  T3              10            251
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WDR7 MUTATED    12   7   3   4
  WDR7 WILD-TYPE 183 166  86  81
D186V5, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  N0           12            183
  N1            7            166
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V6, binary
                cls
clus               0   1
  WDR7 MUTATED    25   0
  WDR7 WILD-TYPE 457  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     25    0
  WDR7 WILD-TYPE  457   38
   clus
vv  WDR7 MUTATED WDR7 WILD-TYPE
  0           25            457
  1            0             38
[1] 2 2
[1] FALSE
D186V7, binary
                cls
clus               0   1
  WDR7 MUTATED    11  18
  WDR7 WILD-TYPE 161 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     11   18
  WDR7 WILD-TYPE  161  388
        clus
vv       WDR7 MUTATED WDR7 WILD-TYPE
  FEMALE           11            161
  MALE             18            388
[1] 2 2
[1] FALSE
D186V8, binary
                cls
clus               0   1
  WDR7 MUTATED    20   3
  WDR7 WILD-TYPE 396  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     20    3
  WDR7 WILD-TYPE  396   99
     clus
vv    WDR7 MUTATED WDR7 WILD-TYPE
  NO            20            396
  YES            3             99
[1] 2 2
[1] FALSE
D186V9, continuous
D186V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WDR7 MUTATED       3                         3
  WDR7 WILD-TYPE   130                        11
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR7 MUTATED                                           0    15
  WDR7 WILD-TYPE                                         1   342
D186V11, multiclass
                                           clus
vv                                          WDR7 MUTATED WDR7 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            3             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V12, binary
                cls
clus               0   1
  WDR7 MUTATED     1  17
  WDR7 WILD-TYPE   9 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED      1   17
  WDR7 WILD-TYPE    9  381
                        clus
vv                       WDR7 MUTATED WDR7 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(187) Variable = FAAH MUTATION ANALYSIS
D187V1, survival
                sevent
clus2              0   1
  FAAH MUTATED     2   3
  FAAH WILD-TYPE 336 213
  FAAH MUTATED FAAH WILD-TYPE 
             5            549 
  FAAH MUTATED FAAH WILD-TYPE 
             3            213 
$`FAAH MUTATED`
TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-A4QL 
       19.56         9.34        14.43        32.25        16.14 

$`FAAH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FAAH MUTATED FAAH WILD-TYPE 
          9.34           0.00 
  FAAH MUTATED FAAH WILD-TYPE 
         32.25         122.30 
  FAAH MUTATED FAAH WILD-TYPE 
         16.14          13.51 
[1] "9.3 - 32.2 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D187V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAAH MUTATED         0        0        0        0         0         1
  FAAH WILD-TYPE      10       20       46       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAAH MUTATED           1          0          1          1        0         0
  FAAH WILD-TYPE        28         84         61         38       43         4
D187V3, multiclass
            clus
vv           FAAH MUTATED FAAH WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FAAH MUTATED       0   0   1   3
  FAAH WILD-TYPE    54 135 260  99
D187V4, multiclass
       clus
vv      FAAH MUTATED FAAH WILD-TYPE
  T0+T1            0             54
  T2               0            135
  T3               1            260
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FAAH MUTATED     1   2   0   2
  FAAH WILD-TYPE 194 171  89  83
D187V5, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  N0            1            194
  N1            2            171
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V6, binary
                cls
clus               0   1
  FAAH MUTATED     5   0
  FAAH WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      5    0
  FAAH WILD-TYPE  477   38
   clus
vv  FAAH MUTATED FAAH WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D187V7, binary
                cls
clus               0   1
  FAAH MUTATED     2   3
  FAAH WILD-TYPE 170 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      2    3
  FAAH WILD-TYPE  170  403
        clus
vv       FAAH MUTATED FAAH WILD-TYPE
  FEMALE            2            170
  MALE              3            403
[1] 2 2
[1] FALSE
D187V8, binary
                cls
clus               0   1
  FAAH MUTATED     5   0
  FAAH WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      5    0
  FAAH WILD-TYPE  411  102
     clus
vv    FAAH MUTATED FAAH WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D187V9, continuous
D187V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FAAH MUTATED       0                         0
  FAAH WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAAH MUTATED                                           0     5
  FAAH WILD-TYPE                                         1   352
D187V11, multiclass
                                           clus
vv                                          FAAH MUTATED FAAH WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V12, binary
                cls
clus               0   1
  FAAH MUTATED     0   5
  FAAH WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      0    5
  FAAH WILD-TYPE   10  393
                        clus
vv                       FAAH MUTATED FAAH WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(188) Variable = EFNB3 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  EFNB3 MUTATED     8   6
  EFNB3 WILD-TYPE 330 210
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             14             540 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              6             210 
$`EFNB3 MUTATED`
TCGA-L5-A8NM TCGA-VR-A8Q7 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8361 
        7.76        52.27        30.90        32.78        30.90        31.10 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-A4CS TCGA-CG-4441 TCGA-D7-A6EY TCGA-HF-A5NB 
        0.26        31.27         1.48        14.01        11.44        30.51 
TCGA-HU-A4H4 TCGA-MX-A5UJ 
       23.84        19.73 

$`EFNB3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        1.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  EFNB3 MUTATED EFNB3 WILD-TYPE 
           0.26            0.00 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
          52.27          122.30 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
         27.175          13.495 
[1] "0.3 - 52.3 (27.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D188V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFNB3 MUTATED         0        0        1        0         1         3
  EFNB3 WILD-TYPE      10       20       45       31        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFNB3 MUTATED           0          4          1          4        0         0
  EFNB3 WILD-TYPE        29         80         61         35       43         4
D188V3, multiclass
            clus
vv           EFNB3 MUTATED EFNB3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFNB3 MUTATED       0   5   5   5
  EFNB3 WILD-TYPE    54 130 256  97
D188V4, multiclass
       clus
vv      EFNB3 MUTATED EFNB3 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFNB3 MUTATED     3   2   5   4
  EFNB3 WILD-TYPE 192 171  84  81
D188V5, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             5              84
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V6, binary
                 cls
clus                0   1
  EFNB3 MUTATED    15   0
  EFNB3 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED     15    0
  EFNB3 WILD-TYPE  467   38
   clus
vv  EFNB3 MUTATED EFNB3 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus                0   1
  EFNB3 MUTATED     9   6
  EFNB3 WILD-TYPE 163 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      9    6
  EFNB3 WILD-TYPE  163  400
        clus
vv       EFNB3 MUTATED EFNB3 WILD-TYPE
  FEMALE             9             163
  MALE               6             400
[1] 2 2
[1] FALSE
D188V8, binary
                 cls
clus                0   1
  EFNB3 MUTATED    13   1
  EFNB3 WILD-TYPE 403 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED     13    1
  EFNB3 WILD-TYPE  403  101
     clus
vv    EFNB3 MUTATED EFNB3 WILD-TYPE
  NO             13             403
  YES             1             101
[1] 2 2
[1] FALSE
D188V9, continuous
[1] "Remove cluster labels:" "EFNB3 MUTATED"         
clus
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
D188V10, continuous
[1] "Remove cluster labels:" "EFNB3 MUTATED"         
clus
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" "EFNB3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EFNB3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFNB3 MUTATED       1                         0
  EFNB3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFNB3 MUTATED                                           0    12
  EFNB3 WILD-TYPE                                         1   345
D188V11, multiclass
                                           clus
vv                                          EFNB3 MUTATED EFNB3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V12, binary
                 cls
clus                0   1
  EFNB3 MUTATED     0  11
  EFNB3 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      0   11
  EFNB3 WILD-TYPE   10  387
                        clus
vv                       EFNB3 MUTATED EFNB3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(189) Variable = MAP3K1 MUTATION ANALYSIS
D189V1, survival
                  sevent
clus2                0   1
  MAP3K1 MUTATED    11  11
  MAP3K1 WILD-TYPE 327 205
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              22              532 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              11              205 
$`MAP3K1 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-LN-A49P TCGA-LN-A4A4 TCGA-M9-A5M8 
       19.99       122.10         7.76        12.33        12.59        33.11 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6852 
        8.12        18.18         6.97        30.90         6.61        44.94 
TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 
        6.18        31.96        11.77         6.02        28.96        21.07 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-VQ-A8PQ 
        0.10         6.51        14.07        15.65 

$`MAP3K1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
             0.1              0.0 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
           122.1            122.3 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
          13.330           13.565 
[1] "0.1 - 122.1 (13.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D189V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP3K1 MUTATED         1        1        1        0         5         2
  MAP3K1 WILD-TYPE       9       19       45       31        79        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K1 MUTATED           2          3          1          3        3
  MAP3K1 WILD-TYPE        27         81         61         36       40
                  vv
clus               STAGE IVA
  MAP3K1 MUTATED           0
  MAP3K1 WILD-TYPE         4
D189V3, multiclass
            clus
vv           MAP3K1 MUTATED MAP3K1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAP3K1 MUTATED       3   4  11   5
  MAP3K1 WILD-TYPE    51 131 250  97
D189V4, multiclass
       clus
vv      MAP3K1 MUTATED MAP3K1 WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                11              250
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP3K1 MUTATED     8   8   4   2
  MAP3K1 WILD-TYPE 187 165  85  83
D189V5, multiclass
    clus
vv   MAP3K1 MUTATED MAP3K1 WILD-TYPE
  N0              8              187
  N1              8              165
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V6, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED    19   2
  MAP3K1 WILD-TYPE 463  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED     19    2
  MAP3K1 WILD-TYPE  463   36
   clus
vv  MAP3K1 MUTATED MAP3K1 WILD-TYPE
  0             19              463
  1              2               36
[1] 2 2
[1] FALSE
D189V7, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     7  16
  MAP3K1 WILD-TYPE 165 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      7   16
  MAP3K1 WILD-TYPE  165  390
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  FEMALE              7              165
  MALE               16              390
[1] 2 2
[1] FALSE
D189V8, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED    20   2
  MAP3K1 WILD-TYPE 396 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED     20    2
  MAP3K1 WILD-TYPE  396  100
     clus
vv    MAP3K1 MUTATED MAP3K1 WILD-TYPE
  NO              20              396
  YES              2              100
[1] 2 2
[1] FALSE
D189V9, continuous
D189V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP3K1 MUTATED       8                         0
  MAP3K1 WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP3K1 MUTATED                                           0    11
  MAP3K1 WILD-TYPE                                         1   346
D189V11, multiclass
                                           clus
vv                                          MAP3K1 MUTATED MAP3K1 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V12, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     0  13
  MAP3K1 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      0   13
  MAP3K1 WILD-TYPE   10  385
                        clus
vv                       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(190) Variable = ZNF124 MUTATION ANALYSIS
D190V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     5   3
  ZNF124 WILD-TYPE 333 213
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              546 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               3              213 
$`ZNF124 MUTATED`
TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8591 TCGA-CD-8528 TCGA-CG-5721 
        6.97        35.84        14.43        28.14        12.33         6.02 
TCGA-CG-5726 TCGA-HU-A4GX 
       28.96        20.25 

$`ZNF124 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF124 MUTATED ZNF124 WILD-TYPE 
            6.02             0.00 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           35.84           122.30 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           17.34            13.53 
[1] "6.0 - 35.8 (17.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D190V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF124 MUTATED         0        1        2        0         0         0
  ZNF124 WILD-TYPE      10       19       44       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           1          2          0          2        1
  ZNF124 WILD-TYPE        28         82         62         37       42
                  vv
clus               STAGE IVA
  ZNF124 MUTATED           0
  ZNF124 WILD-TYPE         4
D190V3, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF124 MUTATED       1   2   1   5
  ZNF124 WILD-TYPE    53 133 260  97
D190V4, multiclass
       clus
vv      ZNF124 MUTATED ZNF124 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 1              260
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF124 MUTATED     4   4   1   1
  ZNF124 WILD-TYPE 191 169  88  84
D190V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V6, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     9   0
  ZNF124 WILD-TYPE 473  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      9    0
  ZNF124 WILD-TYPE  473   38
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              9              473
  1              0               38
[1] 2 2
[1] FALSE
D190V7, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     4   6
  ZNF124 WILD-TYPE 168 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      4    6
  ZNF124 WILD-TYPE  168  400
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  FEMALE              4              168
  MALE                6              400
[1] 2 2
[1] FALSE
D190V8, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     6   1
  ZNF124 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      6    1
  ZNF124 WILD-TYPE  410  101
     clus
vv    ZNF124 MUTATED ZNF124 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D190V9, continuous
D190V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF124 MUTATED       2                         0
  ZNF124 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF124 MUTATED                                           0     5
  ZNF124 WILD-TYPE                                         1   352
D190V11, multiclass
                                           clus
vv                                          ZNF124 MUTATED ZNF124 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V12, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     0   7
  ZNF124 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      0    7
  ZNF124 WILD-TYPE   10  391
                        clus
vv                       ZNF124 MUTATED ZNF124 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(191) Variable = SVIL MUTATION ANALYSIS
D191V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    19  10
  SVIL WILD-TYPE 319 206
  SVIL MUTATED SVIL WILD-TYPE 
            29            525 
  SVIL MUTATED SVIL WILD-TYPE 
            10            206 
$`SVIL MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-CG-4460 TCGA-L7-A56G TCGA-R6-A8WG TCGA-BR-6452 
        4.31        35.97        21.99        10.85        12.69        34.68 
TCGA-BR-6803 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 
       31.20        35.84        29.59        31.10        31.27         1.12 
TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5721 
       31.96        20.42        16.14        11.77         9.01         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV TCGA-D7-A6ET TCGA-D7-A6EY 
      105.07        28.96        65.10         5.92        26.43        11.44 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-VQ-A8P2 
       22.32        22.68        29.98        20.25        38.14 

$`SVIL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       28.34         0.66        32.52        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SVIL MUTATED SVIL WILD-TYPE 
          1.12           0.00 
  SVIL MUTATED SVIL WILD-TYPE 
        105.07         122.30 
  SVIL MUTATED SVIL WILD-TYPE 
         22.68          13.41 
[1] "1.1 - 105.1 (22.7)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D191V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SVIL MUTATED         1        1        3        1         4         5
  SVIL WILD-TYPE       9       19       43       30        80        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SVIL MUTATED           1          3          3          4        5         0
  SVIL WILD-TYPE        28         81         59         35       38         4
D191V3, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             5             78
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            3             59
  STAGE IIIC            4             35
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SVIL MUTATED       3   5  11  13
  SVIL WILD-TYPE    51 130 250  89
D191V4, multiclass
       clus
vv      SVIL MUTATED SVIL WILD-TYPE
  T0+T1            3             51
  T2               5            130
  T3              11            250
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SVIL MUTATED    11  10   4   6
  SVIL WILD-TYPE 184 163  85  79
D191V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           11            184
  N1           10            163
  N2            4             85
  N3            6             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V6, binary
                cls
clus               0   1
  SVIL MUTATED    27   3
  SVIL WILD-TYPE 455  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     27    3
  SVIL WILD-TYPE  455   35
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           27            455
  1            3             35
[1] 2 2
[1] FALSE
D191V7, binary
                cls
clus               0   1
  SVIL MUTATED    19  15
  SVIL WILD-TYPE 153 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     19   15
  SVIL WILD-TYPE  153  391
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  FEMALE           19            153
  MALE             15            391
[1] 2 2
[1] FALSE
D191V8, binary
                cls
clus               0   1
  SVIL MUTATED    24   2
  SVIL WILD-TYPE 392 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     24    2
  SVIL WILD-TYPE  392  100
     clus
vv    SVIL MUTATED SVIL WILD-TYPE
  NO            24            392
  YES            2            100
[1] 2 2
[1] FALSE
D191V9, continuous
D191V10, continuous
[1] "Remove cluster labels:" "SVIL MUTATED"          
clus
  SVIL MUTATED SVIL WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NT 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL     TCGA-IG-A3Y9 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QT 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" "SVIL WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SVIL MUTATED       6                         2
  SVIL WILD-TYPE   127                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SVIL MUTATED                                           0    19
  SVIL WILD-TYPE                                         1   338
D191V11, multiclass
                                           clus
vv                                          SVIL MUTATED SVIL WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V12, binary
                cls
clus               0   1
  SVIL MUTATED     1  23
  SVIL WILD-TYPE   9 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED      1   23
  SVIL WILD-TYPE    9  375
                        clus
vv                       SVIL MUTATED SVIL WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           23            375
[1] 2 2
[1] FALSE

Clustering(192) Variable = TRMT6 MUTATION ANALYSIS
D192V1, survival
                 sevent
clus2               0   1
  TRMT6 MUTATED     8   2
  TRMT6 WILD-TYPE 330 214
  TRMT6 MUTATED TRMT6 WILD-TYPE 
             10             544 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
              2             214 
$`TRMT6 MUTATED`
TCGA-2H-A9GK TCGA-JY-A939 TCGA-L5-A88Z TCGA-BR-7716 TCGA-BR-8589 TCGA-CD-8536 
        7.63        21.70         7.40        39.78        27.12        12.43 
TCGA-CG-4306 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-A4GT 
        1.02         6.02        30.51         6.51 

$`TRMT6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TRMT6 MUTATED TRMT6 WILD-TYPE 
           1.02            0.00 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
          39.78          122.30 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
          10.03           13.63 
[1] "1.0 - 39.8 (10.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D192V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRMT6 MUTATED         0        0        0        1         2         2
  TRMT6 WILD-TYPE      10       20       46       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRMT6 MUTATED           1          0          1          1        2         0
  TRMT6 WILD-TYPE        28         84         61         38       41         4
D192V3, multiclass
            clus
vv           TRMT6 MUTATED TRMT6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TRMT6 MUTATED       2   0   5   3
  TRMT6 WILD-TYPE    52 135 256  99
D192V4, multiclass
       clus
vv      TRMT6 MUTATED TRMT6 WILD-TYPE
  T0+T1             2              52
  T2                0             135
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TRMT6 MUTATED     2   6   1   1
  TRMT6 WILD-TYPE 193 167  88  84
D192V5, multiclass
    clus
vv   TRMT6 MUTATED TRMT6 WILD-TYPE
  N0             2             193
  N1             6             167
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V6, binary
                 cls
clus                0   1
  TRMT6 MUTATED     9   1
  TRMT6 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      9    1
  TRMT6 WILD-TYPE  473   37
   clus
vv  TRMT6 MUTATED TRMT6 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D192V7, binary
                 cls
clus                0   1
  TRMT6 MUTATED     4   6
  TRMT6 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      4    6
  TRMT6 WILD-TYPE  168  400
        clus
vv       TRMT6 MUTATED TRMT6 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D192V8, binary
                 cls
clus                0   1
  TRMT6 MUTATED     8   1
  TRMT6 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      8    1
  TRMT6 WILD-TYPE  408  101
     clus
vv    TRMT6 MUTATED TRMT6 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D192V9, continuous
D192V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRMT6 MUTATED       2                         0
  TRMT6 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRMT6 MUTATED                                           0     4
  TRMT6 WILD-TYPE                                         1   353
D192V11, multiclass
                                           clus
vv                                          TRMT6 MUTATED TRMT6 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V12, binary
                 cls
clus                0   1
  TRMT6 MUTATED     0   4
  TRMT6 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      0    4
  TRMT6 WILD-TYPE   10  394
                        clus
vv                       TRMT6 MUTATED TRMT6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(193) Variable = ATM MUTATION ANALYSIS
D193V1, survival
               sevent
clus2             0   1
  ATM MUTATED    44  10
  ATM WILD-TYPE 294 206
  ATM MUTATED ATM WILD-TYPE 
           54           500 
  ATM MUTATED ATM WILD-TYPE 
           10           206 
$`ATM MUTATED`
TCGA-JY-A938 TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A50L TCGA-JY-A6FD TCGA-JY-A939 
       34.85         8.94         7.69         0.53        68.02        21.70 
TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NL TCGA-L5-A8NQ 
        6.28        26.33         7.40         3.02        13.22        21.37 
TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW 
       13.41        10.36        12.46        12.03        12.85         7.82 
TCGA-R6-A6XG TCGA-VR-A8EX TCGA-Z6-AAPN TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 
       38.40        28.11         2.66         9.67        34.68        32.78 
TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 
       30.90        35.84        18.15        32.25        31.10         0.26 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4J7 
        4.31         1.12        28.14        31.96        34.98        32.52 
TCGA-CD-5798 TCGA-CD-8534 TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-5721 TCGA-CG-5723 
       13.41        12.07        11.77         3.02         6.02       105.07 
TCGA-CG-5728 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8579 TCGA-HF-A5NB TCGA-HU-8249 
       65.10        19.50        18.21        20.91        30.51        28.96 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-RD-A8MV TCGA-VQ-A8P2 TCGA-VQ-AA6K 
        6.51        20.25        74.53       122.30        38.14        12.43 

$`ATM WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.55         7.76         5.49         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         6.18        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53        28.34         0.66        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       20.42         1.15        21.44        16.14         5.13        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19        14.66        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       27.55        17.26 

  ATM MUTATED ATM WILD-TYPE 
         0.26          0.00 
  ATM MUTATED ATM WILD-TYPE 
        122.3         122.1 
  ATM MUTATED ATM WILD-TYPE 
       18.855        13.510 
[1] "0.3 - 122.3 (18.9)" "0.0 - 122.1 (13.5)"
[1] "hr=" "2.8"
D193V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATM MUTATED         1        1        4        3        13         9
  ATM WILD-TYPE       9       19       42       28        71        74
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATM MUTATED           2          8          2          6        5         1
  ATM WILD-TYPE        27         76         60         33       38         3
D193V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              1             9
  STAGE IA             1            19
  STAGE IB             4            42
  STAGE II             3            28
  STAGE IIA           13            71
  STAGE IIB            9            74
  STAGE III            2            27
  STAGE IIIA           8            76
  STAGE IIIB           2            60
  STAGE IIIC           6            33
  STAGE IV             5            38
  STAGE IVA            1             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  ATM MUTATED       8   8  24  16
  ATM WILD-TYPE    46 127 237  86
D193V4, multiclass
       clus
vv      ATM MUTATED ATM WILD-TYPE
  T0+T1           8            46
  T2              8           127
  T3             24           237
  T4             16            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  ATM MUTATED    25  16   9   4
  ATM WILD-TYPE 170 157  80  81
D193V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          25           170
  N1          16           157
  N2           9            80
  N3           4            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V6, binary
               cls
clus              0   1
  ATM MUTATED    52   4
  ATM WILD-TYPE 430  34
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     52    4
  ATM WILD-TYPE  430   34
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          52           430
  1           4            34
[1] 2 2
[1] FALSE
D193V7, binary
               cls
clus              0   1
  ATM MUTATED    23  36
  ATM WILD-TYPE 149 370
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     23   36
  ATM WILD-TYPE  149  370
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          23           149
  MALE            36           370
[1] 2 2
[1] FALSE
D193V8, binary
               cls
clus              0   1
  ATM MUTATED    42   9
  ATM WILD-TYPE 374  93
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     42    9
  ATM WILD-TYPE  374   93
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           42           374
  YES           9            93
[1] 2 2
[1] FALSE
D193V9, continuous
D193V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  ATM MUTATED      13                         0
  ATM WILD-TYPE   120                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATM MUTATED                                           0    39
  ATM WILD-TYPE                                         1   318
D193V11, multiclass
                                           clus
vv                                          ATM MUTATED ATM WILD-TYPE
  ASIAN                                              13           120
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              39           318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V12, binary
               cls
clus              0   1
  ATM MUTATED     1  40
  ATM WILD-TYPE   9 358
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1   40
  ATM WILD-TYPE    9  358
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          40           358
[1] 2 2
[1] FALSE

Clustering(194) Variable = LEMD1 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   1
  LEMD1 WILD-TYPE 335 215
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             550 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              1             215 
$`LEMD1 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-FP-A4BE 
       34.68         6.18         6.58        11.08 

$`LEMD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  LEMD1 MUTATED LEMD1 WILD-TYPE 
           6.18            0.00 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          34.68          122.30 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
           8.83           13.63 
[1] "6.2 - 34.7 (8.8)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LEMD1 MUTATED         0        0        0        0         4         0
  LEMD1 WILD-TYPE      10       20       46       31        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEMD1 MUTATED           0          0          0          0        0         0
  LEMD1 WILD-TYPE        29         84         62         39       43         4
D194V3, multiclass
            clus
vv           LEMD1 MUTATED LEMD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LEMD1 MUTATED       0   0   4   0
  LEMD1 WILD-TYPE    54 135 257 102
D194V4, multiclass
       clus
vv      LEMD1 MUTATED LEMD1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                4             257
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LEMD1 MUTATED     4   0   0   0
  LEMD1 WILD-TYPE 191 173  89  85
D194V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             4             191
  N1             0             173
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V6, binary
                 cls
clus                0   1
  LEMD1 MUTATED     4   0
  LEMD1 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      4    0
  LEMD1 WILD-TYPE  478   38
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D194V7, binary
                 cls
clus                0   1
  LEMD1 MUTATED     1   3
  LEMD1 WILD-TYPE 171 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      1    3
  LEMD1 WILD-TYPE  171  403
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  FEMALE             1             171
  MALE               3             403
[1] 2 2
[1] FALSE
D194V8, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   1
  LEMD1 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    1
  LEMD1 WILD-TYPE  413  101
     clus
vv    LEMD1 MUTATED LEMD1 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D194V9, continuous
D194V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LEMD1 MUTATED       1                         1
  LEMD1 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LEMD1 MUTATED                                           0     2
  LEMD1 WILD-TYPE                                         1   355
D194V11, multiclass
                                           clus
vv                                          LEMD1 MUTATED LEMD1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V12, binary
                 cls
clus                0   1
  LEMD1 MUTATED     0   4
  LEMD1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      0    4
  LEMD1 WILD-TYPE   10  394
                        clus
vv                       LEMD1 MUTATED LEMD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(195) Variable = RASA1 MUTATION ANALYSIS
D195V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    15   8
  RASA1 WILD-TYPE 323 208
  RASA1 MUTATED RASA1 WILD-TYPE 
             23             531 
  RASA1 MUTATED RASA1 WILD-TYPE 
              8             208 
$`RASA1 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-L5-A4OU TCGA-L5-A8NM TCGA-LN-A49U 
       21.99         4.21         7.69        29.00         7.76        15.35 
TCGA-V5-AASX TCGA-Z6-A8JE TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8286 
        8.98         2.10        32.78        44.94        29.56        29.42 
TCGA-BR-8680 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-6527 
       31.96         3.02        15.95         1.02        28.96        10.26 
TCGA-D7-6815 TCGA-D7-A6EY TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-RD-A7BS 
       15.98        11.44        20.25        74.53        11.05 

$`RASA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       18.15        15.32        28.73         3.45         9.07        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20        11.77        12.62        20.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RASA1 MUTATED RASA1 WILD-TYPE 
           1.02            0.00 
  RASA1 MUTATED RASA1 WILD-TYPE 
          74.53          122.30 
  RASA1 MUTATED RASA1 WILD-TYPE 
          15.95           13.51 
[1] "1.0 - 74.5 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D195V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASA1 MUTATED         0        1        0        3         4         4
  RASA1 WILD-TYPE      10       19       46       28        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RASA1 MUTATED           1          2          2          1        5         0
  RASA1 WILD-TYPE        28         82         60         38       38         4
D195V3, multiclass
            clus
vv           RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               3              28
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RASA1 MUTATED       3   4  11   7
  RASA1 WILD-TYPE    51 131 250  95
D195V4, multiclass
       clus
vv      RASA1 MUTATED RASA1 WILD-TYPE
  T0+T1             3              51
  T2                4             131
  T3               11             250
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RASA1 MUTATED     8  10   4   1
  RASA1 WILD-TYPE 187 163  85  84
D195V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             8             187
  N1            10             163
  N2             4              85
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V6, binary
                 cls
clus                0   1
  RASA1 MUTATED    19   5
  RASA1 WILD-TYPE 463  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     19    5
  RASA1 WILD-TYPE  463   33
   clus
vv  RASA1 MUTATED RASA1 WILD-TYPE
  0            19             463
  1             5              33
[1] 2 2
[1] FALSE
D195V7, binary
                 cls
clus                0   1
  RASA1 MUTATED    11  15
  RASA1 WILD-TYPE 161 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     11   15
  RASA1 WILD-TYPE  161  391
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE            11             161
  MALE              15             391
[1] 2 2
[1] FALSE
D195V8, binary
                 cls
clus                0   1
  RASA1 MUTATED    17   3
  RASA1 WILD-TYPE 399  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     17    3
  RASA1 WILD-TYPE  399   99
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO             17             399
  YES             3              99
[1] 2 2
[1] FALSE
D195V9, continuous
D195V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RASA1 MUTATED       3                         0
  RASA1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASA1 MUTATED                                           0    17
  RASA1 WILD-TYPE                                         1   340
D195V11, multiclass
                                           clus
vv                                          RASA1 MUTATED RASA1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V12, binary
                 cls
clus                0   1
  RASA1 MUTATED     1  17
  RASA1 WILD-TYPE   9 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      1   17
  RASA1 WILD-TYPE    9  381
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(196) Variable = CABP5 MUTATION ANALYSIS
D196V1, survival
                 sevent
clus2               0   1
  CABP5 MUTATED     6   1
  CABP5 WILD-TYPE 332 215
  CABP5 MUTATED CABP5 WILD-TYPE 
              7             547 
  CABP5 MUTATED CABP5 WILD-TYPE 
              1             215 
$`CABP5 MUTATED`
TCGA-L7-A6VZ TCGA-LN-A9FP TCGA-BR-6452 TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-A4GQ 
       10.36        12.03        34.68        11.08         1.51         0.10 
TCGA-VQ-A8P2 
       38.14 

$`CABP5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CABP5 MUTATED CABP5 WILD-TYPE 
            0.1             0.0 
  CABP5 MUTATED CABP5 WILD-TYPE 
          38.14          122.30 
  CABP5 MUTATED CABP5 WILD-TYPE 
          11.08           13.68 
[1] "0.1 - 38.1 (11.1)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "2.3"
D196V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CABP5 MUTATED         0        0        1        0         3         0
  CABP5 WILD-TYPE      10       20       45       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CABP5 MUTATED           0          1          0          2        0         0
  CABP5 WILD-TYPE        29         83         62         37       43         4
D196V3, multiclass
            clus
vv           CABP5 MUTATED CABP5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CABP5 MUTATED       0   2   4   2
  CABP5 WILD-TYPE    54 133 257 100
D196V4, multiclass
       clus
vv      CABP5 MUTATED CABP5 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CABP5 MUTATED     4   1   2   1
  CABP5 WILD-TYPE 191 172  87  84
D196V5, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  N0             4             191
  N1             1             172
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V6, binary
                 cls
clus                0   1
  CABP5 MUTATED     7   0
  CABP5 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      7    0
  CABP5 WILD-TYPE  475   38
   clus
vv  CABP5 MUTATED CABP5 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D196V7, binary
                 cls
clus                0   1
  CABP5 MUTATED     2   6
  CABP5 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      2    6
  CABP5 WILD-TYPE  170  400
        clus
vv       CABP5 MUTATED CABP5 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D196V8, binary
                 cls
clus                0   1
  CABP5 MUTATED     3   4
  CABP5 WILD-TYPE 413  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      3    4
  CABP5 WILD-TYPE  413   98
     clus
vv    CABP5 MUTATED CABP5 WILD-TYPE
  NO              3             413
  YES             4              98
[1] 2 2
[1] FALSE
D196V9, continuous
D196V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CABP5 MUTATED       3                         1
  CABP5 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CABP5 MUTATED                                           0     3
  CABP5 WILD-TYPE                                         1   354
D196V11, multiclass
                                           clus
vv                                          CABP5 MUTATED CABP5 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V12, binary
                 cls
clus                0   1
  CABP5 MUTATED     0   6
  CABP5 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      0    6
  CABP5 WILD-TYPE   10  392
                        clus
vv                       CABP5 MUTATED CABP5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(197) Variable = PALB2 MUTATION ANALYSIS
D197V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED     7   5
  PALB2 WILD-TYPE 331 211
  PALB2 MUTATED PALB2 WILD-TYPE 
             12             542 
  PALB2 MUTATED PALB2 WILD-TYPE 
              5             211 
$`PALB2 MUTATED`
TCGA-CG-4460 TCGA-JY-A93D TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8591 
       21.99        31.56        32.78        44.94        31.10        28.14 
TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       16.14         6.02       105.07         0.10        38.14        18.41 

$`PALB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PALB2 MUTATED PALB2 WILD-TYPE 
            0.1             0.0 
  PALB2 MUTATED PALB2 WILD-TYPE 
         105.07          122.30 
  PALB2 MUTATED PALB2 WILD-TYPE 
         29.620          13.445 
[1] "0.1 - 105.1 (29.6)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D197V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PALB2 MUTATED         0        0        0        1         2         0
  PALB2 WILD-TYPE      10       20       46       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PALB2 MUTATED           0          1          2          4        2         0
  PALB2 WILD-TYPE        29         83         60         35       41         4
D197V3, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PALB2 MUTATED       0   2   4   6
  PALB2 WILD-TYPE    54 133 257  96
D197V4, multiclass
       clus
vv      PALB2 MUTATED PALB2 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PALB2 MUTATED     2   4   3   3
  PALB2 WILD-TYPE 193 169  86  82
D197V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V6, binary
                 cls
clus                0   1
  PALB2 MUTATED    11   1
  PALB2 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     11    1
  PALB2 WILD-TYPE  471   37
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D197V7, binary
                 cls
clus                0   1
  PALB2 MUTATED     5   7
  PALB2 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      5    7
  PALB2 WILD-TYPE  167  399
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D197V8, binary
                 cls
clus                0   1
  PALB2 MUTATED     9   3
  PALB2 WILD-TYPE 407  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      9    3
  PALB2 WILD-TYPE  407   99
     clus
vv    PALB2 MUTATED PALB2 WILD-TYPE
  NO              9             407
  YES             3              99
[1] 2 2
[1] FALSE
D197V9, continuous
D197V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PALB2 MUTATED       1                         0
  PALB2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PALB2 MUTATED                                           0     8
  PALB2 WILD-TYPE                                         1   349
D197V11, multiclass
                                           clus
vv                                          PALB2 MUTATED PALB2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V12, binary
                 cls
clus                0   1
  PALB2 MUTATED     0   6
  PALB2 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      0    6
  PALB2 WILD-TYPE   10  392
                        clus
vv                       PALB2 MUTATED PALB2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(198) Variable = RB1CC1 MUTATION ANALYSIS
D198V1, survival
                  sevent
clus2                0   1
  RB1CC1 MUTATED    11   5
  RB1CC1 WILD-TYPE 327 211
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              16              538 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               5              211 
$`RB1CC1 MUTATED`
TCGA-FP-A8CX TCGA-L5-A4OT TCGA-L5-A8NM TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 
        0.23         4.90         7.76        31.10        31.27        28.14 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5723 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-A5NB 
       16.14        15.95       105.07         5.92        11.08        30.51 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-VQ-A8P2 
       29.00        14.07        13.35        38.14 

$`RB1CC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
            0.23             0.00 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
          105.07           122.30 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
          16.045           13.510 
[1] "0.2 - 105.1 (16.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D198V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RB1CC1 MUTATED         0        0        1        2         1         2
  RB1CC1 WILD-TYPE      10       20       45       29        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RB1CC1 MUTATED           0          2          1          6        1
  RB1CC1 WILD-TYPE        29         82         61         33       42
                  vv
clus               STAGE IVA
  RB1CC1 MUTATED           0
  RB1CC1 WILD-TYPE         4
D198V3, multiclass
            clus
vv           RB1CC1 MUTATED RB1CC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              6               33
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RB1CC1 MUTATED       1   4   4   7
  RB1CC1 WILD-TYPE    53 131 257  95
D198V4, multiclass
       clus
vv      RB1CC1 MUTATED RB1CC1 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 4              257
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RB1CC1 MUTATED     1   9   1   6
  RB1CC1 WILD-TYPE 194 164  88  79
D198V5, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  N0              1              194
  N1              9              164
  N2              1               88
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V6, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED    15   1
  RB1CC1 WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED     15    1
  RB1CC1 WILD-TYPE  467   37
   clus
vv  RB1CC1 MUTATED RB1CC1 WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D198V7, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     7  10
  RB1CC1 WILD-TYPE 165 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      7   10
  RB1CC1 WILD-TYPE  165  396
        clus
vv       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  FEMALE              7              165
  MALE               10              396
[1] 2 2
[1] FALSE
D198V8, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED    11   3
  RB1CC1 WILD-TYPE 405  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED     11    3
  RB1CC1 WILD-TYPE  405   99
     clus
vv    RB1CC1 MUTATED RB1CC1 WILD-TYPE
  NO              11              405
  YES              3               99
[1] 2 2
[1] FALSE
D198V9, continuous
D198V10, continuous
[1] "Remove cluster labels:" "RB1CC1 MUTATED"        
clus
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" "RB1CC1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"RB1CC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RB1CC1 MUTATED       2                         1
  RB1CC1 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RB1CC1 MUTATED                                           0    11
  RB1CC1 WILD-TYPE                                         1   346
D198V11, multiclass
                                           clus
vv                                          RB1CC1 MUTATED RB1CC1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V12, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     0  11
  RB1CC1 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      0   11
  RB1CC1 WILD-TYPE   10  387
                        clus
vv                       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(199) Variable = C16ORF63 MUTATION ANALYSIS
D199V1, survival
                    sevent
clus2                  0   1
  C16ORF63 MUTATED     7   2
  C16ORF63 WILD-TYPE 331 214
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 9                545 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 2                214 
$`C16ORF63 MUTATED`
TCGA-IG-A97I TCGA-L5-A43C TCGA-BR-6452 TCGA-BR-8382 TCGA-CD-A48A TCGA-D7-A6EY 
       12.16         3.16        34.68        25.05        12.43        11.44 
TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4H3 
       14.47        22.32        29.00 

$`C16ORF63 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
              3.16               0.00 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
             34.68             122.30 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
             14.47              13.55 
[1] "3.2 - 34.7 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D199V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF63 MUTATED         0        0        1        0         3         1
  C16ORF63 WILD-TYPE      10       20       45       31        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF63 MUTATED           0          0          1          2        0
  C16ORF63 WILD-TYPE        29         84         61         37       43
                    vv
clus                 STAGE IVA
  C16ORF63 MUTATED           0
  C16ORF63 WILD-TYPE         4
D199V3, multiclass
            clus
vv           C16ORF63 MUTATED C16ORF63 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C16ORF63 MUTATED       0   2   3   3
  C16ORF63 WILD-TYPE    54 133 258  99
D199V4, multiclass
       clus
vv      C16ORF63 MUTATED C16ORF63 WILD-TYPE
  T0+T1                0                 54
  T2                   2                133
  T3                   3                258
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C16ORF63 MUTATED     5   1   0   3
  C16ORF63 WILD-TYPE 190 172  89  82
D199V5, multiclass
    clus
vv   C16ORF63 MUTATED C16ORF63 WILD-TYPE
  N0                5                190
  N1                1                172
  N2                0                 89
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V6, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     9   0
  C16ORF63 WILD-TYPE 473  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      9    0
  C16ORF63 WILD-TYPE  473   38
   clus
vv  C16ORF63 MUTATED C16ORF63 WILD-TYPE
  0                9                473
  1                0                 38
[1] 2 2
[1] FALSE
D199V7, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     6   4
  C16ORF63 WILD-TYPE 166 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      6    4
  C16ORF63 WILD-TYPE  166  402
        clus
vv       C16ORF63 MUTATED C16ORF63 WILD-TYPE
  FEMALE                6                166
  MALE                  4                402
[1] 2 2
[1] FALSE
D199V8, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     6   2
  C16ORF63 WILD-TYPE 410 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      6    2
  C16ORF63 WILD-TYPE  410  100
     clus
vv    C16ORF63 MUTATED C16ORF63 WILD-TYPE
  NO                 6                410
  YES                2                100
[1] 2 2
[1] FALSE
D199V9, continuous
D199V10, continuous
[1] "Remove cluster labels:" "C16ORF63 MUTATED"      
clus
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43E         TCGA-L5-A43H 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" "C16ORF63 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C16ORF63 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF63 MUTATED       3                         0
  C16ORF63 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF63 MUTATED                                           0     7
  C16ORF63 WILD-TYPE                                         1   350
D199V11, multiclass
                                           clus
vv                                          C16ORF63 MUTATED C16ORF63 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V12, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     0   9
  C16ORF63 WILD-TYPE  10 389
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      0    9
  C16ORF63 WILD-TYPE   10  389
                        clus
vv                       C16ORF63 MUTATED C16ORF63 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                9                389
[1] 2 2
[1] FALSE

Clustering(200) Variable = ZNF878 MUTATION ANALYSIS
D200V1, survival
                  sevent
clus2                0   1
  ZNF878 MUTATED    12   4
  ZNF878 WILD-TYPE 326 212
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              16              538 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               4              212 
$`ZNF878 MUTATED`
TCGA-L5-A43J TCGA-IG-A6QS TCGA-V5-A7RB TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8360 
        4.31         9.96         5.29         9.67        29.59         6.18 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY 
       31.27         1.12        31.96       105.07        65.10        13.78 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-VQ-A8P2 
       30.51        22.68         6.58        38.14 

$`ZNF878 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        6.02         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZNF878 MUTATED ZNF878 WILD-TYPE 
            1.12             0.00 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
          105.07           122.30 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
           18.23            13.53 
[1] "1.1 - 105.1 (18.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D200V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF878 MUTATED         0        0        1        1         2         5
  ZNF878 WILD-TYPE      10       20       45       30        82        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF878 MUTATED           0          1          1          2        1
  ZNF878 WILD-TYPE        29         83         61         37       42
                  vv
clus               STAGE IVA
  ZNF878 MUTATED           0
  ZNF878 WILD-TYPE         4
D200V3, multiclass
            clus
vv           ZNF878 MUTATED ZNF878 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF878 MUTATED       1   3   6   5
  ZNF878 WILD-TYPE    53 132 255  97
D200V4, multiclass
       clus
vv      ZNF878 MUTATED ZNF878 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 6              255
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF878 MUTATED     5   6   1   3
  ZNF878 WILD-TYPE 190 167  88  82
D200V5, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  N0              5              190
  N1              6              167
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V6, binary
                  cls
clus                 0   1
  ZNF878 MUTATED    13   1
  ZNF878 WILD-TYPE 469  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED     13    1
  ZNF878 WILD-TYPE  469   37
   clus
vv  ZNF878 MUTATED ZNF878 WILD-TYPE
  0             13              469
  1              1               37
[1] 2 2
[1] FALSE
D200V7, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     6  10
  ZNF878 WILD-TYPE 166 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      6   10
  ZNF878 WILD-TYPE  166  396
        clus
vv       ZNF878 MUTATED ZNF878 WILD-TYPE
  FEMALE              6              166
  MALE               10              396
[1] 2 2
[1] FALSE
D200V8, binary
                  cls
clus                 0   1
  ZNF878 MUTATED    11   3
  ZNF878 WILD-TYPE 405  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED     11    3
  ZNF878 WILD-TYPE  405   99
     clus
vv    ZNF878 MUTATED ZNF878 WILD-TYPE
  NO              11              405
  YES              3               99
[1] 2 2
[1] FALSE
D200V9, continuous
[1] "Remove cluster labels:" "ZNF878 MUTATED"        
clus
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" "ZNF878 WILD-TYPE" 
D200V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF878 MUTATED       3                         0
  ZNF878 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF878 MUTATED                                           0     9
  ZNF878 WILD-TYPE                                         1   348
D200V11, multiclass
                                           clus
vv                                          ZNF878 MUTATED ZNF878 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V12, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     1  10
  ZNF878 WILD-TYPE   9 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      1   10
  ZNF878 WILD-TYPE    9  388
                        clus
vv                       ZNF878 MUTATED ZNF878 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(201) Variable = PIK3CA MUTATION ANALYSIS
D201V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    51  26
  PIK3CA WILD-TYPE 287 190
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              77              477 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              190 
$`PIK3CA MUTATED`
TCGA-L5-A43J TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A7DP 
        4.31         7.69        35.21        20.78        18.64        14.86 
TCGA-JY-A6FG TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A8NH TCGA-L5-A8NW TCGA-LN-A49M 
       41.52         7.13        25.12        12.92        46.09        12.66 
TCGA-LN-A4A4 TCGA-LN-A7HW TCGA-R6-A6KZ TCGA-V5-AASV TCGA-VR-A8EW TCGA-XP-A8T7 
       12.59        12.00         5.06        15.35         8.12        41.23 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4253 TCGA-BR-6452 
        2.66        26.70        11.70         9.47         4.08        34.68 
TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       13.87        18.05        19.89        30.90        44.94        21.90 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8487 
       32.25         8.05         6.18         0.95         7.36         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 
       12.79        27.12        28.14         7.53        31.96        20.88 
TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4305 
        1.15        13.15        13.18        12.43        11.77        15.95 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 
        6.02         0.99        65.10        21.07        25.71        12.66 
TCGA-D7-6815 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-D7-A747 TCGA-FP-7735 
       15.98         5.92        36.43        20.32         8.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8602 
       14.07        22.29        77.29        30.51         1.51        22.32 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       21.07        24.30         0.10         6.58        20.25         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-VQ-A8P2 TCGA-VQ-AA69 TCGA-VQ-AA6K 
       29.00        23.84        38.14        28.41        12.43 

$`PIK3CA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        10.45        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       25.08        14.37         3.42         2.10         1.32        19.73 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        15.95        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 
       12.16         8.98        40.21        31.20         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 
       14.43        11.44         0.69        29.59         9.60         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27        14.79        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8592 
        5.39        25.18         9.21        20.22         9.34         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79        32.58         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 
       28.96         4.01        69.04         7.99        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       14.66        21.14        20.91        14.27        16.44        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 
       14.47        72.23        21.27        11.38        19.53        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        6.21        63.06        52.21        26.47         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       28.96        22.82         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H5 
       29.98         8.98         6.51         0.26        12.95        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       16.14        27.55        17.26 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
             0.1              0.0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           77.29           122.30 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           14.86            13.51 
[1] "0.1 - 77.3 (14.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D201V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CA MUTATED         1        0        5        4        13        19
  PIK3CA WILD-TYPE       9       20       41       27        71        64
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           2         15          6         10        6
  PIK3CA WILD-TYPE        27         69         56         29       37
                  vv
clus               STAGE IVA
  PIK3CA MUTATED           0
  PIK3CA WILD-TYPE         4
D201V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                5               41
  STAGE II                4               27
  STAGE IIA              13               71
  STAGE IIB              19               64
  STAGE III               2               27
  STAGE IIIA             15               69
  STAGE IIIB              6               56
  STAGE IIIC             10               29
  STAGE IV                6               37
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PIK3CA MUTATED       3  18  35  27
  PIK3CA WILD-TYPE    51 117 226  75
D201V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T0+T1              3               51
  T2                18              117
  T3                35              226
  T4                27               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3CA MUTATED    29  24  16  11
  PIK3CA WILD-TYPE 166 149  73  74
D201V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             29              166
  N1             24              149
  N2             16               73
  N3             11               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    70   5
  PIK3CA WILD-TYPE 412  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     70    5
  PIK3CA WILD-TYPE  412   33
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             70              412
  1              5               33
[1] 2 2
[1] FALSE
D201V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    27  57
  PIK3CA WILD-TYPE 145 349
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     27   57
  PIK3CA WILD-TYPE  145  349
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             27              145
  MALE               57              349
[1] 2 2
[1] FALSE
D201V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    63  11
  PIK3CA WILD-TYPE 353  91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     63   11
  PIK3CA WILD-TYPE  353   91
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              63              353
  YES             11               91
[1] 2 2
[1] FALSE
D201V9, continuous
D201V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3CA MUTATED      21                         3
  PIK3CA WILD-TYPE   112                        11
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3CA MUTATED                                           0    50
  PIK3CA WILD-TYPE                                         1   307
D201V11, multiclass
                                           clus
vv                                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                                 21              112
  BLACK OR AFRICAN AMERICAN                              3               11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 50              307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V12, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     2  63
  PIK3CA WILD-TYPE   8 335
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2   63
  PIK3CA WILD-TYPE    8  335
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             63              335
[1] 2 2
[1] FALSE

Clustering(202) Variable = SH3KBP1 MUTATION ANALYSIS
D202V1, survival
                   sevent
clus2                 0   1
  SH3KBP1 MUTATED    13   5
  SH3KBP1 WILD-TYPE 325 211
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               18               536 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                5               211 
$`SH3KBP1 MUTATED`
TCGA-JY-A93E TCGA-L5-A8NM TCGA-LN-A5U6 TCGA-Z6-A9VB TCGA-BR-4183 TCGA-BR-4184 
       25.22         7.76        12.33         1.32         6.61         6.97 
TCGA-BR-7704 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4477 
       35.24        32.25         4.31         1.12        31.96        30.97 
TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-R5-A7ZI 
        6.02         5.92         0.10         6.58        20.25        74.53 

$`SH3KBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
              0.1               0.0 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            74.53            122.30 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            7.365            13.730 
[1] "0.1 - 74.5 (7.4)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D202V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH3KBP1 MUTATED         0        0        2        1         1         5
  SH3KBP1 WILD-TYPE      10       20       44       30        83        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3KBP1 MUTATED           0          4          0          2        3
  SH3KBP1 WILD-TYPE        29         80         62         37       40
                   vv
clus                STAGE IVA
  SH3KBP1 MUTATED           0
  SH3KBP1 WILD-TYPE         4
D202V3, multiclass
            clus
vv           SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                5                78
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SH3KBP1 MUTATED       0   4   8   6
  SH3KBP1 WILD-TYPE    54 131 253  96
D202V4, multiclass
       clus
vv      SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  T0+T1               0                54
  T2                  4               131
  T3                  8               253
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SH3KBP1 MUTATED     5  11   3   0
  SH3KBP1 WILD-TYPE 190 162  86  85
D202V5, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  N0               5               190
  N1              11               162
  N2               3                86
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V6, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    16   2
  SH3KBP1 WILD-TYPE 466  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     16    2
  SH3KBP1 WILD-TYPE  466   36
   clus
vv  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  0              16               466
  1               2                36
[1] 2 2
[1] FALSE
D202V7, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    11   8
  SH3KBP1 WILD-TYPE 161 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     11    8
  SH3KBP1 WILD-TYPE  161  398
        clus
vv       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  FEMALE              11               161
  MALE                 8               398
[1] 2 2
[1] FALSE
D202V8, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    16   2
  SH3KBP1 WILD-TYPE 400 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     16    2
  SH3KBP1 WILD-TYPE  400  100
     clus
vv    SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  NO               16               400
  YES               2               100
[1] 2 2
[1] FALSE
D202V9, continuous
[1] "Remove cluster labels:" "SH3KBP1 MUTATED"       
clus
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
D202V10, continuous
[1] "Remove cluster labels:" "SH3KBP1 MUTATED"       
clus
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" "SH3KBP1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SH3KBP1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SH3KBP1 MUTATED       5                         0
  SH3KBP1 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3KBP1 MUTATED                                           0    12
  SH3KBP1 WILD-TYPE                                         1   345
D202V11, multiclass
                                           clus
vv                                          SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V12, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     1  14
  SH3KBP1 WILD-TYPE   9 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      1   14
  SH3KBP1 WILD-TYPE    9  384
                        clus
vv                       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(203) Variable = C2ORF76 MUTATION ANALYSIS
D203V1, survival
                   sevent
clus2                 0   1
  C2ORF76 MUTATED     3   1
  C2ORF76 WILD-TYPE 335 215
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                4               550 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                1               215 
$`C2ORF76 MUTATED`
TCGA-LN-A9FQ TCGA-BR-8591 TCGA-HU-A4GC TCGA-HU-A4GQ 
       12.85        28.14         3.25         0.10 

$`C2ORF76 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
              0.1               0.0 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
            28.14            122.30 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
             8.05             13.63 
[1] "0.1 - 28.1 (8.1)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D203V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF76 MUTATED         0        0        0        0         1         0
  C2ORF76 WILD-TYPE      10       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF76 MUTATED           0          0          1          3        0
  C2ORF76 WILD-TYPE        29         84         61         36       43
                   vv
clus                STAGE IVA
  C2ORF76 MUTATED           0
  C2ORF76 WILD-TYPE         4
D203V3, multiclass
            clus
vv           C2ORF76 MUTATED C2ORF76 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               3                36
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C2ORF76 MUTATED       0   0   1   4
  C2ORF76 WILD-TYPE    54 135 260  98
D203V4, multiclass
       clus
vv      C2ORF76 MUTATED C2ORF76 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  1               260
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C2ORF76 MUTATED     1   0   2   2
  C2ORF76 WILD-TYPE 194 173  87  83
D203V5, multiclass
    clus
vv   C2ORF76 MUTATED C2ORF76 WILD-TYPE
  N0               1               194
  N1               0               173
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V6, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     5   0
  C2ORF76 WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      5    0
  C2ORF76 WILD-TYPE  477   38
   clus
vv  C2ORF76 MUTATED C2ORF76 WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D203V7, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     0   5
  C2ORF76 WILD-TYPE 172 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      0    5
  C2ORF76 WILD-TYPE  172  401
        clus
vv       C2ORF76 MUTATED C2ORF76 WILD-TYPE
  FEMALE               0               172
  MALE                 5               401
[1] 2 2
[1] FALSE
D203V8, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     4   0
  C2ORF76 WILD-TYPE 412 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      4    0
  C2ORF76 WILD-TYPE  412  102
     clus
vv    C2ORF76 MUTATED C2ORF76 WILD-TYPE
  NO                4               412
  YES               0               102
[1] 2 2
[1] FALSE
D203V9, continuous
D203V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C2ORF76 MUTATED       3                         0
  C2ORF76 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2ORF76 MUTATED                                           0     1
  C2ORF76 WILD-TYPE                                         1   356
D203V11, multiclass
                                           clus
vv                                          C2ORF76 MUTATED C2ORF76 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V12, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     0   4
  C2ORF76 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      0    4
  C2ORF76 WILD-TYPE   10  394
                        clus
vv                       C2ORF76 MUTATED C2ORF76 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(204) Variable = CCDC150 MUTATION ANALYSIS
D204V1, survival
                   sevent
clus2                 0   1
  CCDC150 MUTATED     9   2
  CCDC150 WILD-TYPE 329 214
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               11               543 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                2               214 
$`CCDC150 MUTATED`
TCGA-L5-A43J TCGA-KH-A6WC TCGA-L5-A4OP TCGA-VR-A8EZ TCGA-BR-6452 TCGA-BR-8360 
        4.31         6.28         7.17        18.18        34.68         6.18 
TCGA-BR-8372 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       31.27        30.51        22.32        22.68        38.14 

$`CCDC150 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
             4.31              0.00 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            38.14            122.30 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            22.32             13.51 
[1] "4.3 - 38.1 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D204V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC150 MUTATED         1        2        1        0         2         3
  CCDC150 WILD-TYPE       9       18       45       31        82        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC150 MUTATED           0          1          0          3        0
  CCDC150 WILD-TYPE        29         83         62         36       43
                   vv
clus                STAGE IVA
  CCDC150 MUTATED           0
  CCDC150 WILD-TYPE         4
D204V3, multiclass
            clus
vv           CCDC150 MUTATED CCDC150 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                18
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC150 MUTATED       3   1   5   4
  CCDC150 WILD-TYPE    51 134 256  98
D204V4, multiclass
       clus
vv      CCDC150 MUTATED CCDC150 WILD-TYPE
  T0+T1               3                51
  T2                  1               134
  T3                  5               256
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC150 MUTATED     7   3   0   3
  CCDC150 WILD-TYPE 188 170  89  82
D204V5, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  N0               7               188
  N1               3               170
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V6, binary
                   cls
clus                  0   1
  CCDC150 MUTATED    11   0
  CCDC150 WILD-TYPE 471  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED     11    0
  CCDC150 WILD-TYPE  471   38
   clus
vv  CCDC150 MUTATED CCDC150 WILD-TYPE
  0              11               471
  1               0                38
[1] 2 2
[1] FALSE
D204V7, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     6   8
  CCDC150 WILD-TYPE 166 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      6    8
  CCDC150 WILD-TYPE  166  398
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  FEMALE               6               166
  MALE                 8               398
[1] 2 2
[1] FALSE
D204V8, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     7   3
  CCDC150 WILD-TYPE 409  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      7    3
  CCDC150 WILD-TYPE  409   99
     clus
vv    CCDC150 MUTATED CCDC150 WILD-TYPE
  NO                7               409
  YES               3                99
[1] 2 2
[1] FALSE
D204V9, continuous
[1] "Remove cluster labels:" "CCDC150 MUTATED"       
clus
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8Q7 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CCDC150 WILD-TYPE" "CCDC150 WILD-TYPE" 
D204V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC150 MUTATED       2                         1
  CCDC150 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC150 MUTATED                                           0     9
  CCDC150 WILD-TYPE                                         1   348
D204V11, multiclass
                                           clus
vv                                          CCDC150 MUTATED CCDC150 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V12, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     0   8
  CCDC150 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      0    8
  CCDC150 WILD-TYPE   10  390
                        clus
vv                       CCDC150 MUTATED CCDC150 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(205) Variable = ANKRD20A4 MUTATION ANALYSIS
D205V1, survival
                     sevent
clus2                   0   1
  ANKRD20A4 MUTATED     9   1
  ANKRD20A4 WILD-TYPE 329 215
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                 10                 544 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  1                 215 
$`ANKRD20A4 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NW TCGA-LN-A4A2 TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-A4PF 
       19.99        46.09        12.49        14.04        31.27         1.15 
TCGA-D7-A6F2 TCGA-F1-A448 TCGA-HU-A4GT TCGA-VQ-A8P2 
       15.65        21.27         6.51        38.14 

$`ANKRD20A4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
               1.15                0.00 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
              46.09              122.30 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
              17.82               13.51 
[1] "1.1 - 46.1 (17.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.5"
D205V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD20A4 MUTATED         0        0        2        0         2         0
  ANKRD20A4 WILD-TYPE      10       20       44       31        82        83
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD20A4 MUTATED           0          1          3          2        0
  ANKRD20A4 WILD-TYPE        29         83         59         37       43
                     vv
clus                  STAGE IVA
  ANKRD20A4 MUTATED           0
  ANKRD20A4 WILD-TYPE         4
D205V3, multiclass
            clus
vv           ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  STAGE I                    0                  10
  STAGE IA                   0                  20
  STAGE IB                   2                  44
  STAGE II                   0                  31
  STAGE IIA                  2                  82
  STAGE IIB                  0                  83
  STAGE III                  0                  29
  STAGE IIIA                 1                  83
  STAGE IIIB                 3                  59
  STAGE IIIC                 2                  37
  STAGE IV                   0                  43
  STAGE IVA                  0                   4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  ANKRD20A4 MUTATED       0   2   5   3
  ANKRD20A4 WILD-TYPE    54 133 256  99
D205V4, multiclass
       clus
vv      ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  T0+T1                 0                  54
  T2                    2                 133
  T3                    5                 256
  T4                    3                  99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  ANKRD20A4 MUTATED     3   2   1   4
  ANKRD20A4 WILD-TYPE 192 171  88  81
D205V5, multiclass
    clus
vv   ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  N0                 3                 192
  N1                 2                 171
  N2                 1                  88
  N3                 4                  81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V6, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     9   0
  ANKRD20A4 WILD-TYPE 473  38
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      9    0
  ANKRD20A4 WILD-TYPE  473   38
   clus
vv  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  0                 9                 473
  1                 0                  38
[1] 2 2
[1] FALSE
D205V7, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     2   8
  ANKRD20A4 WILD-TYPE 170 398
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      2    8
  ANKRD20A4 WILD-TYPE  170  398
        clus
vv       ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  FEMALE                 2                 170
  MALE                   8                 398
[1] 2 2
[1] FALSE
D205V8, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     7   3
  ANKRD20A4 WILD-TYPE 409  99
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      7    3
  ANKRD20A4 WILD-TYPE  409   99
     clus
vv    ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  NO                  7                 409
  YES                 3                  99
[1] 2 2
[1] FALSE
D205V9, continuous
[1] "Remove cluster labels:" "ANKRD20A4 MUTATED"     
clus
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  1                  67 
         TCGA-IG-A3I8          TCGA-IG-A3QL          TCGA-IG-A3Y9 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A3YA          TCGA-IG-A3YB          TCGA-IG-A3YC 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A51D          TCGA-IG-A5S3          TCGA-IG-A7DP 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-KH-A6WC          TCGA-LN-A49K          TCGA-LN-A49L 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49M          TCGA-LN-A49N          TCGA-LN-A49O 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49P          TCGA-LN-A49R          TCGA-LN-A49S 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49U          TCGA-LN-A49V          TCGA-LN-A49W 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49X          TCGA-LN-A49Y          TCGA-LN-A4A1 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A4A3          TCGA-LN-A4A4          TCGA-LN-A4A5 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A4A6          TCGA-LN-A4A8          TCGA-LN-A4A9 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A4MQ          TCGA-LN-A4MR          TCGA-LN-A5U5 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A5U6          TCGA-LN-A5U7          TCGA-LN-A7HV 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A7HW          TCGA-LN-A7HX          TCGA-LN-A7HY 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A7HZ          TCGA-V5-A7RB          TCGA-V5-A7RC 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-V5-A7RE          TCGA-V5-AASV          TCGA-V5-AASW 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-V5-AASX          TCGA-VR-A8EO          TCGA-VR-A8EP 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8EQ          TCGA-VR-A8ER          TCGA-VR-A8ET 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8EU          TCGA-VR-A8EW          TCGA-VR-A8EX 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8EY          TCGA-VR-A8EZ          TCGA-VR-A8Q7 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-AA4D          TCGA-VR-AA4G          TCGA-VR-AA7B 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-AA7D          TCGA-VR-AA7I          TCGA-XP-A8T6 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-XP-A8T7          TCGA-XP-A8T8          TCGA-Z6-A8JD 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-Z6-A8JE 
"ANKRD20A4 WILD-TYPE" 
D205V10, continuous
[1] "Remove cluster labels:" "ANKRD20A4 MUTATED"     
clus
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  2                  96 
         TCGA-IC-A6RF          TCGA-L5-A43I          TCGA-L5-A43J 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A4OE          TCGA-L5-A4OG          TCGA-L5-A88T 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A88Y          TCGA-L5-A8NG          TCGA-L5-A8NT 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-Q9-A6FU          TCGA-IC-A6RE          TCGA-IG-A3QL 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A3Y9          TCGA-IG-A3YA          TCGA-IG-A3YC 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A4P3          TCGA-IG-A4QT          TCGA-IG-A50L 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A5B8          TCGA-IG-A6QS          TCGA-IG-A8O2 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-IG-A97H          TCGA-JY-A6FA          TCGA-JY-A6FE 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-JY-A6FG          TCGA-JY-A6FH          TCGA-KH-A6WC 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A43C          TCGA-L5-A43E          TCGA-L5-A43H 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A4OH          TCGA-L5-A4OM          TCGA-L5-A4ON 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A4OO          TCGA-L5-A4OP          TCGA-L5-A4OQ 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A4OT          TCGA-L5-A4OU          TCGA-L5-A4OW 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A4OX          TCGA-L5-A88S          TCGA-L5-A88V 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A893          TCGA-L5-A8NE          TCGA-L5-A8NF 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A8NK          TCGA-L5-A8NN          TCGA-L5-A8NQ 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-L5-A8NR          TCGA-L5-A8NS          TCGA-LN-A49O 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49P          TCGA-LN-A49R          TCGA-LN-A49S 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A49U          TCGA-LN-A49V          TCGA-LN-A49W 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A4A3          TCGA-LN-A4A6          TCGA-LN-A4A9 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A5U6          TCGA-LN-A5U7          TCGA-LN-A7HV 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A7HW          TCGA-LN-A7HX          TCGA-LN-A7HZ 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-LN-A8HZ          TCGA-LN-A8I0          TCGA-M9-A5M8 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-Q9-A6FW          TCGA-R6-A6DN          TCGA-R6-A6L4 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-R6-A6XQ          TCGA-R6-A6Y2          TCGA-R6-A8W5 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-R6-A8W8          TCGA-R6-A8WC          TCGA-RE-A7BO 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-V5-A7RB          TCGA-V5-A7RC          TCGA-V5-AASV 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8EP          TCGA-VR-A8ER          TCGA-VR-A8EU 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8EW          TCGA-VR-A8EX          TCGA-VR-A8EZ 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-A8Q7          TCGA-VR-AA4G          TCGA-VR-AA7D 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-VR-AA7I          TCGA-X8-AAAR          TCGA-XP-A8T6 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
         TCGA-XP-A8T7          TCGA-XP-A8T8          TCGA-Z6-AAPN 
"ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" "ANKRD20A4 WILD-TYPE" 
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD20A4 MUTATED       2                         0
  ANKRD20A4 WILD-TYPE   131                        14
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD20A4 MUTATED                                           0     8
  ANKRD20A4 WILD-TYPE                                         1   349
D205V11, multiclass
                                           clus
vv                                          ANKRD20A4 MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     8
                                           clus
vv                                          ANKRD20A4 WILD-TYPE
  ASIAN                                                     131
  BLACK OR AFRICAN AMERICAN                                  14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V12, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     1   6
  ANKRD20A4 WILD-TYPE   9 392
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      1    6
  ANKRD20A4 WILD-TYPE    9  392
                        clus
vv                       ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  HISPANIC OR LATINO                     1                   9
  NOT HISPANIC OR LATINO                 6                 392
[1] 2 2
[1] FALSE

Clustering(206) Variable = RABGAP1 MUTATION ANALYSIS
D206V1, survival
                   sevent
clus2                 0   1
  RABGAP1 MUTATED    17   6
  RABGAP1 WILD-TYPE 321 210
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               23               531 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
                6               210 
$`RABGAP1 MUTATED`
TCGA-L5-A4OI TCGA-JY-A93C TCGA-R6-A6Y2 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 
       19.99        23.18         9.30         9.67        34.68        35.84 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 
       29.59         6.18        31.10         4.31         1.12        31.96 
TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 
       16.14        12.62        15.95        65.10        21.07        21.27 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-VQ-A8P2 
       11.08        26.47         0.10         6.51        38.14 

$`RABGAP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
              0.1               0.0 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
             65.1             122.3 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
            19.99             13.51 
[1] "0.1 - 65.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D206V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RABGAP1 MUTATED         0        0        6        1         5         2
  RABGAP1 WILD-TYPE      10       20       40       30        79        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RABGAP1 MUTATED           0          2          3          3        1
  RABGAP1 WILD-TYPE        29         82         59         36       42
                   vv
clus                STAGE IVA
  RABGAP1 MUTATED           0
  RABGAP1 WILD-TYPE         4
D206V3, multiclass
            clus
vv           RABGAP1 MUTATED RABGAP1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 6                40
  STAGE II                 1                30
  STAGE IIA                5                79
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               3                59
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  RABGAP1 MUTATED       0   8   9   6
  RABGAP1 WILD-TYPE    54 127 252  96
D206V4, multiclass
       clus
vv      RABGAP1 MUTATED RABGAP1 WILD-TYPE
  T0+T1               0                54
  T2                  8               127
  T3                  9               252
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  RABGAP1 MUTATED    13   2   5   3
  RABGAP1 WILD-TYPE 182 171  84  82
D206V5, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  N0              13               182
  N1               2               171
  N2               5                84
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V6, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    21   1
  RABGAP1 WILD-TYPE 461  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     21    1
  RABGAP1 WILD-TYPE  461   37
   clus
vv  RABGAP1 MUTATED RABGAP1 WILD-TYPE
  0              21               461
  1               1                37
[1] 2 2
[1] FALSE
D206V7, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    12  13
  RABGAP1 WILD-TYPE 160 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     12   13
  RABGAP1 WILD-TYPE  160  393
        clus
vv       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  FEMALE              12               160
  MALE                13               393
[1] 2 2
[1] FALSE
D206V8, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    20   3
  RABGAP1 WILD-TYPE 396  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     20    3
  RABGAP1 WILD-TYPE  396   99
     clus
vv    RABGAP1 MUTATED RABGAP1 WILD-TYPE
  NO               20               396
  YES               3                99
[1] 2 2
[1] FALSE
D206V9, continuous
D206V10, continuous
[1] "Remove cluster labels:" "RABGAP1 MUTATED"       
clus
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A8W5        TCGA-R6-A8W8 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" "RABGAP1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RABGAP1 MUTATED       5                         1
  RABGAP1 WILD-TYPE   128                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RABGAP1 MUTATED                                           0    15
  RABGAP1 WILD-TYPE                                         1   342
D206V11, multiclass
                                           clus
vv                                          RABGAP1 MUTATED RABGAP1 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V12, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED     2  16
  RABGAP1 WILD-TYPE   8 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED      2   16
  RABGAP1 WILD-TYPE    8  382
                        clus
vv                       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              16               382
[1] 2 2
[1] FALSE

Clustering(207) Variable = PPARG MUTATION ANALYSIS
D207V1, survival
                 sevent
clus2               0   1
  PPARG MUTATED     5   0
  PPARG WILD-TYPE 333 216
  PPARG MUTATED PPARG WILD-TYPE 
              5             549 
  PPARG MUTATED PPARG WILD-TYPE 
              0             216 
$`PPARG MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FW TCGA-BR-6852 TCGA-CG-4305 TCGA-HU-A4H8 
       19.99         7.82        44.94        15.95        14.07 

$`PPARG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PPARG MUTATED PPARG WILD-TYPE 
           7.82            0.00 
  PPARG MUTATED PPARG WILD-TYPE 
          44.94          122.30 
  PPARG MUTATED PPARG WILD-TYPE 
          15.95           13.51 
[1] "7.8 - 44.9 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr="     "3300000"
D207V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPARG MUTATED         0        0        1        1         1         0
  PPARG WILD-TYPE      10       20       45       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPARG MUTATED           0          0          1          1        0         0
  PPARG WILD-TYPE        29         84         61         38       43         4
D207V3, multiclass
            clus
vv           PPARG MUTATED PPARG WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PPARG MUTATED       1   1   4   0
  PPARG WILD-TYPE    53 134 257 102
D207V4, multiclass
       clus
vv      PPARG MUTATED PPARG WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                4             257
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PPARG MUTATED     1   2   1   1
  PPARG WILD-TYPE 194 171  88  84
D207V5, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  N0             1             194
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V6, binary
                 cls
clus                0   1
  PPARG MUTATED     4   0
  PPARG WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      4    0
  PPARG WILD-TYPE  478   38
   clus
vv  PPARG MUTATED PPARG WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D207V7, binary
                 cls
clus                0   1
  PPARG MUTATED     2   4
  PPARG WILD-TYPE 170 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      2    4
  PPARG WILD-TYPE  170  402
        clus
vv       PPARG MUTATED PPARG WILD-TYPE
  FEMALE             2             170
  MALE               4             402
[1] 2 2
[1] FALSE
D207V8, binary
                 cls
clus                0   1
  PPARG MUTATED     5   0
  PPARG WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      5    0
  PPARG WILD-TYPE  411  102
     clus
vv    PPARG MUTATED PPARG WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D207V9, continuous
D207V10, continuous
[1] "Remove cluster labels:" "PPARG MUTATED"         
clus
  PPARG MUTATED PPARG WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-R6-A6DN      TCGA-R6-A6L4 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" "PPARG WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PPARG MUTATED       1                         0
  PPARG WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPARG MUTATED                                           0     4
  PPARG WILD-TYPE                                         1   353
D207V11, multiclass
                                           clus
vv                                          PPARG MUTATED PPARG WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V12, binary
                 cls
clus                0   1
  PPARG MUTATED     0   4
  PPARG WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      0    4
  PPARG WILD-TYPE   10  394
                        clus
vv                       PPARG MUTATED PPARG WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(208) Variable = TOP2A MUTATION ANALYSIS
D208V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED    11   9
  TOP2A WILD-TYPE 327 207
  TOP2A MUTATED TOP2A WILD-TYPE 
             20             534 
  TOP2A MUTATED TOP2A WILD-TYPE 
              9             207 
$`TOP2A MUTATED`
TCGA-2H-A9GK TCGA-L5-A88Z TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A8I1 TCGA-M9-A5M8 
        7.63         7.40        52.57        10.36        13.18        33.11 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6852 TCGA-BR-8483 TCGA-CD-A4MG TCGA-CG-4305 
        6.97         9.34        44.94         5.39         6.58        15.95 
TCGA-CG-4306 TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5726 TCGA-HU-A4G6 
        1.02        30.97         6.02        15.02        28.96        24.26 
TCGA-KB-A93J TCGA-VQ-A8DL 
       36.95         0.92 

$`TOP2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97         7.07         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 
        0.99         0.99       105.07        12.03        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TOP2A MUTATED TOP2A WILD-TYPE 
           0.92            0.00 
  TOP2A MUTATED TOP2A WILD-TYPE 
          52.57          122.30 
  TOP2A MUTATED TOP2A WILD-TYPE 
          11.77           13.63 
[1] "0.9 - 52.6 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D208V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TOP2A MUTATED         0        2        2        2         7         0
  TOP2A WILD-TYPE      10       18       44       29        77        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2A MUTATED           1          2          0          1        2         0
  TOP2A WILD-TYPE        28         82         62         38       41         4
D208V3, multiclass
            clus
vv           TOP2A MUTATED TOP2A WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              7              77
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TOP2A MUTATED       3   5  10   1
  TOP2A WILD-TYPE    51 130 251 101
D208V4, multiclass
       clus
vv      TOP2A MUTATED TOP2A WILD-TYPE
  T0+T1             3              51
  T2                5             130
  T3               10             251
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TOP2A MUTATED    10   7   2   1
  TOP2A WILD-TYPE 185 166  87  84
D208V5, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  N0            10             185
  N1             7             166
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V6, binary
                 cls
clus                0   1
  TOP2A MUTATED    17   1
  TOP2A WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     17    1
  TOP2A WILD-TYPE  465   37
   clus
vv  TOP2A MUTATED TOP2A WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D208V7, binary
                 cls
clus                0   1
  TOP2A MUTATED     5  15
  TOP2A WILD-TYPE 167 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      5   15
  TOP2A WILD-TYPE  167  391
        clus
vv       TOP2A MUTATED TOP2A WILD-TYPE
  FEMALE             5             167
  MALE              15             391
[1] 2 2
[1] FALSE
D208V8, binary
                 cls
clus                0   1
  TOP2A MUTATED    14   4
  TOP2A WILD-TYPE 402  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     14    4
  TOP2A WILD-TYPE  402   98
     clus
vv    TOP2A MUTATED TOP2A WILD-TYPE
  NO             14             402
  YES             4              98
[1] 2 2
[1] FALSE
D208V9, continuous
D208V10, continuous
[1] "Remove cluster labels:" "TOP2A MUTATED"         
clus
  TOP2A MUTATED TOP2A WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" "TOP2A WILD-TYPE" 
     TCGA-Z6-AAPN 
"TOP2A WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TOP2A MUTATED       3                         0
  TOP2A WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TOP2A MUTATED                                           0     9
  TOP2A WILD-TYPE                                         1   348
D208V11, multiclass
                                           clus
vv                                          TOP2A MUTATED TOP2A WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V12, binary
                 cls
clus                0   1
  TOP2A MUTATED     0   8
  TOP2A WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      0    8
  TOP2A WILD-TYPE   10  390
                        clus
vv                       TOP2A MUTATED TOP2A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(209) Variable = U2AF2 MUTATION ANALYSIS
D209V1, survival
                 sevent
clus2               0   1
  U2AF2 MUTATED     8   6
  U2AF2 WILD-TYPE 330 210
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             14             540 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
              6             210 
$`U2AF2 MUTATED`
TCGA-CG-4460 TCGA-LN-A49K TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-A4MG 
       21.99         5.92        34.68         4.31         1.12         6.58 
TCGA-CD-A4MI TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-KB-A93J 
       11.77         5.92        11.08         0.10         6.51        36.95 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`U2AF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  U2AF2 MUTATED U2AF2 WILD-TYPE 
            0.1             0.0 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
          74.53          122.30 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
           8.83           13.73 
[1] "0.1 - 74.5 (8.8)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D209V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  U2AF2 MUTATED         0        0        1        1         6         1
  U2AF2 WILD-TYPE      10       20       45       30        78        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  U2AF2 MUTATED           0          2          0          1        2         0
  U2AF2 WILD-TYPE        29         82         62         38       41         4
D209V3, multiclass
            clus
vv           U2AF2 MUTATED U2AF2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              6              78
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  U2AF2 MUTATED       0   2   8   4
  U2AF2 WILD-TYPE    54 133 253  98
D209V4, multiclass
       clus
vv      U2AF2 MUTATED U2AF2 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  U2AF2 MUTATED     7   6   1   0
  U2AF2 WILD-TYPE 188 167  88  85
D209V5, multiclass
    clus
vv   U2AF2 MUTATED U2AF2 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V6, binary
                 cls
clus                0   1
  U2AF2 MUTATED    13   2
  U2AF2 WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED     13    2
  U2AF2 WILD-TYPE  469   36
   clus
vv  U2AF2 MUTATED U2AF2 WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D209V7, binary
                 cls
clus                0   1
  U2AF2 MUTATED     8   7
  U2AF2 WILD-TYPE 164 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED      8    7
  U2AF2 WILD-TYPE  164  399
        clus
vv       U2AF2 MUTATED U2AF2 WILD-TYPE
  FEMALE             8             164
  MALE               7             399
[1] 2 2
[1] FALSE
D209V8, binary
                 cls
clus                0   1
  U2AF2 MUTATED    11   3
  U2AF2 WILD-TYPE 405  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED     11    3
  U2AF2 WILD-TYPE  405   99
     clus
vv    U2AF2 MUTATED U2AF2 WILD-TYPE
  NO             11             405
  YES             3              99
[1] 2 2
[1] FALSE
D209V9, continuous
[1] "Remove cluster labels:" "U2AF2 MUTATED"         
clus
  U2AF2 MUTATED U2AF2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49M 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" "U2AF2 WILD-TYPE" 
D209V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  U2AF2 MUTATED       5                         1
  U2AF2 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  U2AF2 MUTATED                                           0     8
  U2AF2 WILD-TYPE                                         1   349
D209V11, multiclass
                                           clus
vv                                          U2AF2 MUTATED U2AF2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V12, binary
                 cls
clus                0   1
  U2AF2 MUTATED     1  11
  U2AF2 WILD-TYPE   9 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED      1   11
  U2AF2 WILD-TYPE    9  387
                        clus
vv                       U2AF2 MUTATED U2AF2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(210) Variable = CCDC153 MUTATION ANALYSIS
D210V1, survival
                   sevent
clus2                 0   1
  CCDC153 MUTATED     5   2
  CCDC153 WILD-TYPE 333 214
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               547 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                2               214 
$`CCDC153 MUTATED`
TCGA-BR-8360 TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-6815 TCGA-D7-A6EY TCGA-F1-6874 
        6.18        11.77         6.02        15.98        11.44        14.47 
TCGA-HU-A4GN 
       29.98 

$`CCDC153 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CCDC153 MUTATED CCDC153 WILD-TYPE 
             6.02              0.00 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
            29.98            122.30 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
            11.77             13.58 
[1] "6.0 - 30.0 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D210V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC153 MUTATED         0        0        1        0         2         1
  CCDC153 WILD-TYPE      10       20       45       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC153 MUTATED           0          1          1          0        1
  CCDC153 WILD-TYPE        29         83         61         39       42
                   vv
clus                STAGE IVA
  CCDC153 MUTATED           0
  CCDC153 WILD-TYPE         4
D210V3, multiclass
            clus
vv           CCDC153 MUTATED CCDC153 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC153 MUTATED       0   3   3   1
  CCDC153 WILD-TYPE    54 132 258 101
D210V4, multiclass
       clus
vv      CCDC153 MUTATED CCDC153 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC153 MUTATED     2   3   1   1
  CCDC153 WILD-TYPE 193 170  88  84
D210V5, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V6, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     7   0
  CCDC153 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      7    0
  CCDC153 WILD-TYPE  475   38
   clus
vv  CCDC153 MUTATED CCDC153 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D210V7, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     2   5
  CCDC153 WILD-TYPE 170 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      2    5
  CCDC153 WILD-TYPE  170  401
        clus
vv       CCDC153 MUTATED CCDC153 WILD-TYPE
  FEMALE               2               170
  MALE                 5               401
[1] 2 2
[1] FALSE
D210V8, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     7   0
  CCDC153 WILD-TYPE 409 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      7    0
  CCDC153 WILD-TYPE  409  102
     clus
vv    CCDC153 MUTATED CCDC153 WILD-TYPE
  NO                7               409
  YES               0               102
[1] 2 2
[1] FALSE
D210V9, continuous
D210V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC153 MUTATED       2                         0
  CCDC153 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC153 MUTATED                                           0     4
  CCDC153 WILD-TYPE                                         1   353
D210V11, multiclass
                                           clus
vv                                          CCDC153 MUTATED CCDC153 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V12, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     0   6
  CCDC153 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      0    6
  CCDC153 WILD-TYPE   10  392
                        clus
vv                       CCDC153 MUTATED CCDC153 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(211) Variable = C5ORF42 MUTATION ANALYSIS
D211V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    29   8
  C5ORF42 WILD-TYPE 309 208
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               37               517 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                8               208 
$`C5ORF42 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OH TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A9FO TCGA-R6-A6DN 
        4.31        32.61        12.59        12.85         0.13         8.02 
TCGA-R6-A6Y2 TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6563 
        9.30         2.66         6.97        30.90        34.68        39.12 
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8487 
       35.84        29.59        31.27        14.79        25.05         1.12 
TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4477 
       27.12        31.96        12.33        12.43         6.58        30.97 
TCGA-D7-6525 TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GH 
       13.35        14.76        21.27        11.08        77.29        11.77 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-A6RS TCGA-MX-A5UJ 
        6.51         6.58        20.25        29.00        12.59        19.73 
TCGA-VQ-A8P3 
       37.22 

$`C5ORF42 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38        13.18        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        19.33        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8384 
        4.31        14.04         3.32        11.80         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY 
       25.81        21.37        29.98         8.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        38.14        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
             0.13              0.00 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            77.29            122.30 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            14.76             13.55 
[1] "0.1 - 77.3 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D211V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C5ORF42 MUTATED         2        2        3        3         7         5
  C5ORF42 WILD-TYPE       8       18       43       28        77        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           1          6          2          4        1
  C5ORF42 WILD-TYPE        28         78         60         35       42
                   vv
clus                STAGE IVA
  C5ORF42 MUTATED           0
  C5ORF42 WILD-TYPE         4
D211V3, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 2                18
  STAGE IB                 3                43
  STAGE II                 3                28
  STAGE IIA                7                77
  STAGE IIB                5                78
  STAGE III                1                28
  STAGE IIIA               6                78
  STAGE IIIB               2                60
  STAGE IIIC               4                35
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C5ORF42 MUTATED       4   9  14  10
  C5ORF42 WILD-TYPE    50 126 247  92
D211V4, multiclass
       clus
vv      C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T0+T1               4                50
  T2                  9               126
  T3                 14               247
  T4                 10                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C5ORF42 MUTATED    18   9   5   4
  C5ORF42 WILD-TYPE 177 164  84  81
D211V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              18               177
  N1               9               164
  N2               5                84
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V6, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    33   1
  C5ORF42 WILD-TYPE 449  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     33    1
  C5ORF42 WILD-TYPE  449   37
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              33               449
  1               1                37
[1] 2 2
[1] FALSE
D211V7, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    14  25
  C5ORF42 WILD-TYPE 158 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     14   25
  C5ORF42 WILD-TYPE  158  381
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  FEMALE              14               158
  MALE                25               381
[1] 2 2
[1] FALSE
D211V8, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    27   8
  C5ORF42 WILD-TYPE 389  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     27    8
  C5ORF42 WILD-TYPE  389   94
     clus
vv    C5ORF42 MUTATED C5ORF42 WILD-TYPE
  NO               27               389
  YES               8                94
[1] 2 2
[1] FALSE
D211V9, continuous
[1] "Remove cluster labels:" "C5ORF42 MUTATED"       
clus
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A5        TCGA-LN-A4A8 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR        TCGA-LN-A5U5 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ        TCGA-V5-A7RB 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-V5-AASW 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C5ORF42 WILD-TYPE" "C5ORF42 WILD-TYPE" 
D211V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C5ORF42 MUTATED      12                         2
  C5ORF42 WILD-TYPE   121                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C5ORF42 MUTATED                                           0    22
  C5ORF42 WILD-TYPE                                         1   335
D211V11, multiclass
                                           clus
vv                                          C5ORF42 MUTATED C5ORF42 WILD-TYPE
  ASIAN                                                  12               121
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V12, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED     2  31
  C5ORF42 WILD-TYPE   8 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED      2   31
  C5ORF42 WILD-TYPE    8  367
                        clus
vv                       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              31               367
[1] 2 2
[1] FALSE

Clustering(212) Variable = JAK1 MUTATION ANALYSIS
D212V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED    11   7
  JAK1 WILD-TYPE 327 209
  JAK1 MUTATED JAK1 WILD-TYPE 
            18            536 
  JAK1 MUTATED JAK1 WILD-TYPE 
             7            209 
$`JAK1 MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-2H-A9GL TCGA-LN-A4A6 TCGA-VR-A8EU TCGA-BR-4201 
       21.99        16.24         5.92        12.85        18.31        30.90 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5728 
       34.68        35.84        14.43        12.43         6.58        65.10 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       11.08        77.29        26.47        22.32        22.68        38.14 

$`JAK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        5.52         6.21        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  JAK1 MUTATED JAK1 WILD-TYPE 
          5.92           0.00 
  JAK1 MUTATED JAK1 WILD-TYPE 
         77.29         122.30 
  JAK1 MUTATED JAK1 WILD-TYPE 
        22.155         13.445 
[1] "5.9 - 77.3 (22.2)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D212V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JAK1 MUTATED         0        0        4        3         3         2
  JAK1 WILD-TYPE      10       20       42       28        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK1 MUTATED           2          1          1          0        2         0
  JAK1 WILD-TYPE        27         83         61         39       41         4
D212V3, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              3             28
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  JAK1 MUTATED       1   7   6   5
  JAK1 WILD-TYPE    53 128 255  97
D212V4, multiclass
       clus
vv      JAK1 MUTATED JAK1 WILD-TYPE
  T0+T1            1             53
  T2               7            128
  T3               6            255
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  JAK1 MUTATED    10   8   0   0
  JAK1 WILD-TYPE 185 165  89  85
D212V5, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  N0           10            185
  N1            8            165
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V6, binary
                cls
clus               0   1
  JAK1 MUTATED    16   2
  JAK1 WILD-TYPE 466  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     16    2
  JAK1 WILD-TYPE  466   36
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           16            466
  1            2             36
[1] 2 2
[1] FALSE
D212V7, binary
                cls
clus               0   1
  JAK1 MUTATED     9  11
  JAK1 WILD-TYPE 163 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      9   11
  JAK1 WILD-TYPE  163  395
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  FEMALE            9            163
  MALE             11            395
[1] 2 2
[1] FALSE
D212V8, binary
                cls
clus               0   1
  JAK1 MUTATED    12   5
  JAK1 WILD-TYPE 404  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     12    5
  JAK1 WILD-TYPE  404   97
     clus
vv    JAK1 MUTATED JAK1 WILD-TYPE
  NO            12            404
  YES            5             97
[1] 2 2
[1] FALSE
D212V9, continuous
[1] "Remove cluster labels:" "JAK1 MUTATED"          
clus
  JAK1 MUTATED JAK1 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EW 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
D212V10, continuous
[1] "Remove cluster labels:" "JAK1 MUTATED"          
clus
  JAK1 MUTATED JAK1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" "JAK1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  JAK1 MUTATED       5                         1
  JAK1 WILD-TYPE   128                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JAK1 MUTATED                                           0     9
  JAK1 WILD-TYPE                                         1   348
D212V11, multiclass
                                           clus
vv                                          JAK1 MUTATED JAK1 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V12, binary
                cls
clus               0   1
  JAK1 MUTATED     0  13
  JAK1 WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      0   13
  JAK1 WILD-TYPE   10  385
                        clus
vv                       JAK1 MUTATED JAK1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(213) Variable = COIL MUTATION ANALYSIS
D213V1, survival
                sevent
clus2              0   1
  COIL MUTATED     7   4
  COIL WILD-TYPE 331 212
  COIL MUTATED COIL WILD-TYPE 
            11            543 
  COIL MUTATED COIL WILD-TYPE 
             4            212 
$`COIL MUTATED`
TCGA-2H-A9GR TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 
       32.45        26.70        29.59         0.26         1.12        31.96 
TCGA-CD-8536 TCGA-CG-4469 TCGA-D7-A4YV TCGA-HU-A4GU TCGA-HU-A4GX 
       12.43         7.07         5.92         6.58        20.25 

$`COIL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  COIL MUTATED COIL WILD-TYPE 
          0.26           0.00 
  COIL MUTATED COIL WILD-TYPE 
         32.45         122.30 
  COIL MUTATED COIL WILD-TYPE 
         12.43          13.58 
[1] "0.3 - 32.5 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D213V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COIL MUTATED         0        0        1        1         2         4
  COIL WILD-TYPE      10       20       45       30        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  COIL MUTATED           0          0          0          1        2         0
  COIL WILD-TYPE        29         84         62         38       41         4
D213V3, multiclass
            clus
vv           COIL MUTATED COIL WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  COIL MUTATED       0   1   6   4
  COIL WILD-TYPE    54 134 255  98
D213V4, multiclass
       clus
vv      COIL MUTATED COIL WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               6            255
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  COIL MUTATED     6   2   2   1
  COIL WILD-TYPE 189 171  87  84
D213V5, multiclass
    clus
vv   COIL MUTATED COIL WILD-TYPE
  N0            6            189
  N1            2            171
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V6, binary
                cls
clus               0   1
  COIL MUTATED    10   1
  COIL WILD-TYPE 472  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED     10    1
  COIL WILD-TYPE  472   37
   clus
vv  COIL MUTATED COIL WILD-TYPE
  0           10            472
  1            1             37
[1] 2 2
[1] FALSE
D213V7, binary
                cls
clus               0   1
  COIL MUTATED     6   5
  COIL WILD-TYPE 166 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      6    5
  COIL WILD-TYPE  166  401
        clus
vv       COIL MUTATED COIL WILD-TYPE
  FEMALE            6            166
  MALE              5            401
[1] 2 2
[1] FALSE
D213V8, binary
                cls
clus               0   1
  COIL MUTATED    10   0
  COIL WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED     10    0
  COIL WILD-TYPE  406  102
     clus
vv    COIL MUTATED COIL WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D213V9, continuous
D213V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  COIL MUTATED       4                         0
  COIL WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COIL MUTATED                                           0     5
  COIL WILD-TYPE                                         1   352
D213V11, multiclass
                                           clus
vv                                          COIL MUTATED COIL WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V12, binary
                cls
clus               0   1
  COIL MUTATED     0   9
  COIL WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      0    9
  COIL WILD-TYPE   10  389
                        clus
vv                       COIL MUTATED COIL WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(214) Variable = TCF20 MUTATION ANALYSIS
D214V1, survival
                 sevent
clus2               0   1
  TCF20 MUTATED    12   7
  TCF20 WILD-TYPE 326 209
  TCF20 MUTATED TCF20 WILD-TYPE 
             19             535 
  TCF20 MUTATED TCF20 WILD-TYPE 
              7             209 
$`TCF20 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NM TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-BR-4184 
        4.31         7.76        12.23        12.03         7.82         6.97 
TCGA-BR-8285 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-5800 TCGA-CD-5813 TCGA-CG-5721 
        0.56         4.31        31.96        13.15        12.39         6.02 
TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-IN-8462 TCGA-MX-A5UJ 
      105.07        11.44         0.10         6.51        18.81        19.73 
TCGA-R5-A7ZI 
       74.53 

$`TCF20 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.00        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26        33.11         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TCF20 MUTATED TCF20 WILD-TYPE 
            0.1             0.0 
  TCF20 MUTATED TCF20 WILD-TYPE 
         105.07          122.30 
  TCF20 MUTATED TCF20 WILD-TYPE 
          11.44           13.87 
[1] "0.1 - 105.1 (11.4)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D214V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCF20 MUTATED         0        0        1        3         2         3
  TCF20 WILD-TYPE      10       20       45       28        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF20 MUTATED           1          2          2          2        3         0
  TCF20 WILD-TYPE        28         82         60         37       40         4
D214V3, multiclass
            clus
vv           TCF20 MUTATED TCF20 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TCF20 MUTATED       0   5  10   5
  TCF20 WILD-TYPE    54 130 251  97
D214V4, multiclass
       clus
vv      TCF20 MUTATED TCF20 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3               10             251
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TCF20 MUTATED     6   8   4   2
  TCF20 WILD-TYPE 189 165  85  83
D214V5, multiclass
    clus
vv   TCF20 MUTATED TCF20 WILD-TYPE
  N0             6             189
  N1             8             165
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V6, binary
                 cls
clus                0   1
  TCF20 MUTATED    17   2
  TCF20 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     17    2
  TCF20 WILD-TYPE  465   36
   clus
vv  TCF20 MUTATED TCF20 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D214V7, binary
                 cls
clus                0   1
  TCF20 MUTATED    11  11
  TCF20 WILD-TYPE 161 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     11   11
  TCF20 WILD-TYPE  161  395
        clus
vv       TCF20 MUTATED TCF20 WILD-TYPE
  FEMALE            11             161
  MALE              11             395
[1] 2 2
[1] FALSE
D214V8, binary
                 cls
clus                0   1
  TCF20 MUTATED    17   1
  TCF20 WILD-TYPE 399 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     17    1
  TCF20 WILD-TYPE  399  101
     clus
vv    TCF20 MUTATED TCF20 WILD-TYPE
  NO             17             399
  YES             1             101
[1] 2 2
[1] FALSE
D214V9, continuous
[1] "Remove cluster labels:" "TCF20 MUTATED"         
clus
  TCF20 MUTATED TCF20 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TCF20 WILD-TYPE" "TCF20 WILD-TYPE" 
D214V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TCF20 MUTATED       7                         0
  TCF20 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCF20 MUTATED                                           0    13
  TCF20 WILD-TYPE                                         1   344
D214V11, multiclass
                                           clus
vv                                          TCF20 MUTATED TCF20 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V12, binary
                 cls
clus                0   1
  TCF20 MUTATED     1  17
  TCF20 WILD-TYPE   9 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED      1   17
  TCF20 WILD-TYPE    9  381
                        clus
vv                       TCF20 MUTATED TCF20 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(215) Variable = TBX4 MUTATION ANALYSIS
D215V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     9   5
  TBX4 WILD-TYPE 329 211
  TBX4 MUTATED TBX4 WILD-TYPE 
            14            540 
  TBX4 MUTATED TBX4 WILD-TYPE 
             5            211 
$`TBX4 MUTATED`
TCGA-VR-AA7I TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-A4QL 
       15.91         6.97        30.90        29.59        28.14        16.14 
TCGA-CD-A4MJ TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-6874 TCGA-FP-A9TM 
       12.62         9.01         6.02        65.10        14.47         6.21 
TCGA-HU-A4GU TCGA-HU-A4H8 
        6.58        14.07 

$`TBX4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TBX4 MUTATED TBX4 WILD-TYPE 
          6.02           0.00 
  TBX4 MUTATED TBX4 WILD-TYPE 
          65.1          122.3 
  TBX4 MUTATED TBX4 WILD-TYPE 
         14.27          13.53 
[1] "6.0 - 65.1 (14.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D215V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBX4 MUTATED         0        0        4        0         0         2
  TBX4 WILD-TYPE      10       20       42       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBX4 MUTATED           1          1          1          1        3         0
  TBX4 WILD-TYPE        28         83         61         38       40         4
D215V3, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TBX4 MUTATED       2   4   3   6
  TBX4 WILD-TYPE    52 131 258  96
D215V4, multiclass
       clus
vv      TBX4 MUTATED TBX4 WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3               3            258
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TBX4 MUTATED     5   5   1   3
  TBX4 WILD-TYPE 190 168  88  82
D215V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0            5            190
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V6, binary
                cls
clus               0   1
  TBX4 MUTATED    13   1
  TBX4 WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     13    1
  TBX4 WILD-TYPE  469   37
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D215V7, binary
                cls
clus               0   1
  TBX4 MUTATED     6   9
  TBX4 WILD-TYPE 166 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      6    9
  TBX4 WILD-TYPE  166  397
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  FEMALE            6            166
  MALE              9            397
[1] 2 2
[1] FALSE
D215V8, binary
                cls
clus               0   1
  TBX4 MUTATED    11   1
  TBX4 WILD-TYPE 405 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     11    1
  TBX4 WILD-TYPE  405  101
     clus
vv    TBX4 MUTATED TBX4 WILD-TYPE
  NO            11            405
  YES            1            101
[1] 2 2
[1] FALSE
D215V9, continuous
[1] "Remove cluster labels:" "TBX4 MUTATED"          
clus
  TBX4 MUTATED TBX4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-XP-A8T6     TCGA-XP-A8T7 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
D215V10, continuous
[1] "Remove cluster labels:" "TBX4 MUTATED"          
clus
  TBX4 MUTATED TBX4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" "TBX4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"TBX4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TBX4 MUTATED       3                         0
  TBX4 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBX4 MUTATED                                           0     9
  TBX4 WILD-TYPE                                         1   348
D215V11, multiclass
                                           clus
vv                                          TBX4 MUTATED TBX4 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V12, binary
                cls
clus               0   1
  TBX4 MUTATED     0  11
  TBX4 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      0   11
  TBX4 WILD-TYPE   10  387
                        clus
vv                       TBX4 MUTATED TBX4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(216) Variable = PRKAB1 MUTATION ANALYSIS
D216V1, survival
                  sevent
clus2                0   1
  PRKAB1 MUTATED     6   5
  PRKAB1 WILD-TYPE 332 211
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
              11              543 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               5              211 
$`PRKAB1 MUTATED`
TCGA-L5-A8NT TCGA-L5-A8NN TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8591 TCGA-CG-5733 
       27.12         5.49         2.66         9.21        28.14        21.07 
TCGA-HU-A4GQ TCGA-IN-AB1X TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PM 
        0.10        13.51        13.25        38.14         1.87 

$`PRKAB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79         5.46        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.41        37.22        22.19        17.85        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
             0.1              0.0 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
           38.14           122.30 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
           13.25            13.68 
[1] "0.1 - 38.1 (13.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.4"
D216V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRKAB1 MUTATED         0        0        1        0         1         1
  PRKAB1 WILD-TYPE      10       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAB1 MUTATED           1          2          0          3        3
  PRKAB1 WILD-TYPE        28         82         62         36       40
                  vv
clus               STAGE IVA
  PRKAB1 MUTATED           0
  PRKAB1 WILD-TYPE         4
D216V3, multiclass
            clus
vv           PRKAB1 MUTATED PRKAB1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PRKAB1 MUTATED       0   2   3   7
  PRKAB1 WILD-TYPE    54 133 258  95
D216V4, multiclass
       clus
vv      PRKAB1 MUTATED PRKAB1 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 3              258
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PRKAB1 MUTATED     3   2   3   4
  PRKAB1 WILD-TYPE 192 171  86  81
D216V5, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V6, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED    11   1
  PRKAB1 WILD-TYPE 471  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED     11    1
  PRKAB1 WILD-TYPE  471   37
   clus
vv  PRKAB1 MUTATED PRKAB1 WILD-TYPE
  0             11              471
  1              1               37
[1] 2 2
[1] FALSE
D216V7, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     4   8
  PRKAB1 WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      4    8
  PRKAB1 WILD-TYPE  168  398
        clus
vv       PRKAB1 MUTATED PRKAB1 WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D216V8, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     9   2
  PRKAB1 WILD-TYPE 407 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      9    2
  PRKAB1 WILD-TYPE  407  100
     clus
vv    PRKAB1 MUTATED PRKAB1 WILD-TYPE
  NO               9              407
  YES              2              100
[1] 2 2
[1] FALSE
D216V9, continuous
D216V10, continuous
[1] "Remove cluster labels:" "PRKAB1 MUTATED"        
clus
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" "PRKAB1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRKAB1 MUTATED       1                         0
  PRKAB1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRKAB1 MUTATED                                           0    10
  PRKAB1 WILD-TYPE                                         1   347
D216V11, multiclass
                                           clus
vv                                          PRKAB1 MUTATED PRKAB1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V12, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     0   6
  PRKAB1 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      0    6
  PRKAB1 WILD-TYPE   10  392
                        clus
vv                       PRKAB1 MUTATED PRKAB1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(217) Variable = CETN3 MUTATION ANALYSIS
D217V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     7   2
  CETN3 WILD-TYPE 331 214
  CETN3 MUTATED CETN3 WILD-TYPE 
              9             545 
  CETN3 MUTATED CETN3 WILD-TYPE 
              2             214 
$`CETN3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5728 
       19.99         7.76        31.96        16.14         6.02        65.10 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-MX-A5UJ 
       29.98         6.51        19.73 

$`CETN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CETN3 MUTATED CETN3 WILD-TYPE 
           6.02            0.00 
  CETN3 MUTATED CETN3 WILD-TYPE 
           65.1           122.3 
  CETN3 MUTATED CETN3 WILD-TYPE 
          19.73           13.51 
[1] "6.0 - 65.1 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D217V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CETN3 MUTATED         0        0        1        0         2         1
  CETN3 WILD-TYPE      10       20       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CETN3 MUTATED           0          1          1          1        3         0
  CETN3 WILD-TYPE        29         83         61         38       40         4
D217V3, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CETN3 MUTATED       1   3   4   3
  CETN3 WILD-TYPE    53 132 257  99
D217V4, multiclass
       clus
vv      CETN3 MUTATED CETN3 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CETN3 MUTATED     2   3   3   2
  CETN3 WILD-TYPE 193 170  86  83
D217V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             2             193
  N1             3             170
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V6, binary
                 cls
clus                0   1
  CETN3 MUTATED     9   1
  CETN3 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      9    1
  CETN3 WILD-TYPE  473   37
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D217V7, binary
                 cls
clus                0   1
  CETN3 MUTATED     7   4
  CETN3 WILD-TYPE 165 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      7    4
  CETN3 WILD-TYPE  165  402
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  FEMALE             7             165
  MALE               4             402
[1] 2 2
[1] FALSE
D217V8, binary
                 cls
clus                0   1
  CETN3 MUTATED     8   0
  CETN3 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      8    0
  CETN3 WILD-TYPE  408  102
     clus
vv    CETN3 MUTATED CETN3 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D217V9, continuous
D217V10, continuous
[1] "Remove cluster labels:" "CETN3 MUTATED"         
clus
  CETN3 MUTATED CETN3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" "CETN3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CETN3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CETN3 MUTATED       3                         0
  CETN3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CETN3 MUTATED                                           0     6
  CETN3 WILD-TYPE                                         1   351
D217V11, multiclass
                                           clus
vv                                          CETN3 MUTATED CETN3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V12, binary
                 cls
clus                0   1
  CETN3 MUTATED     0   7
  CETN3 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      0    7
  CETN3 WILD-TYPE   10  391
                        clus
vv                       CETN3 MUTATED CETN3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(218) Variable = DDX26B MUTATION ANALYSIS
D218V1, survival
                  sevent
clus2                0   1
  DDX26B MUTATED     8   3
  DDX26B WILD-TYPE 330 213
  DDX26B MUTATED DDX26B WILD-TYPE 
              11              543 
  DDX26B MUTATED DDX26B WILD-TYPE 
               3              213 
$`DDX26B MUTATED`
TCGA-L5-A8NM TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8525 
        7.76        35.84        31.10         0.26         1.12        12.59 
TCGA-CG-5728 TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-VQ-AA64 
       65.10         8.98        23.80        14.07        18.41 

$`DDX26B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.39        12.76        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 
       20.81         1.71        42.64        66.81        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DDX26B MUTATED DDX26B WILD-TYPE 
            0.26             0.00 
  DDX26B MUTATED DDX26B WILD-TYPE 
            65.1            122.3 
  DDX26B MUTATED DDX26B WILD-TYPE 
           14.07            13.55 
[1] "0.3 - 65.1 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D218V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX26B MUTATED         1        0        5        0         2         1
  DDX26B WILD-TYPE       9       20       41       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX26B MUTATED           0          1          1          1        0
  DDX26B WILD-TYPE        29         83         61         38       43
                  vv
clus               STAGE IVA
  DDX26B MUTATED           0
  DDX26B WILD-TYPE         4
D218V3, multiclass
            clus
vv           DDX26B MUTATED DDX26B WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                5               41
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DDX26B MUTATED       2   6   3   1
  DDX26B WILD-TYPE    52 129 258 101
D218V4, multiclass
       clus
vv      DDX26B MUTATED DDX26B WILD-TYPE
  T0+T1              2               52
  T2                 6              129
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DDX26B MUTATED     5   5   2   0
  DDX26B WILD-TYPE 190 168  87  85
D218V5, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  N0              5              190
  N1              5              168
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V6, binary
                  cls
clus                 0   1
  DDX26B MUTATED    12   0
  DDX26B WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     12    0
  DDX26B WILD-TYPE  470   38
   clus
vv  DDX26B MUTATED DDX26B WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D218V7, binary
                  cls
clus                 0   1
  DDX26B MUTATED     9   4
  DDX26B WILD-TYPE 163 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      9    4
  DDX26B WILD-TYPE  163  402
        clus
vv       DDX26B MUTATED DDX26B WILD-TYPE
  FEMALE              9              163
  MALE                4              402
[1] 2 2
[1] FALSE
D218V8, binary
                  cls
clus                 0   1
  DDX26B MUTATED     9   2
  DDX26B WILD-TYPE 407 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      9    2
  DDX26B WILD-TYPE  407  100
     clus
vv    DDX26B MUTATED DDX26B WILD-TYPE
  NO               9              407
  YES              2              100
[1] 2 2
[1] FALSE
D218V9, continuous
D218V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DDX26B MUTATED       4                         1
  DDX26B WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX26B MUTATED                                           0     7
  DDX26B WILD-TYPE                                         1   350
D218V11, multiclass
                                           clus
vv                                          DDX26B MUTATED DDX26B WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V12, binary
                  cls
clus                 0   1
  DDX26B MUTATED     0  10
  DDX26B WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      0   10
  DDX26B WILD-TYPE   10  388
                        clus
vv                       DDX26B MUTATED DDX26B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(219) Variable = DLAT MUTATION ANALYSIS
D219V1, survival
                sevent
clus2              0   1
  DLAT MUTATED     6   1
  DLAT WILD-TYPE 332 215
  DLAT MUTATED DLAT WILD-TYPE 
             7            547 
  DLAT MUTATED DLAT WILD-TYPE 
             1            215 
$`DLAT MUTATED`
TCGA-Q9-A6FW TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8360 TCGA-HF-A5NB TCGA-HU-A4G9 
        7.82        26.70        30.90         6.18        30.51        24.20 
TCGA-MX-A5UJ 
       19.73 

$`DLAT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DLAT MUTATED DLAT WILD-TYPE 
          6.18           0.00 
  DLAT MUTATED DLAT WILD-TYPE 
          30.9          122.3 
  DLAT MUTATED DLAT WILD-TYPE 
         24.20          13.51 
[1] "6.2 - 30.9 (24.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.4"
D219V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLAT MUTATED         1        1        0        0         1         1
  DLAT WILD-TYPE       9       19       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DLAT MUTATED           0          2          1          1        0         0
  DLAT WILD-TYPE        29         82         61         38       43         4
D219V3, multiclass
            clus
vv           DLAT MUTATED DLAT WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DLAT MUTATED       2   1   3   3
  DLAT WILD-TYPE    52 134 258  99
D219V4, multiclass
       clus
vv      DLAT MUTATED DLAT WILD-TYPE
  T0+T1            2             52
  T2               1            134
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DLAT MUTATED     4   1   2   1
  DLAT WILD-TYPE 191 172  87  84
D219V5, multiclass
    clus
vv   DLAT MUTATED DLAT WILD-TYPE
  N0            4            191
  N1            1            172
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V6, binary
                cls
clus               0   1
  DLAT MUTATED     8   0
  DLAT WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      8    0
  DLAT WILD-TYPE  474   38
   clus
vv  DLAT MUTATED DLAT WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D219V7, binary
                cls
clus               0   1
  DLAT MUTATED     6   3
  DLAT WILD-TYPE 166 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      6    3
  DLAT WILD-TYPE  166  403
        clus
vv       DLAT MUTATED DLAT WILD-TYPE
  FEMALE            6            166
  MALE              3            403
[1] 2 2
[1] FALSE
D219V8, binary
                cls
clus               0   1
  DLAT MUTATED     7   1
  DLAT WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      7    1
  DLAT WILD-TYPE  409  101
     clus
vv    DLAT MUTATED DLAT WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D219V9, continuous
D219V10, continuous
[1] "Remove cluster labels:" "DLAT MUTATED"          
clus
  DLAT MUTATED DLAT WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-R6-A6DN 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" "DLAT WILD-TYPE" 
    TCGA-Z6-AAPN 
"DLAT WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DLAT MUTATED       1                         1
  DLAT WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLAT MUTATED                                           0     6
  DLAT WILD-TYPE                                         1   351
D219V11, multiclass
                                           clus
vv                                          DLAT MUTATED DLAT WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V12, binary
                cls
clus               0   1
  DLAT MUTATED     0   8
  DLAT WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      0    8
  DLAT WILD-TYPE   10  390
                        clus
vv                       DLAT MUTATED DLAT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(220) Variable = MPRIP MUTATION ANALYSIS
D220V1, survival
                 sevent
clus2               0   1
  MPRIP MUTATED    10   5
  MPRIP WILD-TYPE 328 211
  MPRIP MUTATED MPRIP WILD-TYPE 
             15             539 
  MPRIP MUTATED MPRIP WILD-TYPE 
              5             211 
$`MPRIP MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8368 
       19.99         6.97        32.78        44.94         6.18         4.31 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-HF-A5NB 
        9.34        28.14        16.14         6.58         9.01        30.51 
TCGA-HU-8602 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       22.32        14.07        38.14 

$`MPRIP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MPRIP MUTATED MPRIP WILD-TYPE 
           4.31            0.00 
  MPRIP MUTATED MPRIP WILD-TYPE 
          44.94          122.30 
  MPRIP MUTATED MPRIP WILD-TYPE 
          16.14           13.51 
[1] "4.3 - 44.9 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D220V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MPRIP MUTATED         0        0        2        0         4         1
  MPRIP WILD-TYPE      10       20       44       31        80        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPRIP MUTATED           0          3          1          4        1         0
  MPRIP WILD-TYPE        29         81         61         35       42         4
D220V3, multiclass
            clus
vv           MPRIP MUTATED MPRIP WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MPRIP MUTATED       2   1   8   7
  MPRIP WILD-TYPE    52 134 253  95
D220V4, multiclass
       clus
vv      MPRIP MUTATED MPRIP WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                8             253
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MPRIP MUTATED     7   3   1   5
  MPRIP WILD-TYPE 188 170  88  80
D220V5, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  N0             7             188
  N1             3             170
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V6, binary
                 cls
clus                0   1
  MPRIP MUTATED    14   1
  MPRIP WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     14    1
  MPRIP WILD-TYPE  468   37
   clus
vv  MPRIP MUTATED MPRIP WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D220V7, binary
                 cls
clus                0   1
  MPRIP MUTATED    10   8
  MPRIP WILD-TYPE 162 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     10    8
  MPRIP WILD-TYPE  162  398
        clus
vv       MPRIP MUTATED MPRIP WILD-TYPE
  FEMALE            10             162
  MALE               8             398
[1] 2 2
[1] FALSE
D220V8, binary
                 cls
clus                0   1
  MPRIP MUTATED    12   2
  MPRIP WILD-TYPE 404 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     12    2
  MPRIP WILD-TYPE  404  100
     clus
vv    MPRIP MUTATED MPRIP WILD-TYPE
  NO             12             404
  YES             2             100
[1] 2 2
[1] FALSE
D220V9, continuous
D220V10, continuous
[1] "Remove cluster labels:" "MPRIP MUTATED"         
clus
  MPRIP MUTATED MPRIP WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" "MPRIP WILD-TYPE" 
     TCGA-Z6-AAPN 
"MPRIP WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MPRIP MUTATED       3                         0
  MPRIP WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MPRIP MUTATED                                           0    13
  MPRIP WILD-TYPE                                         1   344
D220V11, multiclass
                                           clus
vv                                          MPRIP MUTATED MPRIP WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V12, binary
                 cls
clus                0   1
  MPRIP MUTATED     0  14
  MPRIP WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED      0   14
  MPRIP WILD-TYPE   10  384
                        clus
vv                       MPRIP MUTATED MPRIP WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(221) Variable = NCAPD3 MUTATION ANALYSIS
D221V1, survival
                  sevent
clus2                0   1
  NCAPD3 MUTATED    18   9
  NCAPD3 WILD-TYPE 320 207
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              27              527 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               9              207 
$`NCAPD3 MUTATED`
TCGA-L5-A43I TCGA-L5-A4OI TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-L5-A4OP 
       18.28        19.99         4.67       122.10        41.52         7.17 
TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-VR-A8EO TCGA-Z6-A9VB TCGA-B7-A5TI 
       55.50        16.47         5.49        25.81         1.32        19.56 
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-A4QL 
       34.68        31.10        27.12        26.73        31.96        16.14 
TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-6524 TCGA-FP-7735 TCGA-FP-A4BE 
        6.58         9.01        28.96        17.85         3.48        11.08 
TCGA-HJ-7597 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       26.47        14.07        74.53 

$`NCAPD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.96        14.86        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.99        14.47        72.23        21.27        11.38        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
            1.32             0.00 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
           122.1            122.3 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
           19.56            13.41 
[1] "1.3 - 122.1 (19.6)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D221V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAPD3 MUTATED         1        2        3        1         4         2
  NCAPD3 WILD-TYPE       9       18       43       30        80        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD3 MUTATED           3          2          4          3        3
  NCAPD3 WILD-TYPE        26         82         58         36       40
                  vv
clus               STAGE IVA
  NCAPD3 MUTATED           0
  NCAPD3 WILD-TYPE         4
D221V3, multiclass
            clus
vv           NCAPD3 MUTATED NCAPD3 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                2               18
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               2               81
  STAGE III               3               26
  STAGE IIIA              2               82
  STAGE IIIB              4               58
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NCAPD3 MUTATED       5   4  13   7
  NCAPD3 WILD-TYPE    49 131 248  95
D221V4, multiclass
       clus
vv      NCAPD3 MUTATED NCAPD3 WILD-TYPE
  T0+T1              5               49
  T2                 4              131
  T3                13              248
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NCAPD3 MUTATED    10  10   3   5
  NCAPD3 WILD-TYPE 185 163  86  80
D221V5, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  N0             10              185
  N1             10              163
  N2              3               86
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V6, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   3
  NCAPD3 WILD-TYPE 460  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    3
  NCAPD3 WILD-TYPE  460   35
   clus
vv  NCAPD3 MUTATED NCAPD3 WILD-TYPE
  0             22              460
  1              3               35
[1] 2 2
[1] FALSE
D221V7, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    10  20
  NCAPD3 WILD-TYPE 162 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     10   20
  NCAPD3 WILD-TYPE  162  386
        clus
vv       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  FEMALE             10              162
  MALE               20              386
[1] 2 2
[1] FALSE
D221V8, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    21   3
  NCAPD3 WILD-TYPE 395  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     21    3
  NCAPD3 WILD-TYPE  395   99
     clus
vv    NCAPD3 MUTATED NCAPD3 WILD-TYPE
  NO              21              395
  YES              3               99
[1] 2 2
[1] FALSE
D221V9, continuous
[1] "Remove cluster labels:" "NCAPD3 MUTATED"        
clus
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EP 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" "NCAPD3 WILD-TYPE" 
D221V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NCAPD3 MUTATED       4                         2
  NCAPD3 WILD-TYPE   129                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCAPD3 MUTATED                                           0    22
  NCAPD3 WILD-TYPE                                         1   335
D221V11, multiclass
                                           clus
vv                                          NCAPD3 MUTATED NCAPD3 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V12, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED     1  18
  NCAPD3 WILD-TYPE   9 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED      1   18
  NCAPD3 WILD-TYPE    9  380
                        clus
vv                       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(222) Variable = CASP8 MUTATION ANALYSIS
D222V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    12   8
  CASP8 WILD-TYPE 326 208
  CASP8 MUTATED CASP8 WILD-TYPE 
             20             534 
  CASP8 MUTATED CASP8 WILD-TYPE 
              8             208 
$`CASP8 MUTATED`
TCGA-IC-A6RF TCGA-EQ-A4SO TCGA-JY-A6F8 TCGA-L5-A8NS TCGA-LN-A4A4 TCGA-LN-A4MR 
       15.68        16.24       122.10        13.41        12.59        13.22 
TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8285 
        9.34         6.61        34.68        44.94        14.43         0.56 
TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-D7-8570 TCGA-D7-A4YV 
        1.12         6.58        11.77         1.02        24.72         5.92 
TCGA-D7-A4Z0 TCGA-HU-A4G8 
       14.76        22.68 

$`CASP8 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        12.33         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44        36.43        13.78        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.56            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
          122.1           122.3 
  CASP8 MUTATED CASP8 WILD-TYPE 
         13.315          13.630 
[1] "0.6 - 122.1 (13.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D222V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASP8 MUTATED         1        1        0        0         5         4
  CASP8 WILD-TYPE       9       19       46       31        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED           3          1          2          1        1         0
  CASP8 WILD-TYPE        26         83         60         38       42         4
D222V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              3              26
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CASP8 MUTATED       3   3  12   3
  CASP8 WILD-TYPE    51 132 249  99
D222V4, multiclass
       clus
vv      CASP8 MUTATED CASP8 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3               12             249
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASP8 MUTATED     8   9   2   2
  CASP8 WILD-TYPE 187 164  87  83
D222V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             8             187
  N1             9             164
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    20   1
  CASP8 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     20    1
  CASP8 WILD-TYPE  462   37
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D222V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    12  11
  CASP8 WILD-TYPE 160 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     12   11
  CASP8 WILD-TYPE  160  395
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            12             160
  MALE              11             395
[1] 2 2
[1] FALSE
D222V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    15   4
  CASP8 WILD-TYPE 401  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     15    4
  CASP8 WILD-TYPE  401   98
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             15             401
  YES             4              98
[1] 2 2
[1] FALSE
D222V9, continuous
[1] "Remove cluster labels:" "CASP8 MUTATED"         
clus
  CASP8 MUTATED CASP8 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A5U5 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
D222V10, continuous
[1] "Remove cluster labels:" "CASP8 MUTATED"         
clus
  CASP8 MUTATED CASP8 WILD-TYPE 
              2              96 
     TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" "CASP8 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASP8 MUTATED       5                         0
  CASP8 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP8 MUTATED                                           0    17
  CASP8 WILD-TYPE                                         1   340
D222V11, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V12, binary
                 cls
clus                0   1
  CASP8 MUTATED     0  20
  CASP8 WILD-TYPE  10 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0   20
  CASP8 WILD-TYPE   10  378
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(223) Variable = BRD8 MUTATION ANALYSIS
D223V1, survival
                sevent
clus2              0   1
  BRD8 MUTATED    19  15
  BRD8 WILD-TYPE 319 201
  BRD8 MUTATED BRD8 WILD-TYPE 
            34            520 
  BRD8 MUTATED BRD8 WILD-TYPE 
            15            201 
$`BRD8 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NM TCGA-LN-A4A9 TCGA-V5-A7RB TCGA-BR-6452 TCGA-BR-6455 
       21.99         7.76        11.54         5.29        34.68        13.87 
TCGA-BR-6564 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 
       26.10         0.69        29.59        32.25         8.05         2.20 
TCGA-BR-8370 TCGA-BR-8591 TCGA-BR-A44U TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 
        3.32        28.14        13.87        12.59        12.53        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CG-5733 TCGA-D7-8572 TCGA-D7-8576 
       12.39        12.59        11.64        21.07        16.80        14.66 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH 
       17.06        59.54        13.58         5.92         0.76        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-VQ-A8P2 
       29.98         8.98         0.10        38.14 

$`BRD8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 
        9.67         6.18         9.57         6.61        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       11.44         9.60         0.56        29.42         2.66        19.96 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        9.86        20.88         8.22        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8527 
       13.35        11.21        12.10        12.39        12.76         7.17 
TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.33        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
       22.29         5.03         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       24.39        28.96        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       25.81        21.37         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BRD8 MUTATED BRD8 WILD-TYPE 
           0.1            0.0 
  BRD8 MUTATED BRD8 WILD-TYPE 
         59.54         122.30 
  BRD8 MUTATED BRD8 WILD-TYPE 
         12.59          13.73 
[1] "0.1 - 59.5 (12.6)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D223V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRD8 MUTATED         0        2        1        2         5         7
  BRD8 WILD-TYPE      10       18       45       29        79        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD8 MUTATED           0          7          4          4        2         0
  BRD8 WILD-TYPE        29         77         58         35       41         4
D223V3, multiclass
            clus
vv           BRD8 MUTATED BRD8 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             5             79
  STAGE IIB             7             76
  STAGE III             0             29
  STAGE IIIA            7             77
  STAGE IIIB            4             58
  STAGE IIIC            4             35
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BRD8 MUTATED       3   7  13  12
  BRD8 WILD-TYPE    51 128 248  90
D223V4, multiclass
       clus
vv      BRD8 MUTATED BRD8 WILD-TYPE
  T0+T1            3             51
  T2               7            128
  T3              13            248
  T4              12             90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BRD8 MUTATED    13  12   4   6
  BRD8 WILD-TYPE 182 161  85  79
D223V5, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  N0           13            182
  N1           12            161
  N2            4             85
  N3            6             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V6, binary
                cls
clus               0   1
  BRD8 MUTATED    30   2
  BRD8 WILD-TYPE 452  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     30    2
  BRD8 WILD-TYPE  452   36
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0           30            452
  1            2             36
[1] 2 2
[1] FALSE
D223V7, binary
                cls
clus               0   1
  BRD8 MUTATED    16  19
  BRD8 WILD-TYPE 156 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     16   19
  BRD8 WILD-TYPE  156  387
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE           16            156
  MALE             19            387
[1] 2 2
[1] FALSE
D223V8, binary
                cls
clus               0   1
  BRD8 MUTATED    26   7
  BRD8 WILD-TYPE 390  95
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     26    7
  BRD8 WILD-TYPE  390   95
     clus
vv    BRD8 MUTATED BRD8 WILD-TYPE
  NO            26            390
  YES            7             95
[1] 2 2
[1] FALSE
D223V9, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
D223V10, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RC 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRD8 MUTATED      13                         0
  BRD8 WILD-TYPE   120                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRD8 MUTATED                                           0    19
  BRD8 WILD-TYPE                                         1   338
D223V11, multiclass
                                           clus
vv                                          BRD8 MUTATED BRD8 WILD-TYPE
  ASIAN                                               13            120
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V12, binary
                cls
clus               0   1
  BRD8 MUTATED     1  30
  BRD8 WILD-TYPE   9 368
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      1   30
  BRD8 WILD-TYPE    9  368
                        clus
vv                       BRD8 MUTATED BRD8 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           30            368
[1] 2 2
[1] FALSE

Clustering(224) Variable = PET112L MUTATION ANALYSIS
D224V1, survival
                   sevent
clus2                 0   1
  PET112L MUTATED     3   8
  PET112L WILD-TYPE 335 208
  PET112L MUTATED PET112L WILD-TYPE 
               11               543 
  PET112L MUTATED PET112L WILD-TYPE 
                8               208 
$`PET112L MUTATED`
TCGA-CG-4460 TCGA-2H-A9GR TCGA-L5-A4OT TCGA-L5-A88W TCGA-BR-4184 TCGA-BR-8382 
       21.99        32.45         4.90        25.12         6.97        25.05 
TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5723 TCGA-D7-A4YV TCGA-HU-A4GN 
       31.96        13.18       105.07         5.92        29.98 

$`PET112L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PET112L MUTATED PET112L WILD-TYPE 
              4.9               0.0 
  PET112L MUTATED PET112L WILD-TYPE 
           105.07            122.30 
  PET112L MUTATED PET112L WILD-TYPE 
            25.05             13.51 
[1] "4.9 - 105.1 (25.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D224V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PET112L MUTATED         0        0        0        1         3         1
  PET112L WILD-TYPE      10       20       46       30        81        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PET112L MUTATED           0          2          0          1        3
  PET112L WILD-TYPE        29         82         62         38       40
                   vv
clus                STAGE IVA
  PET112L MUTATED           0
  PET112L WILD-TYPE         4
D224V3, multiclass
            clus
vv           PET112L MUTATED PET112L WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PET112L MUTATED       0   2   6   3
  PET112L WILD-TYPE    54 133 255  99
D224V4, multiclass
       clus
vv      PET112L MUTATED PET112L WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  6               255
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PET112L MUTATED     2   7   1   1
  PET112L WILD-TYPE 193 166  88  84
D224V5, multiclass
    clus
vv   PET112L MUTATED PET112L WILD-TYPE
  N0               2               193
  N1               7               166
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V6, binary
                   cls
clus                  0   1
  PET112L MUTATED     6   3
  PET112L WILD-TYPE 476  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      6    3
  PET112L WILD-TYPE  476   35
   clus
vv  PET112L MUTATED PET112L WILD-TYPE
  0               6               476
  1               3                35
[1] 2 2
[1] FALSE
D224V7, binary
                   cls
clus                  0   1
  PET112L MUTATED     3   8
  PET112L WILD-TYPE 169 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      3    8
  PET112L WILD-TYPE  169  398
        clus
vv       PET112L MUTATED PET112L WILD-TYPE
  FEMALE               3               169
  MALE                 8               398
[1] 2 2
[1] FALSE
D224V8, binary
                   cls
clus                  0   1
  PET112L MUTATED    10   1
  PET112L WILD-TYPE 406 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED     10    1
  PET112L WILD-TYPE  406  101
     clus
vv    PET112L MUTATED PET112L WILD-TYPE
  NO               10               406
  YES               1               101
[1] 2 2
[1] FALSE
D224V9, continuous
D224V10, continuous
[1] "Remove cluster labels:" "PET112L MUTATED"       
clus
  PET112L MUTATED PET112L WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" "PET112L WILD-TYPE" 
       TCGA-Z6-AAPN 
"PET112L WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PET112L MUTATED       3                         0
  PET112L WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PET112L MUTATED                                           0     5
  PET112L WILD-TYPE                                         1   352
D224V11, multiclass
                                           clus
vv                                          PET112L MUTATED PET112L WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V12, binary
                   cls
clus                  0   1
  PET112L MUTATED     0   6
  PET112L WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      0    6
  PET112L WILD-TYPE   10  392
                        clus
vv                       PET112L MUTATED PET112L WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(225) Variable = RGS9BP MUTATION ANALYSIS
D225V1, survival
                  sevent
clus2                0   1
  RGS9BP MUTATED     5   3
  RGS9BP WILD-TYPE 333 213
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8              546 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               3              213 
$`RGS9BP MUTATED`
TCGA-L5-A4OI TCGA-BR-8059 TCGA-BR-8368 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HU-A4G8 
       19.99        14.43         4.31         1.12        11.44        22.68 
TCGA-HU-A4GQ TCGA-HU-A4HD 
        0.10        33.40 

$`RGS9BP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RGS9BP MUTATED RGS9BP WILD-TYPE 
             0.1              0.0 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
            33.4            122.3 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
          12.935           13.565 
[1] "0.1 - 33.4 (12.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D225V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS9BP MUTATED         0        0        1        0         1         1
  RGS9BP WILD-TYPE      10       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGS9BP MUTATED           1          1          1          2        0
  RGS9BP WILD-TYPE        28         83         61         37       43
                  vv
clus               STAGE IVA
  RGS9BP MUTATED           0
  RGS9BP WILD-TYPE         4
D225V3, multiclass
            clus
vv           RGS9BP MUTATED RGS9BP WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RGS9BP MUTATED       0   1   5   2
  RGS9BP WILD-TYPE    54 134 256 100
D225V4, multiclass
       clus
vv      RGS9BP MUTATED RGS9BP WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RGS9BP MUTATED     2   2   2   2
  RGS9BP WILD-TYPE 193 171  87  83
D225V5, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  N0              2              193
  N1              2              171
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V6, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     8   0
  RGS9BP WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      8    0
  RGS9BP WILD-TYPE  474   38
   clus
vv  RGS9BP MUTATED RGS9BP WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D225V7, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     5   4
  RGS9BP WILD-TYPE 167 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      5    4
  RGS9BP WILD-TYPE  167  402
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  FEMALE              5              167
  MALE                4              402
[1] 2 2
[1] FALSE
D225V8, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     8   0
  RGS9BP WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      8    0
  RGS9BP WILD-TYPE  408  102
     clus
vv    RGS9BP MUTATED RGS9BP WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D225V9, continuous
D225V10, continuous
[1] "Remove cluster labels:" "RGS9BP MUTATED"        
clus
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" "RGS9BP WILD-TYPE" 
      TCGA-Z6-AAPN 
"RGS9BP WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RGS9BP MUTATED       3                         0
  RGS9BP WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS9BP MUTATED                                           0     6
  RGS9BP WILD-TYPE                                         1   351
D225V11, multiclass
                                           clus
vv                                          RGS9BP MUTATED RGS9BP WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V12, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     0   8
  RGS9BP WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      0    8
  RGS9BP WILD-TYPE   10  390
                        clus
vv                       RGS9BP MUTATED RGS9BP WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(226) Variable = OR5M3 MUTATION ANALYSIS
D226V1, survival
                 sevent
clus2               0   1
  OR5M3 MUTATED    16   7
  OR5M3 WILD-TYPE 322 209
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             23             531 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
              7             209 
$`OR5M3 MUTATED`
TCGA-L5-A4OG TCGA-L5-A8NM TCGA-LN-A9FQ TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-VR-A8EZ 
        4.70         7.76        12.85        53.95         2.30        18.18 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8295 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 
       30.90        34.68         2.20        25.05         1.12        12.79 
TCGA-BR-A452 TCGA-CD-8528 TCGA-CG-5725 TCGA-D7-6526 TCGA-HF-7132 TCGA-HU-A4GT 
        7.53        12.33        15.02        17.19        77.29         6.51 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-VQ-AA68 
        6.58        14.07        63.62        74.53        43.66 

$`OR5M3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        3.72         5.39        25.18         9.21        20.22        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  OR5M3 MUTATED OR5M3 WILD-TYPE 
           1.12            0.00 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
          77.29          122.30 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
          14.07           13.55 
[1] "1.1 - 77.3 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D226V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR5M3 MUTATED         1        0        4        1         4         5
  OR5M3 WILD-TYPE       9       20       42       30        80        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5M3 MUTATED           0          3          0          3        1         0
  OR5M3 WILD-TYPE        29         81         62         36       42         4
D226V3, multiclass
            clus
vv           OR5M3 MUTATED OR5M3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OR5M3 MUTATED       3   5   7   8
  OR5M3 WILD-TYPE    51 130 254  94
D226V4, multiclass
       clus
vv      OR5M3 MUTATED OR5M3 WILD-TYPE
  T0+T1             3              51
  T2                5             130
  T3                7             254
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OR5M3 MUTATED    11   7   1   3
  OR5M3 WILD-TYPE 184 166  88  82
D226V5, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  N0            11             184
  N1             7             166
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V6, binary
                 cls
clus                0   1
  OR5M3 MUTATED    22   1
  OR5M3 WILD-TYPE 460  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     22    1
  OR5M3 WILD-TYPE  460   37
   clus
vv  OR5M3 MUTATED OR5M3 WILD-TYPE
  0            22             460
  1             1              37
[1] 2 2
[1] FALSE
D226V7, binary
                 cls
clus                0   1
  OR5M3 MUTATED    14  11
  OR5M3 WILD-TYPE 158 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     14   11
  OR5M3 WILD-TYPE  158  395
        clus
vv       OR5M3 MUTATED OR5M3 WILD-TYPE
  FEMALE            14             158
  MALE              11             395
[1] 2 2
[1] FALSE
D226V8, binary
                 cls
clus                0   1
  OR5M3 MUTATED    19   4
  OR5M3 WILD-TYPE 397  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     19    4
  OR5M3 WILD-TYPE  397   98
     clus
vv    OR5M3 MUTATED OR5M3 WILD-TYPE
  NO             19             397
  YES             4              98
[1] 2 2
[1] FALSE
D226V9, continuous
[1] "Remove cluster labels:" "OR5M3 MUTATED"         
clus
  OR5M3 MUTATED OR5M3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" "OR5M3 WILD-TYPE" 
D226V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR5M3 MUTATED       6                         0
  OR5M3 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR5M3 MUTATED                                           0    15
  OR5M3 WILD-TYPE                                         1   342
D226V11, multiclass
                                           clus
vv                                          OR5M3 MUTATED OR5M3 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V12, binary
                 cls
clus                0   1
  OR5M3 MUTATED     1  16
  OR5M3 WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED      1   16
  OR5M3 WILD-TYPE    9  382
                        clus
vv                       OR5M3 MUTATED OR5M3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(227) Variable = FERMT2 MUTATION ANALYSIS
D227V1, survival
                  sevent
clus2                0   1
  FERMT2 MUTATED    10   2
  FERMT2 WILD-TYPE 328 214
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              12              542 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               2              214 
$`FERMT2 MUTATED`
TCGA-L5-A4OI TCGA-Z6-A8JD TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8361 TCGA-BR-8487 
       19.99         3.42        34.68        35.24        31.10         1.12 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-8238 TCGA-HU-8602 TCGA-VQ-A8P2 TCGA-VQ-A91Q 
       28.14        16.14         1.51        22.32        38.14        20.81 

$`FERMT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U 
       37.22        22.19        17.85         1.87        15.65         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FERMT2 MUTATED FERMT2 WILD-TYPE 
            1.12             0.00 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
           38.14           122.30 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
          21.565           13.495 
[1] "1.1 - 38.1 (21.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.8"
D227V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FERMT2 MUTATED         0        0        0        1         2         2
  FERMT2 WILD-TYPE      10       20       46       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FERMT2 MUTATED           0          2          1          3        1
  FERMT2 WILD-TYPE        29         82         61         36       42
                  vv
clus               STAGE IVA
  FERMT2 MUTATED           0
  FERMT2 WILD-TYPE         4
D227V3, multiclass
            clus
vv           FERMT2 MUTATED FERMT2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FERMT2 MUTATED       0   0   9   5
  FERMT2 WILD-TYPE    54 135 252  97
D227V4, multiclass
       clus
vv      FERMT2 MUTATED FERMT2 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 9              252
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FERMT2 MUTATED     6   1   2   4
  FERMT2 WILD-TYPE 189 172  87  81
D227V5, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  N0              6              189
  N1              1              172
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V6, binary
                  cls
clus                 0   1
  FERMT2 MUTATED    12   0
  FERMT2 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED     12    0
  FERMT2 WILD-TYPE  470   38
   clus
vv  FERMT2 MUTATED FERMT2 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D227V7, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     8   6
  FERMT2 WILD-TYPE 164 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      8    6
  FERMT2 WILD-TYPE  164  400
        clus
vv       FERMT2 MUTATED FERMT2 WILD-TYPE
  FEMALE              8              164
  MALE                6              400
[1] 2 2
[1] FALSE
D227V8, binary
                  cls
clus                 0   1
  FERMT2 MUTATED    10   2
  FERMT2 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED     10    2
  FERMT2 WILD-TYPE  406  100
     clus
vv    FERMT2 MUTATED FERMT2 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D227V9, continuous
[1] "Remove cluster labels:" "FERMT2 MUTATED"        
clus
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JE 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
D227V10, continuous
[1] "Remove cluster labels:" "FERMT2 MUTATED"        
clus
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" "FERMT2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"FERMT2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FERMT2 MUTATED       2                         0
  FERMT2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FERMT2 MUTATED                                           0    11
  FERMT2 WILD-TYPE                                         1   346
D227V11, multiclass
                                           clus
vv                                          FERMT2 MUTATED FERMT2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V12, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     0  11
  FERMT2 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      0   11
  FERMT2 WILD-TYPE   10  387
                        clus
vv                       FERMT2 MUTATED FERMT2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(228) Variable = STX2 MUTATION ANALYSIS
D228V1, survival
                sevent
clus2              0   1
  STX2 MUTATED     5   2
  STX2 WILD-TYPE 333 214
  STX2 MUTATED STX2 WILD-TYPE 
             7            547 
  STX2 MUTATED STX2 WILD-TYPE 
             2            214 
$`STX2 MUTATED`
TCGA-L5-A4OI TCGA-BR-8680 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 
       19.99        31.96        11.44        22.32         0.10        14.07 
TCGA-VQ-A8P2 
       38.14 

$`STX2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  STX2 MUTATED STX2 WILD-TYPE 
           0.1            0.0 
  STX2 MUTATED STX2 WILD-TYPE 
         38.14         122.30 
  STX2 MUTATED STX2 WILD-TYPE 
         19.99          13.51 
[1] "0.1 - 38.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D228V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STX2 MUTATED         0        0        1        0         0         1
  STX2 WILD-TYPE      10       20       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STX2 MUTATED           0          1          1          2        1         0
  STX2 WILD-TYPE        29         83         61         37       42         4
D228V3, multiclass
            clus
vv           STX2 MUTATED STX2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  STX2 MUTATED       1   0   2   4
  STX2 WILD-TYPE    53 135 259  98
D228V4, multiclass
       clus
vv      STX2 MUTATED STX2 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  STX2 MUTATED     1   2   2   2
  STX2 WILD-TYPE 194 171  87  83
D228V5, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  N0            1            194
  N1            2            171
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V6, binary
                cls
clus               0   1
  STX2 MUTATED     5   1
  STX2 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      5    1
  STX2 WILD-TYPE  477   37
   clus
vv  STX2 MUTATED STX2 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D228V7, binary
                cls
clus               0   1
  STX2 MUTATED     2   5
  STX2 WILD-TYPE 170 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      2    5
  STX2 WILD-TYPE  170  401
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  FEMALE            2            170
  MALE              5            401
[1] 2 2
[1] FALSE
D228V8, binary
                cls
clus               0   1
  STX2 MUTATED     6   1
  STX2 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      6    1
  STX2 WILD-TYPE  410  101
     clus
vv    STX2 MUTATED STX2 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D228V9, continuous
D228V10, continuous
[1] "Remove cluster labels:" "STX2 MUTATED"          
clus
  STX2 MUTATED STX2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" "STX2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"STX2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  STX2 MUTATED       4                         0
  STX2 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STX2 MUTATED                                           0     3
  STX2 WILD-TYPE                                         1   354
D228V11, multiclass
                                           clus
vv                                          STX2 MUTATED STX2 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V12, binary
                cls
clus               0   1
  STX2 MUTATED     0   5
  STX2 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      0    5
  STX2 WILD-TYPE   10  393
                        clus
vv                       STX2 MUTATED STX2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(229) Variable = ABCA6 MUTATION ANALYSIS
D229V1, survival
                 sevent
clus2               0   1
  ABCA6 MUTATED     9  11
  ABCA6 WILD-TYPE 329 205
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             20             534 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             11             205 
$`ABCA6 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IG-A4QS TCGA-R6-A6L4 TCGA-R6-A6L6 
       19.99        25.78         7.69         3.88        16.31         7.04 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7704 
       18.31        28.11         6.97        34.68        18.05        35.24 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4465 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 
        1.12        31.96         9.01         5.92        11.08        77.29 
TCGA-RD-A7BW TCGA-VQ-A8P2 
        5.13        38.14 

$`ABCA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ABCA6 MUTATED ABCA6 WILD-TYPE 
           1.12            0.00 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
          77.29          122.30 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
          17.18           13.53 
[1] "1.1 - 77.3 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D229V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA6 MUTATED         0        0        1        2         3         3
  ABCA6 WILD-TYPE      10       20       45       29        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCA6 MUTATED           1          4          1          1        3         1
  ABCA6 WILD-TYPE        28         80         61         38       40         3
D229V3, multiclass
            clus
vv           ABCA6 MUTATED ABCA6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCA6 MUTATED       3   2  10   5
  ABCA6 WILD-TYPE    51 133 251  97
D229V4, multiclass
       clus
vv      ABCA6 MUTATED ABCA6 WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3               10             251
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCA6 MUTATED     7  10   2   2
  ABCA6 WILD-TYPE 188 163  87  83
D229V5, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  N0             7             188
  N1            10             163
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V6, binary
                 cls
clus                0   1
  ABCA6 MUTATED    15   4
  ABCA6 WILD-TYPE 467  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED     15    4
  ABCA6 WILD-TYPE  467   34
   clus
vv  ABCA6 MUTATED ABCA6 WILD-TYPE
  0            15             467
  1             4              34
[1] 2 2
[1] FALSE
D229V7, binary
                 cls
clus                0   1
  ABCA6 MUTATED     8  15
  ABCA6 WILD-TYPE 164 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      8   15
  ABCA6 WILD-TYPE  164  391
        clus
vv       ABCA6 MUTATED ABCA6 WILD-TYPE
  FEMALE             8             164
  MALE              15             391
[1] 2 2
[1] FALSE
D229V8, binary
                 cls
clus                0   1
  ABCA6 MUTATED    15   5
  ABCA6 WILD-TYPE 401  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED     15    5
  ABCA6 WILD-TYPE  401   97
     clus
vv    ABCA6 MUTATED ABCA6 WILD-TYPE
  NO             15             401
  YES             5              97
[1] 2 2
[1] FALSE
D229V9, continuous
[1] "Remove cluster labels:" "ABCA6 MUTATED"         
clus
  ABCA6 MUTATED ABCA6 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCA6 WILD-TYPE" "ABCA6 WILD-TYPE" 
D229V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA6 MUTATED       1                         1
  ABCA6 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA6 MUTATED                                           0    17
  ABCA6 WILD-TYPE                                         1   340
D229V11, multiclass
                                           clus
vv                                          ABCA6 MUTATED ABCA6 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V12, binary
                 cls
clus                0   1
  ABCA6 MUTATED     0  16
  ABCA6 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      0   16
  ABCA6 WILD-TYPE   10  382
                        clus
vv                       ABCA6 MUTATED ABCA6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(230) Variable = PIAS1 MUTATION ANALYSIS
D230V1, survival
                 sevent
clus2               0   1
  PIAS1 MUTATED     9   4
  PIAS1 WILD-TYPE 329 212
  PIAS1 MUTATED PIAS1 WILD-TYPE 
             13             541 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              4             212 
$`PIAS1 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GI TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-L5-A4OH TCGA-BR-4184 
       19.99        14.30        20.78        18.64        32.61         6.97 
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8487 TCGA-CG-5721 
       34.68        31.10        14.79        25.05         1.12         6.02 
TCGA-CG-5723 
      105.07 

$`PIAS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        0.85         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PIAS1 MUTATED PIAS1 WILD-TYPE 
           1.12            0.00 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
         105.07          122.30 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
          19.99           13.48 
[1] "1.1 - 105.1 (20.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D230V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIAS1 MUTATED         2        0        0        1         2         1
  PIAS1 WILD-TYPE       8       20       46       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIAS1 MUTATED           1          3          0          3        1         0
  PIAS1 WILD-TYPE        28         81         62         36       42         4
D230V3, multiclass
            clus
vv           PIAS1 MUTATED PIAS1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PIAS1 MUTATED       2   2   5   5
  PIAS1 WILD-TYPE    52 133 256  97
D230V4, multiclass
       clus
vv      PIAS1 MUTATED PIAS1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PIAS1 MUTATED     4   7   1   2
  PIAS1 WILD-TYPE 191 166  88  83
D230V5, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  N0             4             191
  N1             7             166
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V6, binary
                 cls
clus                0   1
  PIAS1 MUTATED    11   0
  PIAS1 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED     11    0
  PIAS1 WILD-TYPE  471   38
   clus
vv  PIAS1 MUTATED PIAS1 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D230V7, binary
                 cls
clus                0   1
  PIAS1 MUTATED     5   9
  PIAS1 WILD-TYPE 167 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      5    9
  PIAS1 WILD-TYPE  167  397
        clus
vv       PIAS1 MUTATED PIAS1 WILD-TYPE
  FEMALE             5             167
  MALE               9             397
[1] 2 2
[1] FALSE
D230V8, binary
                 cls
clus                0   1
  PIAS1 MUTATED    13   1
  PIAS1 WILD-TYPE 403 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED     13    1
  PIAS1 WILD-TYPE  403  101
     clus
vv    PIAS1 MUTATED PIAS1 WILD-TYPE
  NO             13             403
  YES             1             101
[1] 2 2
[1] FALSE
D230V9, continuous
[1] "Remove cluster labels:" "PIAS1 MUTATED"         
clus
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YB 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" "PIAS1 WILD-TYPE" 
D230V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PIAS1 MUTATED       0                         1
  PIAS1 WILD-TYPE   133                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIAS1 MUTATED                                           0    10
  PIAS1 WILD-TYPE                                         1   347
D230V11, multiclass
                                           clus
vv                                          PIAS1 MUTATED PIAS1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V12, binary
                 cls
clus                0   1
  PIAS1 MUTATED     0   9
  PIAS1 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      0    9
  PIAS1 WILD-TYPE   10  389
                        clus
vv                       PIAS1 MUTATED PIAS1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(231) Variable = USP26 MUTATION ANALYSIS
D231V1, survival
                 sevent
clus2               0   1
  USP26 MUTATED    15   9
  USP26 WILD-TYPE 323 207
  USP26 MUTATED USP26 WILD-TYPE 
             24             530 
  USP26 MUTATED USP26 WILD-TYPE 
              9             207 
$`USP26 MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OX TCGA-L5-A8NF TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 
       24.00         7.43         2.66         6.97         9.34         9.67 
TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-8591 
       34.68        18.05        44.94        35.84        33.63        28.14 
TCGA-BR-8680 TCGA-BR-A4J5 TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-6520 TCGA-EQ-8122 
       31.96        28.34        11.77        65.10        18.84         7.99 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       30.51        22.68        29.98        19.73        19.04        38.14 

$`USP26 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         4.08         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        36.16        35.24        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  USP26 MUTATED USP26 WILD-TYPE 
           2.66            0.00 
  USP26 MUTATED USP26 WILD-TYPE 
           65.1           122.3 
  USP26 MUTATED USP26 WILD-TYPE 
          23.34           13.41 
[1] "2.7 - 65.1 (23.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D231V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP26 MUTATED         0        0        3        0         4         3
  USP26 WILD-TYPE      10       20       43       31        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP26 MUTATED           0          7          1          2        1         1
  USP26 WILD-TYPE        29         77         61         37       42         3
D231V3, multiclass
            clus
vv           USP26 MUTATED USP26 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             7              77
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP26 MUTATED       1   6  10   5
  USP26 WILD-TYPE    53 129 251  97
D231V4, multiclass
       clus
vv      USP26 MUTATED USP26 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3               10             251
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP26 MUTATED     7  10   4   2
  USP26 WILD-TYPE 188 163  85  83
D231V5, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  N0             7             188
  N1            10             163
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V6, binary
                 cls
clus                0   1
  USP26 MUTATED    20   2
  USP26 WILD-TYPE 462  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     20    2
  USP26 WILD-TYPE  462   36
   clus
vv  USP26 MUTATED USP26 WILD-TYPE
  0            20             462
  1             2              36
[1] 2 2
[1] FALSE
D231V7, binary
                 cls
clus                0   1
  USP26 MUTATED    11  14
  USP26 WILD-TYPE 161 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     11   14
  USP26 WILD-TYPE  161  392
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  FEMALE            11             161
  MALE              14             392
[1] 2 2
[1] FALSE
D231V8, binary
                 cls
clus                0   1
  USP26 MUTATED    20   3
  USP26 WILD-TYPE 396  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     20    3
  USP26 WILD-TYPE  396   99
     clus
vv    USP26 MUTATED USP26 WILD-TYPE
  NO             20             396
  YES             3              99
[1] 2 2
[1] FALSE
D231V9, continuous
D231V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP26 MUTATED       5                         0
  USP26 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP26 MUTATED                                           0    18
  USP26 WILD-TYPE                                         1   339
D231V11, multiclass
                                           clus
vv                                          USP26 MUTATED USP26 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V12, binary
                 cls
clus                0   1
  USP26 MUTATED     0  19
  USP26 WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED      0   19
  USP26 WILD-TYPE   10  379
                        clus
vv                       USP26 MUTATED USP26 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(232) Variable = MLH1 MUTATION ANALYSIS
D232V1, survival
                sevent
clus2              0   1
  MLH1 MUTATED     7   2
  MLH1 WILD-TYPE 331 214
  MLH1 MUTATED MLH1 WILD-TYPE 
             9            545 
  MLH1 MUTATED MLH1 WILD-TYPE 
             2            214 
$`MLH1 MUTATED`
TCGA-IC-A6RF TCGA-VR-A8EZ TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-6802 TCGA-CG-5723 
       15.68        18.18        19.56        30.90        30.90       105.07 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-R5-A7ZI 
       14.47        11.08        74.53 

$`MLH1 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MLH1 MUTATED MLH1 WILD-TYPE 
         11.08           0.00 
  MLH1 MUTATED MLH1 WILD-TYPE 
        105.07         122.30 
  MLH1 MUTATED MLH1 WILD-TYPE 
         19.56          13.48 
[1] "11.1 - 105.1 (19.6)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "3.1"
D232V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLH1 MUTATED         0        1        1        1         1         0
  MLH1 WILD-TYPE      10       19       45       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLH1 MUTATED           0          1          0          2        1         0
  MLH1 WILD-TYPE        29         83         62         37       42         4
D232V3, multiclass
            clus
vv           MLH1 MUTATED MLH1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MLH1 MUTATED       1   3   3   2
  MLH1 WILD-TYPE    53 132 258 100
D232V4, multiclass
       clus
vv      MLH1 MUTATED MLH1 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MLH1 MUTATED     3   2   1   2
  MLH1 WILD-TYPE 192 171  88  83
D232V5, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  N0            3            192
  N1            2            171
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V6, binary
                cls
clus               0   1
  MLH1 MUTATED     9   1
  MLH1 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      9    1
  MLH1 WILD-TYPE  473   37
   clus
vv  MLH1 MUTATED MLH1 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D232V7, binary
                cls
clus               0   1
  MLH1 MUTATED     4   6
  MLH1 WILD-TYPE 168 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      4    6
  MLH1 WILD-TYPE  168  400
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE            4            168
  MALE              6            400
[1] 2 2
[1] FALSE
D232V8, binary
                cls
clus               0   1
  MLH1 MUTATED     8   1
  MLH1 WILD-TYPE 408 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      8    1
  MLH1 WILD-TYPE  408  101
     clus
vv    MLH1 MUTATED MLH1 WILD-TYPE
  NO             8            408
  YES            1            101
[1] 2 2
[1] FALSE
D232V9, continuous
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
D232V10, continuous
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             96 
    TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE     TCGA-L5-A4OG 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8Q7 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLH1 MUTATED       0                         1
  MLH1 WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLH1 MUTATED                                           0     8
  MLH1 WILD-TYPE                                         1   349
D232V11, multiclass
                                           clus
vv                                          MLH1 MUTATED MLH1 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V12, binary
                cls
clus               0   1
  MLH1 MUTATED     1   7
  MLH1 WILD-TYPE   9 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      1    7
  MLH1 WILD-TYPE    9  391
                        clus
vv                       MLH1 MUTATED MLH1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(233) Variable = SLC22A6 MUTATION ANALYSIS
D233V1, survival
                   sevent
clus2                 0   1
  SLC22A6 MUTATED     9   6
  SLC22A6 WILD-TYPE 329 210
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               15               539 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                6               210 
$`SLC22A6 MUTATED`
TCGA-IG-A51D TCGA-XP-A8T7 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-8363 
       17.03        41.23         9.34        34.68        13.68         0.26 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-A6EY 
       12.43         6.58        15.95         9.01        28.96        11.44 
TCGA-HF-A5NB TCGA-HU-A4GH TCGA-SW-A7EA 
       30.51        11.77        19.04 

$`SLC22A6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
             0.26              0.00 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
            41.23            122.30 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
            13.68             13.55 
[1] "0.3 - 41.2 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D233V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC22A6 MUTATED         0        2        2        2         4         1
  SLC22A6 WILD-TYPE      10       18       44       29        80        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A6 MUTATED           0          1          1          1        1
  SLC22A6 WILD-TYPE        29         83         61         38       42
                   vv
clus                STAGE IVA
  SLC22A6 MUTATED           0
  SLC22A6 WILD-TYPE         4
D233V3, multiclass
            clus
vv           SLC22A6 MUTATED SLC22A6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                18
  STAGE IB                 2                44
  STAGE II                 2                29
  STAGE IIA                4                80
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC22A6 MUTATED       3   4   5   3
  SLC22A6 WILD-TYPE    51 131 256  99
D233V4, multiclass
       clus
vv      SLC22A6 MUTATED SLC22A6 WILD-TYPE
  T0+T1               3                51
  T2                  4               131
  T3                  5               256
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC22A6 MUTATED    10   3   0   3
  SLC22A6 WILD-TYPE 185 170  89  82
D233V5, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  N0              10               185
  N1               3               170
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V6, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED    15   1
  SLC22A6 WILD-TYPE 467  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED     15    1
  SLC22A6 WILD-TYPE  467   37
   clus
vv  SLC22A6 MUTATED SLC22A6 WILD-TYPE
  0              15               467
  1               1                37
[1] 2 2
[1] FALSE
D233V7, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     8   8
  SLC22A6 WILD-TYPE 164 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      8    8
  SLC22A6 WILD-TYPE  164  398
        clus
vv       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  FEMALE               8               164
  MALE                 8               398
[1] 2 2
[1] FALSE
D233V8, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED    12   1
  SLC22A6 WILD-TYPE 404 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED     12    1
  SLC22A6 WILD-TYPE  404  101
     clus
vv    SLC22A6 MUTATED SLC22A6 WILD-TYPE
  NO               12               404
  YES               1               101
[1] 2 2
[1] FALSE
D233V9, continuous
[1] "Remove cluster labels:" "SLC22A6 MUTATED"       
clus
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A5S3        TCGA-IG-A7DP 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T8 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
D233V10, continuous
[1] "Remove cluster labels:" "SLC22A6 MUTATED"       
clus
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T8 
"SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" "SLC22A6 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SLC22A6 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC22A6 MUTATED       3                         0
  SLC22A6 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC22A6 MUTATED                                           0     9
  SLC22A6 WILD-TYPE                                         1   348
D233V11, multiclass
                                           clus
vv                                          SLC22A6 MUTATED SLC22A6 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V12, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     1  11
  SLC22A6 WILD-TYPE   9 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      1   11
  SLC22A6 WILD-TYPE    9  387
                        clus
vv                       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(234) Variable = EPHA2 MUTATION ANALYSIS
D234V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    22   9
  EPHA2 WILD-TYPE 316 207
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             31             523 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              9             207 
$`EPHA2 MUTATED`
TCGA-2H-A9GN TCGA-IG-A6QS TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A8NM TCGA-LN-A7HY 
        8.94         9.96        29.00        25.12         7.76        12.03 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 
       30.90        34.68        15.95        29.59         1.12        28.14 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-8576 TCGA-F1-A448 TCGA-FP-A4BE 
        6.58         6.02        28.96        14.66        21.27        11.08 
TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       77.29        24.20        11.77        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-AB1X TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.58        20.25        14.07        13.51        19.73        74.53 
TCGA-VQ-A8P2 
       38.14 

$`EPHA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
        4.90         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        6.61        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP 
       22.68         3.25        22.75        25.81        21.37         8.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
            0.1             0.0 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          77.29          122.30 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          15.95           13.48 
[1] "0.1 - 77.3 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D234V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA2 MUTATED         1        3        1        1        10         4
  EPHA2 WILD-TYPE       9       17       45       30        74        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA2 MUTATED           2          3          2          3        2         0
  EPHA2 WILD-TYPE        27         81         60         36       41         4
D234V3, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               3              17
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA             10              74
  STAGE IIB              4              79
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPHA2 MUTATED       5   6  14   8
  EPHA2 WILD-TYPE    49 129 247  94
D234V4, multiclass
       clus
vv      EPHA2 MUTATED EPHA2 WILD-TYPE
  T0+T1             5              49
  T2                6             129
  T3               14             247
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPHA2 MUTATED    13  13   3   3
  EPHA2 WILD-TYPE 182 160  86  82
D234V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0            13             182
  N1            13             160
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED    30   1
  EPHA2 WILD-TYPE 452  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     30    1
  EPHA2 WILD-TYPE  452   37
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0            30             452
  1             1              37
[1] 2 2
[1] FALSE
D234V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED    13  20
  EPHA2 WILD-TYPE 159 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     13   20
  EPHA2 WILD-TYPE  159  386
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE            13             159
  MALE              20             386
[1] 2 2
[1] FALSE
D234V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED    26   5
  EPHA2 WILD-TYPE 390  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     26    5
  EPHA2 WILD-TYPE  390   97
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO             26             390
  YES             5              97
[1] 2 2
[1] FALSE
D234V9, continuous
[1] "Remove cluster labels:" "EPHA2 MUTATED"         
clus
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
D234V10, continuous
[1] "Remove cluster labels:" "EPHA2 MUTATED"         
clus
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" "EPHA2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHA2 MUTATED      10                         2
  EPHA2 WILD-TYPE   123                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHA2 MUTATED                                           0    17
  EPHA2 WILD-TYPE                                         1   340
D234V11, multiclass
                                           clus
vv                                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V12, binary
                 cls
clus                0   1
  EPHA2 MUTATED     2  23
  EPHA2 WILD-TYPE   8 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      2   23
  EPHA2 WILD-TYPE    8  375
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            23             375
[1] 2 2
[1] FALSE

Clustering(235) Variable = DAO MUTATION ANALYSIS
D235V1, survival
               sevent
clus2             0   1
  DAO MUTATED     8   4
  DAO WILD-TYPE 330 212
  DAO MUTATED DAO WILD-TYPE 
           12           542 
  DAO MUTATED DAO WILD-TYPE 
            4           212 
$`DAO MUTATED`
TCGA-CG-4460 TCGA-JY-A93D TCGA-BR-6563 TCGA-BR-6706 TCGA-BR-8382 TCGA-BR-8680 
       21.99        31.56        39.12        18.05        25.05        31.96 
TCGA-BR-A4PE TCGA-CG-4466 TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-HU-A4H6 
       20.42        18.97        21.27        24.20        20.25        21.17 

$`DAO WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        25.61        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DAO MUTATED DAO WILD-TYPE 
        18.05          0.00 
  DAO MUTATED DAO WILD-TYPE 
        39.12        122.30 
  DAO MUTATED DAO WILD-TYPE 
        21.63         13.41 
[1] "18.1 - 39.1 (21.6)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.7"
D235V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DAO MUTATED         1        1        3        0         0         2
  DAO WILD-TYPE       9       19       43       31        84        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAO MUTATED           0          2          1          3        2         0
  DAO WILD-TYPE        29         82         61         36       41         4
D235V3, multiclass
            clus
vv           DAO MUTATED DAO WILD-TYPE
  STAGE I              1             9
  STAGE IA             1            19
  STAGE IB             3            43
  STAGE II             0            31
  STAGE IIA            0            84
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           3            36
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  DAO MUTATED       2   4   4   5
  DAO WILD-TYPE    52 131 257  97
D235V4, multiclass
       clus
vv      DAO MUTATED DAO WILD-TYPE
  T0+T1           2            52
  T2              4           131
  T3              4           257
  T4              5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DAO MUTATED     5   4   3   3
  DAO WILD-TYPE 190 169  86  82
D235V5, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  N0           5           190
  N1           4           169
  N2           3            86
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V6, binary
               cls
clus              0   1
  DAO MUTATED    12   2
  DAO WILD-TYPE 470  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED     12    2
  DAO WILD-TYPE  470   36
   clus
vv  DAO MUTATED DAO WILD-TYPE
  0          12           470
  1           2            36
[1] 2 2
[1] FALSE
D235V7, binary
               cls
clus              0   1
  DAO MUTATED     7   8
  DAO WILD-TYPE 165 398
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      7    8
  DAO WILD-TYPE  165  398
        clus
vv       DAO MUTATED DAO WILD-TYPE
  FEMALE           7           165
  MALE             8           398
[1] 2 2
[1] FALSE
D235V8, binary
               cls
clus              0   1
  DAO MUTATED    12   2
  DAO WILD-TYPE 404 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED     12    2
  DAO WILD-TYPE  404  100
     clus
vv    DAO MUTATED DAO WILD-TYPE
  NO           12           404
  YES           2           100
[1] 2 2
[1] FALSE
D235V9, continuous
D235V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DAO MUTATED       4                         1
  DAO WILD-TYPE   129                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DAO MUTATED                                           0     7
  DAO WILD-TYPE                                         1   350
D235V11, multiclass
                                           clus
vv                                          DAO MUTATED DAO WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V12, binary
               cls
clus              0   1
  DAO MUTATED     1  10
  DAO WILD-TYPE   9 388
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      1   10
  DAO WILD-TYPE    9  388
                        clus
vv                       DAO MUTATED DAO WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          10           388
[1] 2 2
[1] FALSE

Clustering(236) Variable = CD79A MUTATION ANALYSIS
D236V1, survival
                 sevent
clus2               0   1
  CD79A MUTATED     7   2
  CD79A WILD-TYPE 331 214
  CD79A MUTATED CD79A WILD-TYPE 
              9             545 
  CD79A MUTATED CD79A WILD-TYPE 
              2             214 
$`CD79A MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 
       19.99        16.47         6.97        34.68        35.84         1.12 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
        1.02         6.02       105.07 

$`CD79A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CD79A MUTATED CD79A WILD-TYPE 
           1.02            0.00 
  CD79A MUTATED CD79A WILD-TYPE 
         105.07          122.30 
  CD79A MUTATED CD79A WILD-TYPE 
          16.47           13.55 
[1] "1.0 - 105.1 (16.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D236V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD79A MUTATED         0        0        1        1         2         0
  CD79A WILD-TYPE      10       20       45       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD79A MUTATED           1          1          0          1        2         0
  CD79A WILD-TYPE        28         83         62         38       41         4
D236V3, multiclass
            clus
vv           CD79A MUTATED CD79A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CD79A MUTATED       0   2   6   1
  CD79A WILD-TYPE    54 133 255 101
D236V4, multiclass
       clus
vv      CD79A MUTATED CD79A WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CD79A MUTATED     3   4   1   1
  CD79A WILD-TYPE 192 169  88  84
D236V5, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  N0             3             192
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V6, binary
                 cls
clus                0   1
  CD79A MUTATED     6   1
  CD79A WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    1
  CD79A WILD-TYPE  476   37
   clus
vv  CD79A MUTATED CD79A WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D236V7, binary
                 cls
clus                0   1
  CD79A MUTATED     3   6
  CD79A WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      3    6
  CD79A WILD-TYPE  169  400
        clus
vv       CD79A MUTATED CD79A WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D236V8, binary
                 cls
clus                0   1
  CD79A MUTATED     8   0
  CD79A WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      8    0
  CD79A WILD-TYPE  408  102
     clus
vv    CD79A MUTATED CD79A WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D236V9, continuous
D236V10, continuous
[1] "Remove cluster labels:" "CD79A MUTATED"         
clus
  CD79A MUTATED CD79A WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" "CD79A WILD-TYPE" 
     TCGA-Z6-AAPN 
"CD79A WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CD79A MUTATED       0                         0
  CD79A WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD79A MUTATED                                           0     6
  CD79A WILD-TYPE                                         1   351
D236V11, multiclass
                                           clus
vv                                          CD79A MUTATED CD79A WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V12, binary
                 cls
clus                0   1
  CD79A MUTATED     0   4
  CD79A WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      0    4
  CD79A WILD-TYPE   10  394
                        clus
vv                       CD79A MUTATED CD79A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(237) Variable = RAD51AP2 MUTATION ANALYSIS
D237V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED    15   4
  RAD51AP2 WILD-TYPE 323 212
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                19                535 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 4                212 
$`RAD51AP2 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NL TCGA-R6-A8WC TCGA-Z6-A8JD TCGA-BR-4201 TCGA-BR-7703 
       19.99        13.22         2.30         3.42        30.90        36.16 
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8487 TCGA-CG-4306 
       35.84        29.59         2.20        31.10         1.12         1.02 
TCGA-CG-5721 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4HD 
        6.02        30.51        26.47        22.32         6.51        33.40 
TCGA-VQ-A8P2 
       38.14 

$`RAD51AP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       29.42         2.66        19.96         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 
        5.52         6.21        77.29        63.06        52.21         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              1.02               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             38.14             122.30 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             22.32              13.51 
[1] "1.0 - 38.1 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D237V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAD51AP2 MUTATED         0        1        2        0         2         4
  RAD51AP2 WILD-TYPE      10       19       44       31        82        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           1          2          0          3        2
  RAD51AP2 WILD-TYPE        28         82         62         36       41
                    vv
clus                 STAGE IVA
  RAD51AP2 MUTATED           0
  RAD51AP2 WILD-TYPE         4
D237V3, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 4                 79
  STAGE III                 1                 28
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  RAD51AP2 MUTATED       1   3   7   7
  RAD51AP2 WILD-TYPE    53 132 254  95
D237V4, multiclass
       clus
vv      RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                   7                254
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  RAD51AP2 MUTATED     9   3   3   2
  RAD51AP2 WILD-TYPE 186 170  86  83
D237V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0                9                186
  N1                3                170
  N2                3                 86
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V6, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    16   1
  RAD51AP2 WILD-TYPE 466  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     16    1
  RAD51AP2 WILD-TYPE  466   37
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               16                466
  1                1                 37
[1] 2 2
[1] FALSE
D237V7, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    11   9
  RAD51AP2 WILD-TYPE 161 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     11    9
  RAD51AP2 WILD-TYPE  161  397
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  FEMALE               11                161
  MALE                  9                397
[1] 2 2
[1] FALSE
D237V8, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    14   2
  RAD51AP2 WILD-TYPE 402 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     14    2
  RAD51AP2 WILD-TYPE  402  100
     clus
vv    RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  NO                14                402
  YES                2                100
[1] 2 2
[1] FALSE
D237V9, continuous
[1] "Remove cluster labels:" "RAD51AP2 MUTATED"      
clus
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-Z6-A8JE 
"RAD51AP2 WILD-TYPE" 
D237V10, continuous
[1] "Remove cluster labels:" "RAD51AP2 MUTATED"      
clus
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-RE-A7BO 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" "RAD51AP2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  RAD51AP2 MUTATED       3                         0
  RAD51AP2 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAD51AP2 MUTATED                                           0    14
  RAD51AP2 WILD-TYPE                                         1   343
D237V11, multiclass
                                           clus
vv                                          RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V12, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     0  14
  RAD51AP2 WILD-TYPE  10 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      0   14
  RAD51AP2 WILD-TYPE   10  384
                        clus
vv                       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               14                384
[1] 2 2
[1] FALSE

Clustering(238) Variable = IPO5 MUTATION ANALYSIS
D238V1, survival
                sevent
clus2              0   1
  IPO5 MUTATED    15   7
  IPO5 WILD-TYPE 323 209
  IPO5 MUTATED IPO5 WILD-TYPE 
            22            532 
  IPO5 MUTATED IPO5 WILD-TYPE 
             7            209 
$`IPO5 MUTATED`
TCGA-L5-A43J TCGA-L5-A891 TCGA-LN-A8HZ TCGA-Z6-A8JE TCGA-BR-4256 TCGA-BR-6452 
        4.31         3.75        12.33         2.10         9.34        34.68 
TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-A4PF 
        0.69        32.25         8.05        26.33         4.31         1.15 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-F1-6874 
       12.76        12.59        12.33        12.39        11.64        14.47 
TCGA-FP-8211 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       13.58         0.10        38.14        18.41 

$`IPO5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 
       14.43        11.44        29.59         9.60         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19        17.52         0.95        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 
       12.39        12.53         7.17        12.30        12.59        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  IPO5 MUTATED IPO5 WILD-TYPE 
           0.1            0.0 
  IPO5 MUTATED IPO5 WILD-TYPE 
         38.14         122.30 
  IPO5 MUTATED IPO5 WILD-TYPE 
        12.330         13.905 
[1] "0.1 - 38.1 (12.3)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D238V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPO5 MUTATED         0        0        2        3         2         3
  IPO5 WILD-TYPE      10       20       44       28        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPO5 MUTATED           0          5          4          2        1         0
  IPO5 WILD-TYPE        29         79         58         37       42         4
D238V3, multiclass
            clus
vv           IPO5 MUTATED IPO5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              3             28
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            5             79
  STAGE IIIB            4             58
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IPO5 MUTATED       0   3  11   9
  IPO5 WILD-TYPE    54 132 250  93
D238V4, multiclass
       clus
vv      IPO5 MUTATED IPO5 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3              11            250
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IPO5 MUTATED    11   7   4   2
  IPO5 WILD-TYPE 184 166  85  83
D238V5, multiclass
    clus
vv   IPO5 MUTATED IPO5 WILD-TYPE
  N0           11            184
  N1            7            166
  N2            4             85
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V6, binary
                cls
clus               0   1
  IPO5 MUTATED    23   0
  IPO5 WILD-TYPE 459  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     23    0
  IPO5 WILD-TYPE  459   38
   clus
vv  IPO5 MUTATED IPO5 WILD-TYPE
  0           23            459
  1            0             38
[1] 2 2
[1] FALSE
D238V7, binary
                cls
clus               0   1
  IPO5 MUTATED    11  14
  IPO5 WILD-TYPE 161 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     11   14
  IPO5 WILD-TYPE  161  392
        clus
vv       IPO5 MUTATED IPO5 WILD-TYPE
  FEMALE           11            161
  MALE             14            392
[1] 2 2
[1] FALSE
D238V8, binary
                cls
clus               0   1
  IPO5 MUTATED    12   7
  IPO5 WILD-TYPE 404  95
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     12    7
  IPO5 WILD-TYPE  404   95
     clus
vv    IPO5 MUTATED IPO5 WILD-TYPE
  NO            12            404
  YES            7             95
[1] 2 2
[1] FALSE
D238V9, continuous
[1] "Remove cluster labels:" "IPO5 MUTATED"          
clus
  IPO5 MUTATED IPO5 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JD 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
D238V10, continuous
[1] "Remove cluster labels:" "IPO5 MUTATED"          
clus
  IPO5 MUTATED IPO5 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8I0 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" "IPO5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IPO5 MUTATED       7                         0
  IPO5 WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IPO5 MUTATED                                           0    18
  IPO5 WILD-TYPE                                         1   339
D238V11, multiclass
                                           clus
vv                                          IPO5 MUTATED IPO5 WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V12, binary
                cls
clus               0   1
  IPO5 MUTATED     0  21
  IPO5 WILD-TYPE  10 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED      0   21
  IPO5 WILD-TYPE   10  377
                        clus
vv                       IPO5 MUTATED IPO5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           21            377
[1] 2 2
[1] FALSE

Clustering(239) Variable = MYEOV MUTATION ANALYSIS
D239V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     6   5
  MYEOV WILD-TYPE 332 211
  MYEOV MUTATED MYEOV WILD-TYPE 
             11             543 
  MYEOV MUTATED MYEOV WILD-TYPE 
              5             211 
$`MYEOV MUTATED`
TCGA-IG-A4QS TCGA-JY-A93D TCGA-L5-A8NQ TCGA-LN-A7HW TCGA-BR-8078 TCGA-BR-8382 
        3.88        31.56        21.37        12.00        29.59        25.05 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG TCGA-HU-A4G9 
       28.14        31.96        12.43         6.58        24.20 

$`MYEOV WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MYEOV MUTATED MYEOV WILD-TYPE 
           3.88            0.00 
  MYEOV MUTATED MYEOV WILD-TYPE 
          31.96          122.30 
  MYEOV MUTATED MYEOV WILD-TYPE 
          24.20           13.51 
[1] "3.9 - 32.0 (24.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D239V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYEOV MUTATED         1        1        0        1         3         1
  MYEOV WILD-TYPE       9       19       46       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYEOV MUTATED           0          0          1          3        1         0
  MYEOV WILD-TYPE        29         84         61         36       42         4
D239V3, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYEOV MUTATED       3   3   3   4
  MYEOV WILD-TYPE    51 132 258  98
D239V4, multiclass
       clus
vv      MYEOV MUTATED MYEOV WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYEOV MUTATED     6   1   2   3
  MYEOV WILD-TYPE 189 172  87  82
D239V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             6             189
  N1             1             172
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V6, binary
                 cls
clus                0   1
  MYEOV MUTATED    11   1
  MYEOV WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED     11    1
  MYEOV WILD-TYPE  471   37
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D239V7, binary
                 cls
clus                0   1
  MYEOV MUTATED     4   9
  MYEOV WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      4    9
  MYEOV WILD-TYPE  168  397
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D239V8, binary
                 cls
clus                0   1
  MYEOV MUTATED    11   1
  MYEOV WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED     11    1
  MYEOV WILD-TYPE  405  101
     clus
vv    MYEOV MUTATED MYEOV WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D239V9, continuous
[1] "Remove cluster labels:" "MYEOV MUTATED"         
clus
  MYEOV MUTATED MYEOV WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
D239V10, continuous
[1] "Remove cluster labels:" "MYEOV MUTATED"         
clus
  MYEOV MUTATED MYEOV WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" "MYEOV WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYEOV MUTATED       5                         1
  MYEOV WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYEOV MUTATED                                           0     7
  MYEOV WILD-TYPE                                         1   350
D239V11, multiclass
                                           clus
vv                                          MYEOV MUTATED MYEOV WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V12, binary
                 cls
clus                0   1
  MYEOV MUTATED     0  11
  MYEOV WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      0   11
  MYEOV WILD-TYPE   10  387
                        clus
vv                       MYEOV MUTATED MYEOV WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(240) Variable = BCKDHA MUTATION ANALYSIS
D240V1, survival
                  sevent
clus2                0   1
  BCKDHA MUTATED     6   5
  BCKDHA WILD-TYPE 332 211
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              11              543 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               5              211 
$`BCKDHA MUTATED`
TCGA-L5-A4OE TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-CD-A487 
       24.00         6.97        30.90        34.68        32.78        12.30 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-A4BE TCGA-HJ-7597 
       21.14         5.92        14.47        11.08        26.47 

$`BCKDHA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BCKDHA MUTATED BCKDHA WILD-TYPE 
            5.92             0.00 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
           34.68           122.30 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
           21.14            13.51 
[1] "5.9 - 34.7 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D240V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCKDHA MUTATED         0        0        3        0         3         2
  BCKDHA WILD-TYPE      10       20       43       31        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCKDHA MUTATED           0          1          1          0        0
  BCKDHA WILD-TYPE        29         83         61         39       43
                  vv
clus               STAGE IVA
  BCKDHA MUTATED           0
  BCKDHA WILD-TYPE         4
D240V3, multiclass
            clus
vv           BCKDHA MUTATED BCKDHA WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  BCKDHA MUTATED       0   4   7   0
  BCKDHA WILD-TYPE    54 131 254 102
D240V4, multiclass
       clus
vv      BCKDHA MUTATED BCKDHA WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 7              254
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BCKDHA MUTATED     6   3   1   0
  BCKDHA WILD-TYPE 189 170  88  85
D240V5, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  N0              6              189
  N1              3              170
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V6, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     8   0
  BCKDHA WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      8    0
  BCKDHA WILD-TYPE  474   38
   clus
vv  BCKDHA MUTATED BCKDHA WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D240V7, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     5   6
  BCKDHA WILD-TYPE 167 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      5    6
  BCKDHA WILD-TYPE  167  400
        clus
vv       BCKDHA MUTATED BCKDHA WILD-TYPE
  FEMALE              5              167
  MALE                6              400
[1] 2 2
[1] FALSE
D240V8, binary
                  cls
clus                 0   1
  BCKDHA MUTATED    10   1
  BCKDHA WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED     10    1
  BCKDHA WILD-TYPE  406  101
     clus
vv    BCKDHA MUTATED BCKDHA WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D240V9, continuous
D240V10, continuous
[1] "Remove cluster labels:" "BCKDHA MUTATED"        
clus
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OG 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-Z6-AAPN 
"BCKDHA WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCKDHA MUTATED       1                         1
  BCKDHA WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCKDHA MUTATED                                           0     9
  BCKDHA WILD-TYPE                                         1   348
D240V11, multiclass
                                           clus
vv                                          BCKDHA MUTATED BCKDHA WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V12, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     0  10
  BCKDHA WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      0   10
  BCKDHA WILD-TYPE   10  388
                        clus
vv                       BCKDHA MUTATED BCKDHA WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(241) Variable = TRAM1L1 MUTATION ANALYSIS
D241V1, survival
                   sevent
clus2                 0   1
  TRAM1L1 MUTATED    10   7
  TRAM1L1 WILD-TYPE 328 209
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               17               537 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                7               209 
$`TRAM1L1 MUTATED`
TCGA-L5-A4OI TCGA-S8-A6BV TCGA-2H-A9GF TCGA-L5-A4OR TCGA-L5-A891 TCGA-RE-A7BO 
       19.99        20.02        25.78         3.16         3.75         7.00 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8284 TCGA-CD-A4MG TCGA-CG-4437 
        9.34        34.68        29.59         8.05         6.58         8.05 
TCGA-D7-6822 TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       12.33         0.10        19.73        74.53        38.14 

$`TRAM1L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
              0.1               0.0 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            74.53            122.30 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            12.33             13.58 
[1] "0.1 - 74.5 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D241V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRAM1L1 MUTATED         1        1        3        1         2         2
  TRAM1L1 WILD-TYPE       9       19       43       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAM1L1 MUTATED           1          3          0          3        2
  TRAM1L1 WILD-TYPE        28         81         62         36       41
                   vv
clus                STAGE IVA
  TRAM1L1 MUTATED           0
  TRAM1L1 WILD-TYPE         4
D241V3, multiclass
            clus
vv           TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TRAM1L1 MUTATED       3   4   7   6
  TRAM1L1 WILD-TYPE    51 131 254  96
D241V4, multiclass
       clus
vv      TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  T0+T1               3                51
  T2                  4               131
  T3                  7               254
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TRAM1L1 MUTATED     7   9   3   2
  TRAM1L1 WILD-TYPE 188 164  86  83
D241V5, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  N0               7               188
  N1               9               164
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V6, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    16   1
  TRAM1L1 WILD-TYPE 466  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     16    1
  TRAM1L1 WILD-TYPE  466   37
   clus
vv  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  0              16               466
  1               1                37
[1] 2 2
[1] FALSE
D241V7, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     8  13
  TRAM1L1 WILD-TYPE 164 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      8   13
  TRAM1L1 WILD-TYPE  164  393
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  FEMALE               8               164
  MALE                13               393
[1] 2 2
[1] FALSE
D241V8, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    17   1
  TRAM1L1 WILD-TYPE 399 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     17    1
  TRAM1L1 WILD-TYPE  399  101
     clus
vv    TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  NO               17               399
  YES               1               101
[1] 2 2
[1] FALSE
D241V9, continuous
D241V10, continuous
[1] "Remove cluster labels:" "TRAM1L1 MUTATED"       
clus
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-V5-A7RB        TCGA-V5-A7RC 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" "TRAM1L1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TRAM1L1 MUTATED       2                         1
  TRAM1L1 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRAM1L1 MUTATED                                           0    15
  TRAM1L1 WILD-TYPE                                         1   342
D241V11, multiclass
                                           clus
vv                                          TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V12, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     1  13
  TRAM1L1 WILD-TYPE   9 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      1   13
  TRAM1L1 WILD-TYPE    9  385
                        clus
vv                       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              13               385
[1] 2 2
[1] FALSE

Clustering(242) Variable = KIAA1704 MUTATION ANALYSIS
D242V1, survival
                    sevent
clus2                  0   1
  KIAA1704 MUTATED     2   4
  KIAA1704 WILD-TYPE 336 212
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 6                548 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 4                212 
$`KIAA1704 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-VR-A8EW TCGA-CD-A4MG TCGA-FP-7735 TCGA-HF-A5NB 
       19.99         7.76         8.12         6.58         3.48        30.51 

$`KIAA1704 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.99        14.47        72.23        21.27        11.38        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
              3.48               0.00 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
             30.51             122.30 
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
              7.94              13.63 
[1] "3.5 - 30.5 (7.9)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D242V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1704 MUTATED         0        0        1        0         1         1
  KIAA1704 WILD-TYPE      10       20       45       31        83        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1704 MUTATED           0          0          1          2        0
  KIAA1704 WILD-TYPE        29         84         61         37       43
                    vv
clus                 STAGE IVA
  KIAA1704 MUTATED           0
  KIAA1704 WILD-TYPE         4
D242V3, multiclass
            clus
vv           KIAA1704 MUTATED KIAA1704 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1704 MUTATED       0   2   3   1
  KIAA1704 WILD-TYPE    54 133 258 101
D242V4, multiclass
       clus
vv      KIAA1704 MUTATED KIAA1704 WILD-TYPE
  T0+T1                0                 54
  T2                   2                133
  T3                   3                258
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1704 MUTATED     2   1   1   2
  KIAA1704 WILD-TYPE 193 172  88  83
D242V5, multiclass
    clus
vv   KIAA1704 MUTATED KIAA1704 WILD-TYPE
  N0                2                193
  N1                1                172
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V6, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     4   0
  KIAA1704 WILD-TYPE 478  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      4    0
  KIAA1704 WILD-TYPE  478   38
   clus
vv  KIAA1704 MUTATED KIAA1704 WILD-TYPE
  0                4                478
  1                0                 38
[1] 2 2
[1] FALSE
D242V7, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     2   4
  KIAA1704 WILD-TYPE 170 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      2    4
  KIAA1704 WILD-TYPE  170  402
        clus
vv       KIAA1704 MUTATED KIAA1704 WILD-TYPE
  FEMALE                2                170
  MALE                  4                402
[1] 2 2
[1] FALSE
D242V8, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     5   1
  KIAA1704 WILD-TYPE 411 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      5    1
  KIAA1704 WILD-TYPE  411  101
     clus
vv    KIAA1704 MUTATED KIAA1704 WILD-TYPE
  NO                 5                411
  YES                1                101
[1] 2 2
[1] FALSE
D242V9, continuous
[1] "Remove cluster labels:" "KIAA1704 MUTATED"      
clus
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1704 WILD-TYPE" 
D242V10, continuous
[1] "Remove cluster labels:" "KIAA1704 MUTATED"      
clus
  KIAA1704 MUTATED KIAA1704 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" "KIAA1704 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1704 MUTATED       2                         1
  KIAA1704 WILD-TYPE   131                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1704 MUTATED                                           0     2
  KIAA1704 WILD-TYPE                                         1   355
D242V11, multiclass
                                           clus
vv                                          KIAA1704 MUTATED KIAA1704 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V12, binary
                    cls
clus                   0   1
  KIAA1704 MUTATED     0   2
  KIAA1704 WILD-TYPE  10 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1704 MUTATED      0    2
  KIAA1704 WILD-TYPE   10  396
                        clus
vv                       KIAA1704 MUTATED KIAA1704 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                2                396
[1] 2 2
[1] FALSE

Clustering(243) Variable = GPC2 MUTATION ANALYSIS
D243V1, survival
                sevent
clus2              0   1
  GPC2 MUTATED     7   2
  GPC2 WILD-TYPE 331 214
  GPC2 MUTATED GPC2 WILD-TYPE 
             9            545 
  GPC2 MUTATED GPC2 WILD-TYPE 
             2            214 
$`GPC2 MUTATED`
TCGA-L5-A43J TCGA-VR-A8EQ TCGA-B7-A5TJ TCGA-BR-8078 TCGA-CG-5723 TCGA-D7-A4YY 
        4.31        22.82        11.01        29.59       105.07        13.78 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 
        6.51         6.58        14.07 

$`GPC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GPC2 MUTATED GPC2 WILD-TYPE 
          4.31           0.00 
  GPC2 MUTATED GPC2 WILD-TYPE 
        105.07         122.30 
  GPC2 MUTATED GPC2 WILD-TYPE 
         13.78          13.55 
[1] "4.3 - 105.1 (13.8)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D243V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPC2 MUTATED         0        0        1        1         1         4
  GPC2 WILD-TYPE      10       20       45       30        83        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPC2 MUTATED           1          0          1          0        0         0
  GPC2 WILD-TYPE        28         84         61         39       43         4
D243V3, multiclass
            clus
vv           GPC2 MUTATED GPC2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GPC2 MUTATED       1   1   5   2
  GPC2 WILD-TYPE    53 134 256 100
D243V4, multiclass
       clus
vv      GPC2 MUTATED GPC2 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GPC2 MUTATED     3   4   0   1
  GPC2 WILD-TYPE 192 169  89  84
D243V5, multiclass
    clus
vv   GPC2 MUTATED GPC2 WILD-TYPE
  N0            3            192
  N1            4            169
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V6, binary
                cls
clus               0   1
  GPC2 MUTATED     8   0
  GPC2 WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      8    0
  GPC2 WILD-TYPE  474   38
   clus
vv  GPC2 MUTATED GPC2 WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D243V7, binary
                cls
clus               0   1
  GPC2 MUTATED     2   7
  GPC2 WILD-TYPE 170 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      2    7
  GPC2 WILD-TYPE  170  399
        clus
vv       GPC2 MUTATED GPC2 WILD-TYPE
  FEMALE            2            170
  MALE              7            399
[1] 2 2
[1] FALSE
D243V8, binary
                cls
clus               0   1
  GPC2 MUTATED     6   2
  GPC2 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      6    2
  GPC2 WILD-TYPE  410  100
     clus
vv    GPC2 MUTATED GPC2 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D243V9, continuous
[1] "Remove cluster labels:" "GPC2 MUTATED"          
clus
  GPC2 MUTATED GPC2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
D243V10, continuous
[1] "Remove cluster labels:" "GPC2 MUTATED"          
clus
  GPC2 MUTATED GPC2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" "GPC2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"GPC2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GPC2 MUTATED       3                         0
  GPC2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPC2 MUTATED                                           0     5
  GPC2 WILD-TYPE                                         1   352
D243V11, multiclass
                                           clus
vv                                          GPC2 MUTATED GPC2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V12, binary
                cls
clus               0   1
  GPC2 MUTATED     0   6
  GPC2 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      0    6
  GPC2 WILD-TYPE   10  392
                        clus
vv                       GPC2 MUTATED GPC2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(244) Variable = FILIP1L MUTATION ANALYSIS
D244V1, survival
                   sevent
clus2                 0   1
  FILIP1L MUTATED    12   8
  FILIP1L WILD-TYPE 326 208
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               20               534 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
                8               208 
$`FILIP1L MUTATED`
TCGA-L5-A4OE TCGA-CG-4460 TCGA-LN-A5U5 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 
       24.00        21.99         4.47        34.68        29.59         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J1 
       31.10         0.26        31.27        28.14        31.96         0.72 
TCGA-CG-4305 TCGA-D7-6525 TCGA-D7-6820 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-MX-A5UJ 
       15.95        13.35        11.31         0.10        20.25        19.73 
TCGA-SW-A7EA TCGA-VQ-AA6K 
       19.04        12.43 

$`FILIP1L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        2.20         7.40        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        27.55        17.26 

  FILIP1L MUTATED FILIP1L WILD-TYPE 
              0.1               0.0 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
            34.68            122.30 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
           19.385            13.510 
[1] "0.1 - 34.7 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D244V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FILIP1L MUTATED         0        0        3        1         2         2
  FILIP1L WILD-TYPE      10       20       43       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FILIP1L MUTATED           0          4          1          6        3
  FILIP1L WILD-TYPE        29         80         61         33       40
                   vv
clus                STAGE IVA
  FILIP1L MUTATED           0
  FILIP1L WILD-TYPE         4
D244V3, multiclass
            clus
vv           FILIP1L MUTATED FILIP1L WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               6                33
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FILIP1L MUTATED       1   6   5  11
  FILIP1L WILD-TYPE    53 129 256  91
D244V4, multiclass
       clus
vv      FILIP1L MUTATED FILIP1L WILD-TYPE
  T0+T1               1                53
  T2                  6               129
  T3                  5               256
  T4                 11                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FILIP1L MUTATED     7   5   7   3
  FILIP1L WILD-TYPE 188 168  82  82
D244V5, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  N0               7               188
  N1               5               168
  N2               7                82
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V6, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    19   3
  FILIP1L WILD-TYPE 463  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     19    3
  FILIP1L WILD-TYPE  463   35
   clus
vv  FILIP1L MUTATED FILIP1L WILD-TYPE
  0              19               463
  1               3                35
[1] 2 2
[1] FALSE
D244V7, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    10  13
  FILIP1L WILD-TYPE 162 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     10   13
  FILIP1L WILD-TYPE  162  393
        clus
vv       FILIP1L MUTATED FILIP1L WILD-TYPE
  FEMALE              10               162
  MALE                13               393
[1] 2 2
[1] FALSE
D244V8, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    18   1
  FILIP1L WILD-TYPE 398 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     18    1
  FILIP1L WILD-TYPE  398  101
     clus
vv    FILIP1L MUTATED FILIP1L WILD-TYPE
  NO               18               398
  YES               1               101
[1] 2 2
[1] FALSE
D244V9, continuous
[1] "Remove cluster labels:" "FILIP1L MUTATED"       
clus
  FILIP1L MUTATED FILIP1L WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
D244V10, continuous
[1] "Remove cluster labels:" "FILIP1L MUTATED"       
clus
  FILIP1L MUTATED FILIP1L WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OG 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" "FILIP1L WILD-TYPE" 
       TCGA-Z6-AAPN 
"FILIP1L WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FILIP1L MUTATED       5                         0
  FILIP1L WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FILIP1L MUTATED                                           0    15
  FILIP1L WILD-TYPE                                         1   342
D244V11, multiclass
                                           clus
vv                                          FILIP1L MUTATED FILIP1L WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V12, binary
                   cls
clus                  0   1
  FILIP1L MUTATED     0  18
  FILIP1L WILD-TYPE  10 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED      0   18
  FILIP1L WILD-TYPE   10  380
                        clus
vv                       FILIP1L MUTATED FILIP1L WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(245) Variable = GPSM3 MUTATION ANALYSIS
D245V1, survival
                 sevent
clus2               0   1
  GPSM3 MUTATED     7   3
  GPSM3 WILD-TYPE 331 213
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             10             544 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
              3             213 
$`GPSM3 MUTATED`
TCGA-BR-4201 TCGA-BR-7704 TCGA-BR-7707 TCGA-CD-A4MG TCGA-CG-4306 TCGA-HU-A4G9 
       30.90        35.24        35.84         6.58         1.02        24.20 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 
       11.77         8.98         6.58        23.84 

$`GPSM3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 
       31.20        44.94        21.90         9.21        36.16        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GPSM3 MUTATED GPSM3 WILD-TYPE 
           1.02            0.00 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
          35.84          122.30 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
         17.805          13.565 
[1] "1.0 - 35.8 (17.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D245V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPSM3 MUTATED         0        2        1        1         2         3
  GPSM3 WILD-TYPE      10       18       45       30        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPSM3 MUTATED           0          1          0          0        1         0
  GPSM3 WILD-TYPE        29         83         62         39       42         4
D245V3, multiclass
            clus
vv           GPSM3 MUTATED GPSM3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GPSM3 MUTATED       2   4   4   2
  GPSM3 WILD-TYPE    52 131 257 100
D245V4, multiclass
       clus
vv      GPSM3 MUTATED GPSM3 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GPSM3 MUTATED     7   2   2   0
  GPSM3 WILD-TYPE 188 171  87  85
D245V5, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  N0             7             188
  N1             2             171
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V6, binary
                 cls
clus                0   1
  GPSM3 MUTATED    11   1
  GPSM3 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED     11    1
  GPSM3 WILD-TYPE  471   37
   clus
vv  GPSM3 MUTATED GPSM3 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D245V7, binary
                 cls
clus                0   1
  GPSM3 MUTATED     7   5
  GPSM3 WILD-TYPE 165 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      7    5
  GPSM3 WILD-TYPE  165  401
        clus
vv       GPSM3 MUTATED GPSM3 WILD-TYPE
  FEMALE             7             165
  MALE               5             401
[1] 2 2
[1] FALSE
D245V8, binary
                 cls
clus                0   1
  GPSM3 MUTATED    10   0
  GPSM3 WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED     10    0
  GPSM3 WILD-TYPE  406  102
     clus
vv    GPSM3 MUTATED GPSM3 WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D245V9, continuous
D245V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPSM3 MUTATED       6                         0
  GPSM3 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPSM3 MUTATED                                           0     5
  GPSM3 WILD-TYPE                                         1   352
D245V11, multiclass
                                           clus
vv                                          GPSM3 MUTATED GPSM3 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V12, binary
                 cls
clus                0   1
  GPSM3 MUTATED     0  11
  GPSM3 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      0   11
  GPSM3 WILD-TYPE   10  387
                        clus
vv                       GPSM3 MUTATED GPSM3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(246) Variable = FAM82A1 MUTATION ANALYSIS
D246V1, survival
                   sevent
clus2                 0   1
  FAM82A1 MUTATED     2   4
  FAM82A1 WILD-TYPE 336 212
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                6               548 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                4               212 
$`FAM82A1 MUTATED`
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-F1-A448 
       12.92        13.48         1.02         6.02        28.96        21.27 

$`FAM82A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50         2.66        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
             1.02              0.00 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
            28.96            122.30 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
            13.20             13.63 
[1] "1.0 - 29.0 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D246V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM82A1 MUTATED         0        1        0        0         0         0
  FAM82A1 WILD-TYPE      10       19       46       31        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM82A1 MUTATED           1          0          1          0        3
  FAM82A1 WILD-TYPE        28         84         61         39       40
                   vv
clus                STAGE IVA
  FAM82A1 MUTATED           0
  FAM82A1 WILD-TYPE         4
D246V3, multiclass
            clus
vv           FAM82A1 MUTATED FAM82A1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM82A1 MUTATED       2   0   3   1
  FAM82A1 WILD-TYPE    52 135 258 101
D246V4, multiclass
       clus
vv      FAM82A1 MUTATED FAM82A1 WILD-TYPE
  T0+T1               2                52
  T2                  0               135
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM82A1 MUTATED     2   3   1   1
  FAM82A1 WILD-TYPE 193 170  88  84
D246V5, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V6, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     5   2
  FAM82A1 WILD-TYPE 477  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      5    2
  FAM82A1 WILD-TYPE  477   36
   clus
vv  FAM82A1 MUTATED FAM82A1 WILD-TYPE
  0               5               477
  1               2                36
[1] 2 2
[1] FALSE
D246V7, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   6
  FAM82A1 WILD-TYPE 171 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    6
  FAM82A1 WILD-TYPE  171  400
        clus
vv       FAM82A1 MUTATED FAM82A1 WILD-TYPE
  FEMALE               1               171
  MALE                 6               400
[1] 2 2
[1] FALSE
D246V8, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     2   1
  FAM82A1 WILD-TYPE 414 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      2    1
  FAM82A1 WILD-TYPE  414  101
     clus
vv    FAM82A1 MUTATED FAM82A1 WILD-TYPE
  NO                2               414
  YES               1               101
[1] 2 2
[1] FALSE
D246V9, continuous
D246V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM82A1 MUTATED       0                         0
  FAM82A1 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM82A1 MUTATED                                           0     4
  FAM82A1 WILD-TYPE                                         1   353
D246V11, multiclass
                                           clus
vv                                          FAM82A1 MUTATED FAM82A1 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V12, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   1
  FAM82A1 WILD-TYPE   9 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    1
  FAM82A1 WILD-TYPE    9  397
                        clus
vv                       FAM82A1 MUTATED FAM82A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               1               397
[1] 2 2
[1] FALSE

Clustering(247) Variable = KNTC1 MUTATION ANALYSIS
D247V1, survival
                 sevent
clus2               0   1
  KNTC1 MUTATED    14  10
  KNTC1 WILD-TYPE 324 206
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             24             530 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             10             206 
$`KNTC1 MUTATED`
TCGA-L5-A43J TCGA-LN-A7HV TCGA-LN-A9FR TCGA-R6-A6XQ TCGA-VR-A8EQ TCGA-Z6-A8JD 
        4.31        10.52        12.26         6.35        22.82         3.42 
TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-8059 
       26.70        18.35        30.90         9.34         9.67        14.43 
TCGA-BR-8361 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4436 TCGA-CG-5721 
       31.10        31.96         6.58        12.62         7.99         6.02 
TCGA-CG-5723 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HU-8602 TCGA-HU-A4H3 TCGA-VQ-AA6G 
      105.07         0.56         6.21        22.32        29.00        26.04 

$`KNTC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4255 
        6.61         6.97         4.64         7.43         4.08         4.08 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58        11.08         5.52 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KNTC1 MUTATED KNTC1 WILD-TYPE 
           0.56            0.00 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
         105.07          122.30 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
          12.44           13.63 
[1] "0.6 - 105.1 (12.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D247V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KNTC1 MUTATED         0        0        3        1         3         5
  KNTC1 WILD-TYPE      10       20       43       30        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KNTC1 MUTATED           2          1          0          2        2         0
  KNTC1 WILD-TYPE        27         83         62         37       41         4
D247V3, multiclass
            clus
vv           KNTC1 MUTATED KNTC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KNTC1 MUTATED       1   7   6   7
  KNTC1 WILD-TYPE    53 128 255  95
D247V4, multiclass
       clus
vv      KNTC1 MUTATED KNTC1 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3                6             255
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KNTC1 MUTATED    10   9   3   1
  KNTC1 WILD-TYPE 185 164  86  84
D247V5, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  N0            10             185
  N1             9             164
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V6, binary
                 cls
clus                0   1
  KNTC1 MUTATED    22   1
  KNTC1 WILD-TYPE 460  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     22    1
  KNTC1 WILD-TYPE  460   37
   clus
vv  KNTC1 MUTATED KNTC1 WILD-TYPE
  0            22             460
  1             1              37
[1] 2 2
[1] FALSE
D247V7, binary
                 cls
clus                0   1
  KNTC1 MUTATED     7  19
  KNTC1 WILD-TYPE 165 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED      7   19
  KNTC1 WILD-TYPE  165  387
        clus
vv       KNTC1 MUTATED KNTC1 WILD-TYPE
  FEMALE             7             165
  MALE              19             387
[1] 2 2
[1] FALSE
D247V8, binary
                 cls
clus                0   1
  KNTC1 MUTATED    17   4
  KNTC1 WILD-TYPE 399  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     17    4
  KNTC1 WILD-TYPE  399   98
     clus
vv    KNTC1 MUTATED KNTC1 WILD-TYPE
  NO             17             399
  YES             4              98
[1] 2 2
[1] FALSE
D247V9, continuous
D247V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KNTC1 MUTATED       7                         0
  KNTC1 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KNTC1 MUTATED                                           0    15
  KNTC1 WILD-TYPE                                         1   342
D247V11, multiclass
                                           clus
vv                                          KNTC1 MUTATED KNTC1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V12, binary
                 cls
clus                0   1
  KNTC1 MUTATED     0  19
  KNTC1 WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED      0   19
  KNTC1 WILD-TYPE   10  379
                        clus
vv                       KNTC1 MUTATED KNTC1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(248) Variable = ERBB4 MUTATION ANALYSIS
D248V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    39  25
  ERBB4 WILD-TYPE 299 191
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             64             490 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             25             191 
$`ERBB4 MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-IC-A6RE 
       34.85        18.28         4.31        24.00        19.99         7.69 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A8NM 
        3.16        30.25        32.61         3.32         4.90         7.76 
TCGA-L7-A6VZ TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-B7-5816 
       10.36         8.02        16.31        38.40        53.95        26.70 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-7197 
        9.34         9.67         6.61        34.68        25.61         9.21 
TCGA-BR-7703 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8295 TCGA-BR-8361 
       36.16         3.45        29.56        14.43         2.20        31.10 
TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8680 
        0.26         3.32        31.27         9.21         9.34        31.96 
TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8536 TCGA-CD-A48A 
       13.51        13.18        12.39        12.76        12.43        12.43 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-6820 
        6.58         1.02         7.99         7.07         6.02        11.31 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-6874 TCGA-HF-7134 TCGA-HU-A4GT TCGA-HU-A4H8 
        5.92        14.76        14.47        52.21         6.51        14.07 
TCGA-IN-8462 TCGA-MX-A5UJ TCGA-R5-A805 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.81        19.73         9.24        37.41        38.14        37.22 
TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-AA68 
       17.85         1.71        42.64        43.66 

$`ERBB4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         8.94         4.70        22.82         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
       35.97        27.12         5.16        20.02        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
       33.11         7.82         7.59         5.06         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
       30.90         4.08         4.08         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 
       40.21        30.90        31.20        44.94        21.90        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        9.07        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.96         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31        14.04        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.35        11.21        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         6.08         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T 
       22.19         1.87        15.65        20.81        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ERBB4 MUTATED ERBB4 WILD-TYPE 
           0.26            0.00 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
          53.95          122.30 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
          12.97           13.73 
[1] "0.3 - 54.0 (13.0)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D248V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB4 MUTATED         2        2        5        4         4        11
  ERBB4 WILD-TYPE       8       18       41       27        80        72
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB4 MUTATED           2          7          7          8        6         0
  ERBB4 WILD-TYPE        27         77         55         31       37         4
D248V3, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I                2               8
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               4              27
  STAGE IIA              4              80
  STAGE IIB             11              72
  STAGE III              2              27
  STAGE IIIA             7              77
  STAGE IIIB             7              55
  STAGE IIIC             8              31
  STAGE IV               6              37
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ERBB4 MUTATED       7   9  30  13
  ERBB4 WILD-TYPE    47 126 231  89
D248V4, multiclass
       clus
vv      ERBB4 MUTATED ERBB4 WILD-TYPE
  T0+T1             7              47
  T2                9             126
  T3               30             231
  T4               13              89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB4 MUTATED    21  18   9  11
  ERBB4 WILD-TYPE 174 155  80  74
D248V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            21             174
  N1            18             155
  N2             9              80
  N3            11              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V6, binary
                 cls
clus                0   1
  ERBB4 MUTATED    52   4
  ERBB4 WILD-TYPE 430  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     52    4
  ERBB4 WILD-TYPE  430   34
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            52             430
  1             4              34
[1] 2 2
[1] FALSE
D248V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    19  47
  ERBB4 WILD-TYPE 153 359
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     19   47
  ERBB4 WILD-TYPE  153  359
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            19             153
  MALE              47             359
[1] 2 2
[1] FALSE
D248V8, binary
                 cls
clus                0   1
  ERBB4 MUTATED    51   8
  ERBB4 WILD-TYPE 365  94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     51    8
  ERBB4 WILD-TYPE  365   94
     clus
vv    ERBB4 MUTATED ERBB4 WILD-TYPE
  NO             51             365
  YES             8              94
[1] 2 2
[1] FALSE
D248V9, continuous
D248V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB4 MUTATED      10                         0
  ERBB4 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB4 MUTATED                                           0    50
  ERBB4 WILD-TYPE                                         1   307
D248V11, multiclass
                                           clus
vv                                          ERBB4 MUTATED ERBB4 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                50             307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V12, binary
                 cls
clus                0   1
  ERBB4 MUTATED     0  43
  ERBB4 WILD-TYPE  10 355
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED      0   43
  ERBB4 WILD-TYPE   10  355
                        clus
vv                       ERBB4 MUTATED ERBB4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            43             355
[1] 2 2
[1] FALSE

Clustering(249) Variable = NCAPH MUTATION ANALYSIS
D249V1, survival
                 sevent
clus2               0   1
  NCAPH MUTATED     7   3
  NCAPH WILD-TYPE 331 213
  NCAPH MUTATED NCAPH WILD-TYPE 
             10             544 
  NCAPH MUTATED NCAPH WILD-TYPE 
              3             213 
$`NCAPH MUTATED`
TCGA-LN-A9FR TCGA-BR-4184 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5730 
       12.26         6.97         6.02       105.07        28.96         4.01 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-VQ-A8P2 
       11.08        30.51         0.10        38.14 

$`NCAPH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 
        0.99         0.99        12.03        15.02        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NCAPH MUTATED NCAPH WILD-TYPE 
            0.1             0.0 
  NCAPH MUTATED NCAPH WILD-TYPE 
         105.07          122.30 
  NCAPH MUTATED NCAPH WILD-TYPE 
          11.67           13.63 
[1] "0.1 - 105.1 (11.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D249V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAPH MUTATED         0        1        0        1         1         1
  NCAPH WILD-TYPE      10       19       46       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCAPH MUTATED           0          3          0          3        2         0
  NCAPH WILD-TYPE        29         81         62         36       41         4
D249V3, multiclass
            clus
vv           NCAPH MUTATED NCAPH WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NCAPH MUTATED       1   3   2   6
  NCAPH WILD-TYPE    53 132 259  96
D249V4, multiclass
       clus
vv      NCAPH MUTATED NCAPH WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                2             259
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NCAPH MUTATED     3   6   1   2
  NCAPH WILD-TYPE 192 167  88  83
D249V5, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  N0             3             192
  N1             6             167
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V6, binary
                 cls
clus                0   1
  NCAPH MUTATED    11   1
  NCAPH WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED     11    1
  NCAPH WILD-TYPE  471   37
   clus
vv  NCAPH MUTATED NCAPH WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D249V7, binary
                 cls
clus                0   1
  NCAPH MUTATED     4   9
  NCAPH WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      4    9
  NCAPH WILD-TYPE  168  397
        clus
vv       NCAPH MUTATED NCAPH WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D249V8, binary
                 cls
clus                0   1
  NCAPH MUTATED     4   4
  NCAPH WILD-TYPE 412  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      4    4
  NCAPH WILD-TYPE  412   98
     clus
vv    NCAPH MUTATED NCAPH WILD-TYPE
  NO              4             412
  YES             4              98
[1] 2 2
[1] FALSE
D249V9, continuous
D249V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NCAPH MUTATED       2                         1
  NCAPH WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCAPH MUTATED                                           0     4
  NCAPH WILD-TYPE                                         1   353
D249V11, multiclass
                                           clus
vv                                          NCAPH MUTATED NCAPH WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V12, binary
                 cls
clus                0   1
  NCAPH MUTATED     0   6
  NCAPH WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      0    6
  NCAPH WILD-TYPE   10  392
                        clus
vv                       NCAPH MUTATED NCAPH WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(250) Variable = ERBB2 MUTATION ANALYSIS
D250V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    19  10
  ERBB2 WILD-TYPE 319 206
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             29             525 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             10             206 
$`ERBB2 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-2H-A9GH TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A8NM 
       34.85        19.99        31.27        29.00         2.60         7.76 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-BR-4201 
        7.59         5.06         2.89         2.30        12.69        30.90 
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8588 
       32.78        30.90        44.94         7.36         1.12        12.79 
TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-8570 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4H0 
        7.07         4.01        24.72        11.44        77.29         2.10 
TCGA-HU-A4H8 TCGA-IN-8663 TCGA-MX-A5UJ TCGA-VQ-A8DT TCGA-VQ-A8P2 
       14.07         3.39        19.73        48.79        38.14 

$`ERBB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         7.82         8.02        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       38.40         6.35        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
       14.04         3.32        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        3.72         5.39        25.18         9.21        20.22        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           1.12            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          77.29          122.30 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          12.79           13.58 
[1] "1.1 - 77.3 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D250V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB2 MUTATED         0        0        1        1         4         6
  ERBB2 WILD-TYPE      10       20       45       30        80        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED           1          3          3          2        2         0
  ERBB2 WILD-TYPE        28         81         59         37       41         4
D250V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ERBB2 MUTATED       2   5  14   3
  ERBB2 WILD-TYPE    52 130 247  99
D250V4, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3               14             247
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB2 MUTATED     6   8   3   6
  ERBB2 WILD-TYPE 189 165  86  79
D250V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             6             189
  N1             8             165
  N2             3              86
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    22   1
  ERBB2 WILD-TYPE 460  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     22    1
  ERBB2 WILD-TYPE  460   37
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            22             460
  1             1              37
[1] 2 2
[1] FALSE
D250V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED    11  19
  ERBB2 WILD-TYPE 161 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     11   19
  ERBB2 WILD-TYPE  161  387
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE            11             161
  MALE              19             387
[1] 2 2
[1] FALSE
D250V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    22   3
  ERBB2 WILD-TYPE 394  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     22    3
  ERBB2 WILD-TYPE  394   99
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO             22             394
  YES             3              99
[1] 2 2
[1] FALSE
D250V9, continuous
D250V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB2 MUTATED       2                         0
  ERBB2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB2 MUTATED                                           0    23
  ERBB2 WILD-TYPE                                         1   334
D250V11, multiclass
                                           clus
vv                                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V12, binary
                 cls
clus                0   1
  ERBB2 MUTATED     1  18
  ERBB2 WILD-TYPE   9 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      1   18
  ERBB2 WILD-TYPE    9  380
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(251) Variable = ART1 MUTATION ANALYSIS
D251V1, survival
                sevent
clus2              0   1
  ART1 MUTATED     7   1
  ART1 WILD-TYPE 331 215
  ART1 MUTATED ART1 WILD-TYPE 
             8            546 
  ART1 MUTATED ART1 WILD-TYPE 
             1            215 
$`ART1 MUTATED`
TCGA-L5-A4OG TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-CD-5800 
        4.70         6.61        34.68        30.90        29.59        13.15 
TCGA-F1-6874 TCGA-HU-A4H8 
       14.47        14.07 

$`ART1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ART1 MUTATED ART1 WILD-TYPE 
           4.7            0.0 
  ART1 MUTATED ART1 WILD-TYPE 
         34.68         122.30 
  ART1 MUTATED ART1 WILD-TYPE 
         14.27          13.53 
[1] "4.7 - 34.7 (14.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D251V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ART1 MUTATED         1        0        3        1         1         1
  ART1 WILD-TYPE       9       20       43       30        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ART1 MUTATED           1          1          0          0        0         0
  ART1 WILD-TYPE        28         83         62         39       43         4
D251V3, multiclass
            clus
vv           ART1 MUTATED ART1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ART1 MUTATED       2   3   3   1
  ART1 WILD-TYPE    52 132 258 101
D251V4, multiclass
       clus
vv      ART1 MUTATED ART1 WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ART1 MUTATED     6   2   1   0
  ART1 WILD-TYPE 189 171  88  85
D251V5, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  N0            6            189
  N1            2            171
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V6, binary
                cls
clus               0   1
  ART1 MUTATED     9   0
  ART1 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      9    0
  ART1 WILD-TYPE  473   38
   clus
vv  ART1 MUTATED ART1 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D251V7, binary
                cls
clus               0   1
  ART1 MUTATED     5   4
  ART1 WILD-TYPE 167 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      5    4
  ART1 WILD-TYPE  167  402
        clus
vv       ART1 MUTATED ART1 WILD-TYPE
  FEMALE            5            167
  MALE              4            402
[1] 2 2
[1] FALSE
D251V8, binary
                cls
clus               0   1
  ART1 MUTATED     8   0
  ART1 WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      8    0
  ART1 WILD-TYPE  408  102
     clus
vv    ART1 MUTATED ART1 WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D251V9, continuous
D251V10, continuous
[1] "Remove cluster labels:" "ART1 MUTATED"          
clus
  ART1 MUTATED ART1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" "ART1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"ART1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ART1 MUTATED       2                         0
  ART1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ART1 MUTATED                                           0     6
  ART1 WILD-TYPE                                         1   351
D251V11, multiclass
                                           clus
vv                                          ART1 MUTATED ART1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V12, binary
                cls
clus               0   1
  ART1 MUTATED     0   7
  ART1 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      0    7
  ART1 WILD-TYPE   10  391
                        clus
vv                       ART1 MUTATED ART1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(252) Variable = RALGAPB MUTATION ANALYSIS
D252V1, survival
                   sevent
clus2                 0   1
  RALGAPB MUTATED    13   7
  RALGAPB WILD-TYPE 325 209
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               20               534 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
                7               209 
$`RALGAPB MUTATED`
TCGA-L5-A8NM TCGA-LN-A49X TCGA-RE-A7BO TCGA-VR-A8EX TCGA-XP-A8T8 TCGA-BR-4184 
        7.76        12.62         7.00        28.11        14.37         6.97 
TCGA-BR-4256 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J8 
        9.34        32.25         1.12        31.96        10.68        13.51 
TCGA-CG-5733 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT 
       21.07        14.27        13.78        24.20         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 
       20.25        29.00 

$`RALGAPB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD 
       14.17         0.53        28.34         0.66        32.52        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RALGAPB MUTATED RALGAPB WILD-TYPE 
              0.1               0.0 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
            32.25            122.30 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
           13.645            13.565 
[1] "0.1 - 32.2 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D252V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RALGAPB MUTATED         0        1        0        0         3         4
  RALGAPB WILD-TYPE      10       19       46       31        81        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RALGAPB MUTATED           0          3          3          3        1
  RALGAPB WILD-TYPE        29         81         59         36       42
                   vv
clus                STAGE IVA
  RALGAPB MUTATED           1
  RALGAPB WILD-TYPE         3
D252V3, multiclass
            clus
vv           RALGAPB MUTATED RALGAPB WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               3                59
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  RALGAPB MUTATED       5   3   8   5
  RALGAPB WILD-TYPE    49 132 253  97
D252V4, multiclass
       clus
vv      RALGAPB MUTATED RALGAPB WILD-TYPE
  T0+T1               5                49
  T2                  3               132
  T3                  8               253
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  RALGAPB MUTATED     5   6   4   5
  RALGAPB WILD-TYPE 190 167  85  80
D252V5, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  N0               5               190
  N1               6               167
  N2               4                85
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V6, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    18   2
  RALGAPB WILD-TYPE 464  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     18    2
  RALGAPB WILD-TYPE  464   36
   clus
vv  RALGAPB MUTATED RALGAPB WILD-TYPE
  0              18               464
  1               2                36
[1] 2 2
[1] FALSE
D252V7, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    12  10
  RALGAPB WILD-TYPE 160 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     12   10
  RALGAPB WILD-TYPE  160  396
        clus
vv       RALGAPB MUTATED RALGAPB WILD-TYPE
  FEMALE              12               160
  MALE                10               396
[1] 2 2
[1] FALSE
D252V8, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    16   3
  RALGAPB WILD-TYPE 400  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     16    3
  RALGAPB WILD-TYPE  400   99
     clus
vv    RALGAPB MUTATED RALGAPB WILD-TYPE
  NO               16               400
  YES               3                99
[1] 2 2
[1] FALSE
D252V9, continuous
D252V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RALGAPB MUTATED       7                         1
  RALGAPB WILD-TYPE   126                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RALGAPB MUTATED                                           0    12
  RALGAPB WILD-TYPE                                         1   345
D252V11, multiclass
                                           clus
vv                                          RALGAPB MUTATED RALGAPB WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V12, binary
                   cls
clus                  0   1
  RALGAPB MUTATED     1  18
  RALGAPB WILD-TYPE   9 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED      1   18
  RALGAPB WILD-TYPE    9  380
                        clus
vv                       RALGAPB MUTATED RALGAPB WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(253) Variable = CDC14A MUTATION ANALYSIS
D253V1, survival
                  sevent
clus2                0   1
  CDC14A MUTATED     9   5
  CDC14A WILD-TYPE 329 211
  CDC14A MUTATED CDC14A WILD-TYPE 
              14              540 
  CDC14A MUTATED CDC14A WILD-TYPE 
               5              211 
$`CDC14A MUTATED`
TCGA-L5-A4OI TCGA-R6-A6KZ TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 
       19.99         5.06        35.84        29.59         4.31         1.12 
TCGA-BR-A4QL TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-5577 TCGA-HF-7132 
       16.14         9.01         7.07         6.02        25.71        77.29 
TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.58        38.14 

$`CDC14A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CDC14A MUTATED CDC14A WILD-TYPE 
            1.12             0.00 
  CDC14A MUTATED CDC14A WILD-TYPE 
           77.29           122.30 
  CDC14A MUTATED CDC14A WILD-TYPE 
          12.575           13.565 
[1] "1.1 - 77.3 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D253V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC14A MUTATED         1        0        2        1         1         2
  CDC14A WILD-TYPE       9       20       44       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC14A MUTATED           0          3          1          1        3
  CDC14A WILD-TYPE        29         81         61         38       40
                  vv
clus               STAGE IVA
  CDC14A MUTATED           0
  CDC14A WILD-TYPE         4
D253V3, multiclass
            clus
vv           CDC14A MUTATED CDC14A WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CDC14A MUTATED       1   4   5   5
  CDC14A WILD-TYPE    53 131 256  97
D253V4, multiclass
       clus
vv      CDC14A MUTATED CDC14A WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDC14A MUTATED     5   5   0   5
  CDC14A WILD-TYPE 190 168  89  80
D253V5, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  N0              5              190
  N1              5              168
  N2              0               89
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V6, binary
                  cls
clus                 0   1
  CDC14A MUTATED    13   1
  CDC14A WILD-TYPE 469  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED     13    1
  CDC14A WILD-TYPE  469   37
   clus
vv  CDC14A MUTATED CDC14A WILD-TYPE
  0             13              469
  1              1               37
[1] 2 2
[1] FALSE
D253V7, binary
                  cls
clus                 0   1
  CDC14A MUTATED     9   8
  CDC14A WILD-TYPE 163 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      9    8
  CDC14A WILD-TYPE  163  398
        clus
vv       CDC14A MUTATED CDC14A WILD-TYPE
  FEMALE              9              163
  MALE                8              398
[1] 2 2
[1] FALSE
D253V8, binary
                  cls
clus                 0   1
  CDC14A MUTATED    11   2
  CDC14A WILD-TYPE 405 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED     11    2
  CDC14A WILD-TYPE  405  100
     clus
vv    CDC14A MUTATED CDC14A WILD-TYPE
  NO              11              405
  YES              2              100
[1] 2 2
[1] FALSE
D253V9, continuous
D253V10, continuous
[1] "Remove cluster labels:" "CDC14A MUTATED"        
clus
  CDC14A MUTATED CDC14A WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" "CDC14A WILD-TYPE" 
      TCGA-Z6-AAPN 
"CDC14A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDC14A MUTATED       1                         1
  CDC14A WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC14A MUTATED                                           0    11
  CDC14A WILD-TYPE                                         1   346
D253V11, multiclass
                                           clus
vv                                          CDC14A MUTATED CDC14A WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V12, binary
                  cls
clus                 0   1
  CDC14A MUTATED     0  11
  CDC14A WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      0   11
  CDC14A WILD-TYPE   10  387
                        clus
vv                       CDC14A MUTATED CDC14A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(254) Variable = RIF1 MUTATION ANALYSIS
D254V1, survival
                sevent
clus2              0   1
  RIF1 MUTATED    16   5
  RIF1 WILD-TYPE 322 211
  RIF1 MUTATED RIF1 WILD-TYPE 
            21            533 
  RIF1 MUTATED RIF1 WILD-TYPE 
             5            211 
$`RIF1 MUTATED`
TCGA-2H-A9GM TCGA-XP-A8T8 TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7707 
       13.94        14.37        26.70         9.34        34.68        35.84 
TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8536 
       29.59         4.31        31.96        16.14        12.30        12.43 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-6527 TCGA-HF-7132 TCGA-HU-A4GC TCGA-HU-A4GT 
        6.02        28.96        10.26        77.29         3.25         6.51 
TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-AA6J 
       29.00        38.14        27.55 

$`RIF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        17.26 

  RIF1 MUTATED RIF1 WILD-TYPE 
          3.25           0.00 
  RIF1 MUTATED RIF1 WILD-TYPE 
         77.29         122.30 
  RIF1 MUTATED RIF1 WILD-TYPE 
         16.14          13.51 
[1] "3.2 - 77.3 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D254V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RIF1 MUTATED         0        1        3        3         2         5
  RIF1 WILD-TYPE      10       19       43       28        82        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIF1 MUTATED           0          1          3          1        3         0
  RIF1 WILD-TYPE        29         83         59         38       40         4
D254V3, multiclass
            clus
vv           RIF1 MUTATED RIF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              3             28
  STAGE IIA             2             82
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            3             59
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RIF1 MUTATED       3   5   5  10
  RIF1 WILD-TYPE    51 130 256  92
D254V4, multiclass
       clus
vv      RIF1 MUTATED RIF1 WILD-TYPE
  T0+T1            3             51
  T2               5            130
  T3               5            256
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RIF1 MUTATED    11   8   3   2
  RIF1 WILD-TYPE 184 165  86  83
D254V5, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  N0           11            184
  N1            8            165
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V6, binary
                cls
clus               0   1
  RIF1 MUTATED    23   2
  RIF1 WILD-TYPE 459  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     23    2
  RIF1 WILD-TYPE  459   36
   clus
vv  RIF1 MUTATED RIF1 WILD-TYPE
  0           23            459
  1            2             36
[1] 2 2
[1] FALSE
D254V7, binary
                cls
clus               0   1
  RIF1 MUTATED    11  15
  RIF1 WILD-TYPE 161 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     11   15
  RIF1 WILD-TYPE  161  391
        clus
vv       RIF1 MUTATED RIF1 WILD-TYPE
  FEMALE           11            161
  MALE             15            391
[1] 2 2
[1] FALSE
D254V8, binary
                cls
clus               0   1
  RIF1 MUTATED    15   5
  RIF1 WILD-TYPE 401  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     15    5
  RIF1 WILD-TYPE  401   97
     clus
vv    RIF1 MUTATED RIF1 WILD-TYPE
  NO            15            401
  YES            5             97
[1] 2 2
[1] FALSE
D254V9, continuous
[1] "Remove cluster labels:" "RIF1 MUTATED"          
clus
  RIF1 MUTATED RIF1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
D254V10, continuous
[1] "Remove cluster labels:" "RIF1 MUTATED"          
clus
  RIF1 MUTATED RIF1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7 
"RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" "RIF1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"RIF1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RIF1 MUTATED       6                         2
  RIF1 WILD-TYPE   127                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RIF1 MUTATED                                           0    13
  RIF1 WILD-TYPE                                         1   344
D254V11, multiclass
                                           clus
vv                                          RIF1 MUTATED RIF1 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V12, binary
                cls
clus               0   1
  RIF1 MUTATED     1  18
  RIF1 WILD-TYPE   9 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED      1   18
  RIF1 WILD-TYPE    9  380
                        clus
vv                       RIF1 MUTATED RIF1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(255) Variable = STK38 MUTATION ANALYSIS
D255V1, survival
                 sevent
clus2               0   1
  STK38 MUTATED     7   0
  STK38 WILD-TYPE 331 216
  STK38 MUTATED STK38 WILD-TYPE 
              7             547 
  STK38 MUTATED STK38 WILD-TYPE 
              0             216 
$`STK38 MUTATED`
TCGA-L5-A43C TCGA-VR-AA4G TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-CG-5721 
        3.16        18.05        34.68        36.16        31.10         6.02 
TCGA-HU-A4GT 
        6.51 

$`STK38 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  STK38 MUTATED STK38 WILD-TYPE 
           3.16            0.00 
  STK38 MUTATED STK38 WILD-TYPE 
          36.16          122.30 
  STK38 MUTATED STK38 WILD-TYPE 
          18.05           13.55 
[1] "3.2 - 36.2 (18.1)"  "0.0 - 122.3 (13.6)"
[1] "hr="     "9100000"
D255V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK38 MUTATED         0        1        1        0         2         0
  STK38 WILD-TYPE      10       19       45       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK38 MUTATED           0          1          0          1        1         0
  STK38 WILD-TYPE        29         83         62         38       42         4
D255V3, multiclass
            clus
vv           STK38 MUTATED STK38 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  STK38 MUTATED       1   2   2   2
  STK38 WILD-TYPE    53 133 259 100
D255V4, multiclass
       clus
vv      STK38 MUTATED STK38 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK38 MUTATED     4   1   2   0
  STK38 WILD-TYPE 191 172  87  85
D255V5, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  N0             4             191
  N1             1             172
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V6, binary
                 cls
clus                0   1
  STK38 MUTATED     7   0
  STK38 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      7    0
  STK38 WILD-TYPE  475   38
   clus
vv  STK38 MUTATED STK38 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D255V7, binary
                 cls
clus                0   1
  STK38 MUTATED     4   4
  STK38 WILD-TYPE 168 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      4    4
  STK38 WILD-TYPE  168  402
        clus
vv       STK38 MUTATED STK38 WILD-TYPE
  FEMALE             4             168
  MALE               4             402
[1] 2 2
[1] FALSE
D255V8, binary
                 cls
clus                0   1
  STK38 MUTATED     7   0
  STK38 WILD-TYPE 409 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      7    0
  STK38 WILD-TYPE  409  102
     clus
vv    STK38 MUTATED STK38 WILD-TYPE
  NO              7             409
  YES             0             102
[1] 2 2
[1] FALSE
D255V9, continuous
[1] "Remove cluster labels:" "STK38 MUTATED"         
clus
  STK38 MUTATED STK38 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
D255V10, continuous
[1] "Remove cluster labels:" "STK38 MUTATED"         
clus
  STK38 MUTATED STK38 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" "STK38 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STK38 MUTATED       1                         0
  STK38 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STK38 MUTATED                                           0     5
  STK38 WILD-TYPE                                         1   352
D255V11, multiclass
                                           clus
vv                                          STK38 MUTATED STK38 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V12, binary
                 cls
clus                0   1
  STK38 MUTATED     0   4
  STK38 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      0    4
  STK38 WILD-TYPE   10  394
                        clus
vv                       STK38 MUTATED STK38 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(256) Variable = PAPD4 MUTATION ANALYSIS
D256V1, survival
                 sevent
clus2               0   1
  PAPD4 MUTATED     9   3
  PAPD4 WILD-TYPE 329 213
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             12             542 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              3             213 
$`PAPD4 MUTATED`
TCGA-V5-AASV TCGA-Z6-AAPN TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5725 
       15.35         2.66        31.27        31.96        15.95        15.02 
TCGA-CG-5726 TCGA-D7-A6EV TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H3 
       28.96        11.24        22.68         0.10        20.25        29.00 

$`PAPD4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PAPD4 MUTATED PAPD4 WILD-TYPE 
            0.1             0.0 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
          31.96          122.30 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
         18.100          13.495 
[1] "0.1 - 32.0 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D256V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAPD4 MUTATED         0        1        1        1         1         4
  PAPD4 WILD-TYPE      10       19       45       30        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAPD4 MUTATED           0          0          0          4        1         0
  PAPD4 WILD-TYPE        29         84         62         35       42         4
D256V3, multiclass
            clus
vv           PAPD4 MUTATED PAPD4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             4              35
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PAPD4 MUTATED       1   3   3   6
  PAPD4 WILD-TYPE    53 132 258  96
D256V4, multiclass
       clus
vv      PAPD4 MUTATED PAPD4 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PAPD4 MUTATED     5   2   4   2
  PAPD4 WILD-TYPE 190 171  85  83
D256V5, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  N0             5             190
  N1             2             171
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V6, binary
                 cls
clus                0   1
  PAPD4 MUTATED    11   1
  PAPD4 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED     11    1
  PAPD4 WILD-TYPE  471   37
   clus
vv  PAPD4 MUTATED PAPD4 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D256V7, binary
                 cls
clus                0   1
  PAPD4 MUTATED     4   9
  PAPD4 WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      4    9
  PAPD4 WILD-TYPE  168  397
        clus
vv       PAPD4 MUTATED PAPD4 WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D256V8, binary
                 cls
clus                0   1
  PAPD4 MUTATED    10   1
  PAPD4 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED     10    1
  PAPD4 WILD-TYPE  406  101
     clus
vv    PAPD4 MUTATED PAPD4 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D256V9, continuous
[1] "Remove cluster labels:" "PAPD4 MUTATED"         
clus
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
D256V10, continuous
[1] "Remove cluster labels:" "PAPD4 MUTATED"         
clus
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" "PAPD4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PAPD4 MUTATED       5                         1
  PAPD4 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAPD4 MUTATED                                           0     4
  PAPD4 WILD-TYPE                                         1   353
D256V11, multiclass
                                           clus
vv                                          PAPD4 MUTATED PAPD4 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V12, binary
                 cls
clus                0   1
  PAPD4 MUTATED     0  10
  PAPD4 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      0   10
  PAPD4 WILD-TYPE   10  388
                        clus
vv                       PAPD4 MUTATED PAPD4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(257) Variable = ABCB4 MUTATION ANALYSIS
D257V1, survival
                 sevent
clus2               0   1
  ABCB4 MUTATED    14  13
  ABCB4 WILD-TYPE 324 203
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             27             527 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             13             203 
$`ABCB4 MUTATED`
TCGA-L5-A43J TCGA-CG-5727 TCGA-2H-A9GK TCGA-L5-A8NM TCGA-R6-A8WG TCGA-BR-4184 
        4.31        79.07         7.63         7.76        12.69         6.97 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4QL 
       44.94        36.16        31.10        27.12        31.96        16.14 
TCGA-CD-8527 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4469 
        7.17        11.61         6.58        11.77        15.95         7.07 
TCGA-CG-5728 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-F1-6874 TCGA-FP-A4BE TCGA-HF-7132 
       65.10        13.78        11.44        14.47        11.08        77.29 
TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-VQ-A8PQ 
       20.25        23.84        15.65 

$`ABCB4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO 
        5.16        20.02        47.05        21.99        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       30.90        31.20        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.76        12.59        12.53        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.43         6.31        12.30        11.31        12.43        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           4.31            0.00 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          79.07          122.30 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          14.47           13.51 
[1] "4.3 - 79.1 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D257V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCB4 MUTATED         0        1        2        4         3         5
  ABCB4 WILD-TYPE      10       19       44       27        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCB4 MUTATED           1          2          4          2        4         0
  ABCB4 WILD-TYPE        28         82         58         37       39         4
D257V3, multiclass
            clus
vv           ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               4              27
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             4              58
  STAGE IIIC             2              37
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCB4 MUTATED       1   7  14   7
  ABCB4 WILD-TYPE    53 128 247  95
D257V4, multiclass
       clus
vv      ABCB4 MUTATED ABCB4 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3               14             247
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCB4 MUTATED     9  10   5   4
  ABCB4 WILD-TYPE 186 163  84  81
D257V5, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  N0             9             186
  N1            10             163
  N2             5              84
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V6, binary
                 cls
clus                0   1
  ABCB4 MUTATED    24   2
  ABCB4 WILD-TYPE 458  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     24    2
  ABCB4 WILD-TYPE  458   36
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0            24             458
  1             2              36
[1] 2 2
[1] FALSE
D257V7, binary
                 cls
clus                0   1
  ABCB4 MUTATED    13  17
  ABCB4 WILD-TYPE 159 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     13   17
  ABCB4 WILD-TYPE  159  389
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  FEMALE            13             159
  MALE              17             389
[1] 2 2
[1] FALSE
D257V8, binary
                 cls
clus                0   1
  ABCB4 MUTATED    22   3
  ABCB4 WILD-TYPE 394  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     22    3
  ABCB4 WILD-TYPE  394   99
     clus
vv    ABCB4 MUTATED ABCB4 WILD-TYPE
  NO             22             394
  YES             3              99
[1] 2 2
[1] FALSE
D257V9, continuous
D257V10, continuous
[1] "Remove cluster labels:" "ABCB4 MUTATED"         
clus
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ABCB4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCB4 MUTATED       7                         1
  ABCB4 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCB4 MUTATED                                           0    16
  ABCB4 WILD-TYPE                                         1   341
D257V11, multiclass
                                           clus
vv                                          ABCB4 MUTATED ABCB4 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V12, binary
                 cls
clus                0   1
  ABCB4 MUTATED     1  20
  ABCB4 WILD-TYPE   9 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      1   20
  ABCB4 WILD-TYPE    9  378
                        clus
vv                       ABCB4 MUTATED ABCB4 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(258) Variable = DIDO1 MUTATION ANALYSIS
D258V1, survival
                 sevent
clus2               0   1
  DIDO1 MUTATED    30  16
  DIDO1 WILD-TYPE 308 200
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             46             508 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             16             200 
$`DIDO1 MUTATED`
TCGA-L5-A43J TCGA-IG-A3Y9 TCGA-IG-A97H TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NF 
        4.31         0.85        14.50        15.48         3.75         2.66 
TCGA-L5-A8NK TCGA-LN-A7HY TCGA-LN-A9FQ TCGA-R6-A6Y0 TCGA-V5-AASW TCGA-ZR-A9CJ 
       13.55        12.03        12.85        53.95         9.27        19.73 
TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-7703 TCGA-BR-8077 
       19.56         6.61        30.90         9.67        36.16         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4CS 
       29.59        32.25         6.18         1.12        31.96         1.48 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8533 TCGA-CD-A4MG TCGA-CD-A4MJ 
       21.44        16.14        13.18        15.39         6.58        12.62 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6F2 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HU-8602 
        6.02       105.07        15.65        11.08         5.52        22.32 
TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IP-7968 
       24.20         0.10         6.51        20.25        29.00         2.53 
TCGA-MX-A5UJ TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       19.73        13.25        38.14        17.85 

$`DIDO1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.02        55.50        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.66        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       37.25        14.43        11.44         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         8.98         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DIDO1 MUTATED DIDO1 WILD-TYPE 
            0.1             0.0 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
         105.07          122.30 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
          13.40           13.63 
[1] "0.1 - 105.1 (13.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D258V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DIDO1 MUTATED         1        2        4        2         9         4
  DIDO1 WILD-TYPE       9       18       42       29        75        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DIDO1 MUTATED           1          7          4          6        3         1
  DIDO1 WILD-TYPE        28         77         58         33       40         3
D258V3, multiclass
            clus
vv           DIDO1 MUTATED DIDO1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               4              42
  STAGE II               2              29
  STAGE IIA              9              75
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             7              77
  STAGE IIIB             4              58
  STAGE IIIC             6              33
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DIDO1 MUTATED       4   5  23  15
  DIDO1 WILD-TYPE    50 130 238  87
D258V4, multiclass
       clus
vv      DIDO1 MUTATED DIDO1 WILD-TYPE
  T0+T1             4              50
  T2                5             130
  T3               23             238
  T4               15              87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DIDO1 MUTATED    22   9   7   6
  DIDO1 WILD-TYPE 173 164  82  79
D258V5, multiclass
    clus
vv   DIDO1 MUTATED DIDO1 WILD-TYPE
  N0            22             173
  N1             9             164
  N2             7              82
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V6, binary
                 cls
clus                0   1
  DIDO1 MUTATED    40   2
  DIDO1 WILD-TYPE 442  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     40    2
  DIDO1 WILD-TYPE  442   36
   clus
vv  DIDO1 MUTATED DIDO1 WILD-TYPE
  0            40             442
  1             2              36
[1] 2 2
[1] FALSE
D258V7, binary
                 cls
clus                0   1
  DIDO1 MUTATED    19  31
  DIDO1 WILD-TYPE 153 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     19   31
  DIDO1 WILD-TYPE  153  375
        clus
vv       DIDO1 MUTATED DIDO1 WILD-TYPE
  FEMALE            19             153
  MALE              31             375
[1] 2 2
[1] FALSE
D258V8, binary
                 cls
clus                0   1
  DIDO1 MUTATED    37   3
  DIDO1 WILD-TYPE 379  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     37    3
  DIDO1 WILD-TYPE  379   99
     clus
vv    DIDO1 MUTATED DIDO1 WILD-TYPE
  NO             37             379
  YES             3              99
[1] 2 2
[1] FALSE
D258V9, continuous
D258V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DIDO1 MUTATED      14                         2
  DIDO1 WILD-TYPE   119                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DIDO1 MUTATED                                           0    32
  DIDO1 WILD-TYPE                                         1   325
D258V11, multiclass
                                           clus
vv                                          DIDO1 MUTATED DIDO1 WILD-TYPE
  ASIAN                                                14             119
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                32             325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V12, binary
                 cls
clus                0   1
  DIDO1 MUTATED     0  40
  DIDO1 WILD-TYPE  10 358
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      0   40
  DIDO1 WILD-TYPE   10  358
                        clus
vv                       DIDO1 MUTATED DIDO1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            40             358
[1] 2 2
[1] FALSE

Clustering(259) Variable = ADNP MUTATION ANALYSIS
D259V1, survival
                sevent
clus2              0   1
  ADNP MUTATED     9   7
  ADNP WILD-TYPE 329 209
  ADNP MUTATED ADNP WILD-TYPE 
            16            538 
  ADNP MUTATED ADNP WILD-TYPE 
             7            209 
$`ADNP MUTATED`
TCGA-CG-4460 TCGA-LN-A8I1 TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-A4QL 
       21.99        13.18         2.10         6.97        34.68        16.14 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A6EY 
       12.43        11.77         6.02        28.96        13.78        11.44 
TCGA-F1-6874 TCGA-F1-A448 TCGA-HF-A5NB TCGA-IN-A6RR 
       14.47        21.27        30.51         6.74 

$`ADNP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ADNP MUTATED ADNP WILD-TYPE 
           2.1            0.0 
  ADNP MUTATED ADNP WILD-TYPE 
         34.68         122.30 
  ADNP MUTATED ADNP WILD-TYPE 
        13.480         13.565 
[1] "2.1 - 34.7 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D259V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADNP MUTATED         0        1        2        1         2         1
  ADNP WILD-TYPE      10       19       44       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADNP MUTATED           0          4          4          1        3         0
  ADNP WILD-TYPE        29         80         58         38       40         4
D259V3, multiclass
            clus
vv           ADNP MUTATED ADNP WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            4             58
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ADNP MUTATED       2   3  10   5
  ADNP WILD-TYPE    52 132 251  97
D259V4, multiclass
       clus
vv      ADNP MUTATED ADNP WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3              10            251
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ADNP MUTATED     7   6   1   5
  ADNP WILD-TYPE 188 167  88  80
D259V5, multiclass
    clus
vv   ADNP MUTATED ADNP WILD-TYPE
  N0            7            188
  N1            6            167
  N2            1             88
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V6, binary
                cls
clus               0   1
  ADNP MUTATED    18   1
  ADNP WILD-TYPE 464  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED     18    1
  ADNP WILD-TYPE  464   37
   clus
vv  ADNP MUTATED ADNP WILD-TYPE
  0           18            464
  1            1             37
[1] 2 2
[1] FALSE
D259V7, binary
                cls
clus               0   1
  ADNP MUTATED     8  12
  ADNP WILD-TYPE 164 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      8   12
  ADNP WILD-TYPE  164  394
        clus
vv       ADNP MUTATED ADNP WILD-TYPE
  FEMALE            8            164
  MALE             12            394
[1] 2 2
[1] FALSE
D259V8, binary
                cls
clus               0   1
  ADNP MUTATED    12   4
  ADNP WILD-TYPE 404  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED     12    4
  ADNP WILD-TYPE  404   98
     clus
vv    ADNP MUTATED ADNP WILD-TYPE
  NO            12            404
  YES            4             98
[1] 2 2
[1] FALSE
D259V9, continuous
[1] "Remove cluster labels:" "ADNP MUTATED"          
clus
  ADNP MUTATED ADNP WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JD 
"ADNP WILD-TYPE" "ADNP WILD-TYPE" "ADNP WILD-TYPE" 
D259V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ADNP MUTATED       3                         0
  ADNP WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADNP MUTATED                                           0    12
  ADNP WILD-TYPE                                         1   345
D259V11, multiclass
                                           clus
vv                                          ADNP MUTATED ADNP WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V12, binary
                cls
clus               0   1
  ADNP MUTATED     1  14
  ADNP WILD-TYPE   9 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      1   14
  ADNP WILD-TYPE    9  384
                        clus
vv                       ADNP MUTATED ADNP WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(260) Variable = AQP8 MUTATION ANALYSIS
D260V1, survival
                sevent
clus2              0   1
  AQP8 MUTATED     8   4
  AQP8 WILD-TYPE 330 212
  AQP8 MUTATED AQP8 WILD-TYPE 
            12            542 
  AQP8 MUTATED AQP8 WILD-TYPE 
             4            212 
$`AQP8 MUTATED`
TCGA-L5-A8NW TCGA-BR-4280 TCGA-BR-6457 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8487 
       46.09         6.61        13.68         3.32        25.05         1.12 
TCGA-CG-4437 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GC TCGA-VQ-A92D 
        8.05        77.29        30.51        26.47         3.25        66.81 

$`AQP8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        5.52         6.21        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  AQP8 MUTATED AQP8 WILD-TYPE 
          1.12           0.00 
  AQP8 MUTATED AQP8 WILD-TYPE 
         77.29         122.30 
  AQP8 MUTATED AQP8 WILD-TYPE 
        19.365         13.530 
[1] "1.1 - 77.3 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D260V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AQP8 MUTATED         0        0        3        2         2         1
  AQP8 WILD-TYPE      10       20       43       29        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AQP8 MUTATED           1          1          2          2        0         0
  AQP8 WILD-TYPE        28         83         60         37       43         4
D260V3, multiclass
            clus
vv           AQP8 MUTATED AQP8 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  AQP8 MUTATED       0   6   3   5
  AQP8 WILD-TYPE    54 129 258  97
D260V4, multiclass
       clus
vv      AQP8 MUTATED AQP8 WILD-TYPE
  T0+T1            0             54
  T2               6            129
  T3               3            258
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  AQP8 MUTATED     6   4   1   3
  AQP8 WILD-TYPE 189 169  88  82
D260V5, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V6, binary
                cls
clus               0   1
  AQP8 MUTATED    13   0
  AQP8 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED     13    0
  AQP8 WILD-TYPE  469   38
   clus
vv  AQP8 MUTATED AQP8 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D260V7, binary
                cls
clus               0   1
  AQP8 MUTATED     6   8
  AQP8 WILD-TYPE 166 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      6    8
  AQP8 WILD-TYPE  166  398
        clus
vv       AQP8 MUTATED AQP8 WILD-TYPE
  FEMALE            6            166
  MALE              8            398
[1] 2 2
[1] FALSE
D260V8, binary
                cls
clus               0   1
  AQP8 MUTATED    11   2
  AQP8 WILD-TYPE 405 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED     11    2
  AQP8 WILD-TYPE  405  100
     clus
vv    AQP8 MUTATED AQP8 WILD-TYPE
  NO            11            405
  YES            2            100
[1] 2 2
[1] FALSE
D260V9, continuous
D260V10, continuous
[1] "Remove cluster labels:" "AQP8 MUTATED"          
clus
  AQP8 MUTATED AQP8 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-LN-A49O 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" "AQP8 WILD-TYPE" 
    TCGA-Z6-AAPN 
"AQP8 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AQP8 MUTATED       1                         0
  AQP8 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AQP8 MUTATED                                           0    10
  AQP8 WILD-TYPE                                         1   347
D260V11, multiclass
                                           clus
vv                                          AQP8 MUTATED AQP8 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V12, binary
                cls
clus               0   1
  AQP8 MUTATED     0   9
  AQP8 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      0    9
  AQP8 WILD-TYPE   10  389
                        clus
vv                       AQP8 MUTATED AQP8 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(261) Variable = ZC3H13 MUTATION ANALYSIS
D261V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    25  11
  ZC3H13 WILD-TYPE 313 205
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              36              518 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              11              205 
$`ZC3H13 MUTATED`
TCGA-CG-4460 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-L5-A4OH TCGA-L5-A8NE TCGA-L5-A8NL 
       21.99         9.96       122.10        32.61        55.50        13.22 
TCGA-L5-A8NM TCGA-LN-A9FP TCGA-R6-A8WC TCGA-V5-AASW TCGA-VR-AA7B TCGA-BR-4201 
        7.76        12.03         2.30         9.27        11.24        30.90 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8382 
       34.68        15.95        30.90        44.94         6.18        25.05 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4440 
        1.12        31.96         6.58        12.62         1.02         4.01 
TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EV TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4G9 
      105.07         5.92        11.24        11.08        77.29        24.20 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A91Q 
       29.98         0.10         6.58        19.73        19.04        20.81 

$`ZC3H13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57         6.61        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       19.89        12.16         8.98        40.21        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       11.77        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        21.37         8.98         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U 
       37.22        22.19        17.85         1.87        15.65         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
             0.1              0.0 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
           122.1            122.3 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          14.585           13.565 
[1] "0.1 - 122.1 (14.6)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D261V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H13 MUTATED         2        1        3        2         9         7
  ZC3H13 WILD-TYPE       8       19       43       29        75        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           1          3          0          2        6
  ZC3H13 WILD-TYPE        28         81         62         37       37
                  vv
clus               STAGE IVA
  ZC3H13 MUTATED           0
  ZC3H13 WILD-TYPE         4
D261V3, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               9               75
  STAGE IIB               7               76
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                6               37
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZC3H13 MUTATED       4  13  16   6
  ZC3H13 WILD-TYPE    50 122 245  96
D261V4, multiclass
       clus
vv      ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T0+T1              4               50
  T2                13              122
  T3                16              245
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZC3H13 MUTATED    15  11   6   4
  ZC3H13 WILD-TYPE 180 162  83  81
D261V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             15              180
  N1             11              162
  N2              6               83
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V6, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    33   5
  ZC3H13 WILD-TYPE 449  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     33    5
  ZC3H13 WILD-TYPE  449   33
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             33              449
  1              5               33
[1] 2 2
[1] FALSE
D261V7, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    17  24
  ZC3H13 WILD-TYPE 155 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     17   24
  ZC3H13 WILD-TYPE  155  382
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE             17              155
  MALE               24              382
[1] 2 2
[1] FALSE
D261V8, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    28   5
  ZC3H13 WILD-TYPE 388  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     28    5
  ZC3H13 WILD-TYPE  388   97
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO              28              388
  YES              5               97
[1] 2 2
[1] FALSE
D261V9, continuous
[1] "Remove cluster labels:" "ZC3H13 MUTATED"        
clus
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7D 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZC3H13 WILD-TYPE" "ZC3H13 WILD-TYPE" 
D261V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H13 MUTATED       8                         1
  ZC3H13 WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H13 MUTATED                                           0    25
  ZC3H13 WILD-TYPE                                         1   332
D261V11, multiclass
                                           clus
vv                                          ZC3H13 MUTATED ZC3H13 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 25              332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V12, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED     0  28
  ZC3H13 WILD-TYPE  10 370
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      0   28
  ZC3H13 WILD-TYPE   10  370
                        clus
vv                       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             28              370
[1] 2 2
[1] FALSE

Clustering(262) Variable = C10ORF76 MUTATION ANALYSIS
D262V1, survival
                    sevent
clus2                  0   1
  C10ORF76 MUTATED     9   2
  C10ORF76 WILD-TYPE 329 214
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                11                543 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 2                214 
$`C10ORF76 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3YA TCGA-L5-A43H TCGA-L5-A4OJ TCGA-LN-A8I1 TCGA-VR-AA4G 
       19.99        20.78         0.30        21.01        13.18        18.05 
TCGA-CD-A48A TCGA-CG-5721 TCGA-D7-A6EY TCGA-IN-A6RN TCGA-VQ-A8P2 
       12.43         6.02        11.44        19.53        38.14 

$`C10ORF76 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       30.25        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.82        12.43         6.31        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
               0.3                0.0 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
             38.14             122.30 
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
             18.05              13.55 
[1] "0.3 - 38.1 (18.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D262V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C10ORF76 MUTATED         1        0        0        0         3         0
  C10ORF76 WILD-TYPE       9       20       46       31        81        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF76 MUTATED           1          4          1          1        2
  C10ORF76 WILD-TYPE        28         80         61         38       41
                    vv
clus                 STAGE IVA
  C10ORF76 MUTATED           0
  C10ORF76 WILD-TYPE         4
D262V3, multiclass
            clus
vv           C10ORF76 MUTATED C10ORF76 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 0                 83
  STAGE III                 1                 28
  STAGE IIIA                4                 80
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C10ORF76 MUTATED       2   2   4   5
  C10ORF76 WILD-TYPE    52 133 257  97
D262V4, multiclass
       clus
vv      C10ORF76 MUTATED C10ORF76 WILD-TYPE
  T0+T1                2                 52
  T2                   2                133
  T3                   4                257
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C10ORF76 MUTATED     5   3   3   2
  C10ORF76 WILD-TYPE 190 170  86  83
D262V5, multiclass
    clus
vv   C10ORF76 MUTATED C10ORF76 WILD-TYPE
  N0                5                190
  N1                3                170
  N2                3                 86
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V6, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED    12   0
  C10ORF76 WILD-TYPE 470  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED     12    0
  C10ORF76 WILD-TYPE  470   38
   clus
vv  C10ORF76 MUTATED C10ORF76 WILD-TYPE
  0               12                470
  1                0                 38
[1] 2 2
[1] FALSE
D262V7, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     7   6
  C10ORF76 WILD-TYPE 165 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      7    6
  C10ORF76 WILD-TYPE  165  400
        clus
vv       C10ORF76 MUTATED C10ORF76 WILD-TYPE
  FEMALE                7                165
  MALE                  6                400
[1] 2 2
[1] FALSE
D262V8, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     8   3
  C10ORF76 WILD-TYPE 408  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      8    3
  C10ORF76 WILD-TYPE  408   99
     clus
vv    C10ORF76 MUTATED C10ORF76 WILD-TYPE
  NO                 8                408
  YES                3                 99
[1] 2 2
[1] FALSE
D262V9, continuous
[1] "Remove cluster labels:" "C10ORF76 MUTATED"      
clus
  C10ORF76 MUTATED C10ORF76 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A51D 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A7DP         TCGA-KH-A6WC 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA7B         TCGA-VR-AA7D 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" "C10ORF76 WILD-TYPE" 
D262V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C10ORF76 MUTATED       2                         0
  C10ORF76 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C10ORF76 MUTATED                                           0    10
  C10ORF76 WILD-TYPE                                         1   347
D262V11, multiclass
                                           clus
vv                                          C10ORF76 MUTATED C10ORF76 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V12, binary
                    cls
clus                   0   1
  C10ORF76 MUTATED     0   7
  C10ORF76 WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF76 MUTATED      0    7
  C10ORF76 WILD-TYPE   10  391
                        clus
vv                       C10ORF76 MUTATED C10ORF76 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(263) Variable = SYCP1 MUTATION ANALYSIS
D263V1, survival
                 sevent
clus2               0   1
  SYCP1 MUTATED    19   7
  SYCP1 WILD-TYPE 319 209
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             26             528 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              7             209 
$`SYCP1 MUTATED`
TCGA-KH-A6WC TCGA-L5-A891 TCGA-L5-A8NM TCGA-LN-A5U6 TCGA-V5-A7RE TCGA-BR-6452 
        6.28         3.75         7.76        12.33        16.44        34.68 
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8363 TCGA-BR-8373 TCGA-BR-8382 
       44.94        35.84        18.15         0.26        14.79        25.05 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4IV TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4466 
       27.12        28.14        28.57        12.43         6.58        18.97 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6526 TCGA-FP-7735 TCGA-HF-A5NB TCGA-IN-A6RP 
        6.02       105.07        17.19         3.48        30.51         6.44 
TCGA-VQ-A8P2 TCGA-VQ-A92D 
       38.14        66.81 

$`SYCP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        31.27         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
        7.53         6.08        34.98         1.48        27.55        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SYCP1 MUTATED SYCP1 WILD-TYPE 
           0.26            0.00 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
         105.07          122.30 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
         17.670          13.495 
[1] "0.3 - 105.1 (17.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D263V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYCP1 MUTATED         0        1        6        2         3         2
  SYCP1 WILD-TYPE      10       19       40       29        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYCP1 MUTATED           0          3          2          4        2         0
  SYCP1 WILD-TYPE        29         81         60         35       41         4
D263V3, multiclass
            clus
vv           SYCP1 MUTATED SYCP1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               6              40
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SYCP1 MUTATED       3   8   7   9
  SYCP1 WILD-TYPE    51 127 254  93
D263V4, multiclass
       clus
vv      SYCP1 MUTATED SYCP1 WILD-TYPE
  T0+T1             3              51
  T2                8             127
  T3                7             254
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SYCP1 MUTATED    11   9   2   4
  SYCP1 WILD-TYPE 184 164  87  81
D263V5, multiclass
    clus
vv   SYCP1 MUTATED SYCP1 WILD-TYPE
  N0            11             184
  N1             9             164
  N2             2              87
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V6, binary
                 cls
clus                0   1
  SYCP1 MUTATED    26   0
  SYCP1 WILD-TYPE 456  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     26    0
  SYCP1 WILD-TYPE  456   38
   clus
vv  SYCP1 MUTATED SYCP1 WILD-TYPE
  0            26             456
  1             0              38
[1] 2 2
[1] FALSE
D263V7, binary
                 cls
clus                0   1
  SYCP1 MUTATED    11  17
  SYCP1 WILD-TYPE 161 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     11   17
  SYCP1 WILD-TYPE  161  389
        clus
vv       SYCP1 MUTATED SYCP1 WILD-TYPE
  FEMALE            11             161
  MALE              17             389
[1] 2 2
[1] FALSE
D263V8, binary
                 cls
clus                0   1
  SYCP1 MUTATED    19   6
  SYCP1 WILD-TYPE 397  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     19    6
  SYCP1 WILD-TYPE  397   96
     clus
vv    SYCP1 MUTATED SYCP1 WILD-TYPE
  NO             19             397
  YES             6              96
[1] 2 2
[1] FALSE
D263V9, continuous
D263V10, continuous
[1] "Remove cluster labels:" "SYCP1 MUTATED"         
clus
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-L5-A43C 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SYCP1 MUTATED       4                         1
  SYCP1 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYCP1 MUTATED                                           0    19
  SYCP1 WILD-TYPE                                         1   338
D263V11, multiclass
                                           clus
vv                                          SYCP1 MUTATED SYCP1 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V12, binary
                 cls
clus                0   1
  SYCP1 MUTATED     0  20
  SYCP1 WILD-TYPE  10 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      0   20
  SYCP1 WILD-TYPE   10  378
                        clus
vv                       SYCP1 MUTATED SYCP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(264) Variable = SNRK MUTATION ANALYSIS
D264V1, survival
                sevent
clus2              0   1
  SNRK MUTATED     8   7
  SNRK WILD-TYPE 330 209
  SNRK MUTATED SNRK WILD-TYPE 
            15            539 
  SNRK MUTATED SNRK WILD-TYPE 
             7            209 
$`SNRK MUTATED`
TCGA-2H-A9GQ TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8363 
        4.21         6.97         9.67         8.05         6.18         0.26 
TCGA-BR-8367 TCGA-BR-8371 TCGA-CD-8524 TCGA-CD-8530 TCGA-CG-5721 TCGA-D7-8572 
       26.33        11.80        12.76        12.39         6.02        16.80 
TCGA-D7-8574 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       17.19        22.68        38.14 

$`SNRK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 
        0.95         4.31        14.04         3.32        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.39        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 
       12.36        11.31        12.33        24.72        19.50        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SNRK MUTATED SNRK WILD-TYPE 
          0.26           0.00 
  SNRK MUTATED SNRK WILD-TYPE 
         38.14         122.30 
  SNRK MUTATED SNRK WILD-TYPE 
         11.80          13.78 
[1] "0.3 - 38.1 (11.8)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.6"
D264V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNRK MUTATED         0        0        1        2         1         3
  SNRK WILD-TYPE      10       20       45       29        83        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNRK MUTATED           1          4          2          1        1         0
  SNRK WILD-TYPE        28         80         60         38       42         4
D264V3, multiclass
            clus
vv           SNRK MUTATED SNRK WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             1             83
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SNRK MUTATED       0   3   8   5
  SNRK WILD-TYPE    54 132 253  97
D264V4, multiclass
       clus
vv      SNRK MUTATED SNRK WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SNRK MUTATED     6   5   1   4
  SNRK WILD-TYPE 189 168  88  81
D264V5, multiclass
    clus
vv   SNRK MUTATED SNRK WILD-TYPE
  N0            6            189
  N1            5            168
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V6, binary
                cls
clus               0   1
  SNRK MUTATED    16   0
  SNRK WILD-TYPE 466  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED     16    0
  SNRK WILD-TYPE  466   38
   clus
vv  SNRK MUTATED SNRK WILD-TYPE
  0           16            466
  1            0             38
[1] 2 2
[1] FALSE
D264V7, binary
                cls
clus               0   1
  SNRK MUTATED     6  11
  SNRK WILD-TYPE 166 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED      6   11
  SNRK WILD-TYPE  166  395
        clus
vv       SNRK MUTATED SNRK WILD-TYPE
  FEMALE            6            166
  MALE             11            395
[1] 2 2
[1] FALSE
D264V8, binary
                cls
clus               0   1
  SNRK MUTATED    14   2
  SNRK WILD-TYPE 402 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED     14    2
  SNRK WILD-TYPE  402  100
     clus
vv    SNRK MUTATED SNRK WILD-TYPE
  NO            14            402
  YES            2            100
[1] 2 2
[1] FALSE
D264V9, continuous
D264V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SNRK MUTATED       3                         0
  SNRK WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNRK MUTATED                                           0    12
  SNRK WILD-TYPE                                         1   345
D264V11, multiclass
                                           clus
vv                                          SNRK MUTATED SNRK WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V12, binary
                cls
clus               0   1
  SNRK MUTATED     0  14
  SNRK WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED      0   14
  SNRK WILD-TYPE   10  384
                        clus
vv                       SNRK MUTATED SNRK WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(265) Variable = EAF2 MUTATION ANALYSIS
D265V1, survival
                sevent
clus2              0   1
  EAF2 MUTATED     7   3
  EAF2 WILD-TYPE 331 213
  EAF2 MUTATED EAF2 WILD-TYPE 
            10            544 
  EAF2 MUTATED EAF2 WILD-TYPE 
             3            213 
$`EAF2 MUTATED`
TCGA-CG-4460 TCGA-L7-A6VZ TCGA-LN-A4MR TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4QL 
       21.99        10.36        13.22        34.68        28.14        16.14 
TCGA-CG-4305 TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GN 
       15.95        11.44        24.20        29.98 

$`EAF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EAF2 MUTATED EAF2 WILD-TYPE 
         10.36           0.00 
  EAF2 MUTATED EAF2 WILD-TYPE 
         34.68         122.30 
  EAF2 MUTATED EAF2 WILD-TYPE 
        19.065         13.510 
[1] "10.4 - 34.7 (19.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D265V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EAF2 MUTATED         0        1        0        1         3         0
  EAF2 WILD-TYPE      10       19       46       30        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EAF2 MUTATED           0          0          2          2        2         0
  EAF2 WILD-TYPE        29         84         60         37       41         4
D265V3, multiclass
            clus
vv           EAF2 MUTATED EAF2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  EAF2 MUTATED       1   3   4   3
  EAF2 WILD-TYPE    53 132 257  99
D265V4, multiclass
       clus
vv      EAF2 MUTATED EAF2 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EAF2 MUTATED     3   3   1   4
  EAF2 WILD-TYPE 192 170  88  81
D265V5, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  N0            3            192
  N1            3            170
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V6, binary
                cls
clus               0   1
  EAF2 MUTATED     9   1
  EAF2 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      9    1
  EAF2 WILD-TYPE  473   37
   clus
vv  EAF2 MUTATED EAF2 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D265V7, binary
                cls
clus               0   1
  EAF2 MUTATED     6   5
  EAF2 WILD-TYPE 166 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      6    5
  EAF2 WILD-TYPE  166  401
        clus
vv       EAF2 MUTATED EAF2 WILD-TYPE
  FEMALE            6            166
  MALE              5            401
[1] 2 2
[1] FALSE
D265V8, binary
                cls
clus               0   1
  EAF2 MUTATED     9   1
  EAF2 WILD-TYPE 407 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      9    1
  EAF2 WILD-TYPE  407  101
     clus
vv    EAF2 MUTATED EAF2 WILD-TYPE
  NO             9            407
  YES            1            101
[1] 2 2
[1] FALSE
D265V9, continuous
[1] "Remove cluster labels:" "EAF2 MUTATED"          
clus
  EAF2 MUTATED EAF2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
D265V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EAF2 MUTATED       3                         0
  EAF2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EAF2 MUTATED                                           0     6
  EAF2 WILD-TYPE                                         1   351
D265V11, multiclass
                                           clus
vv                                          EAF2 MUTATED EAF2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V12, binary
                cls
clus               0   1
  EAF2 MUTATED     0   9
  EAF2 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    9
  EAF2 WILD-TYPE   10  389
                        clus
vv                       EAF2 MUTATED EAF2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(266) Variable = HSPG2 MUTATION ANALYSIS
D266V1, survival
                 sevent
clus2               0   1
  HSPG2 MUTATED    51  19
  HSPG2 WILD-TYPE 287 197
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             70             484 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             19             197 
$`HSPG2 MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-CG-4460 TCGA-2H-A9GK TCGA-IG-A5S3 TCGA-IG-A7DP 
       60.39        18.28        21.99         7.63        23.41        14.86 
TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-L5-A8NS TCGA-LN-A49U 
        3.16        32.61        21.01         7.76        13.41        15.35 
TCGA-LN-A4A6 TCGA-Z6-A8JD TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-6802 
       12.85         3.42        30.90        34.68        12.16        30.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        9.21        35.24        14.43         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8591 TCGA-BR-A44U TCGA-BR-A4J2 TCGA-CD-5800 
        8.05         6.18        28.14        13.87        14.17        13.15 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4477 
       11.64        12.43         6.58         1.02         9.01        30.97 
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
        6.02        65.10        16.80        19.50        17.19        14.66 
TCGA-D7-A6EY TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-8243 
       11.44        17.06        59.54        13.58        11.08         5.92 
TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GN 
       24.39        22.82        24.26        22.68        24.20        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
       14.07        19.73         5.46        38.14 

$`HSPG2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        26.33        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       40.21        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 
        9.07        29.56        33.21        37.25        11.44         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.76         7.17        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       19.07        12.03         0.00        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       24.72        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8602 
       52.21        30.51        26.47         1.51        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GD 
       21.07         0.76        24.30         5.59         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 
       25.81        11.77        21.37        20.25        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HSPG2 MUTATED HSPG2 WILD-TYPE 
            0.1             0.0 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
           65.1           122.3 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
         13.725          13.530 
[1] "0.1 - 65.1 (13.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSPG2 MUTATED         4        3        5        7        11        12
  HSPG2 WILD-TYPE       6       17       41       24        73        71
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HSPG2 MUTATED           2         13          5          5        5         0
  HSPG2 WILD-TYPE        27         71         57         34       38         4
D266V3, multiclass
            clus
vv           HSPG2 MUTATED HSPG2 WILD-TYPE
  STAGE I                4               6
  STAGE IA               3              17
  STAGE IB               5              41
  STAGE II               7              24
  STAGE IIA             11              73
  STAGE IIB             12              71
  STAGE III              2              27
  STAGE IIIA            13              71
  STAGE IIIB             5              57
  STAGE IIIC             5              34
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HSPG2 MUTATED       9  11  34  20
  HSPG2 WILD-TYPE    45 124 227  82
D266V4, multiclass
       clus
vv      HSPG2 MUTATED HSPG2 WILD-TYPE
  T0+T1             9              45
  T2               11             124
  T3               34             227
  T4               20              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HSPG2 MUTATED    36  19   6  10
  HSPG2 WILD-TYPE 159 154  83  75
D266V5, multiclass
    clus
vv   HSPG2 MUTATED HSPG2 WILD-TYPE
  N0            36             159
  N1            19             154
  N2             6              83
  N3            10              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V6, binary
                 cls
clus                0   1
  HSPG2 MUTATED    65   4
  HSPG2 WILD-TYPE 417  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     65    4
  HSPG2 WILD-TYPE  417   34
   clus
vv  HSPG2 MUTATED HSPG2 WILD-TYPE
  0            65             417
  1             4              34
[1] 2 2
[1] FALSE
D266V7, binary
                 cls
clus                0   1
  HSPG2 MUTATED    33  42
  HSPG2 WILD-TYPE 139 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     33   42
  HSPG2 WILD-TYPE  139  364
        clus
vv       HSPG2 MUTATED HSPG2 WILD-TYPE
  FEMALE            33             139
  MALE              42             364
[1] 2 2
[1] FALSE
D266V8, binary
                 cls
clus                0   1
  HSPG2 MUTATED    55  13
  HSPG2 WILD-TYPE 361  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     55   13
  HSPG2 WILD-TYPE  361   89
     clus
vv    HSPG2 MUTATED HSPG2 WILD-TYPE
  NO             55             361
  YES            13              89
[1] 2 2
[1] FALSE
D266V9, continuous
D266V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HSPG2 MUTATED      27                         2
  HSPG2 WILD-TYPE   106                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPG2 MUTATED                                           0    38
  HSPG2 WILD-TYPE                                         1   319
D266V11, multiclass
                                           clus
vv                                          HSPG2 MUTATED HSPG2 WILD-TYPE
  ASIAN                                                27             106
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                38             319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V12, binary
                 cls
clus                0   1
  HSPG2 MUTATED     0  58
  HSPG2 WILD-TYPE  10 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED      0   58
  HSPG2 WILD-TYPE   10  340
                        clus
vv                       HSPG2 MUTATED HSPG2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            58             340
[1] 2 2
[1] FALSE

Clustering(267) Variable = TP53BP1 MUTATION ANALYSIS
D267V1, survival
                   sevent
clus2                 0   1
  TP53BP1 MUTATED    17   9
  TP53BP1 WILD-TYPE 321 207
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               26               528 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                9               207 
$`TP53BP1 MUTATED`
TCGA-2H-A9GN TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-LN-A49R TCGA-LN-A5U5 TCGA-BR-4201 
        8.94        21.01         7.76        13.38         4.47        30.90 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8370 TCGA-BR-8589 TCGA-CG-4305 
        6.61        34.68        30.90         3.32        27.12        15.95 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6525 TCGA-HU-8244 TCGA-HU-8610 TCGA-HU-A4G8 
        6.02       105.07        13.35        24.39         0.76        22.68 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-KB-A93J TCGA-RD-A7C1 TCGA-VQ-A8DL 
       29.98         6.51        20.25        36.95        16.67         0.92 
TCGA-VQ-A8P2 TCGA-VQ-A91U 
       38.14         1.71 

$`TP53BP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        5.92        28.96        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        21.37         8.98         0.10         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53         5.56        63.62         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D 
       17.85         1.87        15.65        20.81        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
             0.76              0.00 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
           105.07            122.30 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
            16.31             13.53 
[1] "0.8 - 105.1 (16.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D267V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP1 MUTATED         1        2        1        3         4         2
  TP53BP1 WILD-TYPE       9       18       45       28        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP1 MUTATED           3          4          2          1        3
  TP53BP1 WILD-TYPE        26         80         60         38       40
                   vv
clus                STAGE IVA
  TP53BP1 MUTATED           0
  TP53BP1 WILD-TYPE         4
D267V3, multiclass
            clus
vv           TP53BP1 MUTATED TP53BP1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                18
  STAGE IB                 1                45
  STAGE II                 3                28
  STAGE IIA                4                80
  STAGE IIB                2                81
  STAGE III                3                26
  STAGE IIIA               4                80
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TP53BP1 MUTATED       3   9  10   5
  TP53BP1 WILD-TYPE    51 126 251  97
D267V4, multiclass
       clus
vv      TP53BP1 MUTATED TP53BP1 WILD-TYPE
  T0+T1               3                51
  T2                  9               126
  T3                 10               251
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TP53BP1 MUTATED     7  14   4   1
  TP53BP1 WILD-TYPE 188 159  85  84
D267V5, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  N0               7               188
  N1              14               159
  N2               4                85
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V6, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    26   1
  TP53BP1 WILD-TYPE 456  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     26    1
  TP53BP1 WILD-TYPE  456   37
   clus
vv  TP53BP1 MUTATED TP53BP1 WILD-TYPE
  0              26               456
  1               1                37
[1] 2 2
[1] FALSE
D267V7, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    11  16
  TP53BP1 WILD-TYPE 161 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     11   16
  TP53BP1 WILD-TYPE  161  390
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  FEMALE              11               161
  MALE                16               390
[1] 2 2
[1] FALSE
D267V8, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    23   3
  TP53BP1 WILD-TYPE 393  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     23    3
  TP53BP1 WILD-TYPE  393   99
     clus
vv    TP53BP1 MUTATED TP53BP1 WILD-TYPE
  NO               23               393
  YES               3                99
[1] 2 2
[1] FALSE
D267V9, continuous
[1] "Remove cluster labels:" "TP53BP1 MUTATED"       
clus
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ        TCGA-V5-A7RB 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-V5-AASW 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
D267V10, continuous
[1] "Remove cluster labels:" "TP53BP1 MUTATED"       
clus
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49S        TCGA-LN-A49U 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TP53BP1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TP53BP1 MUTATED       9                         0
  TP53BP1 WILD-TYPE   124                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53BP1 MUTATED                                           0    14
  TP53BP1 WILD-TYPE                                         1   343
D267V11, multiclass
                                           clus
vv                                          TP53BP1 MUTATED TP53BP1 WILD-TYPE
  ASIAN                                                   9               124
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V12, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     0  17
  TP53BP1 WILD-TYPE  10 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      0   17
  TP53BP1 WILD-TYPE   10  381
                        clus
vv                       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              17               381
[1] 2 2
[1] FALSE

Clustering(268) Variable = KLC2 MUTATION ANALYSIS
D268V1, survival
                sevent
clus2              0   1
  KLC2 MUTATED    10   6
  KLC2 WILD-TYPE 328 210
  KLC2 MUTATED KLC2 WILD-TYPE 
            16            538 
  KLC2 MUTATED KLC2 WILD-TYPE 
             6            210 
$`KLC2 MUTATED`
TCGA-CG-4460 TCGA-LN-A49W TCGA-LN-A7HY TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 
       21.99        13.25        12.03         6.97        44.94        35.84 
TCGA-BR-8081 TCGA-BR-8487 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY TCGA-EQ-5647 
       32.25         1.12       105.07        21.07        11.44         0.62 
TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-A4GX TCGA-VQ-A8P2 
       13.58        26.47        20.25        38.14 

$`KLC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KLC2 MUTATED KLC2 WILD-TYPE 
          0.62           0.00 
  KLC2 MUTATED KLC2 WILD-TYPE 
        105.07         122.30 
  KLC2 MUTATED KLC2 WILD-TYPE 
         20.66          13.51 
[1] "0.6 - 105.1 (20.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D268V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLC2 MUTATED         0        0        2        1         2         2
  KLC2 WILD-TYPE      10       20       44       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLC2 MUTATED           2          3          1          1        2         0
  KLC2 WILD-TYPE        27         81         61         38       41         4
D268V3, multiclass
            clus
vv           KLC2 MUTATED KLC2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  KLC2 MUTATED       0   4   7   5
  KLC2 WILD-TYPE    54 131 254  97
D268V4, multiclass
       clus
vv      KLC2 MUTATED KLC2 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               7            254
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KLC2 MUTATED     5   7   2   2
  KLC2 WILD-TYPE 190 166  87  83
D268V5, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  N0            5            190
  N1            7            166
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V6, binary
                cls
clus               0   1
  KLC2 MUTATED    11   2
  KLC2 WILD-TYPE 471  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED     11    2
  KLC2 WILD-TYPE  471   36
   clus
vv  KLC2 MUTATED KLC2 WILD-TYPE
  0           11            471
  1            2             36
[1] 2 2
[1] FALSE
D268V7, binary
                cls
clus               0   1
  KLC2 MUTATED    10   6
  KLC2 WILD-TYPE 162 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED     10    6
  KLC2 WILD-TYPE  162  400
        clus
vv       KLC2 MUTATED KLC2 WILD-TYPE
  FEMALE           10            162
  MALE              6            400
[1] 2 2
[1] FALSE
D268V8, binary
                cls
clus               0   1
  KLC2 MUTATED    13   3
  KLC2 WILD-TYPE 403  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED     13    3
  KLC2 WILD-TYPE  403   99
     clus
vv    KLC2 MUTATED KLC2 WILD-TYPE
  NO            13            403
  YES            3             99
[1] 2 2
[1] FALSE
D268V9, continuous
[1] "Remove cluster labels:" "KLC2 MUTATED"          
clus
  KLC2 MUTATED KLC2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
D268V10, continuous
[1] "Remove cluster labels:" "KLC2 MUTATED"          
clus
  KLC2 MUTATED KLC2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A4A3     TCGA-LN-A4A6 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" "KLC2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"KLC2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KLC2 MUTATED       3                         0
  KLC2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLC2 MUTATED                                           0    10
  KLC2 WILD-TYPE                                         1   347
D268V11, multiclass
                                           clus
vv                                          KLC2 MUTATED KLC2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V12, binary
                cls
clus               0   1
  KLC2 MUTATED     0  11
  KLC2 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      0   11
  KLC2 WILD-TYPE   10  387
                        clus
vv                       KLC2 MUTATED KLC2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(269) Variable = SRCIN1 MUTATION ANALYSIS
D269V1, survival
                  sevent
clus2                0   1
  SRCIN1 MUTATED     8   8
  SRCIN1 WILD-TYPE 330 208
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              16              538 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
               8              208 
$`SRCIN1 MUTATED`
TCGA-L5-A4OE TCGA-CG-4460 TCGA-2H-A9GN TCGA-L5-A8NS TCGA-Z6-AAPN TCGA-BR-7707 
       24.00        21.99         8.94        13.41         2.66        35.84 
TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-4469 
        0.26         1.12        12.30         6.58         8.05         7.07 
TCGA-CG-5723 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-VQ-A8DL 
      105.07        11.77         0.10         0.92 

$`SRCIN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
             0.1              0.0 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
          105.07           122.30 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
           8.495           13.870 
[1] "0.1 - 105.1 (8.5)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.7"
D269V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRCIN1 MUTATED         1        1        3        2         4         1
  SRCIN1 WILD-TYPE       9       19       43       29        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRCIN1 MUTATED           1          0          1          1        3
  SRCIN1 WILD-TYPE        28         84         61         38       40
                  vv
clus               STAGE IVA
  SRCIN1 MUTATED           0
  SRCIN1 WILD-TYPE         4
D269V3, multiclass
            clus
vv           SRCIN1 MUTATED SRCIN1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SRCIN1 MUTATED       2   5   8   3
  SRCIN1 WILD-TYPE    52 130 253  99
D269V4, multiclass
       clus
vv      SRCIN1 MUTATED SRCIN1 WILD-TYPE
  T0+T1              2               52
  T2                 5              130
  T3                 8              253
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SRCIN1 MUTATED    10   5   2   1
  SRCIN1 WILD-TYPE 185 168  87  84
D269V5, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  N0             10              185
  N1              5              168
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V6, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED    14   2
  SRCIN1 WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED     14    2
  SRCIN1 WILD-TYPE  468   36
   clus
vv  SRCIN1 MUTATED SRCIN1 WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D269V7, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     5  13
  SRCIN1 WILD-TYPE 167 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      5   13
  SRCIN1 WILD-TYPE  167  393
        clus
vv       SRCIN1 MUTATED SRCIN1 WILD-TYPE
  FEMALE              5              167
  MALE               13              393
[1] 2 2
[1] FALSE
D269V8, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED    14   2
  SRCIN1 WILD-TYPE 402 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED     14    2
  SRCIN1 WILD-TYPE  402  100
     clus
vv    SRCIN1 MUTATED SRCIN1 WILD-TYPE
  NO              14              402
  YES              2              100
[1] 2 2
[1] FALSE
D269V9, continuous
D269V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SRCIN1 MUTATED       4                         1
  SRCIN1 WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRCIN1 MUTATED                                           0     7
  SRCIN1 WILD-TYPE                                         1   350
D269V11, multiclass
                                           clus
vv                                          SRCIN1 MUTATED SRCIN1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V12, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     0   9
  SRCIN1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      0    9
  SRCIN1 WILD-TYPE   10  389
                        clus
vv                       SRCIN1 MUTATED SRCIN1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(270) Variable = FAM98C MUTATION ANALYSIS
D270V1, survival
                  sevent
clus2                0   1
  FAM98C MUTATED     8   0
  FAM98C WILD-TYPE 330 216
  FAM98C MUTATED FAM98C WILD-TYPE 
               8              546 
  FAM98C MUTATED FAM98C WILD-TYPE 
               0              216 
$`FAM98C MUTATED`
TCGA-JY-A6FH TCGA-JY-A93E TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-8680 
       47.38        25.22        44.94        29.59        28.14        31.96 
TCGA-CG-4305 TCGA-HU-A4GT 
       15.95         6.51 

$`FAM98C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FAM98C MUTATED FAM98C WILD-TYPE 
            6.51             0.00 
  FAM98C MUTATED FAM98C WILD-TYPE 
           47.38           122.30 
  FAM98C MUTATED FAM98C WILD-TYPE 
          28.865           13.495 
[1] "6.5 - 47.4 (28.9)"  "0.0 - 122.3 (13.5)"
[1] "hr="     "9300000"
D270V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM98C MUTATED         0        0        1        1         2         2
  FAM98C WILD-TYPE      10       20       45       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM98C MUTATED           0          1          0          1        2
  FAM98C WILD-TYPE        29         83         62         38       41
                  vv
clus               STAGE IVA
  FAM98C MUTATED           0
  FAM98C WILD-TYPE         4
D270V3, multiclass
            clus
vv           FAM98C MUTATED FAM98C WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM98C MUTATED       0   3   3   4
  FAM98C WILD-TYPE    54 132 258  98
D270V4, multiclass
       clus
vv      FAM98C MUTATED FAM98C WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM98C MUTATED     4   3   2   1
  FAM98C WILD-TYPE 191 170  87  84
D270V5, multiclass
    clus
vv   FAM98C MUTATED FAM98C WILD-TYPE
  N0              4              191
  N1              3              170
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V6, binary
                  cls
clus                 0   1
  FAM98C MUTATED     9   1
  FAM98C WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      9    1
  FAM98C WILD-TYPE  473   37
   clus
vv  FAM98C MUTATED FAM98C WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D270V7, binary
                  cls
clus                 0   1
  FAM98C MUTATED     4   6
  FAM98C WILD-TYPE 168 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      4    6
  FAM98C WILD-TYPE  168  400
        clus
vv       FAM98C MUTATED FAM98C WILD-TYPE
  FEMALE              4              168
  MALE                6              400
[1] 2 2
[1] FALSE
D270V8, binary
                  cls
clus                 0   1
  FAM98C MUTATED     8   0
  FAM98C WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      8    0
  FAM98C WILD-TYPE  408  102
     clus
vv    FAM98C MUTATED FAM98C WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D270V9, continuous
D270V10, continuous
[1] "Remove cluster labels:" "FAM98C MUTATED"        
clus
  FAM98C MUTATED FAM98C WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-KH-A6WC       TCGA-L5-A43C 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" "FAM98C WILD-TYPE" 
      TCGA-Z6-AAPN 
"FAM98C WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM98C MUTATED       2                         0
  FAM98C WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM98C MUTATED                                           0     6
  FAM98C WILD-TYPE                                         1   351
D270V11, multiclass
                                           clus
vv                                          FAM98C MUTATED FAM98C WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V12, binary
                  cls
clus                 0   1
  FAM98C MUTATED     0   6
  FAM98C WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      0    6
  FAM98C WILD-TYPE   10  392
                        clus
vv                       FAM98C MUTATED FAM98C WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(271) Variable = PDCD1 MUTATION ANALYSIS
D271V1, survival
                 sevent
clus2               0   1
  PDCD1 MUTATED     3   2
  PDCD1 WILD-TYPE 335 214
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              5             549 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              2             214 
$`PDCD1 MUTATED`
TCGA-L5-A8NM TCGA-BR-8487 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-VQ-A8P3 
        7.76         1.12        11.44        11.08        37.22 

$`PDCD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PDCD1 MUTATED PDCD1 WILD-TYPE 
           1.12            0.00 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
          37.22          122.30 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
          11.08           13.68 
[1] "1.1 - 37.2 (11.1)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.4"
D271V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDCD1 MUTATED         0        0        0        0         2         1
  PDCD1 WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDCD1 MUTATED           0          2          1          0        0         0
  PDCD1 WILD-TYPE        29         82         61         39       43         4
D271V3, multiclass
            clus
vv           PDCD1 MUTATED PDCD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PDCD1 MUTATED       0   1   3   2
  PDCD1 WILD-TYPE    54 134 258 100
D271V4, multiclass
       clus
vv      PDCD1 MUTATED PDCD1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PDCD1 MUTATED     3   2   0   1
  PDCD1 WILD-TYPE 192 171  89  84
D271V5, multiclass
    clus
vv   PDCD1 MUTATED PDCD1 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V6, binary
                 cls
clus                0   1
  PDCD1 MUTATED     6   0
  PDCD1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      6    0
  PDCD1 WILD-TYPE  476   38
   clus
vv  PDCD1 MUTATED PDCD1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D271V7, binary
                 cls
clus                0   1
  PDCD1 MUTATED     4   2
  PDCD1 WILD-TYPE 168 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      4    2
  PDCD1 WILD-TYPE  168  404
        clus
vv       PDCD1 MUTATED PDCD1 WILD-TYPE
  FEMALE             4             168
  MALE               2             404
[1] 2 2
[1] FALSE
D271V8, binary
                 cls
clus                0   1
  PDCD1 MUTATED     3   2
  PDCD1 WILD-TYPE 413 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      3    2
  PDCD1 WILD-TYPE  413  100
     clus
vv    PDCD1 MUTATED PDCD1 WILD-TYPE
  NO              3             413
  YES             2             100
[1] 2 2
[1] FALSE
D271V9, continuous
D271V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDCD1 MUTATED       0                         1
  PDCD1 WILD-TYPE   133                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDCD1 MUTATED                                           0     5
  PDCD1 WILD-TYPE                                         1   352
D271V11, multiclass
                                           clus
vv                                          PDCD1 MUTATED PDCD1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V12, binary
                 cls
clus                0   1
  PDCD1 MUTATED     0   4
  PDCD1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      0    4
  PDCD1 WILD-TYPE   10  394
                        clus
vv                       PDCD1 MUTATED PDCD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(272) Variable = TMC4 MUTATION ANALYSIS
D272V1, survival
                sevent
clus2              0   1
  TMC4 MUTATED    14   6
  TMC4 WILD-TYPE 324 210
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            534 
  TMC4 MUTATED TMC4 WILD-TYPE 
             6            210 
$`TMC4 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-LN-A49S TCGA-XP-A8T6 TCGA-BR-4184 
       21.01        16.47         5.49        13.15        25.08         6.97 
TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8367 TCGA-BR-8370 
       34.68        14.43        29.59         6.18        26.33         3.32 
TCGA-BR-8371 TCGA-CD-8530 TCGA-CG-5723 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       11.80        12.39       105.07        16.80        17.19        14.66 
TCGA-RD-A8N1 TCGA-VQ-A8P2 
      115.69        38.14 

$`TMC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8372 
       22.19        17.52         0.95         4.31        14.04        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       40.64       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TMC4 MUTATED TMC4 WILD-TYPE 
          3.32           0.00 
  TMC4 MUTATED TMC4 WILD-TYPE 
        115.69         122.30 
  TMC4 MUTATED TMC4 WILD-TYPE 
        16.635         13.495 
[1] "3.3 - 115.7 (16.6)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D272V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMC4 MUTATED         1        0        0        2         3         3
  TMC4 WILD-TYPE       9       20       46       29        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMC4 MUTATED           3          3          5          0        0         0
  TMC4 WILD-TYPE        26         81         57         39       43         4
D272V3, multiclass
            clus
vv           TMC4 MUTATED TMC4 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             3             26
  STAGE IIIA            3             81
  STAGE IIIB            5             57
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TMC4 MUTATED       1   4  12   3
  TMC4 WILD-TYPE    53 131 249  99
D272V4, multiclass
       clus
vv      TMC4 MUTATED TMC4 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3              12            249
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TMC4 MUTATED     6   7   2   5
  TMC4 WILD-TYPE 189 166  87  80
D272V5, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  N0            6            189
  N1            7            166
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V6, binary
                cls
clus               0   1
  TMC4 MUTATED    19   0
  TMC4 WILD-TYPE 463  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     19    0
  TMC4 WILD-TYPE  463   38
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0           19            463
  1            0             38
[1] 2 2
[1] FALSE
D272V7, binary
                cls
clus               0   1
  TMC4 MUTATED     4  16
  TMC4 WILD-TYPE 168 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      4   16
  TMC4 WILD-TYPE  168  390
        clus
vv       TMC4 MUTATED TMC4 WILD-TYPE
  FEMALE            4            168
  MALE             16            390
[1] 2 2
[1] FALSE
D272V8, binary
                cls
clus               0   1
  TMC4 MUTATED    16   4
  TMC4 WILD-TYPE 400  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     16    4
  TMC4 WILD-TYPE  400   98
     clus
vv    TMC4 MUTATED TMC4 WILD-TYPE
  NO            16            400
  YES            4             98
[1] 2 2
[1] FALSE
D272V9, continuous
[1] "Remove cluster labels:" "TMC4 MUTATED"          
clus
  TMC4 MUTATED TMC4 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"TMC4 WILD-TYPE" "TMC4 WILD-TYPE" 
D272V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TMC4 MUTATED       2                         1
  TMC4 WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMC4 MUTATED                                           0    16
  TMC4 WILD-TYPE                                         1   341
D272V11, multiclass
                                           clus
vv                                          TMC4 MUTATED TMC4 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V12, binary
                cls
clus               0   1
  TMC4 MUTATED     1  14
  TMC4 WILD-TYPE   9 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      1   14
  TMC4 WILD-TYPE    9  384
                        clus
vv                       TMC4 MUTATED TMC4 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(273) Variable = ACP1 MUTATION ANALYSIS
D273V1, survival
                sevent
clus2              0   1
  ACP1 MUTATED     5   2
  ACP1 WILD-TYPE 333 214
  ACP1 MUTATED ACP1 WILD-TYPE 
             7            547 
  ACP1 MUTATED ACP1 WILD-TYPE 
             2            214 
$`ACP1 MUTATED`
TCGA-BR-4184 TCGA-CD-8536 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
        6.97        12.43         5.92        30.51        22.68        29.98 
TCGA-MX-A5UJ 
       19.73 

$`ACP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ACP1 MUTATED ACP1 WILD-TYPE 
          5.92           0.00 
  ACP1 MUTATED ACP1 WILD-TYPE 
         30.51         122.30 
  ACP1 MUTATED ACP1 WILD-TYPE 
         19.73          13.55 
[1] "5.9 - 30.5 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D273V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACP1 MUTATED         0        0        0        1         1         2
  ACP1 WILD-TYPE      10       20       46       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACP1 MUTATED           0          3          0          1        0         0
  ACP1 WILD-TYPE        29         81         62         38       43         4
D273V3, multiclass
            clus
vv           ACP1 MUTATED ACP1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ACP1 MUTATED       0   1   5   2
  ACP1 WILD-TYPE    54 134 256 100
D273V4, multiclass
       clus
vv      ACP1 MUTATED ACP1 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ACP1 MUTATED     2   5   1   1
  ACP1 WILD-TYPE 193 168  88  84
D273V5, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  N0            2            193
  N1            5            168
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V6, binary
                cls
clus               0   1
  ACP1 MUTATED     8   0
  ACP1 WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      8    0
  ACP1 WILD-TYPE  474   38
   clus
vv  ACP1 MUTATED ACP1 WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D273V7, binary
                cls
clus               0   1
  ACP1 MUTATED     6   3
  ACP1 WILD-TYPE 166 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      6    3
  ACP1 WILD-TYPE  166  403
        clus
vv       ACP1 MUTATED ACP1 WILD-TYPE
  FEMALE            6            166
  MALE              3            403
[1] 2 2
[1] FALSE
D273V8, binary
                cls
clus               0   1
  ACP1 MUTATED     6   1
  ACP1 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      6    1
  ACP1 WILD-TYPE  410  101
     clus
vv    ACP1 MUTATED ACP1 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D273V9, continuous
D273V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ACP1 MUTATED       3                         0
  ACP1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACP1 MUTATED                                           0     5
  ACP1 WILD-TYPE                                         1   352
D273V11, multiclass
                                           clus
vv                                          ACP1 MUTATED ACP1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V12, binary
                cls
clus               0   1
  ACP1 MUTATED     0   8
  ACP1 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      0    8
  ACP1 WILD-TYPE   10  390
                        clus
vv                       ACP1 MUTATED ACP1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(274) Variable = PLOD3 MUTATION ANALYSIS
D274V1, survival
                 sevent
clus2               0   1
  PLOD3 MUTATED    12   6
  PLOD3 WILD-TYPE 326 210
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             18             536 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
              6             210 
$`PLOD3 MUTATED`
TCGA-L5-A43I TCGA-2H-A9GI TCGA-L5-A8NQ TCGA-V5-A7RE TCGA-BR-6452 TCGA-BR-6565 
       18.28        14.30        21.37        16.44        34.68         9.17 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5723 
        4.31        31.27         1.12        11.77         9.01       105.07 
TCGA-D7-A4Z0 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-VQ-A8P2 
       14.76        29.98        20.25        29.00        23.80        38.14 

$`PLOD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       17.29        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       21.37         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLOD3 MUTATED PLOD3 WILD-TYPE 
           1.12            0.00 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
         105.07          122.30 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
         19.265          13.445 
[1] "1.1 - 105.1 (19.3)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D274V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLOD3 MUTATED         0        0        3        1         4         2
  PLOD3 WILD-TYPE      10       20       43       30        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLOD3 MUTATED           1          3          0          3        2         0
  PLOD3 WILD-TYPE        28         81         62         36       41         4
D274V3, multiclass
            clus
vv           PLOD3 MUTATED PLOD3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PLOD3 MUTATED       1   6   6   7
  PLOD3 WILD-TYPE    53 129 255  95
D274V4, multiclass
       clus
vv      PLOD3 MUTATED PLOD3 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                6             255
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PLOD3 MUTATED     7   6   3   3
  PLOD3 WILD-TYPE 188 167  86  82
D274V5, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V6, binary
                 cls
clus                0   1
  PLOD3 MUTATED    17   1
  PLOD3 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED     17    1
  PLOD3 WILD-TYPE  465   37
   clus
vv  PLOD3 MUTATED PLOD3 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D274V7, binary
                 cls
clus                0   1
  PLOD3 MUTATED     8  12
  PLOD3 WILD-TYPE 164 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      8   12
  PLOD3 WILD-TYPE  164  394
        clus
vv       PLOD3 MUTATED PLOD3 WILD-TYPE
  FEMALE             8             164
  MALE              12             394
[1] 2 2
[1] FALSE
D274V8, binary
                 cls
clus                0   1
  PLOD3 MUTATED    12   4
  PLOD3 WILD-TYPE 404  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED     12    4
  PLOD3 WILD-TYPE  404   98
     clus
vv    PLOD3 MUTATED PLOD3 WILD-TYPE
  NO             12             404
  YES             4              98
[1] 2 2
[1] FALSE
D274V9, continuous
[1] "Remove cluster labels:" "PLOD3 MUTATED"         
clus
  PLOD3 MUTATED PLOD3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
D274V10, continuous
[1] "Remove cluster labels:" "PLOD3 MUTATED"         
clus
  PLOD3 MUTATED PLOD3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NR 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" "PLOD3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PLOD3 MUTATED       5                         0
  PLOD3 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLOD3 MUTATED                                           0    12
  PLOD3 WILD-TYPE                                         1   345
D274V11, multiclass
                                           clus
vv                                          PLOD3 MUTATED PLOD3 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V12, binary
                 cls
clus                0   1
  PLOD3 MUTATED     0  14
  PLOD3 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      0   14
  PLOD3 WILD-TYPE   10  384
                        clus
vv                       PLOD3 MUTATED PLOD3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(275) Variable = TMEM41B MUTATION ANALYSIS
D275V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     2   3
  TMEM41B WILD-TYPE 336 213
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               549 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               213 
$`TMEM41B MUTATED`
TCGA-LN-A4A8 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-A4QL TCGA-MX-A5UJ 
       15.52         6.97        30.90        16.14        19.73 

$`TMEM41B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             6.97              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
             30.9             122.3 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            16.14             13.51 
[1] "7.0 - 30.9 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D275V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM41B MUTATED         1        0        0        0         1         0
  TMEM41B WILD-TYPE       9       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          2          1          0        0
  TMEM41B WILD-TYPE        29         82         61         39       43
                   vv
clus                STAGE IVA
  TMEM41B MUTATED           0
  TMEM41B WILD-TYPE         4
D275V3, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM41B MUTATED       1   2   3   0
  TMEM41B WILD-TYPE    53 133 258 102
D275V4, multiclass
       clus
vv      TMEM41B MUTATED TMEM41B WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  3               258
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM41B MUTATED     1   2   1   1
  TMEM41B WILD-TYPE 194 171  88  84
D275V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               1               194
  N1               2               171
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V6, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     4   0
  TMEM41B WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      4    0
  TMEM41B WILD-TYPE  478   38
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D275V7, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     3   3
  TMEM41B WILD-TYPE 169 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      3    3
  TMEM41B WILD-TYPE  169  403
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               3               169
  MALE                 3               403
[1] 2 2
[1] FALSE
D275V8, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     6   0
  TMEM41B WILD-TYPE 410 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      6    0
  TMEM41B WILD-TYPE  410  102
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                6               410
  YES               0               102
[1] 2 2
[1] FALSE
D275V9, continuous
[1] "Remove cluster labels:" "TMEM41B MUTATED"       
clus
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
D275V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM41B MUTATED       1                         1
  TMEM41B WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM41B MUTATED                                           0     4
  TMEM41B WILD-TYPE                                         1   353
D275V11, multiclass
                                           clus
vv                                          TMEM41B MUTATED TMEM41B WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V12, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     0   6
  TMEM41B WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      0    6
  TMEM41B WILD-TYPE   10  392
                        clus
vv                       TMEM41B MUTATED TMEM41B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(276) Variable = ATP2B4 MUTATION ANALYSIS
D276V1, survival
                  sevent
clus2                0   1
  ATP2B4 MUTATED    14   7
  ATP2B4 WILD-TYPE 324 209
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              21              533 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               7              209 
$`ATP2B4 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OH TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A9FP TCGA-R6-A6DQ 
       19.99        32.61        22.39        15.52        12.03         7.59 
TCGA-V5-AASX TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8372 TCGA-CD-8536 
        8.98        19.33        44.94         0.26        31.27        12.43 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A6EX TCGA-D7-A74B TCGA-F1-6874 TCGA-MX-A5UJ 
        6.58       105.07        11.31         7.13        14.47        19.73 
TCGA-RD-A7BT TCGA-SW-A7EA TCGA-VQ-A8P2 
        8.61        19.04        38.14 

$`ATP2B4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.76        12.59        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 
       22.29        15.65         8.38         4.34        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
            0.26             0.00 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          105.07           122.30 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
           15.52            13.51 
[1] "0.3 - 105.1 (15.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D276V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2B4 MUTATED         1        0        3        2         5         1
  ATP2B4 WILD-TYPE       9       20       43       29        79        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B4 MUTATED           0          3          1          2        1
  ATP2B4 WILD-TYPE        29         81         61         37       42
                  vv
clus               STAGE IVA
  ATP2B4 MUTATED           0
  ATP2B4 WILD-TYPE         4
D276V3, multiclass
            clus
vv           ATP2B4 MUTATED ATP2B4 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               5               79
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATP2B4 MUTATED       1   7  10   2
  ATP2B4 WILD-TYPE    53 128 251 100
D276V4, multiclass
       clus
vv      ATP2B4 MUTATED ATP2B4 WILD-TYPE
  T0+T1              1               53
  T2                 7              128
  T3                10              251
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP2B4 MUTATED    10   3   2   4
  ATP2B4 WILD-TYPE 185 170  87  81
D276V5, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  N0             10              185
  N1              3              170
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V6, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    18   0
  ATP2B4 WILD-TYPE 464  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     18    0
  ATP2B4 WILD-TYPE  464   38
   clus
vv  ATP2B4 MUTATED ATP2B4 WILD-TYPE
  0             18              464
  1              0               38
[1] 2 2
[1] FALSE
D276V7, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    10  12
  ATP2B4 WILD-TYPE 162 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     10   12
  ATP2B4 WILD-TYPE  162  394
        clus
vv       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  FEMALE             10              162
  MALE               12              394
[1] 2 2
[1] FALSE
D276V8, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    17   2
  ATP2B4 WILD-TYPE 399 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     17    2
  ATP2B4 WILD-TYPE  399  100
     clus
vv    ATP2B4 MUTATED ATP2B4 WILD-TYPE
  NO              17              399
  YES              2              100
[1] 2 2
[1] FALSE
D276V9, continuous
D276V10, continuous
[1] "Remove cluster labels:" "ATP2B4 MUTATED"        
clus
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" "ATP2B4 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP2B4 MUTATED       5                         0
  ATP2B4 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP2B4 MUTATED                                           1    15
  ATP2B4 WILD-TYPE                                         0   342
D276V11, multiclass
                                           clus
vv                                          ATP2B4 MUTATED ATP2B4 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V12, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED     0  18
  ATP2B4 WILD-TYPE  10 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED      0   18
  ATP2B4 WILD-TYPE   10  380
                        clus
vv                       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(277) Variable = LRRN2 MUTATION ANALYSIS
D277V1, survival
                 sevent
clus2               0   1
  LRRN2 MUTATED    22  12
  LRRN2 WILD-TYPE 316 204
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             34             520 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             12             204 
$`LRRN2 MUTATED`
TCGA-CG-4460 TCGA-LN-A49M TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8078 
       21.99        12.66        34.68        44.94        14.43        29.59 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8382 
        8.05         6.18        26.33         4.31        11.80        25.05 
TCGA-BR-8487 TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-A4J2 TCGA-CD-8525 TCGA-CD-8526 
        1.12        26.73         9.86        14.17        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 
       12.33        12.30        12.39        12.59        11.64        12.07 
TCGA-CD-8536 TCGA-CD-A48A TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-FP-8211 
       12.43        12.43        19.50        17.19        14.66        13.58 
TCGA-HU-8243 TCGA-HU-A4GP TCGA-RD-A7BW TCGA-VQ-A91U 
        5.92         8.98         5.13         1.71 

$`LRRN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 
       31.10         0.26        22.19        17.52         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 
       11.21        12.10        12.39        12.76         7.17        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.82         6.31        12.30        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  LRRN2 MUTATED LRRN2 WILD-TYPE 
           1.12            0.00 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
          44.94          122.30 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
         12.480          13.905 
[1] "1.1 - 44.9 (12.5)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D277V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRN2 MUTATED         0        0        2        4         8         4
  LRRN2 WILD-TYPE      10       20       44       27        76        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRN2 MUTATED           1          6          5          3        2         0
  LRRN2 WILD-TYPE        28         78         57         36       41         4
D277V3, multiclass
            clus
vv           LRRN2 MUTATED LRRN2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               4              27
  STAGE IIA              8              76
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             6              78
  STAGE IIIB             5              57
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LRRN2 MUTATED       0   5  19  11
  LRRN2 WILD-TYPE    54 130 242  91
D277V4, multiclass
       clus
vv      LRRN2 MUTATED LRRN2 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3               19             242
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LRRN2 MUTATED    18   8   1   8
  LRRN2 WILD-TYPE 177 165  88  77
D277V5, multiclass
    clus
vv   LRRN2 MUTATED LRRN2 WILD-TYPE
  N0            18             177
  N1             8             165
  N2             1              88
  N3             8              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V6, binary
                 cls
clus                0   1
  LRRN2 MUTATED    32   2
  LRRN2 WILD-TYPE 450  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     32    2
  LRRN2 WILD-TYPE  450   36
   clus
vv  LRRN2 MUTATED LRRN2 WILD-TYPE
  0            32             450
  1             2              36
[1] 2 2
[1] FALSE
D277V7, binary
                 cls
clus                0   1
  LRRN2 MUTATED    16  19
  LRRN2 WILD-TYPE 156 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     16   19
  LRRN2 WILD-TYPE  156  387
        clus
vv       LRRN2 MUTATED LRRN2 WILD-TYPE
  FEMALE            16             156
  MALE              19             387
[1] 2 2
[1] FALSE
D277V8, binary
                 cls
clus                0   1
  LRRN2 MUTATED    26   9
  LRRN2 WILD-TYPE 390  93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     26    9
  LRRN2 WILD-TYPE  390   93
     clus
vv    LRRN2 MUTATED LRRN2 WILD-TYPE
  NO             26             390
  YES             9              93
[1] 2 2
[1] FALSE
D277V9, continuous
[1] "Remove cluster labels:" "LRRN2 MUTATED"         
clus
  LRRN2 MUTATED LRRN2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" "LRRN2 WILD-TYPE" 
D277V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRRN2 MUTATED      16                         0
  LRRN2 WILD-TYPE   117                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRN2 MUTATED                                           0    18
  LRRN2 WILD-TYPE                                         1   339
D277V11, multiclass
                                           clus
vv                                          LRRN2 MUTATED LRRN2 WILD-TYPE
  ASIAN                                                16             117
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V12, binary
                 cls
clus                0   1
  LRRN2 MUTATED     0  33
  LRRN2 WILD-TYPE  10 365
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED      0   33
  LRRN2 WILD-TYPE   10  365
                        clus
vv                       LRRN2 MUTATED LRRN2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            33             365
[1] 2 2
[1] FALSE

Clustering(278) Variable = OBSCN MUTATION ANALYSIS
D278V1, survival
                 sevent
clus2               0   1
  OBSCN MUTATED    67  41
  OBSCN WILD-TYPE 271 175
  OBSCN MUTATED OBSCN WILD-TYPE 
            108             446 
  OBSCN MUTATED OBSCN WILD-TYPE 
             41             175 
$`OBSCN MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-CG-4460 TCGA-MX-A663 TCGA-2H-A9GJ 
        4.31        24.00        19.99        21.99         9.86        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NQ 
        7.63        13.94        33.27         7.40         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A8I1 
        8.71        52.57        12.46        12.49        12.76        13.18 
TCGA-LN-A9FP TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-V5-AASW TCGA-VR-A8EX TCGA-VR-AA4G 
       12.03         6.35        12.69         9.27        28.11        18.05 
TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6563 
        9.17        41.23         6.97        34.68        13.87        39.12 
TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8059 
       32.78        19.89         9.21        35.24        35.84        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 
       11.44         0.69        29.59        32.25         8.05        29.42 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10         0.26        17.52         0.95 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 
        4.31         3.32         1.12        31.96        13.87         7.53 
TCGA-BR-A4J2 TCGA-BR-A4QL TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       14.17        16.14        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4300 
       12.30        12.59        11.64         6.58        11.77        20.02 
TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
        1.02        29.98         6.02       105.07        65.10        21.07 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-FP-8209 
       16.80        19.50        14.66        11.44        20.32        59.54 
TCGA-FP-8211 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58        11.08        77.29        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GF 
        5.92        28.96        22.32         0.76        22.68        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-R5-A7ZI 
        0.26        29.00        14.07        13.35        19.73        74.53 
TCGA-RD-A7BS TCGA-RD-A8MW TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA68 TCGA-VQ-AA6J 
       11.05        37.91        19.04        38.14        43.66        27.55 

$`OBSCN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        20.05        31.27        14.30         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU 
       16.47        13.55        13.22         5.49        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.59        13.25        12.62        12.59        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.18        12.33        13.38         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       46.19        11.24        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       17.29        13.68        19.33        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       44.94        21.90        36.16        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       37.25         9.60         0.56         2.66        19.96         2.20 
TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       22.19        26.33        14.04        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        34.13         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98         0.72         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8527 
       13.18        13.35        11.21        12.10        12.39         7.17 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.39        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       11.31        12.33        24.72        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.76        26.43        11.24        11.31        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       14.07        22.29        17.06         5.03         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-8608 
        6.21        63.06        52.21        24.39        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.37         6.51         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  OBSCN MUTATED OBSCN WILD-TYPE 
            0.1             0.0 
  OBSCN MUTATED OBSCN WILD-TYPE 
         105.07          122.30 
  OBSCN MUTATED OBSCN WILD-TYPE 
         13.905          13.495 
[1] "0.1 - 105.1 (13.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D278V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OBSCN MUTATED         2        3        9        7        23        15
  OBSCN WILD-TYPE       8       17       37       24        61        68
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OBSCN MUTATED           4         17         10         11        7         1
  OBSCN WILD-TYPE        25         67         52         28       36         3
D278V3, multiclass
            clus
vv           OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I                2               8
  STAGE IA               3              17
  STAGE IB               9              37
  STAGE II               7              24
  STAGE IIA             23              61
  STAGE IIB             15              68
  STAGE III              4              25
  STAGE IIIA            17              67
  STAGE IIIB            10              52
  STAGE IIIC            11              28
  STAGE IV               7              36
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OBSCN MUTATED       9  22  51  28
  OBSCN WILD-TYPE    45 113 210  74
D278V4, multiclass
       clus
vv      OBSCN MUTATED OBSCN WILD-TYPE
  T0+T1             9              45
  T2               22             113
  T3               51             210
  T4               28              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OBSCN MUTATED    46  33  18  13
  OBSCN WILD-TYPE 149 140  71  72
D278V5, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  N0            46             149
  N1            33             140
  N2            18              71
  N3            13              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V6, binary
                 cls
clus                0   1
  OBSCN MUTATED    98   6
  OBSCN WILD-TYPE 384  32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     98    6
  OBSCN WILD-TYPE  384   32
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0            98             384
  1             6              32
[1] 2 2
[1] FALSE
D278V7, binary
                 cls
clus                0   1
  OBSCN MUTATED    49  65
  OBSCN WILD-TYPE 123 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     49   65
  OBSCN WILD-TYPE  123  341
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  FEMALE            49             123
  MALE              65             341
[1] 2 2
[1] FALSE
D278V8, binary
                 cls
clus                0   1
  OBSCN MUTATED    84  19
  OBSCN WILD-TYPE 332  83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     84   19
  OBSCN WILD-TYPE  332   83
     clus
vv    OBSCN MUTATED OBSCN WILD-TYPE
  NO             84             332
  YES            19              83
[1] 2 2
[1] FALSE
D278V9, continuous
D278V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OBSCN MUTATED      33                         3
  OBSCN WILD-TYPE   100                        11
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OBSCN MUTATED                                           0    61
  OBSCN WILD-TYPE                                         1   296
D278V11, multiclass
                                           clus
vv                                          OBSCN MUTATED OBSCN WILD-TYPE
  ASIAN                                                33             100
  BLACK OR AFRICAN AMERICAN                             3              11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                61             296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V12, binary
                 cls
clus                0   1
  OBSCN MUTATED     3  83
  OBSCN WILD-TYPE   7 315
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      3   83
  OBSCN WILD-TYPE    7  315
                        clus
vv                       OBSCN MUTATED OBSCN WILD-TYPE
  HISPANIC OR LATINO                 3               7
  NOT HISPANIC OR LATINO            83             315
[1] 2 2
[1] FALSE

Clustering(279) Variable = KIDINS220 MUTATION ANALYSIS
D279V1, survival
                     sevent
clus2                   0   1
  KIDINS220 MUTATED    17   9
  KIDINS220 WILD-TYPE 321 207
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 26                 528 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  9                 207 
$`KIDINS220 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GJ TCGA-L5-A43H TCGA-L5-A8NM 
       34.85        19.99        21.99        58.55         0.30         7.76 
TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A4A6 TCGA-LN-A7HX TCGA-R6-A6Y2 TCGA-BR-4184 
       21.37        12.66        12.85        12.23         9.30         6.97 
TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5721 
       18.35        34.68        35.84         1.12         6.58         6.02 
TCGA-D7-6815 TCGA-F1-A448 TCGA-HF-7133 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GX 
       15.98        21.27        63.06        22.68        11.77        20.25 
TCGA-HU-A4H3 TCGA-VQ-A8P2 
       29.00        38.14 

$`KIDINS220 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.61         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                0.3                 0.0 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
              63.06              122.30 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
              19.17               13.51 
[1] "0.3 - 63.1 (19.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D279V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIDINS220 MUTATED         1        1        1        1         6         4
  KIDINS220 WILD-TYPE       9       19       45       30        78        79
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIDINS220 MUTATED           1          3          1          3        3
  KIDINS220 WILD-TYPE        28         81         61         36       40
                     vv
clus                  STAGE IVA
  KIDINS220 MUTATED           0
  KIDINS220 WILD-TYPE         4
D279V3, multiclass
            clus
vv           KIDINS220 MUTATED KIDINS220 WILD-TYPE
  STAGE I                    1                   9
  STAGE IA                   1                  19
  STAGE IB                   1                  45
  STAGE II                   1                  30
  STAGE IIA                  6                  78
  STAGE IIB                  4                  79
  STAGE III                  1                  28
  STAGE IIIA                 3                  81
  STAGE IIIB                 1                  61
  STAGE IIIC                 3                  36
  STAGE IV                   3                  40
  STAGE IVA                  0                   4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  KIDINS220 MUTATED       2   8   9   6
  KIDINS220 WILD-TYPE    52 127 252  96
D279V4, multiclass
       clus
vv      KIDINS220 MUTATED KIDINS220 WILD-TYPE
  T0+T1                 2                  52
  T2                    8                 127
  T3                    9                 252
  T4                    6                  96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  KIDINS220 MUTATED    12   8   2   4
  KIDINS220 WILD-TYPE 183 165  87  81
D279V5, multiclass
    clus
vv   KIDINS220 MUTATED KIDINS220 WILD-TYPE
  N0                12                 183
  N1                 8                 165
  N2                 2                  87
  N3                 4                  81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V6, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    24   1
  KIDINS220 WILD-TYPE 458  37
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     24    1
  KIDINS220 WILD-TYPE  458   37
   clus
vv  KIDINS220 MUTATED KIDINS220 WILD-TYPE
  0                24                 458
  1                 1                  37
[1] 2 2
[1] FALSE
D279V7, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    12  16
  KIDINS220 WILD-TYPE 160 390
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     12   16
  KIDINS220 WILD-TYPE  160  390
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  FEMALE                12                 160
  MALE                  16                 390
[1] 2 2
[1] FALSE
D279V8, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    20   5
  KIDINS220 WILD-TYPE 396  97
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     20    5
  KIDINS220 WILD-TYPE  396   97
     clus
vv    KIDINS220 MUTATED KIDINS220 WILD-TYPE
  NO                 20                 396
  YES                 5                  97
[1] 2 2
[1] FALSE
D279V9, continuous
D279V10, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  KIDINS220 MUTATED       8                         0
  KIDINS220 WILD-TYPE   125                        14
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIDINS220 MUTATED                                           0    16
  KIDINS220 WILD-TYPE                                         1   341
D279V11, multiclass
                                           clus
vv                                          KIDINS220 MUTATED
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                    16
                                           clus
vv                                          KIDINS220 WILD-TYPE
  ASIAN                                                     125
  BLACK OR AFRICAN AMERICAN                                  14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V12, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED     2  16
  KIDINS220 WILD-TYPE   8 382
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED      2   16
  KIDINS220 WILD-TYPE    8  382
                        clus
vv                       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  HISPANIC OR LATINO                     2                   8
  NOT HISPANIC OR LATINO                16                 382
[1] 2 2
[1] FALSE

Clustering(280) Variable = NID2 MUTATION ANALYSIS
D280V1, survival
                sevent
clus2              0   1
  NID2 MUTATED    12   8
  NID2 WILD-TYPE 326 208
  NID2 MUTATED NID2 WILD-TYPE 
            20            534 
  NID2 MUTATED NID2 WILD-TYPE 
             8            208 
$`NID2 MUTATED`
TCGA-Q9-A6FU TCGA-L5-A8NJ TCGA-R6-A8W8 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 
        5.16        16.47         2.89        19.56         6.97        30.90 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8381 TCGA-CD-A4MI 
        9.34        34.68        31.10         4.31         7.36        11.77 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6524 TCGA-HF-7132 TCGA-HJ-7597 
       12.62         6.02        21.07        17.85        77.29        26.47 
TCGA-HU-A4GN TCGA-HU-A4GX 
       29.98        20.25 

$`NID2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27        14.79        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61         6.58        12.20        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NID2 MUTATED NID2 WILD-TYPE 
          2.89           0.00 
  NID2 MUTATED NID2 WILD-TYPE 
         77.29         122.30 
  NID2 MUTATED NID2 WILD-TYPE 
         17.16          13.53 
[1] "2.9 - 77.3 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D280V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NID2 MUTATED         0        0        3        2         2         1
  NID2 WILD-TYPE      10       20       43       29        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NID2 MUTATED           1          3          1          3        1         0
  NID2 WILD-TYPE        28         81         61         36       42         4
D280V3, multiclass
            clus
vv           NID2 MUTATED NID2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NID2 MUTATED       1   8   6   4
  NID2 WILD-TYPE    53 127 255  98
D280V4, multiclass
       clus
vv      NID2 MUTATED NID2 WILD-TYPE
  T0+T1            1             53
  T2               8            127
  T3               6            255
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NID2 MUTATED     4  10   4   1
  NID2 WILD-TYPE 191 163  85  84
D280V5, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  N0            4            191
  N1           10            163
  N2            4             85
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V6, binary
                cls
clus               0   1
  NID2 MUTATED    19   0
  NID2 WILD-TYPE 463  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     19    0
  NID2 WILD-TYPE  463   38
   clus
vv  NID2 MUTATED NID2 WILD-TYPE
  0           19            463
  1            0             38
[1] 2 2
[1] FALSE
D280V7, binary
                cls
clus               0   1
  NID2 MUTATED    10  12
  NID2 WILD-TYPE 162 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     10   12
  NID2 WILD-TYPE  162  394
        clus
vv       NID2 MUTATED NID2 WILD-TYPE
  FEMALE           10            162
  MALE             12            394
[1] 2 2
[1] FALSE
D280V8, binary
                cls
clus               0   1
  NID2 MUTATED    19   1
  NID2 WILD-TYPE 397 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     19    1
  NID2 WILD-TYPE  397  101
     clus
vv    NID2 MUTATED NID2 WILD-TYPE
  NO            19            397
  YES            1            101
[1] 2 2
[1] FALSE
D280V9, continuous
D280V10, continuous
[1] "Remove cluster labels:" "NID2 MUTATED"          
clus
  NID2 MUTATED NID2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-IC-A6RE     TCGA-IG-A3QL 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" "NID2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NID2 MUTATED       4                         0
  NID2 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NID2 MUTATED                                           0    15
  NID2 WILD-TYPE                                         1   342
D280V11, multiclass
                                           clus
vv                                          NID2 MUTATED NID2 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V12, binary
                cls
clus               0   1
  NID2 MUTATED     0  18
  NID2 WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      0   18
  NID2 WILD-TYPE   10  380
                        clus
vv                       NID2 MUTATED NID2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(281) Variable = KIRREL MUTATION ANALYSIS
D281V1, survival
                  sevent
clus2                0   1
  KIRREL MUTATED    14  10
  KIRREL WILD-TYPE 324 206
  KIRREL MUTATED KIRREL WILD-TYPE 
              24              530 
  KIRREL MUTATED KIRREL WILD-TYPE 
              10              206 
$`KIRREL MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NK TCGA-LN-A49P TCGA-VR-A8Q7 TCGA-BR-4256 TCGA-BR-4267 
       19.99        13.55        12.33        52.27         9.34         6.18 
TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-A4CS TCGA-CG-5728 TCGA-D7-6525 
       35.84        14.43        31.10         1.48        65.10        13.35 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G8 TCGA-HU-A4GH 
       11.31        11.44        26.47         5.92        22.68        11.77 
TCGA-HU-A4H4 TCGA-IN-8663 TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       23.84         3.39        13.35        19.73        74.53        38.14 

$`KIRREL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.81        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIRREL MUTATED KIRREL WILD-TYPE 
            1.48             0.00 
  KIRREL MUTATED KIRREL WILD-TYPE 
           74.53           122.30 
  KIRREL MUTATED KIRREL WILD-TYPE 
          13.990           13.545 
[1] "1.5 - 74.5 (14.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D281V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIRREL MUTATED         0        1        4        0         2         3
  KIRREL WILD-TYPE      10       19       42       31        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL MUTATED           1          6          1          4        1
  KIRREL WILD-TYPE        28         78         61         35       42
                  vv
clus               STAGE IVA
  KIRREL MUTATED           0
  KIRREL WILD-TYPE         4
D281V3, multiclass
            clus
vv           KIRREL MUTATED KIRREL WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                4               42
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              6               78
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KIRREL MUTATED       1   8   8   6
  KIRREL WILD-TYPE    53 127 253  96
D281V4, multiclass
       clus
vv      KIRREL MUTATED KIRREL WILD-TYPE
  T0+T1              1               53
  T2                 8              127
  T3                 8              253
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KIRREL MUTATED     7   7   6   4
  KIRREL WILD-TYPE 188 166  83  81
D281V5, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  N0              7              188
  N1              7              166
  N2              6               83
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V6, binary
                  cls
clus                 0   1
  KIRREL MUTATED    21   1
  KIRREL WILD-TYPE 461  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     21    1
  KIRREL WILD-TYPE  461   37
   clus
vv  KIRREL MUTATED KIRREL WILD-TYPE
  0             21              461
  1              1               37
[1] 2 2
[1] FALSE
D281V7, binary
                  cls
clus                 0   1
  KIRREL MUTATED    11  13
  KIRREL WILD-TYPE 161 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     11   13
  KIRREL WILD-TYPE  161  393
        clus
vv       KIRREL MUTATED KIRREL WILD-TYPE
  FEMALE             11              161
  MALE               13              393
[1] 2 2
[1] FALSE
D281V8, binary
                  cls
clus                 0   1
  KIRREL MUTATED    20   2
  KIRREL WILD-TYPE 396 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     20    2
  KIRREL WILD-TYPE  396  100
     clus
vv    KIRREL MUTATED KIRREL WILD-TYPE
  NO              20              396
  YES              2              100
[1] 2 2
[1] FALSE
D281V9, continuous
[1] "Remove cluster labels:" "KIRREL MUTATED"        
clus
  KIRREL MUTATED KIRREL WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49R 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KIRREL WILD-TYPE" "KIRREL WILD-TYPE" 
D281V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIRREL MUTATED       5                         0
  KIRREL WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIRREL MUTATED                                           0    18
  KIRREL WILD-TYPE                                         1   339
D281V11, multiclass
                                           clus
vv                                          KIRREL MUTATED KIRREL WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V12, binary
                  cls
clus                 0   1
  KIRREL MUTATED     1  18
  KIRREL WILD-TYPE   9 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      1   18
  KIRREL WILD-TYPE    9  380
                        clus
vv                       KIRREL MUTATED KIRREL WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(282) Variable = PTCH1 MUTATION ANALYSIS
D282V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED    20  14
  PTCH1 WILD-TYPE 318 202
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             34             520 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             14             202 
$`PTCH1 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A3QL TCGA-JY-A6FA TCGA-JY-A93E 
        4.31        19.99        21.99        35.21        44.75        25.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-LN-A49R TCGA-V5-A7RC TCGA-VR-A8EU TCGA-VR-A8EW 
        7.76        21.37        13.38         3.42        18.31         8.12 
TCGA-XP-A8T8 TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8078 
       14.37        26.70        34.68        32.78        36.16        29.59 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8683 
        8.05         6.18         0.26         1.12        27.12         9.86 
TCGA-BR-8690 TCGA-BR-A4CQ TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A6EY TCGA-D7-A747 
       10.68        34.98         6.02        28.96        11.44         8.38 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-8604 TCGA-VQ-A8P2 
       11.08        22.32        22.82        38.14 

$`PTCH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       24.79        31.96        32.58        20.88         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8608 
       26.47         1.51         5.92        24.39        28.96        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.26            0.00 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          44.75          122.30 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          19.15           13.51 
[1] "0.3 - 44.8 (19.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D282V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTCH1 MUTATED         0        2        1        0         8         9
  PTCH1 WILD-TYPE      10       18       45       31        76        74
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH1 MUTATED           1          3          5          2        3         0
  PTCH1 WILD-TYPE        28         81         57         37       40         4
D282V3, multiclass
            clus
vv           PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              8              76
  STAGE IIB              9              74
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             5              57
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTCH1 MUTATED       4   5  14  11
  PTCH1 WILD-TYPE    50 130 247  91
D282V4, multiclass
       clus
vv      PTCH1 MUTATED PTCH1 WILD-TYPE
  T0+T1             4              50
  T2                5             130
  T3               14             247
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTCH1 MUTATED    16  12   2   4
  PTCH1 WILD-TYPE 179 161  87  81
D282V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0            16             179
  N1            12             161
  N2             2              87
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED    30   2
  PTCH1 WILD-TYPE 452  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     30    2
  PTCH1 WILD-TYPE  452   36
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0            30             452
  1             2              36
[1] 2 2
[1] FALSE
D282V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED    13  22
  PTCH1 WILD-TYPE 159 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     13   22
  PTCH1 WILD-TYPE  159  384
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE            13             159
  MALE              22             384
[1] 2 2
[1] FALSE
D282V8, binary
                 cls
clus                0   1
  PTCH1 MUTATED    27   6
  PTCH1 WILD-TYPE 389  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     27    6
  PTCH1 WILD-TYPE  389   96
     clus
vv    PTCH1 MUTATED PTCH1 WILD-TYPE
  NO             27             389
  YES             6              96
[1] 2 2
[1] FALSE
D282V9, continuous
D282V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTCH1 MUTATED       6                         3
  PTCH1 WILD-TYPE   127                        11
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTCH1 MUTATED                                           0    23
  PTCH1 WILD-TYPE                                         1   334
D282V11, multiclass
                                           clus
vv                                          PTCH1 MUTATED PTCH1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             3              11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V12, binary
                 cls
clus                0   1
  PTCH1 MUTATED     1  22
  PTCH1 WILD-TYPE   9 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      1   22
  PTCH1 WILD-TYPE    9  376
                        clus
vv                       PTCH1 MUTATED PTCH1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(283) Variable = NUP35 MUTATION ANALYSIS
D283V1, survival
                 sevent
clus2               0   1
  NUP35 MUTATED     4   2
  NUP35 WILD-TYPE 334 214
  NUP35 MUTATED NUP35 WILD-TYPE 
              6             548 
  NUP35 MUTATED NUP35 WILD-TYPE 
              2             214 
$`NUP35 MUTATED`
TCGA-L5-A43J TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8687 TCGA-CG-5723 TCGA-HU-A4G8 
        4.31        35.84        29.59         8.22       105.07        22.68 

$`NUP35 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NUP35 MUTATED NUP35 WILD-TYPE 
           4.31            0.00 
  NUP35 MUTATED NUP35 WILD-TYPE 
         105.07          122.30 
  NUP35 MUTATED NUP35 WILD-TYPE 
         26.135          13.530 
[1] "4.3 - 105.1 (26.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D283V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUP35 MUTATED         0        0        1        1         0         3
  NUP35 WILD-TYPE      10       20       45       30        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUP35 MUTATED           0          0          0          2        0         0
  NUP35 WILD-TYPE        29         84         62         37       43         4
D283V3, multiclass
            clus
vv           NUP35 MUTATED NUP35 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NUP35 MUTATED       0   2   2   3
  NUP35 WILD-TYPE    54 133 259  99
D283V4, multiclass
       clus
vv      NUP35 MUTATED NUP35 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NUP35 MUTATED     3   2   1   1
  NUP35 WILD-TYPE 192 171  88  84
D283V5, multiclass
    clus
vv   NUP35 MUTATED NUP35 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V6, binary
                 cls
clus                0   1
  NUP35 MUTATED     6   0
  NUP35 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      6    0
  NUP35 WILD-TYPE  476   38
   clus
vv  NUP35 MUTATED NUP35 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D283V7, binary
                 cls
clus                0   1
  NUP35 MUTATED     4   3
  NUP35 WILD-TYPE 168 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      4    3
  NUP35 WILD-TYPE  168  403
        clus
vv       NUP35 MUTATED NUP35 WILD-TYPE
  FEMALE             4             168
  MALE               3             403
[1] 2 2
[1] FALSE
D283V8, binary
                 cls
clus                0   1
  NUP35 MUTATED     5   0
  NUP35 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      5    0
  NUP35 WILD-TYPE  411  102
     clus
vv    NUP35 MUTATED NUP35 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D283V9, continuous
D283V10, continuous
[1] "Remove cluster labels:" "NUP35 MUTATED"         
clus
  NUP35 MUTATED NUP35 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" "NUP35 WILD-TYPE" 
     TCGA-Z6-AAPN 
"NUP35 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NUP35 MUTATED       1                         0
  NUP35 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUP35 MUTATED                                           0     4
  NUP35 WILD-TYPE                                         1   353
D283V11, multiclass
                                           clus
vv                                          NUP35 MUTATED NUP35 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V12, binary
                 cls
clus                0   1
  NUP35 MUTATED     0   4
  NUP35 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      0    4
  NUP35 WILD-TYPE   10  394
                        clus
vv                       NUP35 MUTATED NUP35 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(284) Variable = ZC3H18 MUTATION ANALYSIS
D284V1, survival
                  sevent
clus2                0   1
  ZC3H18 MUTATED    15   8
  ZC3H18 WILD-TYPE 323 208
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              23              531 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               8              208 
$`ZC3H18 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OO TCGA-LN-A4A1 TCGA-R6-A6Y2 TCGA-V5-AASX TCGA-BR-4201 
       19.99         3.32        12.59         9.30         8.98        30.90 
TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CD-A4MH 
        9.67        32.78         0.26        28.14         6.58        12.20 
TCGA-CG-4465 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6815 TCGA-FP-A4BE TCGA-HU-8243 
        9.01        65.10        21.07        15.98        11.08         5.92 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-R5-A7ZI 
       24.20        29.98        20.25        19.73        74.53 

$`ZC3H18 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       21.37         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
            0.26             0.00 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
           74.53           122.30 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
           15.98            13.55 
[1] "0.3 - 74.5 (16.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D284V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H18 MUTATED         0        1        2        0         6         1
  ZC3H18 WILD-TYPE      10       19       44       31        78        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H18 MUTATED           0          2          0          5        2
  ZC3H18 WILD-TYPE        29         82         62         34       41
                  vv
clus               STAGE IVA
  ZC3H18 MUTATED           0
  ZC3H18 WILD-TYPE         4
D284V3, multiclass
            clus
vv           ZC3H18 MUTATED ZC3H18 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               6               78
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              5               34
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZC3H18 MUTATED       1   6   9   5
  ZC3H18 WILD-TYPE    53 129 252  97
D284V4, multiclass
       clus
vv      ZC3H18 MUTATED ZC3H18 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 9              252
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZC3H18 MUTATED     8   2   4   5
  ZC3H18 WILD-TYPE 187 171  85  80
D284V5, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  N0              8              187
  N1              2              171
  N2              4               85
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V6, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    19   2
  ZC3H18 WILD-TYPE 463  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     19    2
  ZC3H18 WILD-TYPE  463   36
   clus
vv  ZC3H18 MUTATED ZC3H18 WILD-TYPE
  0             19              463
  1              2               36
[1] 2 2
[1] FALSE
D284V7, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    15  10
  ZC3H18 WILD-TYPE 157 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     15   10
  ZC3H18 WILD-TYPE  157  396
        clus
vv       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  FEMALE             15              157
  MALE               10              396
[1] 2 2
[1] FALSE
D284V8, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    17   2
  ZC3H18 WILD-TYPE 399 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     17    2
  ZC3H18 WILD-TYPE  399  100
     clus
vv    ZC3H18 MUTATED ZC3H18 WILD-TYPE
  NO              17              399
  YES              2              100
[1] 2 2
[1] FALSE
D284V9, continuous
[1] "Remove cluster labels:" "ZC3H18 MUTATED"        
clus
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A2 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
D284V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H18 MUTATED       7                         1
  ZC3H18 WILD-TYPE   126                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H18 MUTATED                                           0    14
  ZC3H18 WILD-TYPE                                         1   343
D284V11, multiclass
                                           clus
vv                                          ZC3H18 MUTATED ZC3H18 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V12, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     2  18
  ZC3H18 WILD-TYPE   8 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      2   18
  ZC3H18 WILD-TYPE    8  380
                        clus
vv                       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(285) Variable = GLYR1 MUTATION ANALYSIS
D285V1, survival
                 sevent
clus2               0   1
  GLYR1 MUTATED    11   4
  GLYR1 WILD-TYPE 327 212
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             15             539 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
              4             212 
$`GLYR1 MUTATED`
TCGA-L5-A8NM TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-A4QL 
        7.76         2.66         6.97        35.84        28.14        16.14 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CG-4437 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HF-7133 
       12.43        12.30         8.05         5.92        14.47        63.06 
TCGA-HF-A5NB TCGA-R5-A7ZI TCGA-VQ-A8P2 
       30.51        74.53        38.14 

$`GLYR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.82         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        77.29        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GLYR1 MUTATED GLYR1 WILD-TYPE 
           2.66            0.00 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
          74.53          122.30 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
          14.47           13.55 
[1] "2.7 - 74.5 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D285V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLYR1 MUTATED         0        0        2        2         1         3
  GLYR1 WILD-TYPE      10       20       44       29        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLYR1 MUTATED           0          3          1          2        2         0
  GLYR1 WILD-TYPE        29         81         61         37       41         4
D285V3, multiclass
            clus
vv           GLYR1 MUTATED GLYR1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GLYR1 MUTATED       0   5   6   5
  GLYR1 WILD-TYPE    54 130 255  97
D285V4, multiclass
       clus
vv      GLYR1 MUTATED GLYR1 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GLYR1 MUTATED     5   7   0   4
  GLYR1 WILD-TYPE 190 166  89  81
D285V5, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  N0             5             190
  N1             7             166
  N2             0              89
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V6, binary
                 cls
clus                0   1
  GLYR1 MUTATED    15   1
  GLYR1 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED     15    1
  GLYR1 WILD-TYPE  467   37
   clus
vv  GLYR1 MUTATED GLYR1 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D285V7, binary
                 cls
clus                0   1
  GLYR1 MUTATED     9   8
  GLYR1 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      9    8
  GLYR1 WILD-TYPE  163  398
        clus
vv       GLYR1 MUTATED GLYR1 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D285V8, binary
                 cls
clus                0   1
  GLYR1 MUTATED    12   3
  GLYR1 WILD-TYPE 404  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED     12    3
  GLYR1 WILD-TYPE  404   99
     clus
vv    GLYR1 MUTATED GLYR1 WILD-TYPE
  NO             12             404
  YES             3              99
[1] 2 2
[1] FALSE
D285V9, continuous
D285V10, continuous
[1] "Remove cluster labels:" "GLYR1 MUTATED"         
clus
  GLYR1 MUTATED GLYR1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" "GLYR1 WILD-TYPE" 
     TCGA-XP-A8T8 
"GLYR1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GLYR1 MUTATED       2                         0
  GLYR1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLYR1 MUTATED                                           0    12
  GLYR1 WILD-TYPE                                         1   345
D285V11, multiclass
                                           clus
vv                                          GLYR1 MUTATED GLYR1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V12, binary
                 cls
clus                0   1
  GLYR1 MUTATED     1  11
  GLYR1 WILD-TYPE   9 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      1   11
  GLYR1 WILD-TYPE    9  387
                        clus
vv                       GLYR1 MUTATED GLYR1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(286) Variable = FRYL MUTATION ANALYSIS
D286V1, survival
                sevent
clus2              0   1
  FRYL MUTATED    21   9
  FRYL WILD-TYPE 317 207
  FRYL MUTATED FRYL WILD-TYPE 
            30            524 
  FRYL MUTATED FRYL WILD-TYPE 
             9            207 
$`FRYL MUTATED`
TCGA-L5-A43I TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A8NN 
       18.28        44.75        47.38        21.70         6.28         5.49 
TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A7HV TCGA-LN-A9FP TCGA-Z6-AAPN TCGA-BR-4256 
       83.24        13.38        10.52        12.03         2.66         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8285 
        9.67        34.68        30.90        33.21        14.43         0.56 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5730 TCGA-CG-5733 
        4.31         1.12        31.96         6.02         4.01        21.07 
TCGA-D7-6526 TCGA-HF-7132 TCGA-HU-A4GT TCGA-IN-A6RL TCGA-IN-A7NT TCGA-VQ-A8P2 
       17.19        77.29         6.51        13.35        10.62        38.14 

$`FRYL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93C TCGA-JY-A93D 
      122.10        68.02         3.68        41.52        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       29.56        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FRYL MUTATED FRYL WILD-TYPE 
          0.56           0.00 
  FRYL MUTATED FRYL WILD-TYPE 
         83.24         122.30 
  FRYL MUTATED FRYL WILD-TYPE 
        13.365         13.630 
[1] "0.6 - 83.2 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D286V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FRYL MUTATED         0        1        2        1         7         4
  FRYL WILD-TYPE      10       19       44       30        77        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRYL MUTATED           3          8          0          1        3         0
  FRYL WILD-TYPE        26         76         62         38       40         4
D286V3, multiclass
            clus
vv           FRYL MUTATED FRYL WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             7             77
  STAGE IIB             4             79
  STAGE III             3             26
  STAGE IIIA            8             76
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FRYL MUTATED       3  11  10   7
  FRYL WILD-TYPE    51 124 251  95
D286V4, multiclass
       clus
vv      FRYL MUTATED FRYL WILD-TYPE
  T0+T1            3             51
  T2              11            124
  T3              10            251
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FRYL MUTATED    11  16   4   1
  FRYL WILD-TYPE 184 157  85  84
D286V5, multiclass
    clus
vv   FRYL MUTATED FRYL WILD-TYPE
  N0           11            184
  N1           16            157
  N2            4             85
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V6, binary
                cls
clus               0   1
  FRYL MUTATED    32   2
  FRYL WILD-TYPE 450  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     32    2
  FRYL WILD-TYPE  450   36
   clus
vv  FRYL MUTATED FRYL WILD-TYPE
  0           32            450
  1            2             36
[1] 2 2
[1] FALSE
D286V7, binary
                cls
clus               0   1
  FRYL MUTATED    15  20
  FRYL WILD-TYPE 157 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     15   20
  FRYL WILD-TYPE  157  386
        clus
vv       FRYL MUTATED FRYL WILD-TYPE
  FEMALE           15            157
  MALE             20            386
[1] 2 2
[1] FALSE
D286V8, binary
                cls
clus               0   1
  FRYL MUTATED    21   7
  FRYL WILD-TYPE 395  95
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     21    7
  FRYL WILD-TYPE  395   95
     clus
vv    FRYL MUTATED FRYL WILD-TYPE
  NO            21            395
  YES            7             95
[1] 2 2
[1] FALSE
D286V9, continuous
D286V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FRYL MUTATED       6                         0
  FRYL WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FRYL MUTATED                                           0    24
  FRYL WILD-TYPE                                         1   333
D286V11, multiclass
                                           clus
vv                                          FRYL MUTATED FRYL WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               24            333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V12, binary
                cls
clus               0   1
  FRYL MUTATED     0  23
  FRYL WILD-TYPE  10 375
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED      0   23
  FRYL WILD-TYPE   10  375
                        clus
vv                       FRYL MUTATED FRYL WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           23            375
[1] 2 2
[1] FALSE

Clustering(287) Variable = CNBD1 MUTATION ANALYSIS
D287V1, survival
                 sevent
clus2               0   1
  CNBD1 MUTATED    10  10
  CNBD1 WILD-TYPE 328 206
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             20             534 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             10             206 
$`CNBD1 MUTATED`
TCGA-IG-A4QS TCGA-L5-A891 TCGA-L5-A8NR TCGA-ZR-A9CJ TCGA-BR-4256 TCGA-BR-7901 
        3.88         3.75         8.71        19.73         9.34         3.45 
TCGA-BR-A4QM TCGA-CD-A48C TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-A6EY TCGA-HU-8238 
        5.13        11.61        20.55        15.22        11.44         1.51 
TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8663 TCGA-RD-A7C1 TCGA-VQ-A8DU 
       22.32        11.77        33.40         3.39        16.67         5.46 
TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       38.14        17.85 

$`CNBD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44        16.14        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CNBD1 MUTATED CNBD1 WILD-TYPE 
           1.51            0.00 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
          38.14          122.30 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
         11.525          13.730 
[1] "1.5 - 38.1 (11.5)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.8"
D287V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNBD1 MUTATED         0        1        2        0         0         4
  CNBD1 WILD-TYPE      10       19       44       31        84        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNBD1 MUTATED           1          4          3          1        0         0
  CNBD1 WILD-TYPE        28         80         59         38       43         4
D287V3, multiclass
            clus
vv           CNBD1 MUTATED CNBD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CNBD1 MUTATED       1   4  12   2
  CNBD1 WILD-TYPE    53 131 249 100
D287V4, multiclass
       clus
vv      CNBD1 MUTATED CNBD1 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3               12             249
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNBD1 MUTATED     4   7   6   3
  CNBD1 WILD-TYPE 191 166  83  82
D287V5, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  N0             4             191
  N1             7             166
  N2             6              83
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V6, binary
                 cls
clus                0   1
  CNBD1 MUTATED    21   0
  CNBD1 WILD-TYPE 461  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED     21    0
  CNBD1 WILD-TYPE  461   38
   clus
vv  CNBD1 MUTATED CNBD1 WILD-TYPE
  0            21             461
  1             0              38
[1] 2 2
[1] FALSE
D287V7, binary
                 cls
clus                0   1
  CNBD1 MUTATED     6  16
  CNBD1 WILD-TYPE 166 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      6   16
  CNBD1 WILD-TYPE  166  390
        clus
vv       CNBD1 MUTATED CNBD1 WILD-TYPE
  FEMALE             6             166
  MALE              16             390
[1] 2 2
[1] FALSE
D287V8, binary
                 cls
clus                0   1
  CNBD1 MUTATED    17   2
  CNBD1 WILD-TYPE 399 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED     17    2
  CNBD1 WILD-TYPE  399  100
     clus
vv    CNBD1 MUTATED CNBD1 WILD-TYPE
  NO             17             399
  YES             2             100
[1] 2 2
[1] FALSE
D287V9, continuous
D287V10, continuous
[1] "Remove cluster labels:" "CNBD1 MUTATED"         
clus
  CNBD1 MUTATED CNBD1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" "CNBD1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CNBD1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNBD1 MUTATED       5                         0
  CNBD1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNBD1 MUTATED                                           0    16
  CNBD1 WILD-TYPE                                         1   341
D287V11, multiclass
                                           clus
vv                                          CNBD1 MUTATED CNBD1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V12, binary
                 cls
clus                0   1
  CNBD1 MUTATED     0  17
  CNBD1 WILD-TYPE  10 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      0   17
  CNBD1 WILD-TYPE   10  381
                        clus
vv                       CNBD1 MUTATED CNBD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(288) Variable = PANK1 MUTATION ANALYSIS
D288V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     7   4
  PANK1 WILD-TYPE 331 212
  PANK1 MUTATED PANK1 WILD-TYPE 
             11             543 
  PANK1 MUTATED PANK1 WILD-TYPE 
              4             212 
$`PANK1 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-Z6-A8JE TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-8363 
       21.01         7.76         2.10        21.90        36.16         0.26 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-A74A TCGA-HU-8238 
        6.58         1.02       105.07        19.96         1.51 

$`PANK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PANK1 MUTATED PANK1 WILD-TYPE 
           0.26            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
         105.07          122.30 
  PANK1 MUTATED PANK1 WILD-TYPE 
           7.76           13.58 
[1] "0.3 - 105.1 (7.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D288V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PANK1 MUTATED         1        1        2        1         1         2
  PANK1 WILD-TYPE       9       19       44       30        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PANK1 MUTATED           0          2          0          0        2         0
  PANK1 WILD-TYPE        29         82         62         39       41         4
D288V3, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PANK1 MUTATED       2   4   6   1
  PANK1 WILD-TYPE    52 131 255 101
D288V4, multiclass
       clus
vv      PANK1 MUTATED PANK1 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PANK1 MUTATED     6   3   3   1
  PANK1 WILD-TYPE 189 170  86  84
D288V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V6, binary
                 cls
clus                0   1
  PANK1 MUTATED    11   2
  PANK1 WILD-TYPE 471  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED     11    2
  PANK1 WILD-TYPE  471   36
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0            11             471
  1             2              36
[1] 2 2
[1] FALSE
D288V7, binary
                 cls
clus                0   1
  PANK1 MUTATED     4   9
  PANK1 WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      4    9
  PANK1 WILD-TYPE  168  397
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D288V8, binary
                 cls
clus                0   1
  PANK1 MUTATED    11   0
  PANK1 WILD-TYPE 405 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED     11    0
  PANK1 WILD-TYPE  405  102
     clus
vv    PANK1 MUTATED PANK1 WILD-TYPE
  NO             11             405
  YES             0             102
[1] 2 2
[1] FALSE
D288V9, continuous
[1] "Remove cluster labels:" "PANK1 MUTATED"         
clus
  PANK1 MUTATED PANK1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JD 
"PANK1 WILD-TYPE" "PANK1 WILD-TYPE" "PANK1 WILD-TYPE" 
D288V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PANK1 MUTATED       2                         0
  PANK1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PANK1 MUTATED                                           0     8
  PANK1 WILD-TYPE                                         1   349
D288V11, multiclass
                                           clus
vv                                          PANK1 MUTATED PANK1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V12, binary
                 cls
clus                0   1
  PANK1 MUTATED     0   8
  PANK1 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      0    8
  PANK1 WILD-TYPE   10  390
                        clus
vv                       PANK1 MUTATED PANK1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(289) Variable = UGP2 MUTATION ANALYSIS
D289V1, survival
                sevent
clus2              0   1
  UGP2 MUTATED     7   1
  UGP2 WILD-TYPE 331 215
  UGP2 MUTATED UGP2 WILD-TYPE 
             8            546 
  UGP2 MUTATED UGP2 WILD-TYPE 
             1            215 
$`UGP2 MUTATED`
TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-5723 TCGA-CG-5728 
       35.84        28.14        16.14        12.43       105.07        65.10 
TCGA-HF-7134 TCGA-VQ-A8P2 
       52.21        38.14 

$`UGP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
       11.08         5.52         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  UGP2 MUTATED UGP2 WILD-TYPE 
         12.43           0.00 
  UGP2 MUTATED UGP2 WILD-TYPE 
        105.07         122.30 
  UGP2 MUTATED UGP2 WILD-TYPE 
        36.990         13.495 
[1] "12.4 - 105.1 (37.0)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "6.5"
D289V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGP2 MUTATED         0        1        2        2         0         0
  UGP2 WILD-TYPE      10       19       44       29        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UGP2 MUTATED           0          1          1          1        0         0
  UGP2 WILD-TYPE        29         83         61         38       43         4
D289V3, multiclass
            clus
vv           UGP2 MUTATED UGP2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              2             29
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  UGP2 MUTATED       1   3   2   2
  UGP2 WILD-TYPE    53 132 259 100
D289V4, multiclass
       clus
vv      UGP2 MUTATED UGP2 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  UGP2 MUTATED     4   3   0   2
  UGP2 WILD-TYPE 191 170  89  83
D289V5, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  N0            4            191
  N1            3            170
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V6, binary
                cls
clus               0   1
  UGP2 MUTATED     9   0
  UGP2 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      9    0
  UGP2 WILD-TYPE  473   38
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D289V7, binary
                cls
clus               0   1
  UGP2 MUTATED     4   5
  UGP2 WILD-TYPE 168 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      4    5
  UGP2 WILD-TYPE  168  401
        clus
vv       UGP2 MUTATED UGP2 WILD-TYPE
  FEMALE            4            168
  MALE              5            401
[1] 2 2
[1] FALSE
D289V8, binary
                cls
clus               0   1
  UGP2 MUTATED     6   1
  UGP2 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      6    1
  UGP2 WILD-TYPE  410  101
     clus
vv    UGP2 MUTATED UGP2 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D289V9, continuous
D289V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UGP2 MUTATED       1                         0
  UGP2 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGP2 MUTATED                                           0     5
  UGP2 WILD-TYPE                                         1   352
D289V11, multiclass
                                           clus
vv                                          UGP2 MUTATED UGP2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V12, binary
                cls
clus               0   1
  UGP2 MUTATED     0   5
  UGP2 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      0    5
  UGP2 WILD-TYPE   10  393
                        clus
vv                       UGP2 MUTATED UGP2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(290) Variable = CASD1 MUTATION ANALYSIS
D290V1, survival
                 sevent
clus2               0   1
  CASD1 MUTATED    10   4
  CASD1 WILD-TYPE 328 212
  CASD1 MUTATED CASD1 WILD-TYPE 
             14             540 
  CASD1 MUTATED CASD1 WILD-TYPE 
              4             212 
$`CASD1 MUTATED`
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A8I0 TCGA-BR-4201 TCGA-BR-6452 TCGA-CD-A4MG 
        5.92        12.66        13.38        30.90        34.68         6.58 
TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-5733 TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-8602 
       15.95        54.08        21.07        21.27        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4H3 
       22.68        29.00 

$`CASD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CASD1 MUTATED CASD1 WILD-TYPE 
           5.92            0.00 
  CASD1 MUTATED CASD1 WILD-TYPE 
          54.08          122.30 
  CASD1 MUTATED CASD1 WILD-TYPE 
         21.795          13.495 
[1] "5.9 - 54.1 (21.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D290V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASD1 MUTATED         1        0        0        1         5         2
  CASD1 WILD-TYPE       9       20       46       30        79        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASD1 MUTATED           0          1          1          2        1         0
  CASD1 WILD-TYPE        29         83         61         37       42         4
D290V3, multiclass
            clus
vv           CASD1 MUTATED CASD1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CASD1 MUTATED       1   5   5   4
  CASD1 WILD-TYPE    53 130 256  98
D290V4, multiclass
       clus
vv      CASD1 MUTATED CASD1 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASD1 MUTATED     6   3   2   3
  CASD1 WILD-TYPE 189 170  87  82
D290V5, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V6, binary
                 cls
clus                0   1
  CASD1 MUTATED    14   0
  CASD1 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED     14    0
  CASD1 WILD-TYPE  468   38
   clus
vv  CASD1 MUTATED CASD1 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D290V7, binary
                 cls
clus                0   1
  CASD1 MUTATED     7   8
  CASD1 WILD-TYPE 165 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      7    8
  CASD1 WILD-TYPE  165  398
        clus
vv       CASD1 MUTATED CASD1 WILD-TYPE
  FEMALE             7             165
  MALE               8             398
[1] 2 2
[1] FALSE
D290V8, binary
                 cls
clus                0   1
  CASD1 MUTATED    10   3
  CASD1 WILD-TYPE 406  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED     10    3
  CASD1 WILD-TYPE  406   99
     clus
vv    CASD1 MUTATED CASD1 WILD-TYPE
  NO             10             406
  YES             3              99
[1] 2 2
[1] FALSE
D290V9, continuous
[1] "Remove cluster labels:" "CASD1 MUTATED"         
clus
  CASD1 MUTATED CASD1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49N 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A49X 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2      TCGA-LN-A4A3 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
D290V10, continuous
[1] "Remove cluster labels:" "CASD1 MUTATED"         
clus
  CASD1 MUTATED CASD1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" "CASD1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CASD1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASD1 MUTATED       7                         1
  CASD1 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASD1 MUTATED                                           0     3
  CASD1 WILD-TYPE                                         1   354
D290V11, multiclass
                                           clus
vv                                          CASD1 MUTATED CASD1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V12, binary
                 cls
clus                0   1
  CASD1 MUTATED     1  10
  CASD1 WILD-TYPE   9 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      1   10
  CASD1 WILD-TYPE    9  388
                        clus
vv                       CASD1 MUTATED CASD1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(291) Variable = NT5M MUTATION ANALYSIS
D291V1, survival
                sevent
clus2              0   1
  NT5M MUTATED     3   2
  NT5M WILD-TYPE 335 214
  NT5M MUTATED NT5M WILD-TYPE 
             5            549 
  NT5M MUTATED NT5M WILD-TYPE 
             2            214 
$`NT5M MUTATED`
TCGA-2H-A9GL TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A4QL TCGA-IN-A6RP 
        5.92        29.59         1.12        16.14         6.44 

$`NT5M WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  NT5M MUTATED NT5M WILD-TYPE 
          1.12           0.00 
  NT5M MUTATED NT5M WILD-TYPE 
         29.59         122.30 
  NT5M MUTATED NT5M WILD-TYPE 
          6.44          13.58 
[1] "1.1 - 29.6 (6.4)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D291V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NT5M MUTATED         0        0        0        0         1         1
  NT5M WILD-TYPE      10       20       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NT5M MUTATED           1          1          1          1        1         0
  NT5M WILD-TYPE        28         83         61         38       42         4
D291V3, multiclass
            clus
vv           NT5M MUTATED NT5M WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NT5M MUTATED       1   0   3   3
  NT5M WILD-TYPE    53 135 258  99
D291V4, multiclass
       clus
vv      NT5M MUTATED NT5M WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NT5M MUTATED     3   1   1   2
  NT5M WILD-TYPE 192 172  88  83
D291V5, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  N0            3            192
  N1            1            172
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V6, binary
                cls
clus               0   1
  NT5M MUTATED     7   0
  NT5M WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      7    0
  NT5M WILD-TYPE  475   38
   clus
vv  NT5M MUTATED NT5M WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D291V7, binary
                cls
clus               0   1
  NT5M MUTATED     5   2
  NT5M WILD-TYPE 167 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      5    2
  NT5M WILD-TYPE  167  404
        clus
vv       NT5M MUTATED NT5M WILD-TYPE
  FEMALE            5            167
  MALE              2            404
[1] 2 2
[1] FALSE
D291V8, binary
                cls
clus               0   1
  NT5M MUTATED     4   1
  NT5M WILD-TYPE 412 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      4    1
  NT5M WILD-TYPE  412  101
     clus
vv    NT5M MUTATED NT5M WILD-TYPE
  NO             4            412
  YES            1            101
[1] 2 2
[1] FALSE
D291V9, continuous
D291V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NT5M MUTATED       0                         0
  NT5M WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NT5M MUTATED                                           0     6
  NT5M WILD-TYPE                                         1   351
D291V11, multiclass
                                           clus
vv                                          NT5M MUTATED NT5M WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V12, binary
                cls
clus               0   1
  NT5M MUTATED     0   6
  NT5M WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      0    6
  NT5M WILD-TYPE   10  392
                        clus
vv                       NT5M MUTATED NT5M WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(292) Variable = AZGP1 MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  AZGP1 MUTATED     2   2
  AZGP1 WILD-TYPE 336 214
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             550 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              2             214 
$`AZGP1 MUTATED`
TCGA-BR-8361 TCGA-CD-8527 TCGA-CD-A4MG TCGA-VQ-A8P2 
       31.10         7.17         6.58        38.14 

$`AZGP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  AZGP1 MUTATED AZGP1 WILD-TYPE 
           6.58            0.00 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
          38.14          122.30 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
         19.135          13.565 
[1] "6.6 - 38.1 (19.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AZGP1 MUTATED         0        0        0        1         1         0
  AZGP1 WILD-TYPE      10       20       46       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AZGP1 MUTATED           0          1          0          1        0         0
  AZGP1 WILD-TYPE        29         83         62         38       43         4
D292V3, multiclass
            clus
vv           AZGP1 MUTATED AZGP1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AZGP1 MUTATED       0   1   1   2
  AZGP1 WILD-TYPE    54 134 260 100
D292V4, multiclass
       clus
vv      AZGP1 MUTATED AZGP1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AZGP1 MUTATED     1   2   1   0
  AZGP1 WILD-TYPE 194 171  88  85
D292V5, multiclass
    clus
vv   AZGP1 MUTATED AZGP1 WILD-TYPE
  N0             1             194
  N1             2             171
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V6, binary
                 cls
clus                0   1
  AZGP1 MUTATED     4   0
  AZGP1 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      4    0
  AZGP1 WILD-TYPE  478   38
   clus
vv  AZGP1 MUTATED AZGP1 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D292V7, binary
                 cls
clus                0   1
  AZGP1 MUTATED     2   2
  AZGP1 WILD-TYPE 170 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      2    2
  AZGP1 WILD-TYPE  170  404
        clus
vv       AZGP1 MUTATED AZGP1 WILD-TYPE
  FEMALE             2             170
  MALE               2             404
[1] 2 2
[1] FALSE
D292V8, binary
                 cls
clus                0   1
  AZGP1 MUTATED     3   1
  AZGP1 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      3    1
  AZGP1 WILD-TYPE  413  101
     clus
vv    AZGP1 MUTATED AZGP1 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D292V9, continuous
D292V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AZGP1 MUTATED       2                         0
  AZGP1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AZGP1 MUTATED                                           0     2
  AZGP1 WILD-TYPE                                         1   355
D292V11, multiclass
                                           clus
vv                                          AZGP1 MUTATED AZGP1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V12, binary
                 cls
clus                0   1
  AZGP1 MUTATED     0   3
  AZGP1 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      0    3
  AZGP1 WILD-TYPE   10  395
                        clus
vv                       AZGP1 MUTATED AZGP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(293) Variable = RAB42 MUTATION ANALYSIS
D293V1, survival
                 sevent
clus2               0   1
  RAB42 MUTATED     3   2
  RAB42 WILD-TYPE 335 214
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             549 
  RAB42 MUTATED RAB42 WILD-TYPE 
              2             214 
$`RAB42 MUTATED`
TCGA-BR-4280 TCGA-BR-7703 TCGA-D7-A6EY TCGA-HF-7132 TCGA-MX-A5UJ 
        6.61        36.16        11.44        77.29        19.73 

$`RAB42 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RAB42 MUTATED RAB42 WILD-TYPE 
           6.61            0.00 
  RAB42 MUTATED RAB42 WILD-TYPE 
          77.29          122.30 
  RAB42 MUTATED RAB42 WILD-TYPE 
          19.73           13.55 
[1] "6.6 - 77.3 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D293V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAB42 MUTATED         0        1        0        1         0         0
  RAB42 WILD-TYPE      10       19       46       30        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB42 MUTATED           1          1          1          0        0         0
  RAB42 WILD-TYPE        28         83         61         39       43         4
D293V3, multiclass
            clus
vv           RAB42 MUTATED RAB42 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RAB42 MUTATED       1   2   2   0
  RAB42 WILD-TYPE    53 133 259 102
D293V4, multiclass
       clus
vv      RAB42 MUTATED RAB42 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RAB42 MUTATED     1   2   1   1
  RAB42 WILD-TYPE 194 171  88  84
D293V5, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  N0             1             194
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V6, binary
                 cls
clus                0   1
  RAB42 MUTATED     5   0
  RAB42 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      5    0
  RAB42 WILD-TYPE  477   38
   clus
vv  RAB42 MUTATED RAB42 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D293V7, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   2
  RAB42 WILD-TYPE 169 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    2
  RAB42 WILD-TYPE  169  404
        clus
vv       RAB42 MUTATED RAB42 WILD-TYPE
  FEMALE             3             169
  MALE               2             404
[1] 2 2
[1] FALSE
D293V8, binary
                 cls
clus                0   1
  RAB42 MUTATED     4   1
  RAB42 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      4    1
  RAB42 WILD-TYPE  412  101
     clus
vv    RAB42 MUTATED RAB42 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D293V9, continuous
D293V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAB42 MUTATED       0                         0
  RAB42 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB42 MUTATED                                           0     4
  RAB42 WILD-TYPE                                         1   353
D293V11, multiclass
                                           clus
vv                                          RAB42 MUTATED RAB42 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V12, binary
                 cls
clus                0   1
  RAB42 MUTATED     0   4
  RAB42 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      0    4
  RAB42 WILD-TYPE   10  394
                        clus
vv                       RAB42 MUTATED RAB42 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(294) Variable = C11ORF80 MUTATION ANALYSIS
D294V1, survival
                    sevent
clus2                  0   1
  C11ORF80 MUTATED     7   1
  C11ORF80 WILD-TYPE 331 215
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 8                546 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 1                215 
$`C11ORF80 MUTATED`
TCGA-R6-A6L6 TCGA-XP-A8T7 TCGA-Z6-AAPN TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8591 
        7.04        41.23         2.66        35.84        31.10        28.14 
TCGA-BR-A4PF TCGA-HU-A4GT 
        1.15         6.51 

$`C11ORF80 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
              1.15               0.00 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
             41.23             122.30 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
            17.590             13.565 
[1] "1.1 - 41.2 (17.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3.2"
D294V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF80 MUTATED         0        0        2        0         3         0
  C11ORF80 WILD-TYPE      10       20       44       31        81        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF80 MUTATED           0          0          1          2        0
  C11ORF80 WILD-TYPE        29         84         61         37       43
                    vv
clus                 STAGE IVA
  C11ORF80 MUTATED           0
  C11ORF80 WILD-TYPE         4
D294V3, multiclass
            clus
vv           C11ORF80 MUTATED C11ORF80 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C11ORF80 MUTATED       0   3   2   3
  C11ORF80 WILD-TYPE    54 132 259  99
D294V4, multiclass
       clus
vv      C11ORF80 MUTATED C11ORF80 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   2                259
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C11ORF80 MUTATED     5   0   2   1
  C11ORF80 WILD-TYPE 190 173  87  84
D294V5, multiclass
    clus
vv   C11ORF80 MUTATED C11ORF80 WILD-TYPE
  N0                5                190
  N1                0                173
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V6, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     8   0
  C11ORF80 WILD-TYPE 474  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      8    0
  C11ORF80 WILD-TYPE  474   38
   clus
vv  C11ORF80 MUTATED C11ORF80 WILD-TYPE
  0                8                474
  1                0                 38
[1] 2 2
[1] FALSE
D294V7, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     4   5
  C11ORF80 WILD-TYPE 168 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      4    5
  C11ORF80 WILD-TYPE  168  401
        clus
vv       C11ORF80 MUTATED C11ORF80 WILD-TYPE
  FEMALE                4                168
  MALE                  5                401
[1] 2 2
[1] FALSE
D294V8, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     8   0
  C11ORF80 WILD-TYPE 408 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      8    0
  C11ORF80 WILD-TYPE  408  102
     clus
vv    C11ORF80 MUTATED C11ORF80 WILD-TYPE
  NO                 8                408
  YES                0                102
[1] 2 2
[1] FALSE
D294V9, continuous
[1] "Remove cluster labels:" "C11ORF80 MUTATED"      
clus
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-Z6-A8JE 
"C11ORF80 WILD-TYPE" 
D294V10, continuous
[1] "Remove cluster labels:" "C11ORF80 MUTATED"      
clus
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U6 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HZ         TCGA-LN-A8HZ 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-LN-A8I0         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-R6-A6DN         TCGA-R6-A6L4         TCGA-R6-A6XQ 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-R6-A6Y2         TCGA-R6-A8W5         TCGA-R6-A8W8 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-R6-A8WC         TCGA-RE-A7BO         TCGA-V5-A7RB 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-AASV         TCGA-VR-A8EP 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8EU         TCGA-VR-A8EW 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7D         TCGA-VR-AA7I 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
        TCGA-X8-AAAR         TCGA-XP-A8T6         TCGA-XP-A8T8 
"C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" "C11ORF80 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF80 MUTATED       1                         0
  C11ORF80 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF80 MUTATED                                           0     7
  C11ORF80 WILD-TYPE                                         1   350
D294V11, multiclass
                                           clus
vv                                          C11ORF80 MUTATED C11ORF80 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V12, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     1   7
  C11ORF80 WILD-TYPE   9 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      1    7
  C11ORF80 WILD-TYPE    9  391
                        clus
vv                       C11ORF80 MUTATED C11ORF80 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(295) Variable = OXNAD1 MUTATION ANALYSIS
D295V1, survival
                  sevent
clus2                0   1
  OXNAD1 MUTATED     6   3
  OXNAD1 WILD-TYPE 332 213
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               9              545 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               3              213 
$`OXNAD1 MUTATED`
TCGA-L5-A8NM TCGA-LN-A49R TCGA-R6-A6XG TCGA-BR-8080 TCGA-BR-8487 TCGA-BR-A4PE 
        7.76        13.38        38.40         9.60         1.12        20.42 
TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-VQ-A8P2 
        6.58        22.68        38.14 

$`OXNAD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
            1.12             0.00 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
            38.4            122.3 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
           13.38            13.58 
[1] "1.1 - 38.4 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D295V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OXNAD1 MUTATED         0        0        1        0         2         2
  OXNAD1 WILD-TYPE      10       20       45       31        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OXNAD1 MUTATED           1          1          0          1        0
  OXNAD1 WILD-TYPE        28         83         62         38       43
                  vv
clus               STAGE IVA
  OXNAD1 MUTATED           0
  OXNAD1 WILD-TYPE         4
D295V3, multiclass
            clus
vv           OXNAD1 MUTATED OXNAD1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OXNAD1 MUTATED       0   2   4   2
  OXNAD1 WILD-TYPE    54 133 257 100
D295V4, multiclass
       clus
vv      OXNAD1 MUTATED OXNAD1 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OXNAD1 MUTATED     3   4   0   1
  OXNAD1 WILD-TYPE 192 169  89  84
D295V5, multiclass
    clus
vv   OXNAD1 MUTATED OXNAD1 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V6, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     8   0
  OXNAD1 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      8    0
  OXNAD1 WILD-TYPE  474   38
   clus
vv  OXNAD1 MUTATED OXNAD1 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D295V7, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     5   4
  OXNAD1 WILD-TYPE 167 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      5    4
  OXNAD1 WILD-TYPE  167  402
        clus
vv       OXNAD1 MUTATED OXNAD1 WILD-TYPE
  FEMALE              5              167
  MALE                4              402
[1] 2 2
[1] FALSE
D295V8, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     7   2
  OXNAD1 WILD-TYPE 409 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      7    2
  OXNAD1 WILD-TYPE  409  100
     clus
vv    OXNAD1 MUTATED OXNAD1 WILD-TYPE
  NO               7              409
  YES              2              100
[1] 2 2
[1] FALSE
D295V9, continuous
[1] "Remove cluster labels:" "OXNAD1 MUTATED"        
clus
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
D295V10, continuous
[1] "Remove cluster labels:" "OXNAD1 MUTATED"        
clus
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49S       TCGA-LN-A49U 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" "OXNAD1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"OXNAD1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OXNAD1 MUTATED       3                         0
  OXNAD1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OXNAD1 MUTATED                                           0     6
  OXNAD1 WILD-TYPE                                         1   351
D295V11, multiclass
                                           clus
vv                                          OXNAD1 MUTATED OXNAD1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V12, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     0   7
  OXNAD1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      0    7
  OXNAD1 WILD-TYPE   10  391
                        clus
vv                       OXNAD1 MUTATED OXNAD1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(296) Variable = KLRK1 MUTATION ANALYSIS
D296V1, survival
                 sevent
clus2               0   1
  KLRK1 MUTATED     3   4
  KLRK1 WILD-TYPE 335 212
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              7             547 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              4             212 
$`KLRK1 MUTATED`
TCGA-IG-A4P3 TCGA-L5-A43H TCGA-L5-A8NS TCGA-BR-8487 TCGA-BR-A4QL TCGA-D7-A6EY 
       18.64         0.30        13.41         1.12        16.14        11.44 
TCGA-HU-A4GT 
        6.51 

$`KLRK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KLRK1 MUTATED KLRK1 WILD-TYPE 
            0.3             0.0 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
          18.64          122.30 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
          11.44           13.68 
[1] "0.3 - 18.6 (11.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "2.7"
D296V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLRK1 MUTATED         0        0        0        0         2         2
  KLRK1 WILD-TYPE      10       20       46       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLRK1 MUTATED           1          0          2          0        1         0
  KLRK1 WILD-TYPE        28         84         60         39       42         4
D296V3, multiclass
            clus
vv           KLRK1 MUTATED KLRK1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KLRK1 MUTATED       0   1   6   1
  KLRK1 WILD-TYPE    54 134 255 101
D296V4, multiclass
       clus
vv      KLRK1 MUTATED KLRK1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KLRK1 MUTATED     3   2   1   2
  KLRK1 WILD-TYPE 192 171  88  83
D296V5, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V6, binary
                 cls
clus                0   1
  KLRK1 MUTATED     8   0
  KLRK1 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      8    0
  KLRK1 WILD-TYPE  474   38
   clus
vv  KLRK1 MUTATED KLRK1 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D296V7, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   3
  KLRK1 WILD-TYPE 167 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    3
  KLRK1 WILD-TYPE  167  403
        clus
vv       KLRK1 MUTATED KLRK1 WILD-TYPE
  FEMALE             5             167
  MALE               3             403
[1] 2 2
[1] FALSE
D296V8, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   2
  KLRK1 WILD-TYPE 411 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    2
  KLRK1 WILD-TYPE  411  100
     clus
vv    KLRK1 MUTATED KLRK1 WILD-TYPE
  NO              5             411
  YES             2             100
[1] 2 2
[1] FALSE
D296V9, continuous
D296V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KLRK1 MUTATED       1                         0
  KLRK1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLRK1 MUTATED                                           0     7
  KLRK1 WILD-TYPE                                         1   350
D296V11, multiclass
                                           clus
vv                                          KLRK1 MUTATED KLRK1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V12, binary
                 cls
clus                0   1
  KLRK1 MUTATED     0   6
  KLRK1 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      0    6
  KLRK1 WILD-TYPE   10  392
                        clus
vv                       KLRK1 MUTATED KLRK1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(297) Variable = IPO11 MUTATION ANALYSIS
D297V1, survival
                 sevent
clus2               0   1
  IPO11 MUTATED     9   3
  IPO11 WILD-TYPE 329 213
  IPO11 MUTATED IPO11 WILD-TYPE 
             12             542 
  IPO11 MUTATED IPO11 WILD-TYPE 
              3             213 
$`IPO11 MUTATED`
TCGA-L5-A88T TCGA-LN-A49W TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-8360 TCGA-BR-8589 
       22.82        13.25        26.70         9.67         6.18        27.12 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-D7-6818 TCGA-F1-6874 TCGA-FP-A4BE TCGA-MX-A5UJ 
       12.43        11.77        12.36        14.47        11.08        19.73 

$`IPO11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  IPO11 MUTATED IPO11 WILD-TYPE 
           6.18            0.00 
  IPO11 MUTATED IPO11 WILD-TYPE 
          27.12          122.30 
  IPO11 MUTATED IPO11 WILD-TYPE 
          12.84           13.63 
[1] "6.2 - 27.1 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D297V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPO11 MUTATED         0        0        1        1         2         2
  IPO11 WILD-TYPE      10       20       45       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPO11 MUTATED           1          4          1          0        0         0
  IPO11 WILD-TYPE        28         80         61         39       43         4
D297V3, multiclass
            clus
vv           IPO11 MUTATED IPO11 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IPO11 MUTATED       0   3   6   3
  IPO11 WILD-TYPE    54 132 255  99
D297V4, multiclass
       clus
vv      IPO11 MUTATED IPO11 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IPO11 MUTATED     6   4   1   1
  IPO11 WILD-TYPE 189 169  88  84
D297V5, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V6, binary
                 cls
clus                0   1
  IPO11 MUTATED    13   0
  IPO11 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     13    0
  IPO11 WILD-TYPE  469   38
   clus
vv  IPO11 MUTATED IPO11 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D297V7, binary
                 cls
clus                0   1
  IPO11 MUTATED     4   9
  IPO11 WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      4    9
  IPO11 WILD-TYPE  168  397
        clus
vv       IPO11 MUTATED IPO11 WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D297V8, binary
                 cls
clus                0   1
  IPO11 MUTATED     9   3
  IPO11 WILD-TYPE 407  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      9    3
  IPO11 WILD-TYPE  407   99
     clus
vv    IPO11 MUTATED IPO11 WILD-TYPE
  NO              9             407
  YES             3              99
[1] 2 2
[1] FALSE
D297V9, continuous
[1] "Remove cluster labels:" "IPO11 MUTATED"         
clus
  IPO11 MUTATED IPO11 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
D297V10, continuous
[1] "Remove cluster labels:" "IPO11 MUTATED"         
clus
  IPO11 MUTATED IPO11 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88Y      TCGA-L5-A8NG 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" "IPO11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IPO11 MUTATED       3                         1
  IPO11 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IPO11 MUTATED                                           0     9
  IPO11 WILD-TYPE                                         1   348
D297V11, multiclass
                                           clus
vv                                          IPO11 MUTATED IPO11 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V12, binary
                 cls
clus                0   1
  IPO11 MUTATED     0  11
  IPO11 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      0   11
  IPO11 WILD-TYPE   10  387
                        clus
vv                       IPO11 MUTATED IPO11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(298) Variable = GAS6 MUTATION ANALYSIS
D298V1, survival
                sevent
clus2              0   1
  GAS6 MUTATED    10   7
  GAS6 WILD-TYPE 328 209
  GAS6 MUTATED GAS6 WILD-TYPE 
            17            537 
  GAS6 MUTATED GAS6 WILD-TYPE 
             7            209 
$`GAS6 MUTATED`
TCGA-LN-A7HY TCGA-Z6-A8JD TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8591 
       12.03         3.42         6.97         9.67        34.68        28.14 
TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 
       34.98        16.14         6.58         1.02         6.02        28.96 
TCGA-CG-5728 TCGA-D7-A4YV TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 
       65.10         5.92        22.68        20.25        38.14 

$`GAS6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GAS6 MUTATED GAS6 WILD-TYPE 
          1.02           0.00 
  GAS6 MUTATED GAS6 WILD-TYPE 
          65.1          122.3 
  GAS6 MUTATED GAS6 WILD-TYPE 
         16.14          13.55 
[1] "1.0 - 65.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D298V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAS6 MUTATED         0        1        1        0         2         3
  GAS6 WILD-TYPE      10       19       45       31        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAS6 MUTATED           1          3          1          2        3         0
  GAS6 WILD-TYPE        28         81         61         37       40         4
D298V3, multiclass
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GAS6 MUTATED       1   1   9   6
  GAS6 WILD-TYPE    53 134 252  96
D298V4, multiclass
       clus
vv      GAS6 MUTATED GAS6 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               9            252
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GAS6 MUTATED     5   7   3   2
  GAS6 WILD-TYPE 190 166  86  83
D298V5, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  N0            5            190
  N1            7            166
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V6, binary
                cls
clus               0   1
  GAS6 MUTATED    16   1
  GAS6 WILD-TYPE 466  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED     16    1
  GAS6 WILD-TYPE  466   37
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0           16            466
  1            1             37
[1] 2 2
[1] FALSE
D298V7, binary
                cls
clus               0   1
  GAS6 MUTATED     8  10
  GAS6 WILD-TYPE 164 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      8   10
  GAS6 WILD-TYPE  164  396
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  FEMALE            8            164
  MALE             10            396
[1] 2 2
[1] FALSE
D298V8, binary
                cls
clus               0   1
  GAS6 MUTATED    13   1
  GAS6 WILD-TYPE 403 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED     13    1
  GAS6 WILD-TYPE  403  101
     clus
vv    GAS6 MUTATED GAS6 WILD-TYPE
  NO            13            403
  YES            1            101
[1] 2 2
[1] FALSE
D298V9, continuous
[1] "Remove cluster labels:" "GAS6 MUTATED"          
clus
  GAS6 MUTATED GAS6 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JE 
"GAS6 WILD-TYPE" "GAS6 WILD-TYPE" 
D298V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GAS6 MUTATED       4                         0
  GAS6 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GAS6 MUTATED                                           0    10
  GAS6 WILD-TYPE                                         1   347
D298V11, multiclass
                                           clus
vv                                          GAS6 MUTATED GAS6 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V12, binary
                cls
clus               0   1
  GAS6 MUTATED     0  13
  GAS6 WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0   13
  GAS6 WILD-TYPE   10  385
                        clus
vv                       GAS6 MUTATED GAS6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(299) Variable = DMXL2 MUTATION ANALYSIS
D299V1, survival
                 sevent
clus2               0   1
  DMXL2 MUTATED    34  15
  DMXL2 WILD-TYPE 304 201
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             49             505 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             15             201 
$`DMXL2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A4OR TCGA-R6-A6DN 
       19.99        21.99       122.10        25.22         3.16         8.02 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-VR-AA4G TCGA-VR-AA7B TCGA-BR-4191 TCGA-BR-4256 
        2.30        12.69        18.05        11.24        18.35         9.34 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       34.68        35.84        14.43         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8384 TCGA-BR-8589 
        8.05         6.18        31.10         0.26         3.72        27.12 
TCGA-BR-8680 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 
       31.96        12.76        12.59        12.53        12.30        12.39 
TCGA-CD-8531 TCGA-CD-A4MI TCGA-CG-4305 TCGA-D7-8573 TCGA-D7-8576 TCGA-F1-6874 
       12.59        11.77        15.95        19.50        14.66        14.47 
TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-HF-7132 TCGA-HU-8243 
       72.23        17.06        59.54        13.58        77.29         5.92 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-RD-A8N1 
       11.77         8.98         0.10         6.58         0.26       115.69 
TCGA-VQ-A8P2 
       38.14 

$`DMXL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        52.27        46.19         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
        7.43        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 
        9.07        29.56        33.21        37.25        11.44         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
        7.17        12.33        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37        29.98         6.51        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DMXL2 MUTATED DMXL2 WILD-TYPE 
            0.1             0.0 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
          122.1           122.3 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
          13.58           13.55 
[1] "0.1 - 122.1 (13.6)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D299V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DMXL2 MUTATED         1        3        4        4         5         4
  DMXL2 WILD-TYPE       9       17       42       27        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DMXL2 MUTATED           1          9          4          6        4         0
  DMXL2 WILD-TYPE        28         75         58         33       39         4
D299V3, multiclass
            clus
vv           DMXL2 MUTATED DMXL2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               3              17
  STAGE IB               4              42
  STAGE II               4              27
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             9              75
  STAGE IIIB             4              58
  STAGE IIIC             6              33
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DMXL2 MUTATED       3   9  17  16
  DMXL2 WILD-TYPE    51 126 244  86
D299V4, multiclass
       clus
vv      DMXL2 MUTATED DMXL2 WILD-TYPE
  T0+T1             3              51
  T2                9             126
  T3               17             244
  T4               16              86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DMXL2 MUTATED    18  18   6   5
  DMXL2 WILD-TYPE 177 155  83  80
D299V5, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  N0            18             177
  N1            18             155
  N2             6              83
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V6, binary
                 cls
clus                0   1
  DMXL2 MUTATED    39   4
  DMXL2 WILD-TYPE 443  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     39    4
  DMXL2 WILD-TYPE  443   34
   clus
vv  DMXL2 MUTATED DMXL2 WILD-TYPE
  0            39             443
  1             4              34
[1] 2 2
[1] FALSE
D299V7, binary
                 cls
clus                0   1
  DMXL2 MUTATED    19  31
  DMXL2 WILD-TYPE 153 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     19   31
  DMXL2 WILD-TYPE  153  375
        clus
vv       DMXL2 MUTATED DMXL2 WILD-TYPE
  FEMALE            19             153
  MALE              31             375
[1] 2 2
[1] FALSE
D299V8, binary
                 cls
clus                0   1
  DMXL2 MUTATED    37   9
  DMXL2 WILD-TYPE 379  93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     37    9
  DMXL2 WILD-TYPE  379   93
     clus
vv    DMXL2 MUTATED DMXL2 WILD-TYPE
  NO             37             379
  YES             9              93
[1] 2 2
[1] FALSE
D299V9, continuous
[1] "Remove cluster labels:" "DMXL2 MUTATED"         
clus
  DMXL2 MUTATED DMXL2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7D 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"DMXL2 WILD-TYPE" "DMXL2 WILD-TYPE" 
D299V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DMXL2 MUTATED      14                         1
  DMXL2 WILD-TYPE   119                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DMXL2 MUTATED                                           0    32
  DMXL2 WILD-TYPE                                         1   325
D299V11, multiclass
                                           clus
vv                                          DMXL2 MUTATED DMXL2 WILD-TYPE
  ASIAN                                                14             119
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                32             325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V12, binary
                 cls
clus                0   1
  DMXL2 MUTATED     1  39
  DMXL2 WILD-TYPE   9 359
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED      1   39
  DMXL2 WILD-TYPE    9  359
                        clus
vv                       DMXL2 MUTATED DMXL2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            39             359
[1] 2 2
[1] FALSE

Clustering(300) Variable = IRS1 MUTATION ANALYSIS
D300V1, survival
                sevent
clus2              0   1
  IRS1 MUTATED    15   8
  IRS1 WILD-TYPE 323 208
  IRS1 MUTATED IRS1 WILD-TYPE 
            23            531 
  IRS1 MUTATED IRS1 WILD-TYPE 
             8            208 
$`IRS1 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GJ TCGA-L5-A8NI TCGA-LN-A8I1 TCGA-BR-4256 
        4.31        19.99        58.55        13.48        13.18         9.34 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL 
       34.68        29.59         0.26         1.12        31.96        16.14 
TCGA-CD-5804 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YY TCGA-HF-7132 
       12.10         6.02       105.07        28.96        13.78        77.29 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8P2 
       26.47        29.98         6.51        29.00        38.14 

$`IRS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
       13.02        13.15        13.18        13.35        11.21        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        1.02         0.99         0.99        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IRS1 MUTATED IRS1 WILD-TYPE 
          0.26           0.00 
  IRS1 MUTATED IRS1 WILD-TYPE 
        105.07         122.30 
  IRS1 MUTATED IRS1 WILD-TYPE 
         19.99          13.51 
[1] "0.3 - 105.1 (20.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D300V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS1 MUTATED         1        1        2        2         5         3
  IRS1 WILD-TYPE       9       19       44       29        79        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRS1 MUTATED           1          2          2          2        2         0
  IRS1 WILD-TYPE        28         82         60         37       41         4
D300V3, multiclass
            clus
vv           IRS1 MUTATED IRS1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              2             29
  STAGE IIA             5             79
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IRS1 MUTATED       2   6   9   7
  IRS1 WILD-TYPE    52 129 252  95
D300V4, multiclass
       clus
vv      IRS1 MUTATED IRS1 WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3               9            252
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRS1 MUTATED    12   9   1   4
  IRS1 WILD-TYPE 183 164  88  81
D300V5, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  N0           12            183
  N1            9            164
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V6, binary
                cls
clus               0   1
  IRS1 MUTATED    22   1
  IRS1 WILD-TYPE 460  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     22    1
  IRS1 WILD-TYPE  460   37
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0           22            460
  1            1             37
[1] 2 2
[1] FALSE
D300V7, binary
                cls
clus               0   1
  IRS1 MUTATED    11  15
  IRS1 WILD-TYPE 161 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     11   15
  IRS1 WILD-TYPE  161  391
        clus
vv       IRS1 MUTATED IRS1 WILD-TYPE
  FEMALE           11            161
  MALE             15            391
[1] 2 2
[1] FALSE
D300V8, binary
                cls
clus               0   1
  IRS1 MUTATED    17   4
  IRS1 WILD-TYPE 399  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     17    4
  IRS1 WILD-TYPE  399   98
     clus
vv    IRS1 MUTATED IRS1 WILD-TYPE
  NO            17            399
  YES            4             98
[1] 2 2
[1] FALSE
D300V9, continuous
D300V10, continuous
[1] "Remove cluster labels:" "IRS1 MUTATED"          
clus
  IRS1 MUTATED IRS1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG     TCGA-L5-A8NT 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL     TCGA-IG-A3Y9 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QT 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" "IRS1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRS1 MUTATED       6                         0
  IRS1 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRS1 MUTATED                                           0    15
  IRS1 WILD-TYPE                                         1   342
D300V11, multiclass
                                           clus
vv                                          IRS1 MUTATED IRS1 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V12, binary
                cls
clus               0   1
  IRS1 MUTATED     0  17
  IRS1 WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      0   17
  IRS1 WILD-TYPE   10  381
                        clus
vv                       IRS1 MUTATED IRS1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(301) Variable = HIST1H1A MUTATION ANALYSIS
D301V1, survival
                    sevent
clus2                  0   1
  HIST1H1A MUTATED     7   3
  HIST1H1A WILD-TYPE 331 213
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                10                544 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 3                213 
$`HIST1H1A MUTATED`
TCGA-CG-4460 TCGA-LN-A49Y TCGA-LN-A5U6 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 
       21.99        12.46        12.33         6.97        30.90        32.78 
TCGA-BR-8360 TCGA-BR-8591 TCGA-CG-5723 TCGA-D7-6521 
        6.18        28.14       105.07        18.54 

$`HIST1H1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
              6.18               0.00 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
            105.07             122.30 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
            20.265             13.530 
[1] "6.2 - 105.1 (20.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D301V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIST1H1A MUTATED         0        0        0        1         3         1
  HIST1H1A WILD-TYPE      10       20       46       30        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1A MUTATED           0          1          0          1        1
  HIST1H1A WILD-TYPE        29         83         62         38       42
                    vv
clus                 STAGE IVA
  HIST1H1A MUTATED           0
  HIST1H1A WILD-TYPE         4
D301V3, multiclass
            clus
vv           HIST1H1A MUTATED HIST1H1A WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  HIST1H1A MUTATED       0   4   4   2
  HIST1H1A WILD-TYPE    54 131 257 100
D301V4, multiclass
       clus
vv      HIST1H1A MUTATED HIST1H1A WILD-TYPE
  T0+T1                0                 54
  T2                   4                131
  T3                   4                257
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  HIST1H1A MUTATED     3   5   1   1
  HIST1H1A WILD-TYPE 192 168  88  84
D301V5, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  N0                3                192
  N1                5                168
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V6, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   1
  HIST1H1A WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    1
  HIST1H1A WILD-TYPE  473   37
   clus
vv  HIST1H1A MUTATED HIST1H1A WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D301V7, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     4   7
  HIST1H1A WILD-TYPE 168 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      4    7
  HIST1H1A WILD-TYPE  168  399
        clus
vv       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  FEMALE                4                168
  MALE                  7                399
[1] 2 2
[1] FALSE
D301V8, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   1
  HIST1H1A WILD-TYPE 407 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    1
  HIST1H1A WILD-TYPE  407  101
     clus
vv    HIST1H1A MUTATED HIST1H1A WILD-TYPE
  NO                 9                407
  YES                1                101
[1] 2 2
[1] FALSE
D301V9, continuous
[1] "Remove cluster labels:" "HIST1H1A MUTATED"      
clus
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A4A1         TCGA-LN-A4A2 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-A7RE 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-V5-AASV         TCGA-V5-AASW         TCGA-V5-AASX 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
D301V10, continuous
[1] "Remove cluster labels:" "HIST1H1A MUTATED"      
clus
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U7 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" "HIST1H1A WILD-TYPE" 
        TCGA-Z6-AAPN 
"HIST1H1A WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HIST1H1A MUTATED       2                         0
  HIST1H1A WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIST1H1A MUTATED                                           0     7
  HIST1H1A WILD-TYPE                                         1   350
D301V11, multiclass
                                           clus
vv                                          HIST1H1A MUTATED HIST1H1A WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V12, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     0   9
  HIST1H1A WILD-TYPE  10 389
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      0    9
  HIST1H1A WILD-TYPE   10  389
                        clus
vv                       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                9                389
[1] 2 2
[1] FALSE

Clustering(302) Variable = CTSO MUTATION ANALYSIS
D302V1, survival
                sevent
clus2              0   1
  CTSO MUTATED     6   1
  CTSO WILD-TYPE 332 215
  CTSO MUTATED CTSO WILD-TYPE 
             7            547 
  CTSO MUTATED CTSO WILD-TYPE 
             1            215 
$`CTSO MUTATED`
TCGA-L5-A8NG TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-8524 TCGA-HU-8602 
       35.97         6.61        34.68        31.96        12.76        22.32 
TCGA-VQ-AA6A 
       38.93 

$`CTSO WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.39        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CTSO MUTATED CTSO WILD-TYPE 
          6.61           0.00 
  CTSO MUTATED CTSO WILD-TYPE 
         38.93         122.30 
  CTSO MUTATED CTSO WILD-TYPE 
         31.96          13.51 
[1] "6.6 - 38.9 (32.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4"  
D302V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSO MUTATED         0        0        0        1         1         1
  CTSO WILD-TYPE      10       20       46       30        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSO MUTATED           2          0          0          1        1         0
  CTSO WILD-TYPE        27         84         62         38       42         4
D302V3, multiclass
            clus
vv           CTSO MUTATED CTSO WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             2             27
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTSO MUTATED       0   1   3   3
  CTSO WILD-TYPE    54 134 258  99
D302V4, multiclass
       clus
vv      CTSO MUTATED CTSO WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTSO MUTATED     3   2   1   1
  CTSO WILD-TYPE 192 171  88  84
D302V5, multiclass
    clus
vv   CTSO MUTATED CTSO WILD-TYPE
  N0            3            192
  N1            2            171
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V6, binary
                cls
clus               0   1
  CTSO MUTATED     6   1
  CTSO WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      6    1
  CTSO WILD-TYPE  476   37
   clus
vv  CTSO MUTATED CTSO WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D302V7, binary
                cls
clus               0   1
  CTSO MUTATED     4   3
  CTSO WILD-TYPE 168 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      4    3
  CTSO WILD-TYPE  168  403
        clus
vv       CTSO MUTATED CTSO WILD-TYPE
  FEMALE            4            168
  MALE              3            403
[1] 2 2
[1] FALSE
D302V8, binary
                cls
clus               0   1
  CTSO MUTATED     6   1
  CTSO WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      6    1
  CTSO WILD-TYPE  410  101
     clus
vv    CTSO MUTATED CTSO WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D302V9, continuous
D302V10, continuous
[1] "Remove cluster labels:" "CTSO MUTATED"          
clus
  CTSO MUTATED CTSO WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" "CTSO WILD-TYPE" 
    TCGA-Z6-AAPN 
"CTSO WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSO MUTATED       3                         0
  CTSO WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSO MUTATED                                           0     4
  CTSO WILD-TYPE                                         1   353
D302V11, multiclass
                                           clus
vv                                          CTSO MUTATED CTSO WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V12, binary
                cls
clus               0   1
  CTSO MUTATED     0   5
  CTSO WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      0    5
  CTSO WILD-TYPE   10  393
                        clus
vv                       CTSO MUTATED CTSO WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(303) Variable = CASC3 MUTATION ANALYSIS
D303V1, survival
                 sevent
clus2               0   1
  CASC3 MUTATED     6   5
  CASC3 WILD-TYPE 332 211
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             543 
  CASC3 MUTATED CASC3 WILD-TYPE 
              5             211 
$`CASC3 MUTATED`
TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A44U TCGA-BR-A4QL TCGA-CD-A487 
        8.05        31.27        28.14        13.87        16.14        12.30 
TCGA-D7-8579 TCGA-D7-A6EZ TCGA-EQ-8122 TCGA-HF-7132 TCGA-VQ-A92D 
       20.91        20.32         7.99        77.29        66.81 

$`CASC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        42.64        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CASC3 MUTATED CASC3 WILD-TYPE 
           7.99            0.00 
  CASC3 MUTATED CASC3 WILD-TYPE 
          77.29          122.30 
  CASC3 MUTATED CASC3 WILD-TYPE 
          20.32           13.51 
[1] "8.0 - 77.3 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D303V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASC3 MUTATED         0        0        1        1         0         3
  CASC3 WILD-TYPE      10       20       45       30        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC3 MUTATED           0          1          2          3        0         0
  CASC3 WILD-TYPE        29         83         60         36       43         4
D303V3, multiclass
            clus
vv           CASC3 MUTATED CASC3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CASC3 MUTATED       0   3   5   3
  CASC3 WILD-TYPE    54 132 256  99
D303V4, multiclass
       clus
vv      CASC3 MUTATED CASC3 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASC3 MUTATED     1   3   2   5
  CASC3 WILD-TYPE 194 170  87  80
D303V5, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  N0             1             194
  N1             3             170
  N2             2              87
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V6, binary
                 cls
clus                0   1
  CASC3 MUTATED    10   0
  CASC3 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED     10    0
  CASC3 WILD-TYPE  472   38
   clus
vv  CASC3 MUTATED CASC3 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D303V7, binary
                 cls
clus                0   1
  CASC3 MUTATED     4   7
  CASC3 WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      4    7
  CASC3 WILD-TYPE  168  399
        clus
vv       CASC3 MUTATED CASC3 WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D303V8, binary
                 cls
clus                0   1
  CASC3 MUTATED     8   3
  CASC3 WILD-TYPE 408  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      8    3
  CASC3 WILD-TYPE  408   99
     clus
vv    CASC3 MUTATED CASC3 WILD-TYPE
  NO              8             408
  YES             3              99
[1] 2 2
[1] FALSE
D303V9, continuous
D303V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASC3 MUTATED       1                         0
  CASC3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASC3 MUTATED                                           0     9
  CASC3 WILD-TYPE                                         1   348
D303V11, multiclass
                                           clus
vv                                          CASC3 MUTATED CASC3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V12, binary
                 cls
clus                0   1
  CASC3 MUTATED     0   9
  CASC3 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      0    9
  CASC3 WILD-TYPE   10  389
                        clus
vv                       CASC3 MUTATED CASC3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(304) Variable = TNFSF10 MUTATION ANALYSIS
D304V1, survival
                   sevent
clus2                 0   1
  TNFSF10 MUTATED     4   5
  TNFSF10 WILD-TYPE 334 211
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                9               545 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                5               211 
$`TNFSF10 MUTATED`
TCGA-V5-AASW TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-A4QL TCGA-CD-A4MG 
        9.27         6.97         9.67        30.90        16.14         6.58 
TCGA-CG-4300 TCGA-HU-8249 TCGA-VQ-A8P2 
       20.02        28.96        38.14 

$`TNFSF10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.43        11.61        12.20        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
             6.58              0.00 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
            38.14            122.30 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
            16.14             13.55 
[1] "6.6 - 38.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D304V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFSF10 MUTATED         0        0        0        0         1         0
  TNFSF10 WILD-TYPE      10       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFSF10 MUTATED           0          4          2          0        0
  TNFSF10 WILD-TYPE        29         80         60         39       43
                   vv
clus                STAGE IVA
  TNFSF10 MUTATED           0
  TNFSF10 WILD-TYPE         4
D304V3, multiclass
            clus
vv           TNFSF10 MUTATED TNFSF10 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TNFSF10 MUTATED       0   0   6   1
  TNFSF10 WILD-TYPE    54 135 255 101
D304V4, multiclass
       clus
vv      TNFSF10 MUTATED TNFSF10 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  6               255
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TNFSF10 MUTATED     1   2   3   1
  TNFSF10 WILD-TYPE 194 171  86  84
D304V5, multiclass
    clus
vv   TNFSF10 MUTATED TNFSF10 WILD-TYPE
  N0               1               194
  N1               2               171
  N2               3                86
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V6, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     7   0
  TNFSF10 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      7    0
  TNFSF10 WILD-TYPE  475   38
   clus
vv  TNFSF10 MUTATED TNFSF10 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D304V7, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     2   7
  TNFSF10 WILD-TYPE 170 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      2    7
  TNFSF10 WILD-TYPE  170  399
        clus
vv       TNFSF10 MUTATED TNFSF10 WILD-TYPE
  FEMALE               2               170
  MALE                 7               399
[1] 2 2
[1] FALSE
D304V8, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     6   2
  TNFSF10 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      6    2
  TNFSF10 WILD-TYPE  410  100
     clus
vv    TNFSF10 MUTATED TNFSF10 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D304V9, continuous
[1] "Remove cluster labels:" "TNFSF10 MUTATED"       
clus
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" "TNFSF10 WILD-TYPE" 
D304V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFSF10 MUTATED       2                         0
  TNFSF10 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFSF10 MUTATED                                           0     6
  TNFSF10 WILD-TYPE                                         1   351
D304V11, multiclass
                                           clus
vv                                          TNFSF10 MUTATED TNFSF10 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V12, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     0   7
  TNFSF10 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      0    7
  TNFSF10 WILD-TYPE   10  391
                        clus
vv                       TNFSF10 MUTATED TNFSF10 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(305) Variable = RIC3 MUTATION ANALYSIS
D305V1, survival
                sevent
clus2              0   1
  RIC3 MUTATED     7   2
  RIC3 WILD-TYPE 331 214
  RIC3 MUTATED RIC3 WILD-TYPE 
             9            545 
  RIC3 MUTATED RIC3 WILD-TYPE 
             2            214 
$`RIC3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NM TCGA-L5-A8NS TCGA-BR-6452 TCGA-CG-5721 
        4.31        19.99         7.76        13.41        34.68         6.02 
TCGA-F1-6874 TCGA-HU-A4H8 TCGA-SW-A7EA 
       14.47        14.07        19.04 

$`RIC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RIC3 MUTATED RIC3 WILD-TYPE 
          4.31           0.00 
  RIC3 MUTATED RIC3 WILD-TYPE 
         34.68         122.30 
  RIC3 MUTATED RIC3 WILD-TYPE 
         14.07          13.55 
[1] "4.3 - 34.7 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D305V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RIC3 MUTATED         0        0        3        0         1         3
  RIC3 WILD-TYPE      10       20       43       31        83        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIC3 MUTATED           0          0          0          1        1         0
  RIC3 WILD-TYPE        29         84         62         38       42         4
D305V3, multiclass
            clus
vv           RIC3 MUTATED RIC3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RIC3 MUTATED       1   3   4   1
  RIC3 WILD-TYPE    53 132 257 101
D305V4, multiclass
       clus
vv      RIC3 MUTATED RIC3 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               4            257
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RIC3 MUTATED     5   3   0   1
  RIC3 WILD-TYPE 190 170  89  84
D305V5, multiclass
    clus
vv   RIC3 MUTATED RIC3 WILD-TYPE
  N0            5            190
  N1            3            170
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V6, binary
                cls
clus               0   1
  RIC3 MUTATED     7   0
  RIC3 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      7    0
  RIC3 WILD-TYPE  475   38
   clus
vv  RIC3 MUTATED RIC3 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D305V7, binary
                cls
clus               0   1
  RIC3 MUTATED     3   6
  RIC3 WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      3    6
  RIC3 WILD-TYPE  169  400
        clus
vv       RIC3 MUTATED RIC3 WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D305V8, binary
                cls
clus               0   1
  RIC3 MUTATED     7   1
  RIC3 WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      7    1
  RIC3 WILD-TYPE  409  101
     clus
vv    RIC3 MUTATED RIC3 WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D305V9, continuous
D305V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RIC3 MUTATED       1                         0
  RIC3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RIC3 MUTATED                                           0     7
  RIC3 WILD-TYPE                                         1   350
D305V11, multiclass
                                           clus
vv                                          RIC3 MUTATED RIC3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V12, binary
                cls
clus               0   1
  RIC3 MUTATED     0   4
  RIC3 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIC3 MUTATED      0    4
  RIC3 WILD-TYPE   10  394
                        clus
vv                       RIC3 MUTATED RIC3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(306) Variable = FAM108A1 MUTATION ANALYSIS
D306V1, survival
                    sevent
clus2                  0   1
  FAM108A1 MUTATED     5   1
  FAM108A1 WILD-TYPE 333 215
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 6                548 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 1                215 
$`FAM108A1 MUTATED`
TCGA-S8-A6BV TCGA-L5-A4OS TCGA-LN-A8HZ TCGA-VR-A8EY TCGA-BR-8590 TCGA-FP-A4BE 
       20.02        58.59        12.33        33.70         9.34        11.08 

$`FAM108A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
              9.34               0.00 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
             58.59             122.30 
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
            16.175             13.565 
[1] "9.3 - 58.6 (16.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3"  
D306V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM108A1 MUTATED         0        0        0        0         3         1
  FAM108A1 WILD-TYPE      10       20       46       31        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM108A1 MUTATED           0          1          0          1        0
  FAM108A1 WILD-TYPE        29         83         62         38       43
                    vv
clus                 STAGE IVA
  FAM108A1 MUTATED           0
  FAM108A1 WILD-TYPE         4
D306V3, multiclass
            clus
vv           FAM108A1 MUTATED FAM108A1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  FAM108A1 MUTATED       0   2   3   1
  FAM108A1 WILD-TYPE    54 133 258 101
D306V4, multiclass
       clus
vv      FAM108A1 MUTATED FAM108A1 WILD-TYPE
  T0+T1                0                 54
  T2                   2                133
  T3                   3                258
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  FAM108A1 MUTATED     3   2   1   0
  FAM108A1 WILD-TYPE 192 171  88  85
D306V5, multiclass
    clus
vv   FAM108A1 MUTATED FAM108A1 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V6, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     5   0
  FAM108A1 WILD-TYPE 477  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      5    0
  FAM108A1 WILD-TYPE  477   38
   clus
vv  FAM108A1 MUTATED FAM108A1 WILD-TYPE
  0                5                477
  1                0                 38
[1] 2 2
[1] FALSE
D306V7, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     2   4
  FAM108A1 WILD-TYPE 170 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      2    4
  FAM108A1 WILD-TYPE  170  402
        clus
vv       FAM108A1 MUTATED FAM108A1 WILD-TYPE
  FEMALE                2                170
  MALE                  4                402
[1] 2 2
[1] FALSE
D306V8, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     4   2
  FAM108A1 WILD-TYPE 412 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      4    2
  FAM108A1 WILD-TYPE  412  100
     clus
vv    FAM108A1 MUTATED FAM108A1 WILD-TYPE
  NO                 4                412
  YES                2                100
[1] 2 2
[1] FALSE
D306V9, continuous
[1] "Remove cluster labels:" "FAM108A1 MUTATED"      
clus
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"FAM108A1 WILD-TYPE" 
D306V10, continuous
[1] "Remove cluster labels:" "FAM108A1 MUTATED"      
clus
  FAM108A1 MUTATED FAM108A1 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U6 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HZ         TCGA-LN-A8I0 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" "FAM108A1 WILD-TYPE" 
        TCGA-Z6-AAPN 
"FAM108A1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  FAM108A1 MUTATED       1                         1
  FAM108A1 WILD-TYPE   132                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM108A1 MUTATED                                           0     4
  FAM108A1 WILD-TYPE                                         1   353
D306V11, multiclass
                                           clus
vv                                          FAM108A1 MUTATED FAM108A1 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V12, binary
                    cls
clus                   0   1
  FAM108A1 MUTATED     0   4
  FAM108A1 WILD-TYPE  10 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM108A1 MUTATED      0    4
  FAM108A1 WILD-TYPE   10  394
                        clus
vv                       FAM108A1 MUTATED FAM108A1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                4                394
[1] 2 2
[1] FALSE

Clustering(307) Variable = GAB2 MUTATION ANALYSIS
D307V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED     7   4
  GAB2 WILD-TYPE 331 212
  GAB2 MUTATED GAB2 WILD-TYPE 
            11            543 
  GAB2 MUTATED GAB2 WILD-TYPE 
             4            212 
$`GAB2 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GM TCGA-IG-A50L TCGA-B7-5816 TCGA-BR-8483 TCGA-BR-8487 
       21.99        13.94         0.53        26.70         5.39         1.12 
TCGA-BR-A4CS TCGA-CD-A487 TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H8 
        1.48        12.30         5.52         6.51        14.07 

$`GAB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56        11.08         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GAB2 MUTATED GAB2 WILD-TYPE 
          0.53           0.00 
  GAB2 MUTATED GAB2 WILD-TYPE 
          26.7          122.3 
  GAB2 MUTATED GAB2 WILD-TYPE 
          6.51          13.68 
[1] "0.5 - 26.7 (6.5)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.6"
D307V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAB2 MUTATED         0        0        1        0         2         4
  GAB2 WILD-TYPE      10       20       45       31        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAB2 MUTATED           0          3          0          2        1         0
  GAB2 WILD-TYPE        29         81         62         37       42         4
D307V3, multiclass
            clus
vv           GAB2 MUTATED GAB2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GAB2 MUTATED       2   0   6   5
  GAB2 WILD-TYPE    52 135 255  97
D307V4, multiclass
       clus
vv      GAB2 MUTATED GAB2 WILD-TYPE
  T0+T1            2             52
  T2               0            135
  T3               6            255
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GAB2 MUTATED     4   5   2   2
  GAB2 WILD-TYPE 191 168  87  83
D307V5, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  N0            4            191
  N1            5            168
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V6, binary
                cls
clus               0   1
  GAB2 MUTATED    12   1
  GAB2 WILD-TYPE 470  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED     12    1
  GAB2 WILD-TYPE  470   37
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0           12            470
  1            1             37
[1] 2 2
[1] FALSE
D307V7, binary
                cls
clus               0   1
  GAB2 MUTATED     5   8
  GAB2 WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      5    8
  GAB2 WILD-TYPE  167  398
        clus
vv       GAB2 MUTATED GAB2 WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D307V8, binary
                cls
clus               0   1
  GAB2 MUTATED    12   0
  GAB2 WILD-TYPE 404 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED     12    0
  GAB2 WILD-TYPE  404  102
     clus
vv    GAB2 MUTATED GAB2 WILD-TYPE
  NO            12            404
  YES            0            102
[1] 2 2
[1] FALSE
D307V9, continuous
D307V10, continuous
[1] "Remove cluster labels:" "GAB2 MUTATED"          
clus
  GAB2 MUTATED GAB2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A5B8     TCGA-IG-A6QS 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"GAB2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GAB2 MUTATED       4                         0
  GAB2 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GAB2 MUTATED                                           0     7
  GAB2 WILD-TYPE                                         1   350
D307V11, multiclass
                                           clus
vv                                          GAB2 MUTATED GAB2 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V12, binary
                cls
clus               0   1
  GAB2 MUTATED     0  11
  GAB2 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      0   11
  GAB2 WILD-TYPE   10  387
                        clus
vv                       GAB2 MUTATED GAB2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(308) Variable = BAHCC1 MUTATION ANALYSIS
D308V1, survival
                  sevent
clus2                0   1
  BAHCC1 MUTATED     8   8
  BAHCC1 WILD-TYPE 330 208
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              16              538 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
               8              208 
$`BAHCC1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GF TCGA-JY-A939 TCGA-L5-A8NU TCGA-Z6-A8JD 
       19.99        21.99        25.78        21.70        83.24         3.42 
TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CG-4441 TCGA-CG-5726 
        9.67        13.87        29.59        16.14        14.01        28.96 
TCGA-HU-8604 TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       22.82        23.84        74.53        38.14 

$`BAHCC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
            3.42             0.00 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
           83.24           122.30 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
          22.405           13.410 
[1] "3.4 - 83.2 (22.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.2"
D308V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAHCC1 MUTATED         0        1        0        0         2         6
  BAHCC1 WILD-TYPE      10       19       46       31        82        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAHCC1 MUTATED           1          2          1          1        2
  BAHCC1 WILD-TYPE        28         82         61         38       41
                  vv
clus               STAGE IVA
  BAHCC1 MUTATED           0
  BAHCC1 WILD-TYPE         4
D308V3, multiclass
            clus
vv           BAHCC1 MUTATED BAHCC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               6               77
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  BAHCC1 MUTATED       2   3   6   5
  BAHCC1 WILD-TYPE    52 132 255  97
D308V4, multiclass
       clus
vv      BAHCC1 MUTATED BAHCC1 WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 6              255
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BAHCC1 MUTATED     6   6   2   2
  BAHCC1 WILD-TYPE 189 167  87  83
D308V5, multiclass
    clus
vv   BAHCC1 MUTATED BAHCC1 WILD-TYPE
  N0              6              189
  N1              6              167
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V6, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED    14   2
  BAHCC1 WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED     14    2
  BAHCC1 WILD-TYPE  468   36
   clus
vv  BAHCC1 MUTATED BAHCC1 WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D308V7, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED     7  10
  BAHCC1 WILD-TYPE 165 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED      7   10
  BAHCC1 WILD-TYPE  165  396
        clus
vv       BAHCC1 MUTATED BAHCC1 WILD-TYPE
  FEMALE              7              165
  MALE               10              396
[1] 2 2
[1] FALSE
D308V8, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED    13   1
  BAHCC1 WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED     13    1
  BAHCC1 WILD-TYPE  403  101
     clus
vv    BAHCC1 MUTATED BAHCC1 WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D308V9, continuous
[1] "Remove cluster labels:" "BAHCC1 MUTATED"        
clus
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JE 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
D308V10, continuous
[1] "Remove cluster labels:" "BAHCC1 MUTATED"        
clus
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" "BAHCC1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"BAHCC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BAHCC1 MUTATED       2                         0
  BAHCC1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAHCC1 MUTATED                                           0    11
  BAHCC1 WILD-TYPE                                         1   346
D308V11, multiclass
                                           clus
vv                                          BAHCC1 MUTATED BAHCC1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V12, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED     1   8
  BAHCC1 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED      1    8
  BAHCC1 WILD-TYPE    9  390
                        clus
vv                       BAHCC1 MUTATED BAHCC1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(309) Variable = ARHGAP18 MUTATION ANALYSIS
D309V1, survival
                    sevent
clus2                  0   1
  ARHGAP18 MUTATED     4   5
  ARHGAP18 WILD-TYPE 334 211
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 9                545 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 5                211 
$`ARHGAP18 MUTATED`
TCGA-VR-A8EU TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CD-A48C 
       18.31         9.67        35.24         0.26        16.14        11.61 
TCGA-D7-6815 TCGA-HU-A4GN TCGA-VQ-A8P2 
       15.98        29.98        38.14 

$`ARHGAP18 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
              0.26               0.00 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             38.14             122.30 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             16.14              13.51 
[1] "0.3 - 38.1 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D309V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGAP18 MUTATED         0        0        1        1         1         2
  ARHGAP18 WILD-TYPE      10       20       45       30        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP18 MUTATED           0          1          1          0        1
  ARHGAP18 WILD-TYPE        29         83         61         39       42
                    vv
clus                 STAGE IVA
  ARHGAP18 MUTATED           0
  ARHGAP18 WILD-TYPE         4
D309V3, multiclass
            clus
vv           ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ARHGAP18 MUTATED       2   3   3   1
  ARHGAP18 WILD-TYPE    52 132 258 101
D309V4, multiclass
       clus
vv      ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  T0+T1                2                 52
  T2                   3                132
  T3                   3                258
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ARHGAP18 MUTATED     2   4   1   1
  ARHGAP18 WILD-TYPE 193 169  88  84
D309V5, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  N0                2                193
  N1                4                169
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V6, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     9   1
  ARHGAP18 WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      9    1
  ARHGAP18 WILD-TYPE  473   37
   clus
vv  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D309V7, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     7   3
  ARHGAP18 WILD-TYPE 165 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      7    3
  ARHGAP18 WILD-TYPE  165  403
        clus
vv       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  FEMALE                7                165
  MALE                  3                403
[1] 2 2
[1] FALSE
D309V8, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     7   2
  ARHGAP18 WILD-TYPE 409 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      7    2
  ARHGAP18 WILD-TYPE  409  100
     clus
vv    ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  NO                 7                409
  YES                2                100
[1] 2 2
[1] FALSE
D309V9, continuous
[1] "Remove cluster labels:" "ARHGAP18 MUTATED"      
clus
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-Z6-A8JE 
"ARHGAP18 WILD-TYPE" 
D309V10, continuous
[1] "Remove cluster labels:" "ARHGAP18 MUTATED"      
clus
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U6 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HZ         TCGA-LN-A8HZ 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-LN-A8I0         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-R6-A6DN         TCGA-R6-A6L4         TCGA-R6-A6XQ 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-R6-A6Y2         TCGA-R6-A8W5         TCGA-R6-A8W8 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-R6-A8WC         TCGA-RE-A7BO         TCGA-V5-A7RB 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-AASV         TCGA-VR-A8EP 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-Z6-AAPN 
"ARHGAP18 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGAP18 MUTATED       2                         0
  ARHGAP18 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP18 MUTATED                                           0     8
  ARHGAP18 WILD-TYPE                                         1   349
D309V11, multiclass
                                           clus
vv                                          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V12, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     0   8
  ARHGAP18 WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      0    8
  ARHGAP18 WILD-TYPE   10  390
                        clus
vv                       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(310) Variable = FHDC1 MUTATION ANALYSIS
D310V1, survival
                 sevent
clus2               0   1
  FHDC1 MUTATED     5  12
  FHDC1 WILD-TYPE 333 204
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             17             537 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             12             204 
$`FHDC1 MUTATED`
TCGA-IG-A5B8 TCGA-R6-A6XQ TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-8059 
        0.79         6.35        30.90         9.34         9.67        14.43 
TCGA-BR-8081 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-5577 
       32.25        25.05        28.14         6.58         1.02        25.71 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-A4G8 TCGA-VQ-AA6G 
       11.44        14.47        21.27        22.68        26.04 

$`FHDC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       37.25        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         7.13         0.62         7.99        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FHDC1 MUTATED FHDC1 WILD-TYPE 
           0.79            0.00 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          32.25          122.30 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          14.47           13.51 
[1] "0.8 - 32.2 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D310V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHDC1 MUTATED         0        0        2        0         2         2
  FHDC1 WILD-TYPE      10       20       44       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FHDC1 MUTATED           1          3          2          2        1         0
  FHDC1 WILD-TYPE        28         81         60         37       42         4
D310V3, multiclass
            clus
vv           FHDC1 MUTATED FHDC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FHDC1 MUTATED       0   3   8   5
  FHDC1 WILD-TYPE    54 132 253  97
D310V4, multiclass
       clus
vv      FHDC1 MUTATED FHDC1 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                8             253
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FHDC1 MUTATED     6   4   1   5
  FHDC1 WILD-TYPE 189 169  88  80
D310V5, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V6, binary
                 cls
clus                0   1
  FHDC1 MUTATED    17   1
  FHDC1 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED     17    1
  FHDC1 WILD-TYPE  465   37
   clus
vv  FHDC1 MUTATED FHDC1 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D310V7, binary
                 cls
clus                0   1
  FHDC1 MUTATED     8  11
  FHDC1 WILD-TYPE 164 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      8   11
  FHDC1 WILD-TYPE  164  395
        clus
vv       FHDC1 MUTATED FHDC1 WILD-TYPE
  FEMALE             8             164
  MALE              11             395
[1] 2 2
[1] FALSE
D310V8, binary
                 cls
clus                0   1
  FHDC1 MUTATED    15   2
  FHDC1 WILD-TYPE 401 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED     15    2
  FHDC1 WILD-TYPE  401  100
     clus
vv    FHDC1 MUTATED FHDC1 WILD-TYPE
  NO             15             401
  YES             2             100
[1] 2 2
[1] FALSE
D310V9, continuous
D310V10, continuous
[1] "Remove cluster labels:" "FHDC1 MUTATED"         
clus
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A6QS 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FHDC1 MUTATED       2                         0
  FHDC1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FHDC1 MUTATED                                           0    15
  FHDC1 WILD-TYPE                                         1   342
D310V11, multiclass
                                           clus
vv                                          FHDC1 MUTATED FHDC1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V12, binary
                 cls
clus                0   1
  FHDC1 MUTATED     1  15
  FHDC1 WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      1   15
  FHDC1 WILD-TYPE    9  383
                        clus
vv                       FHDC1 MUTATED FHDC1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(311) Variable = CCDC148 MUTATION ANALYSIS
D311V1, survival
                   sevent
clus2                 0   1
  CCDC148 MUTATED     7   3
  CCDC148 WILD-TYPE 331 213
  CCDC148 MUTATED CCDC148 WILD-TYPE 
               10               544 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                3               213 
$`CCDC148 MUTATED`
TCGA-L5-A43J TCGA-LN-A7HY TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-A4G8 
        4.31        12.03        16.14        28.96        17.85        22.68 
TCGA-HU-A4GN TCGA-HU-A4GU TCGA-VQ-A8P2 TCGA-VQ-A91V 
       29.98         6.58        38.14        42.64 

$`CCDC148 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CCDC148 MUTATED CCDC148 WILD-TYPE 
             4.31              0.00 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
            42.64            122.30 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
           20.265            13.510 
[1] "4.3 - 42.6 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D311V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC148 MUTATED         0        1        0        1         1         3
  CCDC148 WILD-TYPE      10       19       46       30        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC148 MUTATED           1          2          1          0        0
  CCDC148 WILD-TYPE        28         82         61         39       43
                   vv
clus                STAGE IVA
  CCDC148 MUTATED           0
  CCDC148 WILD-TYPE         4
D311V3, multiclass
            clus
vv           CCDC148 MUTATED CCDC148 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC148 MUTATED       1   2   6   1
  CCDC148 WILD-TYPE    53 133 255 101
D311V4, multiclass
       clus
vv      CCDC148 MUTATED CCDC148 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  6               255
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC148 MUTATED     2   6   1   1
  CCDC148 WILD-TYPE 193 167  88  84
D311V5, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  N0               2               193
  N1               6               167
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V6, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     9   0
  CCDC148 WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      9    0
  CCDC148 WILD-TYPE  473   38
   clus
vv  CCDC148 MUTATED CCDC148 WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D311V7, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     2   8
  CCDC148 WILD-TYPE 170 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      2    8
  CCDC148 WILD-TYPE  170  398
        clus
vv       CCDC148 MUTATED CCDC148 WILD-TYPE
  FEMALE               2               170
  MALE                 8               398
[1] 2 2
[1] FALSE
D311V8, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     6   2
  CCDC148 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      6    2
  CCDC148 WILD-TYPE  410  100
     clus
vv    CCDC148 MUTATED CCDC148 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D311V9, continuous
[1] "Remove cluster labels:" "CCDC148 MUTATED"       
clus
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
D311V10, continuous
[1] "Remove cluster labels:" "CCDC148 MUTATED"       
clus
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" "CCDC148 WILD-TYPE" 
       TCGA-Z6-AAPN 
"CCDC148 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC148 MUTATED       4                         0
  CCDC148 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC148 MUTATED                                           0     4
  CCDC148 WILD-TYPE                                         1   353
D311V11, multiclass
                                           clus
vv                                          CCDC148 MUTATED CCDC148 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V12, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     0   6
  CCDC148 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      0    6
  CCDC148 WILD-TYPE   10  392
                        clus
vv                       CCDC148 MUTATED CCDC148 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(312) Variable = SF3B3 MUTATION ANALYSIS
D312V1, survival
                 sevent
clus2               0   1
  SF3B3 MUTATED    15   8
  SF3B3 WILD-TYPE 323 208
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             23             531 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
              8             208 
$`SF3B3 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-L5-A8NS TCGA-VR-A8EX TCGA-Z6-A8JE TCGA-BR-4255 
        4.31        21.99        13.41        28.11         2.10         4.08 
TCGA-BR-6452 TCGA-BR-7716 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 
       34.68        39.78        32.25         8.05         2.20         4.31 
TCGA-BR-8680 TCGA-BR-A44U TCGA-CD-8525 TCGA-CD-8530 TCGA-CD-8534 TCGA-CD-8536 
       31.96        13.87        12.59        12.39        12.07        12.43 
TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU 
       14.66        13.58        11.77         6.51         6.58 

$`SF3B3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69        29.59         9.60         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       15.39        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SF3B3 MUTATED SF3B3 WILD-TYPE 
            2.1             0.0 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
          39.78          122.30 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
          12.43           13.87 
[1] "2.1 - 39.8 (12.4)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.1"
D312V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SF3B3 MUTATED         0        1        2        3         2         7
  SF3B3 WILD-TYPE      10       19       44       28        82        76
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF3B3 MUTATED           0          3          2          1        2         1
  SF3B3 WILD-TYPE        29         81         60         38       41         3
D312V3, multiclass
            clus
vv           SF3B3 MUTATED SF3B3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              7              76
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SF3B3 MUTATED       2   2  15   5
  SF3B3 WILD-TYPE    52 133 246  97
D312V4, multiclass
       clus
vv      SF3B3 MUTATED SF3B3 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3               15             246
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SF3B3 MUTATED    12   8   1   3
  SF3B3 WILD-TYPE 183 165  88  82
D312V5, multiclass
    clus
vv   SF3B3 MUTATED SF3B3 WILD-TYPE
  N0            12             183
  N1             8             165
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V6, binary
                 cls
clus                0   1
  SF3B3 MUTATED    19   3
  SF3B3 WILD-TYPE 463  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     19    3
  SF3B3 WILD-TYPE  463   35
   clus
vv  SF3B3 MUTATED SF3B3 WILD-TYPE
  0            19             463
  1             3              35
[1] 2 2
[1] FALSE
D312V7, binary
                 cls
clus                0   1
  SF3B3 MUTATED    11  13
  SF3B3 WILD-TYPE 161 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     11   13
  SF3B3 WILD-TYPE  161  393
        clus
vv       SF3B3 MUTATED SF3B3 WILD-TYPE
  FEMALE            11             161
  MALE              13             393
[1] 2 2
[1] FALSE
D312V8, binary
                 cls
clus                0   1
  SF3B3 MUTATED    18   4
  SF3B3 WILD-TYPE 398  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     18    4
  SF3B3 WILD-TYPE  398   98
     clus
vv    SF3B3 MUTATED SF3B3 WILD-TYPE
  NO             18             398
  YES             4              98
[1] 2 2
[1] FALSE
D312V9, continuous
[1] "Remove cluster labels:" "SF3B3 MUTATED"         
clus
  SF3B3 MUTATED SF3B3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD 
"SF3B3 WILD-TYPE" "SF3B3 WILD-TYPE" 
D312V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SF3B3 MUTATED       8                         0
  SF3B3 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SF3B3 MUTATED                                           0    13
  SF3B3 WILD-TYPE                                         1   344
D312V11, multiclass
                                           clus
vv                                          SF3B3 MUTATED SF3B3 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V12, binary
                 cls
clus                0   1
  SF3B3 MUTATED     0  19
  SF3B3 WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED      0   19
  SF3B3 WILD-TYPE   10  379
                        clus
vv                       SF3B3 MUTATED SF3B3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(313) Variable = PPIP5K2 MUTATION ANALYSIS
D313V1, survival
                   sevent
clus2                 0   1
  PPIP5K2 MUTATED     8   5
  PPIP5K2 WILD-TYPE 330 211
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               13               541 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
                5               211 
$`PPIP5K2 MUTATED`
TCGA-IG-A3Y9 TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8360 TCGA-BR-8363 
        0.85        20.38         6.97         6.61         6.18         0.26 
TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-4466 TCGA-CG-5721 TCGA-D7-A6F0 TCGA-HU-A4GY 
       13.18        15.95        18.97         6.02        22.29         0.26 
TCGA-VQ-A8P2 
       38.14 

$`PPIP5K2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
             0.26              0.00 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
            38.14            122.30 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
             6.97             13.68 
[1] "0.3 - 38.1 (7.0)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.5"
D313V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPIP5K2 MUTATED         0        0        5        1         1         0
  PPIP5K2 WILD-TYPE      10       20       41       30        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPIP5K2 MUTATED           1          6          0          0        2
  PPIP5K2 WILD-TYPE        28         78         62         39       41
                   vv
clus                STAGE IVA
  PPIP5K2 MUTATED           0
  PPIP5K2 WILD-TYPE         4
D313V3, multiclass
            clus
vv           PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 5                41
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               6                78
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PPIP5K2 MUTATED       0   7   3   6
  PPIP5K2 WILD-TYPE    54 128 258  96
D313V4, multiclass
       clus
vv      PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  T0+T1               0                54
  T2                  7               128
  T3                  3               258
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PPIP5K2 MUTATED     8   7   1   0
  PPIP5K2 WILD-TYPE 187 166  88  85
D313V5, multiclass
    clus
vv   PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  N0               8               187
  N1               7               166
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V6, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED    14   0
  PPIP5K2 WILD-TYPE 468  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED     14    0
  PPIP5K2 WILD-TYPE  468   38
   clus
vv  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  0              14               468
  1               0                38
[1] 2 2
[1] FALSE
D313V7, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED     7   9
  PPIP5K2 WILD-TYPE 165 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED      7    9
  PPIP5K2 WILD-TYPE  165  397
        clus
vv       PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  FEMALE               7               165
  MALE                 9               397
[1] 2 2
[1] FALSE
D313V8, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED    12   1
  PPIP5K2 WILD-TYPE 404 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED     12    1
  PPIP5K2 WILD-TYPE  404  101
     clus
vv    PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  NO               12               404
  YES               1               101
[1] 2 2
[1] FALSE
D313V9, continuous
[1] "Remove cluster labels:" "PPIP5K2 MUTATED"       
clus
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
D313V10, continuous
[1] "Remove cluster labels:" "PPIP5K2 MUTATED"       
clus
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" "PPIP5K2 WILD-TYPE" 
       TCGA-Z6-AAPN 
"PPIP5K2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PPIP5K2 MUTATED       2                         0
  PPIP5K2 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIP5K2 MUTATED                                           0    10
  PPIP5K2 WILD-TYPE                                         1   347
D313V11, multiclass
                                           clus
vv                                          PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V12, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED     0  11
  PPIP5K2 WILD-TYPE  10 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED      0   11
  PPIP5K2 WILD-TYPE   10  387
                        clus
vv                       PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(314) Variable = PTCHD3 MUTATION ANALYSIS
D314V1, survival
                  sevent
clus2                0   1
  PTCHD3 MUTATED    14  10
  PTCHD3 WILD-TYPE 324 206
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              24              530 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              10              206 
$`PTCHD3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A43C TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A5U7 TCGA-VR-A8Q7 
       19.99         3.16         8.71        46.09        25.25        52.27 
TCGA-XP-A8T6 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 
       25.08         6.97        30.90        34.68        35.84         1.12 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4465 
       31.96        16.14        12.43        20.02        15.95         9.01 
TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A6EZ TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-RD-A8N9 
        6.02         5.92        20.32        24.20         0.10        35.61 

$`PTCHD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
        5.49        21.37        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       11.77        12.62         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
             0.1              0.0 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
           52.27           122.30 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
          20.005           13.495 
[1] "0.1 - 52.3 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D314V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTCHD3 MUTATED         1        1        3        3         3         2
  PTCHD3 WILD-TYPE       9       19       43       28        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTCHD3 MUTATED           1          3          2          2        3
  PTCHD3 WILD-TYPE        28         81         60         37       40
                  vv
clus               STAGE IVA
  PTCHD3 MUTATED           0
  PTCHD3 WILD-TYPE         4
D314V3, multiclass
            clus
vv           PTCHD3 MUTATED PTCHD3 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PTCHD3 MUTATED       2   8  11   4
  PTCHD3 WILD-TYPE    52 127 250  98
D314V4, multiclass
       clus
vv      PTCHD3 MUTATED PTCHD3 WILD-TYPE
  T0+T1              2               52
  T2                 8              127
  T3                11              250
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTCHD3 MUTATED     7  10   4   3
  PTCHD3 WILD-TYPE 188 163  85  82
D314V5, multiclass
    clus
vv   PTCHD3 MUTATED PTCHD3 WILD-TYPE
  N0              7              188
  N1             10              163
  N2              4               85
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V6, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED    20   2
  PTCHD3 WILD-TYPE 462  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED     20    2
  PTCHD3 WILD-TYPE  462   36
   clus
vv  PTCHD3 MUTATED PTCHD3 WILD-TYPE
  0             20              462
  1              2               36
[1] 2 2
[1] FALSE
D314V7, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED    10  16
  PTCHD3 WILD-TYPE 162 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED     10   16
  PTCHD3 WILD-TYPE  162  390
        clus
vv       PTCHD3 MUTATED PTCHD3 WILD-TYPE
  FEMALE             10              162
  MALE               16              390
[1] 2 2
[1] FALSE
D314V8, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED    22   1
  PTCHD3 WILD-TYPE 394 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED     22    1
  PTCHD3 WILD-TYPE  394  101
     clus
vv    PTCHD3 MUTATED PTCHD3 WILD-TYPE
  NO              22              394
  YES              1              101
[1] 2 2
[1] FALSE
D314V9, continuous
D314V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTCHD3 MUTATED       6                         2
  PTCHD3 WILD-TYPE   127                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTCHD3 MUTATED                                           0    12
  PTCHD3 WILD-TYPE                                         1   345
D314V11, multiclass
                                           clus
vv                                          PTCHD3 MUTATED PTCHD3 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V12, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED     1  15
  PTCHD3 WILD-TYPE   9 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED      1   15
  PTCHD3 WILD-TYPE    9  383
                        clus
vv                       PTCHD3 MUTATED PTCHD3 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(315) Variable = DLGAP3 MUTATION ANALYSIS
D315V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    20   3
  DLGAP3 WILD-TYPE 318 213
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              23              531 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               3              213 
$`DLGAP3 MUTATED`
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A8I0 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8078 
        5.92        12.66        13.38        30.90        32.78        29.59 
TCGA-BR-8680 TCGA-BR-A4J7 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6822 TCGA-HF-7132 
       31.96        32.52         6.02        65.10        12.33        77.29 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         6.51         6.58         0.26        29.00        23.84 
TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IP-7968 TCGA-VQ-A8P2 TCGA-VQ-A91U 
       14.07        18.81         2.53        38.14         1.71 

$`DLGAP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34         0.66        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 
       11.77        21.37         8.98         0.10        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
            0.26             0.00 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           77.29           122.30 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           18.81            13.51 
[1] "0.3 - 77.3 (18.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.8"
D315V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLGAP3 MUTATED         0        0        3        1         6         5
  DLGAP3 WILD-TYPE      10       20       43       30        78        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           0          3          1          1        2
  DLGAP3 WILD-TYPE        29         81         61         38       41
                  vv
clus               STAGE IVA
  DLGAP3 MUTATED           0
  DLGAP3 WILD-TYPE         4
D315V3, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DLGAP3 MUTATED       1   9   6   7
  DLGAP3 WILD-TYPE    53 126 255  95
D315V4, multiclass
       clus
vv      DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T0+T1              1               53
  T2                 9              126
  T3                 6              255
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DLGAP3 MUTATED     8   9   3   1
  DLGAP3 WILD-TYPE 187 164  86  84
D315V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0              8              187
  N1              9              164
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V6, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    21   1
  DLGAP3 WILD-TYPE 461  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     21    1
  DLGAP3 WILD-TYPE  461   37
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             21              461
  1              1               37
[1] 2 2
[1] FALSE
D315V7, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     8  15
  DLGAP3 WILD-TYPE 164 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      8   15
  DLGAP3 WILD-TYPE  164  391
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  FEMALE              8              164
  MALE               15              391
[1] 2 2
[1] FALSE
D315V8, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    17   3
  DLGAP3 WILD-TYPE 399  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     17    3
  DLGAP3 WILD-TYPE  399   99
     clus
vv    DLGAP3 MUTATED DLGAP3 WILD-TYPE
  NO              17              399
  YES              3               99
[1] 2 2
[1] FALSE
D315V9, continuous
[1] "Remove cluster labels:" "DLGAP3 MUTATED"        
clus
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49L       TCGA-LN-A49N 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A49X 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
D315V10, continuous
[1] "Remove cluster labels:" "DLGAP3 MUTATED"        
clus
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" "DLGAP3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"DLGAP3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DLGAP3 MUTATED      13                         0
  DLGAP3 WILD-TYPE   120                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLGAP3 MUTATED                                           0     7
  DLGAP3 WILD-TYPE                                         1   350
D315V11, multiclass
                                           clus
vv                                          DLGAP3 MUTATED DLGAP3 WILD-TYPE
  ASIAN                                                 13              120
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V12, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     0  18
  DLGAP3 WILD-TYPE  10 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      0   18
  DLGAP3 WILD-TYPE   10  380
                        clus
vv                       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(316) Variable = KIN MUTATION ANALYSIS
D316V1, survival
               sevent
clus2             0   1
  KIN MUTATED     6   2
  KIN WILD-TYPE 332 214
  KIN MUTATED KIN WILD-TYPE 
            8           546 
  KIN MUTATED KIN WILD-TYPE 
            2           214 
$`KIN MUTATED`
TCGA-R6-A6Y2 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 
        9.30        34.68        44.94        32.25         1.12        31.96 
TCGA-D7-A4YV TCGA-HF-7132 
        5.92        77.29 

$`KIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KIN MUTATED KIN WILD-TYPE 
         1.12          0.00 
  KIN MUTATED KIN WILD-TYPE 
        77.29        122.30 
  KIN MUTATED KIN WILD-TYPE 
       32.105        13.530 
[1] "1.1 - 77.3 (32.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D316V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIN MUTATED         0        0        0        1         3         2
  KIN WILD-TYPE      10       20       46       30        81        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIN MUTATED           0          0          0          0        1         0
  KIN WILD-TYPE        29         84         62         39       42         4
D316V3, multiclass
            clus
vv           KIN MUTATED KIN WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             1            30
  STAGE IIA            3            81
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           0            84
  STAGE IIIB           0            62
  STAGE IIIC           0            39
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  KIN MUTATED       0   1   4   2
  KIN WILD-TYPE    54 134 257 100
D316V4, multiclass
       clus
vv      KIN MUTATED KIN WILD-TYPE
  T0+T1           0            54
  T2              1           134
  T3              4           257
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  KIN MUTATED     4   2   1   0
  KIN WILD-TYPE 191 171  88  85
D316V5, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  N0           4           191
  N1           2           171
  N2           1            88
  N3           0            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V6, binary
               cls
clus              0   1
  KIN MUTATED     6   1
  KIN WILD-TYPE 476  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      6    1
  KIN WILD-TYPE  476   37
   clus
vv  KIN MUTATED KIN WILD-TYPE
  0           6           476
  1           1            37
[1] 2 2
[1] FALSE
D316V7, binary
               cls
clus              0   1
  KIN MUTATED     5   3
  KIN WILD-TYPE 167 403
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      5    3
  KIN WILD-TYPE  167  403
        clus
vv       KIN MUTATED KIN WILD-TYPE
  FEMALE           5           167
  MALE             3           403
[1] 2 2
[1] FALSE
D316V8, binary
               cls
clus              0   1
  KIN MUTATED     7   1
  KIN WILD-TYPE 409 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      7    1
  KIN WILD-TYPE  409  101
     clus
vv    KIN MUTATED KIN WILD-TYPE
  NO            7           409
  YES           1           101
[1] 2 2
[1] FALSE
D316V9, continuous
D316V10, continuous
[1] "Remove cluster labels:" "KIN MUTATED"           
clus
  KIN MUTATED KIN WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A4OX    TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A8NF    TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-L5-A8NS    TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-LN-A4A6    TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-M9-A5M8    TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" "KIN WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"KIN WILD-TYPE" "KIN WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  KIN MUTATED       1                         0
  KIN WILD-TYPE   132                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIN MUTATED                                           0     6
  KIN WILD-TYPE                                         1   351
D316V11, multiclass
                                           clus
vv                                          KIN MUTATED KIN WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               6           351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V12, binary
               cls
clus              0   1
  KIN MUTATED     1   6
  KIN WILD-TYPE   9 392
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      1    6
  KIN WILD-TYPE    9  392
                        clus
vv                       KIN MUTATED KIN WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO           6           392
[1] 2 2
[1] FALSE

Clustering(317) Variable = KPNA1 MUTATION ANALYSIS
D317V1, survival
                 sevent
clus2               0   1
  KPNA1 MUTATED     2   4
  KPNA1 WILD-TYPE 336 212
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              6             548 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
              4             212 
$`KPNA1 MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A4P3 TCGA-JY-A93D TCGA-L5-A4OH TCGA-LN-A8I0 
        5.92         4.21        18.64        31.56        32.61        13.38 

$`KPNA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KPNA1 MUTATED KPNA1 WILD-TYPE 
           4.21            0.00 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
          32.61          122.30 
  KPNA1 MUTATED KPNA1 WILD-TYPE 
         16.010          13.565 
[1] "4.2 - 32.6 (16.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D317V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KPNA1 MUTATED         1        0        0        0         1         1
  KPNA1 WILD-TYPE       9       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNA1 MUTATED           2          0          0          1        0         0
  KPNA1 WILD-TYPE        27         84         62         38       43         4
D317V3, multiclass
            clus
vv           KPNA1 MUTATED KPNA1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KPNA1 MUTATED       1   3   2   0
  KPNA1 WILD-TYPE    53 132 259 102
D317V4, multiclass
       clus
vv      KPNA1 MUTATED KPNA1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                2             259
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KPNA1 MUTATED     2   3   0   1
  KPNA1 WILD-TYPE 193 170  89  84
D317V5, multiclass
    clus
vv   KPNA1 MUTATED KPNA1 WILD-TYPE
  N0             2             193
  N1             3             170
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V6, binary
                 cls
clus                0   1
  KPNA1 MUTATED     6   0
  KPNA1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      6    0
  KPNA1 WILD-TYPE  476   38
   clus
vv  KPNA1 MUTATED KPNA1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D317V7, binary
                 cls
clus                0   1
  KPNA1 MUTATED     0   6
  KPNA1 WILD-TYPE 172 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      0    6
  KPNA1 WILD-TYPE  172  400
        clus
vv       KPNA1 MUTATED KPNA1 WILD-TYPE
  FEMALE             0             172
  MALE               6             400
[1] 2 2
[1] FALSE
D317V8, binary
                 cls
clus                0   1
  KPNA1 MUTATED     4   2
  KPNA1 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      4    2
  KPNA1 WILD-TYPE  412  100
     clus
vv    KPNA1 MUTATED KPNA1 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D317V9, continuous
D317V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KPNA1 MUTATED       1                         0
  KPNA1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KPNA1 MUTATED                                           0     3
  KPNA1 WILD-TYPE                                         1   354
D317V11, multiclass
                                           clus
vv                                          KPNA1 MUTATED KPNA1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V12, binary
                 cls
clus                0   1
  KPNA1 MUTATED     0   2
  KPNA1 WILD-TYPE  10 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA1 MUTATED      0    2
  KPNA1 WILD-TYPE   10  396
                        clus
vv                       KPNA1 MUTATED KPNA1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             2             396
[1] 2 2
[1] FALSE

Clustering(318) Variable = KIAA0649 MUTATION ANALYSIS
D318V1, survival
                    sevent
clus2                  0   1
  KIAA0649 MUTATED    12   7
  KIAA0649 WILD-TYPE 326 209
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                19                535 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                 7                209 
$`KIAA0649 MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A8NM TCGA-Q9-A6FW TCGA-BR-6452 TCGA-BR-6458 
       24.00        19.99         7.76         7.82        34.68        19.33 
TCGA-BR-6802 TCGA-BR-8080 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QI 
       30.90         9.60        31.27         1.12        28.14        21.44 
TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6818 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 
       15.95         6.02        12.36        11.44        22.32        24.20 
TCGA-VQ-A8P2 
       38.14 

$`KIAA0649 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
              1.12               0.00 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             38.14             122.30 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             19.99              13.51 
[1] "1.1 - 38.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D318V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0649 MUTATED         1        1        1        1         3         4
  KIAA0649 WILD-TYPE       9       19       45       30        81        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0649 MUTATED           0          3          3          4        1
  KIAA0649 WILD-TYPE        29         81         59         35       42
                    vv
clus                 STAGE IVA
  KIAA0649 MUTATED           0
  KIAA0649 WILD-TYPE         4
D318V3, multiclass
            clus
vv           KIAA0649 MUTATED KIAA0649 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 4                 79
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                3                 59
  STAGE IIIC                4                 35
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0649 MUTATED       2   4   9   7
  KIAA0649 WILD-TYPE    52 131 252  95
D318V4, multiclass
       clus
vv      KIAA0649 MUTATED KIAA0649 WILD-TYPE
  T0+T1                2                 52
  T2                   4                131
  T3                   9                252
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0649 MUTATED     7   6   3   6
  KIAA0649 WILD-TYPE 188 167  86  79
D318V5, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  N0                7                188
  N1                6                167
  N2                3                 86
  N3                6                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V6, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED    19   0
  KIAA0649 WILD-TYPE 463  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED     19    0
  KIAA0649 WILD-TYPE  463   38
   clus
vv  KIAA0649 MUTATED KIAA0649 WILD-TYPE
  0               19                463
  1                0                 38
[1] 2 2
[1] FALSE
D318V7, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     9  13
  KIAA0649 WILD-TYPE 163 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      9   13
  KIAA0649 WILD-TYPE  163  393
        clus
vv       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  FEMALE                9                163
  MALE                 13                393
[1] 2 2
[1] FALSE
D318V8, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED    19   2
  KIAA0649 WILD-TYPE 397 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED     19    2
  KIAA0649 WILD-TYPE  397  100
     clus
vv    KIAA0649 MUTATED KIAA0649 WILD-TYPE
  NO                19                397
  YES                2                100
[1] 2 2
[1] FALSE
D318V9, continuous
D318V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0649 MUTATED       2                         1
  KIAA0649 WILD-TYPE   131                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0649 MUTATED                                           0    16
  KIAA0649 WILD-TYPE                                         1   341
D318V11, multiclass
                                           clus
vv                                          KIAA0649 MUTATED KIAA0649 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V12, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     0  15
  KIAA0649 WILD-TYPE  10 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      0   15
  KIAA0649 WILD-TYPE   10  383
                        clus
vv                       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               15                383
[1] 2 2
[1] FALSE

Clustering(319) Variable = NIN MUTATION ANALYSIS
D319V1, survival
               sevent
clus2             0   1
  NIN MUTATED    23   9
  NIN WILD-TYPE 315 207
  NIN MUTATED NIN WILD-TYPE 
           32           522 
  NIN MUTATED NIN WILD-TYPE 
            9           207 
$`NIN MUTATED`
TCGA-IG-A3I8 TCGA-JY-A6FH TCGA-L5-A8NU TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-Q9-A6FW 
       33.27        47.38        83.24        13.22        25.25         7.82 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-VR-A8EX TCGA-B7-A5TI TCGA-BR-4184 
       53.95         2.89        12.69        28.11        19.56         6.97 
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-7958 TCGA-BR-8361 
       30.90         9.67        34.68        35.24        29.56        31.10 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-5804 TCGA-CD-A4MJ TCGA-CG-4477 
        4.31         1.12        31.96        12.10        12.62        30.97 
TCGA-D7-6524 TCGA-D7-A74A TCGA-F1-6875 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
       17.85        19.96        72.23        22.68        29.98         6.51 
TCGA-IN-A6RR TCGA-MX-A5UJ 
        6.74        19.73 

$`NIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       18.15        15.32        28.73         3.45         9.07        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NIN MUTATED NIN WILD-TYPE 
         1.12          0.00 
  NIN MUTATED NIN WILD-TYPE 
        83.24        122.30 
  NIN MUTATED NIN WILD-TYPE 
       21.320        13.445 
[1] "1.1 - 83.2 (21.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.9"
D319V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NIN MUTATED         0        1        3        2         8         3
  NIN WILD-TYPE      10       19       43       29        76        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIN MUTATED           0          4          2          2        1         1
  NIN WILD-TYPE        29         80         60         37       42         3
D319V3, multiclass
            clus
vv           NIN MUTATED NIN WILD-TYPE
  STAGE I              0            10
  STAGE IA             1            19
  STAGE IB             3            43
  STAGE II             2            29
  STAGE IIA            8            76
  STAGE IIB            3            80
  STAGE III            0            29
  STAGE IIIA           4            80
  STAGE IIIB           2            60
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            1             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  NIN MUTATED       1  11  12   5
  NIN WILD-TYPE    53 124 249  97
D319V4, multiclass
       clus
vv      NIN MUTATED NIN WILD-TYPE
  T0+T1           1            53
  T2             11           124
  T3             12           249
  T4              5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NIN MUTATED    14   8   5   1
  NIN WILD-TYPE 181 165  84  84
D319V5, multiclass
    clus
vv   NIN MUTATED NIN WILD-TYPE
  N0          14           181
  N1           8           165
  N2           5            84
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V6, binary
               cls
clus              0   1
  NIN MUTATED    27   2
  NIN WILD-TYPE 455  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     27    2
  NIN WILD-TYPE  455   36
   clus
vv  NIN MUTATED NIN WILD-TYPE
  0          27           455
  1           2            36
[1] 2 2
[1] FALSE
D319V7, binary
               cls
clus              0   1
  NIN MUTATED    13  20
  NIN WILD-TYPE 159 386
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     13   20
  NIN WILD-TYPE  159  386
        clus
vv       NIN MUTATED NIN WILD-TYPE
  FEMALE          13           159
  MALE            20           386
[1] 2 2
[1] FALSE
D319V8, binary
               cls
clus              0   1
  NIN MUTATED    31   1
  NIN WILD-TYPE 385 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     31    1
  NIN WILD-TYPE  385  101
     clus
vv    NIN MUTATED NIN WILD-TYPE
  NO           31           385
  YES           1           101
[1] 2 2
[1] FALSE
D319V9, continuous
D319V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NIN MUTATED       8                         1
  NIN WILD-TYPE   125                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NIN MUTATED                                           0    22
  NIN WILD-TYPE                                         1   335
D319V11, multiclass
                                           clus
vv                                          NIN MUTATED NIN WILD-TYPE
  ASIAN                                               8           125
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              22           335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V12, binary
               cls
clus              0   1
  NIN MUTATED     1  28
  NIN WILD-TYPE   9 370
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED      1   28
  NIN WILD-TYPE    9  370
                        clus
vv                       NIN MUTATED NIN WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          28           370
[1] 2 2
[1] FALSE

Clustering(320) Variable = CTSC MUTATION ANALYSIS
D320V1, survival
                sevent
clus2              0   1
  CTSC MUTATED     5   4
  CTSC WILD-TYPE 333 212
  CTSC MUTATED CTSC WILD-TYPE 
             9            545 
  CTSC MUTATED CTSC WILD-TYPE 
             4            212 
$`CTSC MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-A4QL 
       30.90         9.34        35.84        29.59        31.27        16.14 
TCGA-CD-A4MI TCGA-HU-A4G8 TCGA-MX-A5UJ 
       11.77        22.68        19.73 

$`CTSC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CTSC MUTATED CTSC WILD-TYPE 
          9.34           0.00 
  CTSC MUTATED CTSC WILD-TYPE 
         35.84         122.30 
  CTSC MUTATED CTSC WILD-TYPE 
         22.68          13.51 
[1] "9.3 - 35.8 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D320V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSC MUTATED         0        0        1        0         0         2
  CTSC WILD-TYPE      10       20       45       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSC MUTATED           0          3          1          1        0         0
  CTSC WILD-TYPE        29         81         61         38       43         4
D320V3, multiclass
            clus
vv           CTSC MUTATED CTSC WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTSC MUTATED       0   2   4   3
  CTSC WILD-TYPE    54 133 257  99
D320V4, multiclass
       clus
vv      CTSC MUTATED CTSC WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTSC MUTATED     3   4   1   2
  CTSC WILD-TYPE 192 169  88  83
D320V5, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  N0            3            192
  N1            4            169
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V6, binary
                cls
clus               0   1
  CTSC MUTATED    11   0
  CTSC WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED     11    0
  CTSC WILD-TYPE  471   38
   clus
vv  CTSC MUTATED CTSC WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D320V7, binary
                cls
clus               0   1
  CTSC MUTATED     8   3
  CTSC WILD-TYPE 164 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      8    3
  CTSC WILD-TYPE  164  403
        clus
vv       CTSC MUTATED CTSC WILD-TYPE
  FEMALE            8            164
  MALE              3            403
[1] 2 2
[1] FALSE
D320V8, binary
                cls
clus               0   1
  CTSC MUTATED     9   0
  CTSC WILD-TYPE 407 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      9    0
  CTSC WILD-TYPE  407  102
     clus
vv    CTSC MUTATED CTSC WILD-TYPE
  NO             9            407
  YES            0            102
[1] 2 2
[1] FALSE
D320V9, continuous
D320V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSC MUTATED       2                         0
  CTSC WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSC MUTATED                                           0     9
  CTSC WILD-TYPE                                         1   348
D320V11, multiclass
                                           clus
vv                                          CTSC MUTATED CTSC WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V12, binary
                cls
clus               0   1
  CTSC MUTATED     0  11
  CTSC WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      0   11
  CTSC WILD-TYPE   10  387
                        clus
vv                       CTSC MUTATED CTSC WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(321) Variable = TYRO3 MUTATION ANALYSIS
D321V1, survival
                 sevent
clus2               0   1
  TYRO3 MUTATED    11   6
  TYRO3 WILD-TYPE 327 210
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             17             537 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              6             210 
$`TYRO3 MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A8NV TCGA-R6-A6DN TCGA-R6-A6XG 
       60.39        18.28        19.99        52.57         8.02        38.40 
TCGA-BR-7958 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 TCGA-F1-6874 
       29.56         1.12         6.58        15.95         6.02        14.47 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-VQ-A8P2 TCGA-VQ-AA6G 
        0.10        20.25         0.26        38.14        26.04 

$`TYRO3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03        12.85        12.26        33.11         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TYRO3 MUTATED TYRO3 WILD-TYPE 
            0.1             0.0 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          60.39          122.30 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          18.28           13.51 
[1] "0.1 - 60.4 (18.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D321V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TYRO3 MUTATED         1        0        1        1         4         0
  TYRO3 WILD-TYPE       9       20       45       30        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TYRO3 MUTATED           0          3          1          3        1         0
  TYRO3 WILD-TYPE        29         81         61         36       42         4
D321V3, multiclass
            clus
vv           TYRO3 MUTATED TYRO3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TYRO3 MUTATED       1   2   6   6
  TYRO3 WILD-TYPE    53 133 255  96
D321V4, multiclass
       clus
vv      TYRO3 MUTATED TYRO3 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                6             255
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TYRO3 MUTATED     7   5   2   1
  TYRO3 WILD-TYPE 188 168  87  84
D321V5, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  N0             7             188
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V6, binary
                 cls
clus                0   1
  TYRO3 MUTATED    13   0
  TYRO3 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED     13    0
  TYRO3 WILD-TYPE  469   38
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D321V7, binary
                 cls
clus                0   1
  TYRO3 MUTATED     3  14
  TYRO3 WILD-TYPE 169 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      3   14
  TYRO3 WILD-TYPE  169  392
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  FEMALE             3             169
  MALE              14             392
[1] 2 2
[1] FALSE
D321V8, binary
                 cls
clus                0   1
  TYRO3 MUTATED    14   2
  TYRO3 WILD-TYPE 402 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED     14    2
  TYRO3 WILD-TYPE  402  100
     clus
vv    TYRO3 MUTATED TYRO3 WILD-TYPE
  NO             14             402
  YES             2             100
[1] 2 2
[1] FALSE
D321V9, continuous
D321V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TYRO3 MUTATED       4                         0
  TYRO3 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TYRO3 MUTATED                                           0    11
  TYRO3 WILD-TYPE                                         1   346
D321V11, multiclass
                                           clus
vv                                          TYRO3 MUTATED TYRO3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V12, binary
                 cls
clus                0   1
  TYRO3 MUTATED     0   9
  TYRO3 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      0    9
  TYRO3 WILD-TYPE   10  389
                        clus
vv                       TYRO3 MUTATED TYRO3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(322) Variable = C2ORF42 MUTATION ANALYSIS
D322V1, survival
                   sevent
clus2                 0   1
  C2ORF42 MUTATED     8   5
  C2ORF42 WILD-TYPE 330 211
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               13               541 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
                5               211 
$`C2ORF42 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-IG-A6QS TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7901 
        4.31        19.99         9.96         9.67        34.68         3.45 
TCGA-BR-8081 TCGA-BR-8361 TCGA-CD-A4MI TCGA-CG-4477 TCGA-FP-A4BE TCGA-HU-A4H3 
       32.25        31.10        11.77        30.97        11.08        29.00 
TCGA-IN-7806 
       36.36 

$`C2ORF42 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
             3.45              0.00 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
            36.36            122.30 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
            19.99             13.55 
[1] "3.5 - 36.4 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D322V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF42 MUTATED         0        0        1        0         2         5
  C2ORF42 WILD-TYPE      10       20       45       31        82        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF42 MUTATED           0          1          0          3        1
  C2ORF42 WILD-TYPE        29         83         62         36       42
                   vv
clus                STAGE IVA
  C2ORF42 MUTATED           0
  C2ORF42 WILD-TYPE         4
D322V3, multiclass
            clus
vv           C2ORF42 MUTATED C2ORF42 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                5                78
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C2ORF42 MUTATED       0   2   8   4
  C2ORF42 WILD-TYPE    54 133 253  98
D322V4, multiclass
       clus
vv      C2ORF42 MUTATED C2ORF42 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  8               253
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C2ORF42 MUTATED     5   4   2   2
  C2ORF42 WILD-TYPE 190 169  87  83
D322V5, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V6, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED    12   0
  C2ORF42 WILD-TYPE 470  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED     12    0
  C2ORF42 WILD-TYPE  470   38
   clus
vv  C2ORF42 MUTATED C2ORF42 WILD-TYPE
  0              12               470
  1               0                38
[1] 2 2
[1] FALSE
D322V7, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     8   7
  C2ORF42 WILD-TYPE 164 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      8    7
  C2ORF42 WILD-TYPE  164  399
        clus
vv       C2ORF42 MUTATED C2ORF42 WILD-TYPE
  FEMALE               8               164
  MALE                 7               399
[1] 2 2
[1] FALSE
D322V8, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     9   2
  C2ORF42 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      9    2
  C2ORF42 WILD-TYPE  407  100
     clus
vv    C2ORF42 MUTATED C2ORF42 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D322V9, continuous
D322V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C2ORF42 MUTATED       2                         1
  C2ORF42 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2ORF42 MUTATED                                           0    11
  C2ORF42 WILD-TYPE                                         1   346
D322V11, multiclass
                                           clus
vv                                          C2ORF42 MUTATED C2ORF42 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V12, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     0  12
  C2ORF42 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      0   12
  C2ORF42 WILD-TYPE   10  386
                        clus
vv                       C2ORF42 MUTATED C2ORF42 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(323) Variable = COL12A1 MUTATION ANALYSIS
D323V1, survival
                   sevent
clus2                 0   1
  COL12A1 MUTATED    36  24
  COL12A1 WILD-TYPE 302 192
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               60               494 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               24               192 
$`COL12A1 MUTATED`
TCGA-IC-A6RF TCGA-CG-4444 TCGA-CG-5727 TCGA-2H-A9GR TCGA-JY-A6FD TCGA-JY-A6FH 
       15.68        47.05        79.07        32.45        68.02        47.38 
TCGA-JY-A93D TCGA-L5-A4OT TCGA-L5-A8NM TCGA-L5-A8NW TCGA-LN-A8I0 TCGA-LN-A9FP 
       31.56         4.90         7.76        46.09        13.38        12.03 
TCGA-R6-A8WC TCGA-XP-A8T8 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 
        2.30        14.37        11.70         6.97         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8487 
       13.87        19.33         2.66        31.10        22.19         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8530 TCGA-CD-A48C TCGA-CD-A4MG 
       28.14        31.96        16.14        12.39        11.61         6.58 
TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       11.77        15.95         1.02         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6527 TCGA-D7-6822 TCGA-D7-A6EY TCGA-D7-A6EZ 
       28.96        65.10        10.26        12.33        11.44        20.32 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GN 
        7.99        14.47        21.27        11.08        77.29        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-IN-A6RP 
        8.98         6.51        20.25         0.26        14.07         6.44 
TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8P3 
       19.73        16.67        57.44         8.94         5.46        37.22 

$`COL12A1 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX 
        5.16        20.02        21.99        22.98        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        44.75         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.03        13.18        12.33        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.67         6.18         9.57        15.95        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
       29.42        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        15.02         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.31        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
        4.34        19.96         7.13         0.62        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 
       25.81        11.77        21.37         0.10         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
      116.38        71.38        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  COL12A1 MUTATED COL12A1 WILD-TYPE 
             0.26              0.00 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
           105.07            122.30 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
            14.22             13.51 
[1] "0.3 - 105.1 (14.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D323V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL12A1 MUTATED         1        2        8        6        11         7
  COL12A1 WILD-TYPE       9       18       38       25        73        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL12A1 MUTATED           1         10          3          7        7
  COL12A1 WILD-TYPE        28         74         59         32       36
                   vv
clus                STAGE IVA
  COL12A1 MUTATED           0
  COL12A1 WILD-TYPE         4
D323V3, multiclass
            clus
vv           COL12A1 MUTATED COL12A1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 2                18
  STAGE IB                 8                38
  STAGE II                 6                25
  STAGE IIA               11                73
  STAGE IIB                7                76
  STAGE III                1                28
  STAGE IIIA              10                74
  STAGE IIIB               3                59
  STAGE IIIC               7                32
  STAGE IV                 7                36
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  COL12A1 MUTATED       6  21  25  11
  COL12A1 WILD-TYPE    48 114 236  91
D323V4, multiclass
       clus
vv      COL12A1 MUTATED COL12A1 WILD-TYPE
  T0+T1               6                48
  T2                 21               114
  T3                 25               236
  T4                 11                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  COL12A1 MUTATED    19  25  12   8
  COL12A1 WILD-TYPE 176 148  77  77
D323V5, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  N0              19               176
  N1              25               148
  N2              12                77
  N3               8                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V6, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    56   5
  COL12A1 WILD-TYPE 426  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     56    5
  COL12A1 WILD-TYPE  426   33
   clus
vv  COL12A1 MUTATED COL12A1 WILD-TYPE
  0              56               426
  1               5                33
[1] 2 2
[1] FALSE
D323V7, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    24  41
  COL12A1 WILD-TYPE 148 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     24   41
  COL12A1 WILD-TYPE  148  365
        clus
vv       COL12A1 MUTATED COL12A1 WILD-TYPE
  FEMALE              24               148
  MALE                41               365
[1] 2 2
[1] FALSE
D323V8, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    43  13
  COL12A1 WILD-TYPE 373  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     43   13
  COL12A1 WILD-TYPE  373   89
     clus
vv    COL12A1 MUTATED COL12A1 WILD-TYPE
  NO               43               373
  YES              13                89
[1] 2 2
[1] FALSE
D323V9, continuous
[1] "Remove cluster labels:" "COL12A1 MUTATED"       
clus
  COL12A1 MUTATED COL12A1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
       TCGA-XP-A8T7        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" "COL12A1 WILD-TYPE" 
D323V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL12A1 MUTATED      14                         3
  COL12A1 WILD-TYPE   119                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL12A1 MUTATED                                           0    35
  COL12A1 WILD-TYPE                                         1   322
D323V11, multiclass
                                           clus
vv                                          COL12A1 MUTATED COL12A1 WILD-TYPE
  ASIAN                                                  14               119
  BLACK OR AFRICAN AMERICAN                               3                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  35               322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V12, binary
                   cls
clus                  0   1
  COL12A1 MUTATED     2  42
  COL12A1 WILD-TYPE   8 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED      2   42
  COL12A1 WILD-TYPE    8  356
                        clus
vv                       COL12A1 MUTATED COL12A1 WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              42               356
[1] 2 2
[1] FALSE

Clustering(324) Variable = FAM60A MUTATION ANALYSIS
D324V1, survival
                  sevent
clus2                0   1
  FAM60A MUTATED     2   1
  FAM60A WILD-TYPE 336 215
  FAM60A MUTATED FAM60A WILD-TYPE 
               3              551 
  FAM60A MUTATED FAM60A WILD-TYPE 
               1              215 
$`FAM60A MUTATED`
TCGA-L5-A8NJ TCGA-BR-A4QL TCGA-IP-7968 
       16.47        16.14         2.53 

$`FAM60A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM60A MUTATED FAM60A WILD-TYPE 
            2.53             0.00 
  FAM60A MUTATED FAM60A WILD-TYPE 
           16.47           122.30 
  FAM60A MUTATED FAM60A WILD-TYPE 
           16.14            13.55 
[1] "2.5 - 16.5 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D324V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM60A MUTATED         0        0        0        0         0         0
  FAM60A WILD-TYPE      10       20       46       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM60A MUTATED           1          0          2          0        1
  FAM60A WILD-TYPE        28         84         60         39       42
                  vv
clus               STAGE IVA
  FAM60A MUTATED           0
  FAM60A WILD-TYPE         4
D324V3, multiclass
            clus
vv           FAM60A MUTATED FAM60A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM60A MUTATED       0   0   3   1
  FAM60A WILD-TYPE    54 135 258 101
D324V4, multiclass
       clus
vv      FAM60A MUTATED FAM60A WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM60A MUTATED     0   1   2   1
  FAM60A WILD-TYPE 195 172  87  84
D324V5, multiclass
    clus
vv   FAM60A MUTATED FAM60A WILD-TYPE
  N0              0              195
  N1              1              172
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V6, binary
                  cls
clus                 0   1
  FAM60A MUTATED     3   0
  FAM60A WILD-TYPE 479  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      3    0
  FAM60A WILD-TYPE  479   38
   clus
vv  FAM60A MUTATED FAM60A WILD-TYPE
  0              3              479
  1              0               38
[1] 2 2
[1] FALSE
D324V7, binary
                  cls
clus                 0   1
  FAM60A MUTATED     2   2
  FAM60A WILD-TYPE 170 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      2    2
  FAM60A WILD-TYPE  170  404
        clus
vv       FAM60A MUTATED FAM60A WILD-TYPE
  FEMALE              2              170
  MALE                2              404
[1] 2 2
[1] FALSE
D324V8, binary
                  cls
clus                 0   1
  FAM60A MUTATED     2   0
  FAM60A WILD-TYPE 414 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      2    0
  FAM60A WILD-TYPE  414  102
     clus
vv    FAM60A MUTATED FAM60A WILD-TYPE
  NO               2              414
  YES              0              102
[1] 2 2
[1] FALSE
D324V9, continuous
D324V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM60A MUTATED       0                         0
  FAM60A WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM60A MUTATED                                           0     4
  FAM60A WILD-TYPE                                         1   353
D324V11, multiclass
                                           clus
vv                                          FAM60A MUTATED FAM60A WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V12, binary
                  cls
clus                 0   1
  FAM60A MUTATED     0   3
  FAM60A WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      0    3
  FAM60A WILD-TYPE   10  395
                        clus
vv                       FAM60A MUTATED FAM60A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(325) Variable = CBWD6 MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 333 215
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              6             548 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              1             215 
$`CBWD6 MUTATED`
TCGA-BR-8680 TCGA-CD-A4MG TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H8 
       31.96         6.58        30.51        22.68         6.51        14.07 

$`CBWD6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CBWD6 MUTATED CBWD6 WILD-TYPE 
           6.51            0.00 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
          31.96          122.30 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
         18.375          13.530 
[1] "6.5 - 32.0 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D325V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBWD6 MUTATED         0        0        1        0         2         1
  CBWD6 WILD-TYPE      10       20       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBWD6 MUTATED           0          0          0          1        1         0
  CBWD6 WILD-TYPE        29         84         62         38       42         4
D325V3, multiclass
            clus
vv           CBWD6 MUTATED CBWD6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CBWD6 MUTATED       1   0   4   2
  CBWD6 WILD-TYPE    53 135 257 100
D325V4, multiclass
       clus
vv      CBWD6 MUTATED CBWD6 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CBWD6 MUTATED     2   2   1   1
  CBWD6 WILD-TYPE 193 171  88  84
D325V5, multiclass
    clus
vv   CBWD6 MUTATED CBWD6 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V6, binary
                 cls
clus                0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 477  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      5    1
  CBWD6 WILD-TYPE  477   37
   clus
vv  CBWD6 MUTATED CBWD6 WILD-TYPE
  0             5             477
  1             1              37
[1] 2 2
[1] FALSE
D325V7, binary
                 cls
clus                0   1
  CBWD6 MUTATED     4   3
  CBWD6 WILD-TYPE 168 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      4    3
  CBWD6 WILD-TYPE  168  403
        clus
vv       CBWD6 MUTATED CBWD6 WILD-TYPE
  FEMALE             4             168
  MALE               3             403
[1] 2 2
[1] FALSE
D325V8, binary
                 cls
clus                0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      5    1
  CBWD6 WILD-TYPE  411  101
     clus
vv    CBWD6 MUTATED CBWD6 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D325V9, continuous
D325V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBWD6 MUTATED       5                         0
  CBWD6 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBWD6 MUTATED                                           0     1
  CBWD6 WILD-TYPE                                         1   356
D325V11, multiclass
                                           clus
vv                                          CBWD6 MUTATED CBWD6 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V12, binary
                 cls
clus                0   1
  CBWD6 MUTATED     0   6
  CBWD6 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      0    6
  CBWD6 WILD-TYPE   10  392
                        clus
vv                       CBWD6 MUTATED CBWD6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(326) Variable = SPG20 MUTATION ANALYSIS
D326V1, survival
                 sevent
clus2               0   1
  SPG20 MUTATED    15   8
  SPG20 WILD-TYPE 323 208
  SPG20 MUTATED SPG20 WILD-TYPE 
             23             531 
  SPG20 MUTATED SPG20 WILD-TYPE 
              8             208 
$`SPG20 MUTATED`
TCGA-2H-A9GM TCGA-R6-A6Y0 TCGA-RE-A7BO TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 
       13.94        53.95         7.00        26.70         6.97        30.90 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-8078 
        9.34         9.67        34.68        13.68        19.33        29.59 
TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5723 
       32.25         1.12        28.14        16.14        15.95       105.07 
TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8P2 
       22.32        24.30         6.51        29.00        38.14 

$`SPG20 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       18.35         4.08         4.08         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        17.29        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44         0.69         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SPG20 MUTATED SPG20 WILD-TYPE 
           1.12            0.00 
  SPG20 MUTATED SPG20 WILD-TYPE 
         105.07          122.30 
  SPG20 MUTATED SPG20 WILD-TYPE 
          22.32           13.41 
[1] "1.1 - 105.1 (22.3)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D326V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPG20 MUTATED         0        0        0        2         4         8
  SPG20 WILD-TYPE      10       20       46       29        80        75
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPG20 MUTATED           0          2          1          2        0         0
  SPG20 WILD-TYPE        29         82         61         37       43         4
D326V3, multiclass
            clus
vv           SPG20 MUTATED SPG20 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              8              75
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SPG20 MUTATED       2   3   8   7
  SPG20 WILD-TYPE    52 132 253  95
D326V4, multiclass
       clus
vv      SPG20 MUTATED SPG20 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                8             253
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SPG20 MUTATED     8  10   0   3
  SPG20 WILD-TYPE 187 163  89  82
D326V5, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  N0             8             187
  N1            10             163
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V6, binary
                 cls
clus                0   1
  SPG20 MUTATED    23   0
  SPG20 WILD-TYPE 459  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     23    0
  SPG20 WILD-TYPE  459   38
   clus
vv  SPG20 MUTATED SPG20 WILD-TYPE
  0            23             459
  1             0              38
[1] 2 2
[1] FALSE
D326V7, binary
                 cls
clus                0   1
  SPG20 MUTATED    14  11
  SPG20 WILD-TYPE 158 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     14   11
  SPG20 WILD-TYPE  158  395
        clus
vv       SPG20 MUTATED SPG20 WILD-TYPE
  FEMALE            14             158
  MALE              11             395
[1] 2 2
[1] FALSE
D326V8, binary
                 cls
clus                0   1
  SPG20 MUTATED    21   1
  SPG20 WILD-TYPE 395 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     21    1
  SPG20 WILD-TYPE  395  101
     clus
vv    SPG20 MUTATED SPG20 WILD-TYPE
  NO             21             395
  YES             1             101
[1] 2 2
[1] FALSE
D326V9, continuous
D326V10, continuous
[1] "Remove cluster labels:" "SPG20 MUTATED"         
clus
  SPG20 MUTATED SPG20 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-V5-A7RB 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" "SPG20 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SPG20 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SPG20 MUTATED       4                         0
  SPG20 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPG20 MUTATED                                           0    18
  SPG20 WILD-TYPE                                         1   339
D326V11, multiclass
                                           clus
vv                                          SPG20 MUTATED SPG20 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V12, binary
                 cls
clus                0   1
  SPG20 MUTATED     0  21
  SPG20 WILD-TYPE  10 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED      0   21
  SPG20 WILD-TYPE   10  377
                        clus
vv                       SPG20 MUTATED SPG20 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            21             377
[1] 2 2
[1] FALSE

Clustering(327) Variable = BPTF MUTATION ANALYSIS
D327V1, survival
                sevent
clus2              0   1
  BPTF MUTATED    19  15
  BPTF WILD-TYPE 319 201
  BPTF MUTATED BPTF WILD-TYPE 
            34            520 
  BPTF MUTATED BPTF WILD-TYPE 
            15            201 
$`BPTF MUTATED`
TCGA-L5-A43I TCGA-CG-4460 TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-L5-A4OW TCGA-LN-A49X 
       18.28        21.99         7.69        18.64         7.13        12.62 
TCGA-LN-A4A2 TCGA-LN-A7HZ TCGA-R6-A8WG TCGA-VR-A8ER TCGA-B7-A5TN TCGA-BR-4184 
       12.49        13.18        12.69        12.43         9.44         6.97 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 
        6.61        34.68        35.84        14.43        32.25         8.05 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MJ 
       31.10         0.26        31.96        16.14        12.43        12.62 
TCGA-CG-4305 TCGA-D7-6528 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-8608 TCGA-HU-A4GU 
       15.95        15.22         5.92        21.27        21.07         6.58 
TCGA-HU-A4H5 TCGA-RD-A7BT TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       23.80         8.61        38.14        17.85 

$`BPTF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        9.60         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        22.82         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BPTF MUTATED BPTF WILD-TYPE 
          0.26           0.00 
  BPTF MUTATED BPTF WILD-TYPE 
         38.14         122.30 
  BPTF MUTATED BPTF WILD-TYPE 
        13.805         13.565 
[1] "0.3 - 38.1 (13.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D327V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BPTF MUTATED         1        0        5        2         4         8
  BPTF WILD-TYPE       9       20       41       29        80        75
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BPTF MUTATED           3          4          4          2        4         0
  BPTF WILD-TYPE        26         80         58         37       39         4
D327V3, multiclass
            clus
vv           BPTF MUTATED BPTF WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              5             41
  STAGE II              2             29
  STAGE IIA             4             80
  STAGE IIB             8             75
  STAGE III             3             26
  STAGE IIIA            4             80
  STAGE IIIB            4             58
  STAGE IIIC            2             37
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BPTF MUTATED       2  10  12  13
  BPTF WILD-TYPE    52 125 249  89
D327V4, multiclass
       clus
vv      BPTF MUTATED BPTF WILD-TYPE
  T0+T1            2             52
  T2              10            125
  T3              12            249
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BPTF MUTATED    13  15   4   5
  BPTF WILD-TYPE 182 158  85  80
D327V5, multiclass
    clus
vv   BPTF MUTATED BPTF WILD-TYPE
  N0           13            182
  N1           15            158
  N2            4             85
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V6, binary
                cls
clus               0   1
  BPTF MUTATED    33   2
  BPTF WILD-TYPE 449  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     33    2
  BPTF WILD-TYPE  449   36
   clus
vv  BPTF MUTATED BPTF WILD-TYPE
  0           33            449
  1            2             36
[1] 2 2
[1] FALSE
D327V7, binary
                cls
clus               0   1
  BPTF MUTATED    15  24
  BPTF WILD-TYPE 157 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     15   24
  BPTF WILD-TYPE  157  382
        clus
vv       BPTF MUTATED BPTF WILD-TYPE
  FEMALE           15            157
  MALE             24            382
[1] 2 2
[1] FALSE
D327V8, binary
                cls
clus               0   1
  BPTF MUTATED    28   8
  BPTF WILD-TYPE 388  94
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     28    8
  BPTF WILD-TYPE  388   94
     clus
vv    BPTF MUTATED BPTF WILD-TYPE
  NO            28            388
  YES            8             94
[1] 2 2
[1] FALSE
D327V9, continuous
D327V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BPTF MUTATED       9                         1
  BPTF WILD-TYPE   124                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BPTF MUTATED                                           1    24
  BPTF WILD-TYPE                                         0   333
D327V11, multiclass
                                           clus
vv                                          BPTF MUTATED BPTF WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               24            333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V12, binary
                cls
clus               0   1
  BPTF MUTATED     2  30
  BPTF WILD-TYPE   8 368
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED      2   30
  BPTF WILD-TYPE    8  368
                        clus
vv                       BPTF MUTATED BPTF WILD-TYPE
  HISPANIC OR LATINO                2              8
  NOT HISPANIC OR LATINO           30            368
[1] 2 2
[1] FALSE

Clustering(328) Variable = MAP2K1 MUTATION ANALYSIS
D328V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     5   4
  MAP2K1 WILD-TYPE 333 212
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               9              545 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               4              212 
$`MAP2K1 MUTATED`
TCGA-L5-A43J TCGA-R6-A8WG TCGA-BR-6566 TCGA-BR-8368 TCGA-BR-8683 TCGA-CG-5723 
        4.31        12.69        32.78         4.31         9.86       105.07 
TCGA-D7-5577 TCGA-IN-A6RP TCGA-VQ-AA6J 
       25.71         6.44        27.55 

$`MAP2K1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        17.26 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
            4.31             0.00 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
          105.07           122.30 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           12.69            13.58 
[1] "4.3 - 105.1 (12.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D328V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP2K1 MUTATED         0        0        1        1         1         1
  MAP2K1 WILD-TYPE      10       20       45       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED           0          1          2          1        0
  MAP2K1 WILD-TYPE        29         83         60         38       43
                  vv
clus               STAGE IVA
  MAP2K1 MUTATED           0
  MAP2K1 WILD-TYPE         4
D328V3, multiclass
            clus
vv           MAP2K1 MUTATED MAP2K1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAP2K1 MUTATED       1   3   2   2
  MAP2K1 WILD-TYPE    53 132 259 100
D328V4, multiclass
       clus
vv      MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 2              259
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP2K1 MUTATED     3   1   2   2
  MAP2K1 WILD-TYPE 192 172  87  83
D328V5, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              3              192
  N1              1              172
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V6, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     7   0
  MAP2K1 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      7    0
  MAP2K1 WILD-TYPE  475   38
   clus
vv  MAP2K1 MUTATED MAP2K1 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D328V7, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     3   6
  MAP2K1 WILD-TYPE 169 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      3    6
  MAP2K1 WILD-TYPE  169  400
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              3              169
  MALE                6              400
[1] 2 2
[1] FALSE
D328V8, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     7   1
  MAP2K1 WILD-TYPE 409 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      7    1
  MAP2K1 WILD-TYPE  409  101
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               7              409
  YES              1              101
[1] 2 2
[1] FALSE
D328V9, continuous
D328V10, continuous
[1] "Remove cluster labels:" "MAP2K1 MUTATED"        
clus
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A4OE       TCGA-L5-A4OG 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" "MAP2K1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"MAP2K1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP2K1 MUTATED       1                         1
  MAP2K1 WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP2K1 MUTATED                                           0     6
  MAP2K1 WILD-TYPE                                         1   351
D328V11, multiclass
                                           clus
vv                                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V12, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     1   5
  MAP2K1 WILD-TYPE   9 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      1    5
  MAP2K1 WILD-TYPE    9  393
                        clus
vv                       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(329) Variable = RAI1 MUTATION ANALYSIS
D329V1, survival
                sevent
clus2              0   1
  RAI1 MUTATED    20   6
  RAI1 WILD-TYPE 318 210
  RAI1 MUTATED RAI1 WILD-TYPE 
            26            528 
  RAI1 MUTATED RAI1 WILD-TYPE 
             6            210 
$`RAI1 MUTATED`
TCGA-L5-A4OI TCGA-LN-A49O TCGA-R6-A8W8 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 
       19.99        13.41         2.89        44.94        36.16        35.84 
TCGA-BR-7716 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG 
       39.78         2.66         5.39        28.14        16.14         6.58 
TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YT TCGA-HF-7132 TCGA-HJ-7597 
       11.77         6.02       105.07        14.27        77.29        26.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-A7NT 
       22.32        22.68        24.20         6.58        14.07        10.62 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`RAI1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        35.24        33.63        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RAI1 MUTATED RAI1 WILD-TYPE 
          2.66           0.00 
  RAI1 MUTATED RAI1 WILD-TYPE 
        105.07         122.30 
  RAI1 MUTATED RAI1 WILD-TYPE 
        19.515         13.445 
[1] "2.7 - 105.1 (19.5)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D329V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAI1 MUTATED         0        2        4        2         3         6
  RAI1 WILD-TYPE      10       18       42       29        81        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAI1 MUTATED           0          5          1          2        3         0
  RAI1 WILD-TYPE        29         79         61         37       40         4
D329V3, multiclass
            clus
vv           RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              2             29
  STAGE IIA             3             81
  STAGE IIB             6             77
  STAGE III             0             29
  STAGE IIIA            5             79
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RAI1 MUTATED       4   6  11   8
  RAI1 WILD-TYPE    50 129 250  94
D329V4, multiclass
       clus
vv      RAI1 MUTATED RAI1 WILD-TYPE
  T0+T1            4             50
  T2               6            129
  T3              11            250
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAI1 MUTATED    11  11   2   5
  RAI1 WILD-TYPE 184 162  87  80
D329V5, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  N0           11            184
  N1           11            162
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V6, binary
                cls
clus               0   1
  RAI1 MUTATED    28   1
  RAI1 WILD-TYPE 454  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     28    1
  RAI1 WILD-TYPE  454   37
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0           28            454
  1            1             37
[1] 2 2
[1] FALSE
D329V7, binary
                cls
clus               0   1
  RAI1 MUTATED    15  17
  RAI1 WILD-TYPE 157 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     15   17
  RAI1 WILD-TYPE  157  389
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE           15            157
  MALE             17            389
[1] 2 2
[1] FALSE
D329V8, binary
                cls
clus               0   1
  RAI1 MUTATED    24   3
  RAI1 WILD-TYPE 392  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     24    3
  RAI1 WILD-TYPE  392   99
     clus
vv    RAI1 MUTATED RAI1 WILD-TYPE
  NO            24            392
  YES            3             99
[1] 2 2
[1] FALSE
D329V9, continuous
[1] "Remove cluster labels:" "RAI1 MUTATED"          
clus
  RAI1 MUTATED RAI1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49P     TCGA-LN-A49R 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
D329V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RAI1 MUTATED       8                         0
  RAI1 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAI1 MUTATED                                           0    21
  RAI1 WILD-TYPE                                         1   336
D329V11, multiclass
                                           clus
vv                                          RAI1 MUTATED RAI1 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               21            336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V12, binary
                cls
clus               0   1
  RAI1 MUTATED     0  27
  RAI1 WILD-TYPE  10 371
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      0   27
  RAI1 WILD-TYPE   10  371
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           27            371
[1] 2 2
[1] FALSE

Clustering(330) Variable = TRUB1 MUTATION ANALYSIS
D330V1, survival
                 sevent
clus2               0   1
  TRUB1 MUTATED     8   3
  TRUB1 WILD-TYPE 330 213
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             11             543 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              3             213 
$`TRUB1 MUTATED`
TCGA-JY-A6FG TCGA-BR-4256 TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
       41.52         9.34        30.90        31.27         1.12        28.14 
TCGA-BR-8680 TCGA-CD-8536 TCGA-CG-5721 TCGA-F1-6874 TCGA-IN-7808 
       31.96        12.43         6.02        14.47         3.45 

$`TRUB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TRUB1 MUTATED TRUB1 WILD-TYPE 
           1.12            0.00 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          41.52          122.30 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          14.47           13.55 
[1] "1.1 - 41.5 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D330V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRUB1 MUTATED         0        0        1        1         1         0
  TRUB1 WILD-TYPE      10       20       45       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRUB1 MUTATED           1          1          0          2        2         0
  TRUB1 WILD-TYPE        28         83         62         37       41         4
D330V3, multiclass
            clus
vv           TRUB1 MUTATED TRUB1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TRUB1 MUTATED       0   1   6   4
  TRUB1 WILD-TYPE    54 134 255  98
D330V4, multiclass
       clus
vv      TRUB1 MUTATED TRUB1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                6             255
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TRUB1 MUTATED     3   3   2   3
  TRUB1 WILD-TYPE 192 170  87  82
D330V5, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V6, binary
                 cls
clus                0   1
  TRUB1 MUTATED     9   2
  TRUB1 WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      9    2
  TRUB1 WILD-TYPE  473   36
   clus
vv  TRUB1 MUTATED TRUB1 WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D330V7, binary
                 cls
clus                0   1
  TRUB1 MUTATED     1  11
  TRUB1 WILD-TYPE 171 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      1   11
  TRUB1 WILD-TYPE  171  395
        clus
vv       TRUB1 MUTATED TRUB1 WILD-TYPE
  FEMALE             1             171
  MALE              11             395
[1] 2 2
[1] FALSE
D330V8, binary
                 cls
clus                0   1
  TRUB1 MUTATED    11   0
  TRUB1 WILD-TYPE 405 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED     11    0
  TRUB1 WILD-TYPE  405  102
     clus
vv    TRUB1 MUTATED TRUB1 WILD-TYPE
  NO             11             405
  YES             0             102
[1] 2 2
[1] FALSE
D330V9, continuous
D330V10, continuous
[1] "Remove cluster labels:" "TRUB1 MUTATED"         
clus
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" "TRUB1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"TRUB1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRUB1 MUTATED       2                         0
  TRUB1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRUB1 MUTATED                                           0     9
  TRUB1 WILD-TYPE                                         1   348
D330V11, multiclass
                                           clus
vv                                          TRUB1 MUTATED TRUB1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V12, binary
                 cls
clus                0   1
  TRUB1 MUTATED     0  10
  TRUB1 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      0   10
  TRUB1 WILD-TYPE   10  388
                        clus
vv                       TRUB1 MUTATED TRUB1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(331) Variable = SPATA20 MUTATION ANALYSIS
D331V1, survival
                   sevent
clus2                 0   1
  SPATA20 MUTATED    11   7
  SPATA20 WILD-TYPE 327 209
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               18               536 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
                7               209 
$`SPATA20 MUTATED`
TCGA-Q9-A6FW TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8284 
        7.82         6.61        34.68        35.84        14.43         8.05 
TCGA-BR-8368 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-8572 
        4.31        12.53        12.39         6.58         1.02        16.80 
TCGA-D7-8574 TCGA-D7-A4YY TCGA-D7-A74A TCGA-FP-8209 TCGA-HU-A4GQ TCGA-HU-A4H3 
       17.19        13.78        19.96        59.54         0.10        29.00 

$`SPATA20 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       12.76        12.59         7.17        12.33        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 
       12.36        11.31        12.33        24.72        19.50        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       20.32        22.29        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        17.06         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SPATA20 MUTATED SPATA20 WILD-TYPE 
              0.1               0.0 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
            59.54            122.30 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
           13.155            13.565 
[1] "0.1 - 59.5 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D331V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA20 MUTATED         0        0        3        1         2         1
  SPATA20 WILD-TYPE      10       20       43       30        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA20 MUTATED           2          3          2          3        1
  SPATA20 WILD-TYPE        27         81         60         36       42
                   vv
clus                STAGE IVA
  SPATA20 MUTATED           0
  SPATA20 WILD-TYPE         4
D331V3, multiclass
            clus
vv           SPATA20 MUTATED SPATA20 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                2                27
  STAGE IIIA               3                81
  STAGE IIIB               2                60
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SPATA20 MUTATED       0   6   8   4
  SPATA20 WILD-TYPE    54 129 253  98
D331V4, multiclass
       clus
vv      SPATA20 MUTATED SPATA20 WILD-TYPE
  T0+T1               0                54
  T2                  6               129
  T3                  8               253
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SPATA20 MUTATED     6   3   5   4
  SPATA20 WILD-TYPE 189 170  84  81
D331V5, multiclass
    clus
vv   SPATA20 MUTATED SPATA20 WILD-TYPE
  N0               6               189
  N1               3               170
  N2               5                84
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V6, binary
                   cls
clus                  0   1
  SPATA20 MUTATED    17   1
  SPATA20 WILD-TYPE 465  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED     17    1
  SPATA20 WILD-TYPE  465   37
   clus
vv  SPATA20 MUTATED SPATA20 WILD-TYPE
  0              17               465
  1               1                37
[1] 2 2
[1] FALSE
D331V7, binary
                   cls
clus                  0   1
  SPATA20 MUTATED     8  10
  SPATA20 WILD-TYPE 164 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED      8   10
  SPATA20 WILD-TYPE  164  396
        clus
vv       SPATA20 MUTATED SPATA20 WILD-TYPE
  FEMALE               8               164
  MALE                10               396
[1] 2 2
[1] FALSE
D331V8, binary
                   cls
clus                  0   1
  SPATA20 MUTATED    13   3
  SPATA20 WILD-TYPE 403  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED     13    3
  SPATA20 WILD-TYPE  403   99
     clus
vv    SPATA20 MUTATED SPATA20 WILD-TYPE
  NO               13               403
  YES               3                99
[1] 2 2
[1] FALSE
D331V9, continuous
D331V10, continuous
[1] "Remove cluster labels:" "SPATA20 MUTATED"       
clus
  SPATA20 MUTATED SPATA20 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-R6-A6DN 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" "SPATA20 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SPATA20 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPATA20 MUTATED       5                         0
  SPATA20 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA20 MUTATED                                           0    12
  SPATA20 WILD-TYPE                                         1   345
D331V11, multiclass
                                           clus
vv                                          SPATA20 MUTATED SPATA20 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V12, binary
                   cls
clus                  0   1
  SPATA20 MUTATED     0  17
  SPATA20 WILD-TYPE  10 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED      0   17
  SPATA20 WILD-TYPE   10  381
                        clus
vv                       SPATA20 MUTATED SPATA20 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              17               381
[1] 2 2
[1] FALSE

Clustering(332) Variable = NOS3 MUTATION ANALYSIS
D332V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED    12   6
  NOS3 WILD-TYPE 326 210
  NOS3 MUTATED NOS3 WILD-TYPE 
            18            536 
  NOS3 MUTATED NOS3 WILD-TYPE 
             6            210 
$`NOS3 MUTATED`
TCGA-L5-A43J TCGA-CG-4444 TCGA-CG-4460 TCGA-IG-A50L TCGA-L5-A8NM TCGA-LN-A49K 
        4.31        47.05        21.99         0.53         7.76         5.92 
TCGA-LN-A5U7 TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8284 TCGA-CD-8526 TCGA-CG-5723 
       25.25         9.67        29.59         8.05        12.53       105.07 
TCGA-F1-6874 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-R5-A7ZI 
       14.47        19.53        30.51         6.51        29.00        74.53 

$`NOS3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
        5.16        20.02        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NOS3 MUTATED NOS3 WILD-TYPE 
          0.53           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
        105.07         122.30 
  NOS3 MUTATED NOS3 WILD-TYPE 
         17.00          13.53 
[1] "0.5 - 105.1 (17.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D332V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOS3 MUTATED         1        0        2        1         3         4
  NOS3 WILD-TYPE       9       20       44       30        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOS3 MUTATED           0          3          0          3        2         0
  NOS3 WILD-TYPE        29         81         62         36       41         4
D332V3, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NOS3 MUTATED       1   6   6   6
  NOS3 WILD-TYPE    53 129 255  96
D332V4, multiclass
       clus
vv      NOS3 MUTATED NOS3 WILD-TYPE
  T0+T1            1             53
  T2               6            129
  T3               6            255
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NOS3 MUTATED     7   8   1   3
  NOS3 WILD-TYPE 188 165  88  82
D332V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0            7            188
  N1            8            165
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V6, binary
                cls
clus               0   1
  NOS3 MUTATED    16   2
  NOS3 WILD-TYPE 466  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     16    2
  NOS3 WILD-TYPE  466   36
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0           16            466
  1            2             36
[1] 2 2
[1] FALSE
D332V7, binary
                cls
clus               0   1
  NOS3 MUTATED    10  10
  NOS3 WILD-TYPE 162 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     10   10
  NOS3 WILD-TYPE  162  396
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE           10            162
  MALE             10            396
[1] 2 2
[1] FALSE
D332V8, binary
                cls
clus               0   1
  NOS3 MUTATED    13   3
  NOS3 WILD-TYPE 403  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     13    3
  NOS3 WILD-TYPE  403   99
     clus
vv    NOS3 MUTATED NOS3 WILD-TYPE
  NO            13            403
  YES            3             99
[1] 2 2
[1] FALSE
D332V9, continuous
[1] "Remove cluster labels:" "NOS3 MUTATED"          
clus
  NOS3 MUTATED NOS3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49L     TCGA-LN-A49M 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A7HV     TCGA-LN-A7HW 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"NOS3 WILD-TYPE" "NOS3 WILD-TYPE" 
D332V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOS3 MUTATED       6                         1
  NOS3 WILD-TYPE   127                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOS3 MUTATED                                           0     8
  NOS3 WILD-TYPE                                         1   349
D332V11, multiclass
                                           clus
vv                                          NOS3 MUTATED NOS3 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V12, binary
                cls
clus               0   1
  NOS3 MUTATED     1  12
  NOS3 WILD-TYPE   9 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      1   12
  NOS3 WILD-TYPE    9  386
                        clus
vv                       NOS3 MUTATED NOS3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(333) Variable = FAM155B MUTATION ANALYSIS
D333V1, survival
                   sevent
clus2                 0   1
  FAM155B MUTATED     8   5
  FAM155B WILD-TYPE 330 211
  FAM155B MUTATED FAM155B WILD-TYPE 
               13               541 
  FAM155B MUTATED FAM155B WILD-TYPE 
                5               211 
$`FAM155B MUTATED`
TCGA-L5-A4OI TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 
       19.99        36.16        35.84        31.10        31.27         1.12 
TCGA-BR-8591 TCGA-CD-8532 TCGA-CD-A4MG TCGA-HF-7132 TCGA-RD-A7C1 TCGA-VQ-A8DZ 
       28.14        11.64         6.58        77.29        16.67        13.02 
TCGA-VQ-A94T 
       11.24 

$`FAM155B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       31.20        44.94        21.90         9.21        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.25        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        66.81        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FAM155B MUTATED FAM155B WILD-TYPE 
             1.12              0.00 
  FAM155B MUTATED FAM155B WILD-TYPE 
            77.29            122.30 
  FAM155B MUTATED FAM155B WILD-TYPE 
            19.99             13.51 
[1] "1.1 - 77.3 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D333V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM155B MUTATED         0        1        2        2         2         0
  FAM155B WILD-TYPE      10       19       44       29        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM155B MUTATED           0          0          1          4        2
  FAM155B WILD-TYPE        29         84         61         35       41
                   vv
clus                STAGE IVA
  FAM155B MUTATED           0
  FAM155B WILD-TYPE         4
D333V3, multiclass
            clus
vv           FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 2                29
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM155B MUTATED       1   3   5   5
  FAM155B WILD-TYPE    53 132 256  97
D333V4, multiclass
       clus
vv      FAM155B MUTATED FAM155B WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  5               256
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM155B MUTATED     6   1   3   4
  FAM155B WILD-TYPE 189 172  86  81
D333V5, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  N0               6               189
  N1               1               172
  N2               3                86
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V6, binary
                   cls
clus                  0   1
  FAM155B MUTATED    12   1
  FAM155B WILD-TYPE 470  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED     12    1
  FAM155B WILD-TYPE  470   37
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0              12               470
  1               1                37
[1] 2 2
[1] FALSE
D333V7, binary
                   cls
clus                  0   1
  FAM155B MUTATED     4  10
  FAM155B WILD-TYPE 168 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      4   10
  FAM155B WILD-TYPE  168  396
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  FEMALE               4               168
  MALE                10               396
[1] 2 2
[1] FALSE
D333V8, binary
                   cls
clus                  0   1
  FAM155B MUTATED    12   1
  FAM155B WILD-TYPE 404 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED     12    1
  FAM155B WILD-TYPE  404  101
     clus
vv    FAM155B MUTATED FAM155B WILD-TYPE
  NO               12               404
  YES               1               101
[1] 2 2
[1] FALSE
D333V9, continuous
D333V10, continuous
[1] "Remove cluster labels:" "FAM155B MUTATED"       
clus
  FAM155B MUTATED FAM155B WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-Z6-AAPN 
"FAM155B WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM155B MUTATED       2                         1
  FAM155B WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM155B MUTATED                                           0     9
  FAM155B WILD-TYPE                                         1   348
D333V11, multiclass
                                           clus
vv                                          FAM155B MUTATED FAM155B WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V12, binary
                   cls
clus                  0   1
  FAM155B MUTATED     0  10
  FAM155B WILD-TYPE  10 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      0   10
  FAM155B WILD-TYPE   10  388
                        clus
vv                       FAM155B MUTATED FAM155B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(334) Variable = MDM2 MUTATION ANALYSIS
D334V1, survival
                sevent
clus2              0   1
  MDM2 MUTATED     4   5
  MDM2 WILD-TYPE 334 211
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            545 
  MDM2 MUTATED MDM2 WILD-TYPE 
             5            211 
$`MDM2 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-LN-A7HX TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8365 
        4.31        21.99        12.23         6.97        34.68        17.52 
TCGA-HJ-7597 TCGA-HU-A4GU TCGA-VQ-A8P2 
       26.47         6.58        38.14 

$`MDM2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MDM2 MUTATED MDM2 WILD-TYPE 
          4.31           0.00 
  MDM2 MUTATED MDM2 WILD-TYPE 
         38.14         122.30 
  MDM2 MUTATED MDM2 WILD-TYPE 
         17.52          13.55 
[1] "4.3 - 38.1 (17.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D334V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MDM2 MUTATED         0        0        1        0         3         2
  MDM2 WILD-TYPE      10       20       45       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDM2 MUTATED           0          2          0          0        1         0
  MDM2 WILD-TYPE        29         82         62         39       42         4
D334V3, multiclass
            clus
vv           MDM2 MUTATED MDM2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MDM2 MUTATED       0   2   5   2
  MDM2 WILD-TYPE    54 133 256 100
D334V4, multiclass
       clus
vv      MDM2 MUTATED MDM2 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MDM2 MUTATED     5   4   0   0
  MDM2 WILD-TYPE 190 169  89  85
D334V5, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  N0            5            190
  N1            4            169
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V6, binary
                cls
clus               0   1
  MDM2 MUTATED     5   1
  MDM2 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      5    1
  MDM2 WILD-TYPE  477   37
   clus
vv  MDM2 MUTATED MDM2 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D334V7, binary
                cls
clus               0   1
  MDM2 MUTATED     4   5
  MDM2 WILD-TYPE 168 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      4    5
  MDM2 WILD-TYPE  168  401
        clus
vv       MDM2 MUTATED MDM2 WILD-TYPE
  FEMALE            4            168
  MALE              5            401
[1] 2 2
[1] FALSE
D334V8, binary
                cls
clus               0   1
  MDM2 MUTATED     6   2
  MDM2 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      6    2
  MDM2 WILD-TYPE  410  100
     clus
vv    MDM2 MUTATED MDM2 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D334V9, continuous
[1] "Remove cluster labels:" "MDM2 MUTATED"          
clus
  MDM2 MUTATED MDM2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
D334V10, continuous
[1] "Remove cluster labels:" "MDM2 MUTATED"          
clus
  MDM2 MUTATED MDM2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" "MDM2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MDM2 MUTATED       2                         0
  MDM2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MDM2 MUTATED                                           0     6
  MDM2 WILD-TYPE                                         1   351
D334V11, multiclass
                                           clus
vv                                          MDM2 MUTATED MDM2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V12, binary
                cls
clus               0   1
  MDM2 MUTATED     0   6
  MDM2 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      0    6
  MDM2 WILD-TYPE   10  392
                        clus
vv                       MDM2 MUTATED MDM2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(335) Variable = ASB11 MUTATION ANALYSIS
D335V1, survival
                 sevent
clus2               0   1
  ASB11 MUTATED     8   3
  ASB11 WILD-TYPE 330 213
  ASB11 MUTATED ASB11 WILD-TYPE 
             11             543 
  ASB11 MUTATED ASB11 WILD-TYPE 
              3             213 
$`ASB11 MUTATED`
TCGA-Z6-A8JD TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL 
        3.42        34.68        44.94        31.27        31.96        16.14 
TCGA-CD-5813 TCGA-CG-4306 TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4GT 
       12.39         1.02         6.02        14.47         6.51 

$`ASB11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ASB11 MUTATED ASB11 WILD-TYPE 
           1.02            0.00 
  ASB11 MUTATED ASB11 WILD-TYPE 
          44.94          122.30 
  ASB11 MUTATED ASB11 WILD-TYPE 
          14.47           13.55 
[1] "1.0 - 44.9 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASB11 MUTATED         0        0        1        1         3         1
  ASB11 WILD-TYPE      10       20       45       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASB11 MUTATED           0          0          1          1        3         0
  ASB11 WILD-TYPE        29         84         61         38       40         4
D335V3, multiclass
            clus
vv           ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ASB11 MUTATED       0   1   7   3
  ASB11 WILD-TYPE    54 134 254  99
D335V4, multiclass
       clus
vv      ASB11 MUTATED ASB11 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASB11 MUTATED     6   1   2   2
  ASB11 WILD-TYPE 189 172  87  83
D335V5, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  N0             6             189
  N1             1             172
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V6, binary
                 cls
clus                0   1
  ASB11 MUTATED     9   2
  ASB11 WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      9    2
  ASB11 WILD-TYPE  473   36
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D335V7, binary
                 cls
clus                0   1
  ASB11 MUTATED     4   7
  ASB11 WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      4    7
  ASB11 WILD-TYPE  168  399
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D335V8, binary
                 cls
clus                0   1
  ASB11 MUTATED    10   0
  ASB11 WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED     10    0
  ASB11 WILD-TYPE  406  102
     clus
vv    ASB11 MUTATED ASB11 WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D335V9, continuous
[1] "Remove cluster labels:" "ASB11 MUTATED"         
clus
  ASB11 MUTATED ASB11 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JE 
"ASB11 WILD-TYPE" "ASB11 WILD-TYPE" "ASB11 WILD-TYPE" 
D335V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASB11 MUTATED       3                         0
  ASB11 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASB11 MUTATED                                           0     6
  ASB11 WILD-TYPE                                         1   351
D335V11, multiclass
                                           clus
vv                                          ASB11 MUTATED ASB11 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V12, binary
                 cls
clus                0   1
  ASB11 MUTATED     0   9
  ASB11 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      0    9
  ASB11 WILD-TYPE   10  389
                        clus
vv                       ASB11 MUTATED ASB11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(336) Variable = TAS2R10 MUTATION ANALYSIS
D336V1, survival
                   sevent
clus2                 0   1
  TAS2R10 MUTATED     2   2
  TAS2R10 WILD-TYPE 336 214
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                4               550 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                2               214 
$`TAS2R10 MUTATED`
TCGA-Q9-A6FU TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-VQ-A8PK 
        5.16        22.68         6.58        17.85 

$`TAS2R10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
             5.16              0.00 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
            22.68            122.30 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
           12.215            13.565 
[1] "5.2 - 22.7 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D336V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAS2R10 MUTATED         1        0        0        0         0         2
  TAS2R10 WILD-TYPE       9       20       46       31        84        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R10 MUTATED           0          0          2          0        0
  TAS2R10 WILD-TYPE        29         84         60         39       43
                   vv
clus                STAGE IVA
  TAS2R10 MUTATED           0
  TAS2R10 WILD-TYPE         4
D336V3, multiclass
            clus
vv           TAS2R10 MUTATED TAS2R10 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TAS2R10 MUTATED       1   0   4   0
  TAS2R10 WILD-TYPE    53 135 257 102
D336V4, multiclass
       clus
vv      TAS2R10 MUTATED TAS2R10 WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  4               257
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TAS2R10 MUTATED     0   3   1   1
  TAS2R10 WILD-TYPE 195 170  88  84
D336V5, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  N0               0               195
  N1               3               170
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V6, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     4   0
  TAS2R10 WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      4    0
  TAS2R10 WILD-TYPE  478   38
   clus
vv  TAS2R10 MUTATED TAS2R10 WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D336V7, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     2   3
  TAS2R10 WILD-TYPE 170 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      2    3
  TAS2R10 WILD-TYPE  170  403
        clus
vv       TAS2R10 MUTATED TAS2R10 WILD-TYPE
  FEMALE               2               170
  MALE                 3               403
[1] 2 2
[1] FALSE
D336V8, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     5   0
  TAS2R10 WILD-TYPE 411 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      5    0
  TAS2R10 WILD-TYPE  411  102
     clus
vv    TAS2R10 MUTATED TAS2R10 WILD-TYPE
  NO                5               411
  YES               0               102
[1] 2 2
[1] FALSE
D336V9, continuous
D336V10, continuous
[1] "Remove cluster labels:" "TAS2R10 MUTATED"       
clus
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" "TAS2R10 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TAS2R10 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TAS2R10 MUTATED       2                         1
  TAS2R10 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAS2R10 MUTATED                                           0     2
  TAS2R10 WILD-TYPE                                         1   355
D336V11, multiclass
                                           clus
vv                                          TAS2R10 MUTATED TAS2R10 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V12, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     0   4
  TAS2R10 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      0    4
  TAS2R10 WILD-TYPE   10  394
                        clus
vv                       TAS2R10 MUTATED TAS2R10 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(337) Variable = B4GALT6 MUTATION ANALYSIS
D337V1, survival
                   sevent
clus2                 0   1
  B4GALT6 MUTATED     4   2
  B4GALT6 WILD-TYPE 334 214
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                6               548 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2               214 
$`B4GALT6 MUTATED`
TCGA-IG-A3YC TCGA-R6-A6DQ TCGA-V5-AASV TCGA-BR-8485 TCGA-CD-A4MG TCGA-HF-A5NB 
       20.12         7.59        15.35         9.21         6.58        30.51 

$`B4GALT6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
       33.27        35.21         0.85        20.78         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             6.58              0.00 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            30.51            122.30 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
           12.280            13.565 
[1] "6.6 - 30.5 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D337V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B4GALT6 MUTATED         1        1        1        0         1         1
  B4GALT6 WILD-TYPE       9       19       45       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALT6 MUTATED           0          1          0          2        0
  B4GALT6 WILD-TYPE        29         83         62         37       43
                   vv
clus                STAGE IVA
  B4GALT6 MUTATED           0
  B4GALT6 WILD-TYPE         4
D337V3, multiclass
            clus
vv           B4GALT6 MUTATED B4GALT6 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  B4GALT6 MUTATED       2   1   3   2
  B4GALT6 WILD-TYPE    52 134 258 100
D337V4, multiclass
       clus
vv      B4GALT6 MUTATED B4GALT6 WILD-TYPE
  T0+T1               2                52
  T2                  1               134
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  B4GALT6 MUTATED     4   2   0   2
  B4GALT6 WILD-TYPE 191 171  89  83
D337V5, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  N0               4               191
  N1               2               171
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V6, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     6   0
  B4GALT6 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      6    0
  B4GALT6 WILD-TYPE  476   38
   clus
vv  B4GALT6 MUTATED B4GALT6 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D337V7, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     3   6
  B4GALT6 WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      3    6
  B4GALT6 WILD-TYPE  169  400
        clus
vv       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D337V8, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     4   3
  B4GALT6 WILD-TYPE 412  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      4    3
  B4GALT6 WILD-TYPE  412   99
     clus
vv    B4GALT6 MUTATED B4GALT6 WILD-TYPE
  NO                4               412
  YES               3                99
[1] 2 2
[1] FALSE
D337V9, continuous
[1] "Remove cluster labels:" "B4GALT6 MUTATED"       
clus
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASW 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
D337V10, continuous
[1] "Remove cluster labels:" "B4GALT6 MUTATED"       
clus
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A4P3 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" "B4GALT6 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  B4GALT6 MUTATED       2                         2
  B4GALT6 WILD-TYPE   131                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B4GALT6 MUTATED                                           0     3
  B4GALT6 WILD-TYPE                                         1   354
D337V11, multiclass
                                           clus
vv                                          B4GALT6 MUTATED B4GALT6 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V12, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     0   7
  B4GALT6 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      0    7
  B4GALT6 WILD-TYPE   10  391
                        clus
vv                       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(338) Variable = SNAPC2 MUTATION ANALYSIS
D338V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     8   1
  SNAPC2 WILD-TYPE 330 215
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              545 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               1              215 
$`SNAPC2 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-CG-5721 TCGA-D7-A4YY 
       34.68        36.16        29.59        31.10         6.02        13.78 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H8 
        0.10         6.58        14.07 

$`SNAPC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
             0.1              0.0 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           36.16           122.30 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           14.07            13.51 
[1] "0.1 - 36.2 (14.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.8"
D338V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNAPC2 MUTATED         0        1        1        0         1         2
  SNAPC2 WILD-TYPE      10       19       45       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           0          0          1          2        1
  SNAPC2 WILD-TYPE        29         84         61         37       42
                  vv
clus               STAGE IVA
  SNAPC2 MUTATED           0
  SNAPC2 WILD-TYPE         4
D338V3, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SNAPC2 MUTATED       2   0   3   4
  SNAPC2 WILD-TYPE    52 135 258  98
D338V4, multiclass
       clus
vv      SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T0+T1              2               52
  T2                 0              135
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SNAPC2 MUTATED     3   3   2   1
  SNAPC2 WILD-TYPE 192 170  87  84
D338V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              3              192
  N1              3              170
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V6, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     9   0
  SNAPC2 WILD-TYPE 473  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      9    0
  SNAPC2 WILD-TYPE  473   38
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0              9              473
  1              0               38
[1] 2 2
[1] FALSE
D338V7, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     3   6
  SNAPC2 WILD-TYPE 169 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      3    6
  SNAPC2 WILD-TYPE  169  400
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  FEMALE              3              169
  MALE                6              400
[1] 2 2
[1] FALSE
D338V8, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     8   1
  SNAPC2 WILD-TYPE 408 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      8    1
  SNAPC2 WILD-TYPE  408  101
     clus
vv    SNAPC2 MUTATED SNAPC2 WILD-TYPE
  NO               8              408
  YES              1              101
[1] 2 2
[1] FALSE
D338V9, continuous
D338V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SNAPC2 MUTATED       3                         0
  SNAPC2 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNAPC2 MUTATED                                           0     5
  SNAPC2 WILD-TYPE                                         1   352
D338V11, multiclass
                                           clus
vv                                          SNAPC2 MUTATED SNAPC2 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V12, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     0   8
  SNAPC2 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      0    8
  SNAPC2 WILD-TYPE   10  390
                        clus
vv                       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(339) Variable = TCHP MUTATION ANALYSIS
D339V1, survival
                sevent
clus2              0   1
  TCHP MUTATED     9   4
  TCHP WILD-TYPE 329 212
  TCHP MUTATED TCHP WILD-TYPE 
            13            541 
  TCHP MUTATED TCHP WILD-TYPE 
             4            212 
$`TCHP MUTATED`
TCGA-L5-A43J TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8372 
        4.31        26.70         6.97         6.61        29.59        31.27 
TCGA-CD-A4MG TCGA-D7-8572 TCGA-D7-A4YT TCGA-HU-A4GX TCGA-KB-A6F5 TCGA-MX-A5UJ 
        6.58        16.80        14.27        20.25         5.56        19.73 
TCGA-VQ-A8P2 
       38.14 

$`TCHP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        2.53        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TCHP MUTATED TCHP WILD-TYPE 
          4.31           0.00 
  TCHP MUTATED TCHP WILD-TYPE 
         38.14         122.30 
  TCHP MUTATED TCHP WILD-TYPE 
         16.80          13.51 
[1] "4.3 - 38.1 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D339V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCHP MUTATED         0        0        0        0         1         4
  TCHP WILD-TYPE      10       20       46       31        83        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCHP MUTATED           1          5          0          2        0         0
  TCHP WILD-TYPE        28         79         62         37       43         4
D339V3, multiclass
            clus
vv           TCHP MUTATED TCHP WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            5             79
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TCHP MUTATED       0   3   5   5
  TCHP WILD-TYPE    54 132 256  97
D339V4, multiclass
       clus
vv      TCHP MUTATED TCHP WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               5            256
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TCHP MUTATED     4   3   4   2
  TCHP WILD-TYPE 191 170  85  83
D339V5, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  N0            4            191
  N1            3            170
  N2            4             85
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V6, binary
                cls
clus               0   1
  TCHP MUTATED    11   0
  TCHP WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED     11    0
  TCHP WILD-TYPE  471   38
   clus
vv  TCHP MUTATED TCHP WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D339V7, binary
                cls
clus               0   1
  TCHP MUTATED     5   8
  TCHP WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      5    8
  TCHP WILD-TYPE  167  398
        clus
vv       TCHP MUTATED TCHP WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D339V8, binary
                cls
clus               0   1
  TCHP MUTATED    11   1
  TCHP WILD-TYPE 405 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED     11    1
  TCHP WILD-TYPE  405  101
     clus
vv    TCHP MUTATED TCHP WILD-TYPE
  NO            11            405
  YES            1            101
[1] 2 2
[1] FALSE
D339V9, continuous
D339V10, continuous
[1] "Remove cluster labels:" "TCHP MUTATED"          
clus
  TCHP MUTATED TCHP WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" "TCHP WILD-TYPE" 
    TCGA-Z6-AAPN 
"TCHP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TCHP MUTATED       2                         0
  TCHP WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCHP MUTATED                                           0    10
  TCHP WILD-TYPE                                         1   347
D339V11, multiclass
                                           clus
vv                                          TCHP MUTATED TCHP WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V12, binary
                cls
clus               0   1
  TCHP MUTATED     0  10
  TCHP WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      0   10
  TCHP WILD-TYPE   10  388
                        clus
vv                       TCHP MUTATED TCHP WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(340) Variable = ADNP2 MUTATION ANALYSIS
D340V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    17   3
  ADNP2 WILD-TYPE 321 213
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             20             534 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              3             213 
$`ADNP2 MUTATED`
TCGA-JY-A93F TCGA-VR-AA7B TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 
       24.03        11.24        11.70         6.97        34.68        44.94 
TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8487 TCGA-CD-8536 TCGA-CG-4305 
       36.16        29.59         6.18         1.12        12.43        15.95 
TCGA-CG-5726 TCGA-D7-A4YY TCGA-EQ-8122 TCGA-F1-A448 TCGA-HU-A4GT TCGA-HU-A4GX 
       28.96        13.78         7.99        21.27         6.51        20.25 
TCGA-HU-A4H0 TCGA-VQ-A8P2 
        2.10        38.14 

$`ADNP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        25.22         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       40.21        30.90        31.20        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        7.13         0.62        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.58         0.26        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
           1.12            0.00 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
          44.94          122.30 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
         14.865          13.530 
[1] "1.1 - 44.9 (14.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.8"
D340V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADNP2 MUTATED         0        2        2        2         5         2
  ADNP2 WILD-TYPE      10       18       44       29        79        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADNP2 MUTATED           0          3          2          2        1         0
  ADNP2 WILD-TYPE        29         81         60         37       42         4
D340V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              5              79
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ADNP2 MUTATED       2   3  11   5
  ADNP2 WILD-TYPE    52 132 250  97
D340V4, multiclass
       clus
vv      ADNP2 MUTATED ADNP2 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3               11             250
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ADNP2 MUTATED    12   4   1   4
  ADNP2 WILD-TYPE 183 169  88  81
D340V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            12             183
  N1             4             169
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V6, binary
                 cls
clus                0   1
  ADNP2 MUTATED    18   1
  ADNP2 WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     18    1
  ADNP2 WILD-TYPE  464   37
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D340V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED    10  11
  ADNP2 WILD-TYPE 162 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     10   11
  ADNP2 WILD-TYPE  162  395
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE            10             162
  MALE              11             395
[1] 2 2
[1] FALSE
D340V8, binary
                 cls
clus                0   1
  ADNP2 MUTATED    15   4
  ADNP2 WILD-TYPE 401  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     15    4
  ADNP2 WILD-TYPE  401   98
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO             15             401
  YES             4              98
[1] 2 2
[1] FALSE
D340V9, continuous
[1] "Remove cluster labels:" "ADNP2 MUTATED"         
clus
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" "ADNP2 WILD-TYPE" 
D340V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ADNP2 MUTATED       4                         0
  ADNP2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADNP2 MUTATED                                           0    15
  ADNP2 WILD-TYPE                                         1   342
D340V11, multiclass
                                           clus
vv                                          ADNP2 MUTATED ADNP2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V12, binary
                 cls
clus                0   1
  ADNP2 MUTATED     1  15
  ADNP2 WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      1   15
  ADNP2 WILD-TYPE    9  383
                        clus
vv                       ADNP2 MUTATED ADNP2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(341) Variable = PUS7L MUTATION ANALYSIS
D341V1, survival
                 sevent
clus2               0   1
  PUS7L MUTATED     4   4
  PUS7L WILD-TYPE 334 212
  PUS7L MUTATED PUS7L WILD-TYPE 
              8             546 
  PUS7L MUTATED PUS7L WILD-TYPE 
              4             212 
$`PUS7L MUTATED`
TCGA-CG-4460 TCGA-JY-A93E TCGA-BR-4184 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5733 
       21.99        25.22         6.97         6.02        12.03        21.07 
TCGA-HU-A4GN TCGA-HU-A4H4 
       29.98        23.84 

$`PUS7L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PUS7L MUTATED PUS7L WILD-TYPE 
           6.02            0.00 
  PUS7L MUTATED PUS7L WILD-TYPE 
          29.98          122.30 
  PUS7L MUTATED PUS7L WILD-TYPE 
          21.53           13.53 
[1] "6.0 - 30.0 (21.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D341V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PUS7L MUTATED         0        0        0        0         1         1
  PUS7L WILD-TYPE      10       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PUS7L MUTATED           0          3          0          0        4         0
  PUS7L WILD-TYPE        29         81         62         39       39         4
D341V3, multiclass
            clus
vv           PUS7L MUTATED PUS7L WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PUS7L MUTATED       1   3   3   3
  PUS7L WILD-TYPE    53 132 258  99
D341V4, multiclass
       clus
vv      PUS7L MUTATED PUS7L WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PUS7L MUTATED     0   5   3   1
  PUS7L WILD-TYPE 195 168  86  84
D341V5, multiclass
    clus
vv   PUS7L MUTATED PUS7L WILD-TYPE
  N0             0             195
  N1             5             168
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V6, binary
                 cls
clus                0   1
  PUS7L MUTATED     7   2
  PUS7L WILD-TYPE 475  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      7    2
  PUS7L WILD-TYPE  475   36
   clus
vv  PUS7L MUTATED PUS7L WILD-TYPE
  0             7             475
  1             2              36
[1] 2 2
[1] FALSE
D341V7, binary
                 cls
clus                0   1
  PUS7L MUTATED     5   5
  PUS7L WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      5    5
  PUS7L WILD-TYPE  167  401
        clus
vv       PUS7L MUTATED PUS7L WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D341V8, binary
                 cls
clus                0   1
  PUS7L MUTATED     8   0
  PUS7L WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      8    0
  PUS7L WILD-TYPE  408  102
     clus
vv    PUS7L MUTATED PUS7L WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D341V9, continuous
D341V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PUS7L MUTATED       2                         0
  PUS7L WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PUS7L MUTATED                                           0     4
  PUS7L WILD-TYPE                                         1   353
D341V11, multiclass
                                           clus
vv                                          PUS7L MUTATED PUS7L WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V12, binary
                 cls
clus                0   1
  PUS7L MUTATED     0   5
  PUS7L WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      0    5
  PUS7L WILD-TYPE   10  393
                        clus
vv                       PUS7L MUTATED PUS7L WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(342) Variable = NCOA7 MUTATION ANALYSIS
D342V1, survival
                 sevent
clus2               0   1
  NCOA7 MUTATED    11   5
  NCOA7 WILD-TYPE 327 211
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             16             538 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              5             211 
$`NCOA7 MUTATED`
TCGA-CG-5727 TCGA-JY-A6FE TCGA-LN-A7HY TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
       79.07         3.68        12.03         6.97        30.90        34.68 
TCGA-BR-7704 TCGA-BR-8077 TCGA-BR-8382 TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-A6EY 
       35.24         0.69        25.05        15.95        65.10        11.44 
TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       30.51        23.84        14.07        74.53 

$`NCOA7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
           0.69            0.00 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          79.07          122.30 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
         24.445          13.495 
[1] "0.7 - 79.1 (24.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D342V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCOA7 MUTATED         0        0        2        3         2         1
  NCOA7 WILD-TYPE      10       20       44       28        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA7 MUTATED           2          1          2          2        1         0
  NCOA7 WILD-TYPE        27         83         60         37       42         4
D342V3, multiclass
            clus
vv           NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NCOA7 MUTATED       1   4   8   4
  NCOA7 WILD-TYPE    53 131 253  98
D342V4, multiclass
       clus
vv      NCOA7 MUTATED NCOA7 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NCOA7 MUTATED     5   8   1   3
  NCOA7 WILD-TYPE 190 165  88  82
D342V5, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  N0             5             190
  N1             8             165
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V6, binary
                 cls
clus                0   1
  NCOA7 MUTATED    16   1
  NCOA7 WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     16    1
  NCOA7 WILD-TYPE  466   37
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D342V7, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   7
  NCOA7 WILD-TYPE 161 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    7
  NCOA7 WILD-TYPE  161  399
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  FEMALE            11             161
  MALE               7             399
[1] 2 2
[1] FALSE
D342V8, binary
                 cls
clus                0   1
  NCOA7 MUTATED    13   1
  NCOA7 WILD-TYPE 403 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     13    1
  NCOA7 WILD-TYPE  403  101
     clus
vv    NCOA7 MUTATED NCOA7 WILD-TYPE
  NO             13             403
  YES             1             101
[1] 2 2
[1] FALSE
D342V9, continuous
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
D342V10, continuous
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-Z6-AAPN 
"NCOA7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NCOA7 MUTATED       3                         0
  NCOA7 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCOA7 MUTATED                                           0    11
  NCOA7 WILD-TYPE                                         1   346
D342V11, multiclass
                                           clus
vv                                          NCOA7 MUTATED NCOA7 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V12, binary
                 cls
clus                0   1
  NCOA7 MUTATED     1  12
  NCOA7 WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      1   12
  NCOA7 WILD-TYPE    9  386
                        clus
vv                       NCOA7 MUTATED NCOA7 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(343) Variable = RAD50 MUTATION ANALYSIS
D343V1, survival
                 sevent
clus2               0   1
  RAD50 MUTATED     7   7
  RAD50 WILD-TYPE 331 209
  RAD50 MUTATED RAD50 WILD-TYPE 
             14             540 
  RAD50 MUTATED RAD50 WILD-TYPE 
              7             209 
$`RAD50 MUTATED`
TCGA-JY-A6FE TCGA-L7-A6VZ TCGA-VR-A8EQ TCGA-BR-4257 TCGA-BR-8367 TCGA-BR-8382 
        3.68        10.36        22.82         9.67        26.33        25.05 
TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4GN 
       16.14        12.62         1.02         6.02        21.27        29.98 
TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.51        38.14 

$`RAD50 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RAD50 MUTATED RAD50 WILD-TYPE 
           1.02            0.00 
  RAD50 MUTATED RAD50 WILD-TYPE 
          38.14          122.30 
  RAD50 MUTATED RAD50 WILD-TYPE 
         14.380          13.565 
[1] "1.0 - 38.1 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D343V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAD50 MUTATED         0        0        1        0         2         0
  RAD50 WILD-TYPE      10       20       45       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAD50 MUTATED           2          1          3          2        2         0
  RAD50 WILD-TYPE        27         83         59         37       41         4
D343V3, multiclass
            clus
vv           RAD50 MUTATED RAD50 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RAD50 MUTATED       1   2   8   3
  RAD50 WILD-TYPE    53 133 253  99
D343V4, multiclass
       clus
vv      RAD50 MUTATED RAD50 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                8             253
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RAD50 MUTATED     2   5   1   5
  RAD50 WILD-TYPE 193 168  88  80
D343V5, multiclass
    clus
vv   RAD50 MUTATED RAD50 WILD-TYPE
  N0             2             193
  N1             5             168
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V6, binary
                 cls
clus                0   1
  RAD50 MUTATED    13   1
  RAD50 WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED     13    1
  RAD50 WILD-TYPE  469   37
   clus
vv  RAD50 MUTATED RAD50 WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D343V7, binary
                 cls
clus                0   1
  RAD50 MUTATED     5  10
  RAD50 WILD-TYPE 167 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      5   10
  RAD50 WILD-TYPE  167  396
        clus
vv       RAD50 MUTATED RAD50 WILD-TYPE
  FEMALE             5             167
  MALE              10             396
[1] 2 2
[1] FALSE
D343V8, binary
                 cls
clus                0   1
  RAD50 MUTATED     9   4
  RAD50 WILD-TYPE 407  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      9    4
  RAD50 WILD-TYPE  407   98
     clus
vv    RAD50 MUTATED RAD50 WILD-TYPE
  NO              9             407
  YES             4              98
[1] 2 2
[1] FALSE
D343V9, continuous
[1] "Remove cluster labels:" "RAD50 MUTATED"         
clus
  RAD50 MUTATED RAD50 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
D343V10, continuous
[1] "Remove cluster labels:" "RAD50 MUTATED"         
clus
  RAD50 MUTATED RAD50 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" "RAD50 WILD-TYPE" 
     TCGA-Z6-AAPN 
"RAD50 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAD50 MUTATED       3                         0
  RAD50 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAD50 MUTATED                                           0    10
  RAD50 WILD-TYPE                                         1   347
D343V11, multiclass
                                           clus
vv                                          RAD50 MUTATED RAD50 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V12, binary
                 cls
clus                0   1
  RAD50 MUTATED     1   9
  RAD50 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      1    9
  RAD50 WILD-TYPE    9  389
                        clus
vv                       RAD50 MUTATED RAD50 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(344) Variable = KIAA1009 MUTATION ANALYSIS
D344V1, survival
                    sevent
clus2                  0   1
  KIAA1009 MUTATED    12   6
  KIAA1009 WILD-TYPE 326 210
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                18                536 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                 6                210 
$`KIAA1009 MUTATED`
TCGA-Q9-A6FU TCGA-LN-A7HW TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-8078 
        5.16        12.00        30.90        34.68         9.17        29.59 
TCGA-BR-8289 TCGA-BR-8382 TCGA-CD-A4MG TCGA-CG-5723 TCGA-F1-A448 TCGA-HU-A4GN 
        2.66        25.05         6.58       105.07        21.27        29.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-VQ-A8P2 
        6.51         6.58        20.25        29.00        19.73        38.14 

$`KIAA1009 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56        29.42        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY 
       25.81        11.77        21.37         8.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
              2.66               0.00 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
            105.07             122.30 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
             20.76              13.51 
[1] "2.7 - 105.1 (20.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D344V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1009 MUTATED         0        0        0        1         5         3
  KIAA1009 WILD-TYPE      10       20       46       30        79        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1009 MUTATED           0          2          2          3        1
  KIAA1009 WILD-TYPE        29         82         60         36       42
                    vv
clus                 STAGE IVA
  KIAA1009 MUTATED           0
  KIAA1009 WILD-TYPE         4
D344V3, multiclass
            clus
vv           KIAA1009 MUTATED KIAA1009 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 5                 79
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                2                 60
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1009 MUTATED       0   4   7   7
  KIAA1009 WILD-TYPE    54 131 254  95
D344V4, multiclass
       clus
vv      KIAA1009 MUTATED KIAA1009 WILD-TYPE
  T0+T1                0                 54
  T2                   4                131
  T3                   7                254
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1009 MUTATED     6   4   3   4
  KIAA1009 WILD-TYPE 189 169  86  81
D344V5, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  N0                6                189
  N1                4                169
  N2                3                 86
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V6, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED    17   1
  KIAA1009 WILD-TYPE 465  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED     17    1
  KIAA1009 WILD-TYPE  465   37
   clus
vv  KIAA1009 MUTATED KIAA1009 WILD-TYPE
  0               17                465
  1                1                 37
[1] 2 2
[1] FALSE
D344V7, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     9   9
  KIAA1009 WILD-TYPE 163 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      9    9
  KIAA1009 WILD-TYPE  163  397
        clus
vv       KIAA1009 MUTATED KIAA1009 WILD-TYPE
  FEMALE                9                163
  MALE                  9                397
[1] 2 2
[1] FALSE
D344V8, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED    15   2
  KIAA1009 WILD-TYPE 401 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED     15    2
  KIAA1009 WILD-TYPE  401  100
     clus
vv    KIAA1009 MUTATED KIAA1009 WILD-TYPE
  NO                15                401
  YES                2                100
[1] 2 2
[1] FALSE
D344V9, continuous
[1] "Remove cluster labels:" "KIAA1009 MUTATED"      
clus
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1009 WILD-TYPE" 
D344V10, continuous
[1] "Remove cluster labels:" "KIAA1009 MUTATED"      
clus
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-IC-A6RE         TCGA-IG-A3QL 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" "KIAA1009 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1009 MUTATED       7                         0
  KIAA1009 WILD-TYPE   126                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1009 MUTATED                                           0    10
  KIAA1009 WILD-TYPE                                         1   347
D344V11, multiclass
                                           clus
vv                                          KIAA1009 MUTATED KIAA1009 WILD-TYPE
  ASIAN                                                    7                126
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V12, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     1  15
  KIAA1009 WILD-TYPE   9 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      1   15
  KIAA1009 WILD-TYPE    9  383
                        clus
vv                       KIAA1009 MUTATED KIAA1009 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               15                383
[1] 2 2
[1] FALSE

Clustering(345) Variable = PFKP MUTATION ANALYSIS
D345V1, survival
                sevent
clus2              0   1
  PFKP MUTATED    10   6
  PFKP WILD-TYPE 328 210
  PFKP MUTATED PFKP WILD-TYPE 
            16            538 
  PFKP MUTATED PFKP WILD-TYPE 
             6            210 
$`PFKP MUTATED`
TCGA-2H-A9GK TCGA-R6-A6Y2 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 
        7.63         9.30         6.97        30.90        34.68        32.78 
TCGA-BR-7723 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8591 TCGA-CG-5726 TCGA-HU-A4G2 
       28.73        29.59        32.25        28.14        28.96        24.30 
TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-VQ-A8P2 
        6.58        21.17        14.07        38.14 

$`PFKP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.80        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PFKP MUTATED PFKP WILD-TYPE 
          6.58           0.00 
  PFKP MUTATED PFKP WILD-TYPE 
         38.14         122.30 
  PFKP MUTATED PFKP WILD-TYPE 
        28.435         13.445 
[1] "6.6 - 38.1 (28.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D345V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PFKP MUTATED         0        1        1        0         2         5
  PFKP WILD-TYPE      10       19       45       31        82        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PFKP MUTATED           1          4          1          1        0         0
  PFKP WILD-TYPE        28         80         61         38       43         4
D345V3, multiclass
            clus
vv           PFKP MUTATED PFKP WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             5             78
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PFKP MUTATED       3   1   8   6
  PFKP WILD-TYPE    51 134 253  96
D345V4, multiclass
       clus
vv      PFKP MUTATED PFKP WILD-TYPE
  T0+T1            3             51
  T2               1            134
  T3               8            253
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PFKP MUTATED     7   6   1   2
  PFKP WILD-TYPE 188 167  88  83
D345V5, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  N0            7            188
  N1            6            167
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V6, binary
                cls
clus               0   1
  PFKP MUTATED    18   0
  PFKP WILD-TYPE 464  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED     18    0
  PFKP WILD-TYPE  464   38
   clus
vv  PFKP MUTATED PFKP WILD-TYPE
  0           18            464
  1            0             38
[1] 2 2
[1] FALSE
D345V7, binary
                cls
clus               0   1
  PFKP MUTATED     9  11
  PFKP WILD-TYPE 163 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      9   11
  PFKP WILD-TYPE  163  395
        clus
vv       PFKP MUTATED PFKP WILD-TYPE
  FEMALE            9            163
  MALE             11            395
[1] 2 2
[1] FALSE
D345V8, binary
                cls
clus               0   1
  PFKP MUTATED    15   1
  PFKP WILD-TYPE 401 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED     15    1
  PFKP WILD-TYPE  401  101
     clus
vv    PFKP MUTATED PFKP WILD-TYPE
  NO            15            401
  YES            1            101
[1] 2 2
[1] FALSE
D345V9, continuous
D345V10, continuous
[1] "Remove cluster labels:" "PFKP MUTATED"          
clus
  PFKP MUTATED PFKP WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A8W5 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" "PFKP WILD-TYPE" 
    TCGA-Z6-AAPN 
"PFKP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PFKP MUTATED       4                         0
  PFKP WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PFKP MUTATED                                           0    14
  PFKP WILD-TYPE                                         1   343
D345V11, multiclass
                                           clus
vv                                          PFKP MUTATED PFKP WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V12, binary
                cls
clus               0   1
  PFKP MUTATED     1  16
  PFKP WILD-TYPE   9 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      1   16
  PFKP WILD-TYPE    9  382
                        clus
vv                       PFKP MUTATED PFKP WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           16            382
[1] 2 2
[1] FALSE

Clustering(346) Variable = NT5DC1 MUTATION ANALYSIS
D346V1, survival
                  sevent
clus2                0   1
  NT5DC1 MUTATED     5   3
  NT5DC1 WILD-TYPE 333 213
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              546 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               3              213 
$`NT5DC1 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-A4YV 
       34.68         0.26         1.12        12.43         6.58         5.92 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`NT5DC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
            0.26             0.00 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
           38.14           122.30 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
           9.505           13.630 
[1] "0.3 - 38.1 (9.5)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D346V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NT5DC1 MUTATED         0        0        1        1         3         1
  NT5DC1 WILD-TYPE      10       20       45       30        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC1 MUTATED           0          2          0          0        0
  NT5DC1 WILD-TYPE        29         82         62         39       43
                  vv
clus               STAGE IVA
  NT5DC1 MUTATED           0
  NT5DC1 WILD-TYPE         4
D346V3, multiclass
            clus
vv           NT5DC1 MUTATED NT5DC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NT5DC1 MUTATED       0   1   6   1
  NT5DC1 WILD-TYPE    54 134 255 101
D346V4, multiclass
       clus
vv      NT5DC1 MUTATED NT5DC1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 6              255
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NT5DC1 MUTATED     5   2   1   0
  NT5DC1 WILD-TYPE 190 171  88  85
D346V5, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  N0              5              190
  N1              2              171
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V6, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     8   0
  NT5DC1 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      8    0
  NT5DC1 WILD-TYPE  474   38
   clus
vv  NT5DC1 MUTATED NT5DC1 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D346V7, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     5   3
  NT5DC1 WILD-TYPE 167 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      5    3
  NT5DC1 WILD-TYPE  167  403
        clus
vv       NT5DC1 MUTATED NT5DC1 WILD-TYPE
  FEMALE              5              167
  MALE                3              403
[1] 2 2
[1] FALSE
D346V8, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     7   1
  NT5DC1 WILD-TYPE 409 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      7    1
  NT5DC1 WILD-TYPE  409  101
     clus
vv    NT5DC1 MUTATED NT5DC1 WILD-TYPE
  NO               7              409
  YES              1              101
[1] 2 2
[1] FALSE
D346V9, continuous
D346V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NT5DC1 MUTATED       2                         0
  NT5DC1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NT5DC1 MUTATED                                           0     6
  NT5DC1 WILD-TYPE                                         1   351
D346V11, multiclass
                                           clus
vv                                          NT5DC1 MUTATED NT5DC1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V12, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     0   7
  NT5DC1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      0    7
  NT5DC1 WILD-TYPE   10  391
                        clus
vv                       NT5DC1 MUTATED NT5DC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(347) Variable = TM7SF4 MUTATION ANALYSIS
D347V1, survival
                  sevent
clus2                0   1
  TM7SF4 MUTATED    16   6
  TM7SF4 WILD-TYPE 322 210
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              22              532 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               6              210 
$`TM7SF4 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-L5-A43E TCGA-L5-A4ON TCGA-B7-A5TI 
       19.99        58.55         7.69        30.25        18.35        19.56 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-8372 TCGA-BR-A452 TCGA-BR-A4QL TCGA-CD-5801 
        9.21        36.16        31.27         7.53        16.14        13.18 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5723 TCGA-D7-6528 TCGA-F1-6874 TCGA-FP-A9TM 
       12.43        11.77       105.07        15.22        14.47         6.21 
TCGA-HU-8602 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A91V 
       22.32        38.14        37.22        42.64 

$`TM7SF4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       20.88         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.41        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
            6.21             0.00 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
          105.07           122.30 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
          18.955           13.445 
[1] "6.2 - 105.1 (19.0)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D347V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM7SF4 MUTATED         2        1        2        3         0         3
  TM7SF4 WILD-TYPE       8       19       44       28        84        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF4 MUTATED           0          6          1          3        1
  TM7SF4 WILD-TYPE        29         78         61         36       42
                  vv
clus               STAGE IVA
  TM7SF4 MUTATED           0
  TM7SF4 WILD-TYPE         4
D347V3, multiclass
            clus
vv           TM7SF4 MUTATED TM7SF4 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                3               28
  STAGE IIA               0               84
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              6               78
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TM7SF4 MUTATED       7   3   7   7
  TM7SF4 WILD-TYPE    47 132 254  95
D347V4, multiclass
       clus
vv      TM7SF4 MUTATED TM7SF4 WILD-TYPE
  T0+T1              7               47
  T2                 3              132
  T3                 7              254
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TM7SF4 MUTATED     8   9   2   4
  TM7SF4 WILD-TYPE 187 164  87  81
D347V5, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  N0              8              187
  N1              9              164
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V6, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED    22   0
  TM7SF4 WILD-TYPE 460  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED     22    0
  TM7SF4 WILD-TYPE  460   38
   clus
vv  TM7SF4 MUTATED TM7SF4 WILD-TYPE
  0             22              460
  1              0               38
[1] 2 2
[1] FALSE
D347V7, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     5  19
  TM7SF4 WILD-TYPE 167 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      5   19
  TM7SF4 WILD-TYPE  167  387
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  FEMALE              5              167
  MALE               19              387
[1] 2 2
[1] FALSE
D347V8, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED    17   4
  TM7SF4 WILD-TYPE 399  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED     17    4
  TM7SF4 WILD-TYPE  399   98
     clus
vv    TM7SF4 MUTATED TM7SF4 WILD-TYPE
  NO              17              399
  YES              4               98
[1] 2 2
[1] FALSE
D347V9, continuous
D347V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM7SF4 MUTATED       5                         0
  TM7SF4 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM7SF4 MUTATED                                           0    16
  TM7SF4 WILD-TYPE                                         1   341
D347V11, multiclass
                                           clus
vv                                          TM7SF4 MUTATED TM7SF4 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V12, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     0  16
  TM7SF4 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      0   16
  TM7SF4 WILD-TYPE   10  382
                        clus
vv                       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(348) Variable = PKN2 MUTATION ANALYSIS
D348V1, survival
                sevent
clus2              0   1
  PKN2 MUTATED    12   5
  PKN2 WILD-TYPE 326 211
  PKN2 MUTATED PKN2 WILD-TYPE 
            17            537 
  PKN2 MUTATED PKN2 WILD-TYPE 
             5            211 
$`PKN2 MUTATED`
TCGA-LN-A7HW TCGA-VR-A8EZ TCGA-BR-4280 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 
       12.00        18.18         6.61        11.44         9.60        32.25 
TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-6524 
        4.31        31.96        16.14        15.95        65.10        17.85 
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-R5-A7ZI TCGA-SW-A7EA 
       22.68         6.58        14.07        74.53        19.04 

$`PKN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 
       19.13        20.55        18.84        18.54        18.61        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PKN2 MUTATED PKN2 WILD-TYPE 
          4.31           0.00 
  PKN2 MUTATED PKN2 WILD-TYPE 
         74.53         122.30 
  PKN2 MUTATED PKN2 WILD-TYPE 
         16.14          13.51 
[1] "4.3 - 74.5 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D348V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKN2 MUTATED         0        0        4        2         1         4
  PKN2 WILD-TYPE      10       20       42       29        83        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKN2 MUTATED           1          0          1          2        2         0
  PKN2 WILD-TYPE        28         84         61         37       41         4
D348V3, multiclass
            clus
vv           PKN2 MUTATED PKN2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              2             29
  STAGE IIA             1             83
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PKN2 MUTATED       1   8   4   4
  PKN2 WILD-TYPE    53 127 257  98
D348V4, multiclass
       clus
vv      PKN2 MUTATED PKN2 WILD-TYPE
  T0+T1            1             53
  T2               8            127
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PKN2 MUTATED     5   7   2   3
  PKN2 WILD-TYPE 190 166  87  82
D348V5, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  N0            5            190
  N1            7            166
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V6, binary
                cls
clus               0   1
  PKN2 MUTATED    16   2
  PKN2 WILD-TYPE 466  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     16    2
  PKN2 WILD-TYPE  466   36
   clus
vv  PKN2 MUTATED PKN2 WILD-TYPE
  0           16            466
  1            2             36
[1] 2 2
[1] FALSE
D348V7, binary
                cls
clus               0   1
  PKN2 MUTATED    11   7
  PKN2 WILD-TYPE 161 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     11    7
  PKN2 WILD-TYPE  161  399
        clus
vv       PKN2 MUTATED PKN2 WILD-TYPE
  FEMALE           11            161
  MALE              7            399
[1] 2 2
[1] FALSE
D348V8, binary
                cls
clus               0   1
  PKN2 MUTATED    16   0
  PKN2 WILD-TYPE 400 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     16    0
  PKN2 WILD-TYPE  400  102
     clus
vv    PKN2 MUTATED PKN2 WILD-TYPE
  NO            16            400
  YES            0            102
[1] 2 2
[1] FALSE
D348V9, continuous
[1] "Remove cluster labels:" "PKN2 MUTATED"          
clus
  PKN2 MUTATED PKN2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8Q7 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
D348V10, continuous
[1] "Remove cluster labels:" "PKN2 MUTATED"          
clus
  PKN2 MUTATED PKN2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8Q7 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" "PKN2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKN2 MUTATED       5                         0
  PKN2 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKN2 MUTATED                                           0    11
  PKN2 WILD-TYPE                                         1   346
D348V11, multiclass
                                           clus
vv                                          PKN2 MUTATED PKN2 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V12, binary
                cls
clus               0   1
  PKN2 MUTATED     1  14
  PKN2 WILD-TYPE   9 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED      1   14
  PKN2 WILD-TYPE    9  384
                        clus
vv                       PKN2 MUTATED PKN2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(349) Variable = THEMIS MUTATION ANALYSIS
D349V1, survival
                  sevent
clus2                0   1
  THEMIS MUTATED     7   6
  THEMIS WILD-TYPE 331 210
  THEMIS MUTATED THEMIS WILD-TYPE 
              13              541 
  THEMIS MUTATED THEMIS WILD-TYPE 
               6              210 
$`THEMIS MUTATED`
TCGA-2H-A9GF TCGA-IG-A4QS TCGA-L5-A4OU TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 
       25.78         3.88        29.00         6.97         7.43        30.90 
TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5723 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       34.68        31.96        16.14       105.07        19.73        38.14 
TCGA-ZA-A8F6 
       17.26 

$`THEMIS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K 
       12.43 

  THEMIS MUTATED THEMIS WILD-TYPE 
            3.88             0.00 
  THEMIS MUTATED THEMIS WILD-TYPE 
          105.07           122.30 
  THEMIS MUTATED THEMIS WILD-TYPE 
           25.78            13.48 
[1] "3.9 - 105.1 (25.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D349V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THEMIS MUTATED         1        0        1        1         2         0
  THEMIS WILD-TYPE       9       20       45       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED           1          3          2          0        1
  THEMIS WILD-TYPE        28         81         60         39       42
                  vv
clus               STAGE IVA
  THEMIS MUTATED           0
  THEMIS WILD-TYPE         4
D349V3, multiclass
            clus
vv           THEMIS MUTATED THEMIS WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  THEMIS MUTATED       1   3   7   2
  THEMIS WILD-TYPE    53 132 254 100
D349V4, multiclass
       clus
vv      THEMIS MUTATED THEMIS WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 7              254
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  THEMIS MUTATED     3   6   3   1
  THEMIS WILD-TYPE 192 167  86  84
D349V5, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0              3              192
  N1              6              167
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V6, binary
                  cls
clus                 0   1
  THEMIS MUTATED    10   1
  THEMIS WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     10    1
  THEMIS WILD-TYPE  472   37
   clus
vv  THEMIS MUTATED THEMIS WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D349V7, binary
                  cls
clus                 0   1
  THEMIS MUTATED     5   9
  THEMIS WILD-TYPE 167 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      5    9
  THEMIS WILD-TYPE  167  397
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              5              167
  MALE                9              397
[1] 2 2
[1] FALSE
D349V8, binary
                  cls
clus                 0   1
  THEMIS MUTATED    13   1
  THEMIS WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     13    1
  THEMIS WILD-TYPE  403  101
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D349V9, continuous
D349V10, continuous
[1] "Remove cluster labels:" "THEMIS MUTATED"        
clus
  THEMIS MUTATED THEMIS WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OW       TCGA-L5-A4OX 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-Z6-AAPN 
"THEMIS WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  THEMIS MUTATED       1                         1
  THEMIS WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THEMIS MUTATED                                           0    10
  THEMIS WILD-TYPE                                         1   347
D349V11, multiclass
                                           clus
vv                                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V12, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0  10
  THEMIS WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0   10
  THEMIS WILD-TYPE   10  388
                        clus
vv                       THEMIS MUTATED THEMIS WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(350) Variable = GCC2 MUTATION ANALYSIS
D350V1, survival
                sevent
clus2              0   1
  GCC2 MUTATED    11   7
  GCC2 WILD-TYPE 327 209
  GCC2 MUTATED GCC2 WILD-TYPE 
            18            536 
  GCC2 MUTATED GCC2 WILD-TYPE 
             7            209 
$`GCC2 MUTATED`
TCGA-IG-A5B8 TCGA-JY-A93F TCGA-LN-A5U6 TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-Z6-A8JE 
        0.79        24.03        12.33        53.95        20.38         2.10 
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 
       26.70        30.90         9.67        25.05        27.12        31.96 
TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5733 TCGA-D7-A6EZ TCGA-HU-A4H3 TCGA-VQ-A8P2 
        6.02        15.02        21.07        20.32        29.00        38.14 

$`GCC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        25.22         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GCC2 MUTATED GCC2 WILD-TYPE 
          0.79           0.00 
  GCC2 MUTATED GCC2 WILD-TYPE 
         53.95         122.30 
  GCC2 MUTATED GCC2 WILD-TYPE 
        22.550         13.445 
[1] "0.8 - 54.0 (22.6)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D350V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCC2 MUTATED         0        0        4        0         0         2
  GCC2 WILD-TYPE      10       20       42       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCC2 MUTATED           0          4          1          2        2         0
  GCC2 WILD-TYPE        29         80         61         37       41         4
D350V3, multiclass
            clus
vv           GCC2 MUTATED GCC2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GCC2 MUTATED       0   6   4   7
  GCC2 WILD-TYPE    54 129 257  95
D350V4, multiclass
       clus
vv      GCC2 MUTATED GCC2 WILD-TYPE
  T0+T1            0             54
  T2               6            129
  T3               4            257
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GCC2 MUTATED     5   6   3   2
  GCC2 WILD-TYPE 190 167  86  83
D350V5, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  N0            5            190
  N1            6            167
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V6, binary
                cls
clus               0   1
  GCC2 MUTATED    16   1
  GCC2 WILD-TYPE 466  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED     16    1
  GCC2 WILD-TYPE  466   37
   clus
vv  GCC2 MUTATED GCC2 WILD-TYPE
  0           16            466
  1            1             37
[1] 2 2
[1] FALSE
D350V7, binary
                cls
clus               0   1
  GCC2 MUTATED     9  11
  GCC2 WILD-TYPE 163 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      9   11
  GCC2 WILD-TYPE  163  395
        clus
vv       GCC2 MUTATED GCC2 WILD-TYPE
  FEMALE            9            163
  MALE             11            395
[1] 2 2
[1] FALSE
D350V8, binary
                cls
clus               0   1
  GCC2 MUTATED    15   2
  GCC2 WILD-TYPE 401 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED     15    2
  GCC2 WILD-TYPE  401  100
     clus
vv    GCC2 MUTATED GCC2 WILD-TYPE
  NO            15            401
  YES            2            100
[1] 2 2
[1] FALSE
D350V9, continuous
[1] "Remove cluster labels:" "GCC2 MUTATED"          
clus
  GCC2 MUTATED GCC2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
D350V10, continuous
[1] "Remove cluster labels:" "GCC2 MUTATED"          
clus
  GCC2 MUTATED GCC2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A6QS 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" "GCC2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GCC2 MUTATED       3                         0
  GCC2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCC2 MUTATED                                           0    14
  GCC2 WILD-TYPE                                         1   343
D350V11, multiclass
                                           clus
vv                                          GCC2 MUTATED GCC2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V12, binary
                cls
clus               0   1
  GCC2 MUTATED     0  15
  GCC2 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      0   15
  GCC2 WILD-TYPE   10  383
                        clus
vv                       GCC2 MUTATED GCC2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(351) Variable = FAM70B MUTATION ANALYSIS
D351V1, survival
                  sevent
clus2                0   1
  FAM70B MUTATED     7   5
  FAM70B WILD-TYPE 331 211
  FAM70B MUTATED FAM70B WILD-TYPE 
              12              542 
  FAM70B MUTATED FAM70B WILD-TYPE 
               5              211 
$`FAM70B MUTATED`
TCGA-L5-A4OR TCGA-BR-4256 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PF 
        3.16         9.34         6.18         1.12        31.96         1.15 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4G9 
        6.58        11.77         9.01         6.02        21.27        24.20 

$`FAM70B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM70B MUTATED FAM70B WILD-TYPE 
            1.12             0.00 
  FAM70B MUTATED FAM70B WILD-TYPE 
           31.96           122.30 
  FAM70B MUTATED FAM70B WILD-TYPE 
           7.795           13.825 
[1] "1.1 - 32.0 (7.8)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "1.8"
D351V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM70B MUTATED         0        2        1        0         3         0
  FAM70B WILD-TYPE      10       18       45       31        81        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70B MUTATED           0          1          2          0        3
  FAM70B WILD-TYPE        29         83         60         39       40
                  vv
clus               STAGE IVA
  FAM70B MUTATED           0
  FAM70B WILD-TYPE         4
D351V3, multiclass
            clus
vv           FAM70B MUTATED FAM70B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM70B MUTATED       2   1   5   4
  FAM70B WILD-TYPE    52 134 256  98
D351V4, multiclass
       clus
vv      FAM70B MUTATED FAM70B WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 5              256
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM70B MUTATED     6   4   2   2
  FAM70B WILD-TYPE 189 169  87  83
D351V5, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  N0              6              189
  N1              4              169
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V6, binary
                  cls
clus                 0   1
  FAM70B MUTATED    11   2
  FAM70B WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED     11    2
  FAM70B WILD-TYPE  471   36
   clus
vv  FAM70B MUTATED FAM70B WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D351V7, binary
                  cls
clus                 0   1
  FAM70B MUTATED     4  10
  FAM70B WILD-TYPE 168 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      4   10
  FAM70B WILD-TYPE  168  396
        clus
vv       FAM70B MUTATED FAM70B WILD-TYPE
  FEMALE              4              168
  MALE               10              396
[1] 2 2
[1] FALSE
D351V8, binary
                  cls
clus                 0   1
  FAM70B MUTATED    10   1
  FAM70B WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED     10    1
  FAM70B WILD-TYPE  406  101
     clus
vv    FAM70B MUTATED FAM70B WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D351V9, continuous
D351V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM70B MUTATED       4                         0
  FAM70B WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM70B MUTATED                                           0     7
  FAM70B WILD-TYPE                                         1   350
D351V11, multiclass
                                           clus
vv                                          FAM70B MUTATED FAM70B WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V12, binary
                  cls
clus                 0   1
  FAM70B MUTATED     1   9
  FAM70B WILD-TYPE   9 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      1    9
  FAM70B WILD-TYPE    9  389
                        clus
vv                       FAM70B MUTATED FAM70B WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(352) Variable = C16ORF74 MUTATION ANALYSIS
D352V1, survival
                    sevent
clus2                  0   1
  C16ORF74 MUTATED     1   1
  C16ORF74 WILD-TYPE 337 215
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 2                552 
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 1                215 
$`C16ORF74 MUTATED`
TCGA-R6-A6XG TCGA-HJ-7597 
       38.40        26.47 

$`C16ORF74 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
             26.47               0.00 
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
              38.4              122.3 
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
            32.435             13.530 
[1] "26.5 - 38.4 (32.4)" "0.0 - 122.3 (13.5)"
[1] "Remove cluster labels:" "C16ORF74 MUTATED"      
D352V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF74 MUTATED         0        0        1        0         0         0
  C16ORF74 WILD-TYPE      10       20       45       31        84        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF74 MUTATED           0          1          0          0        0
  C16ORF74 WILD-TYPE        29         83         62         39       43
                    vv
clus                 STAGE IVA
  C16ORF74 MUTATED           0
  C16ORF74 WILD-TYPE         4
D352V3, multiclass
[1] "Remove cluster labels:" "C16ORF74 MUTATED"      
clus
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 2                533 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A4OE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NG         TCGA-L5-A8NT         TCGA-Q9-A6FU 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-S8-A6BV         TCGA-CG-4444         TCGA-CG-4460 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-5716 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5727         TCGA-EQ-A4SO         TCGA-F1-6177 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-A8CX         TCGA-HF-7131         TCGA-KB-A93G 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-MX-A663         TCGA-2H-A9GF         TCGA-2H-A9GG 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GH         TCGA-2H-A9GI         TCGA-2H-A9GJ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GK         TCGA-2H-A9GL         TCGA-2H-A9GM 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GN         TCGA-2H-A9GO         TCGA-2H-A9GQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GR         TCGA-IC-A6RE         TCGA-IG-A3I8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A4P3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A4QS         TCGA-IG-A4QT         TCGA-IG-A50L 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5B8         TCGA-IG-A5S3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A625         TCGA-IG-A6QS         TCGA-IG-A7DP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-IG-A97I 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6F8         TCGA-JY-A6FA         TCGA-JY-A6FD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A939         TCGA-JY-A93C         TCGA-JY-A93D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A93E         TCGA-JY-A93F         TCGA-KH-A6WC 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43E         TCGA-L5-A43H         TCGA-L5-A4OF 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OJ         TCGA-L5-A4OM 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OR         TCGA-L5-A4OS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88W         TCGA-L5-A88Z         TCGA-L5-A893 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NI         TCGA-L5-A8NJ         TCGA-L5-A8NK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NL         TCGA-L5-A8NM         TCGA-L5-A8NN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NU         TCGA-L5-A8NV         TCGA-L5-A8NW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L7-A6VZ         TCGA-LN-A49K         TCGA-LN-A49L 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-LN-A8HZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A8I0         TCGA-LN-A8I1         TCGA-LN-A9FO 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A9FP         TCGA-LN-A9FQ         TCGA-LN-A9FR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A8W5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-S8-A6BW         TCGA-V5-A7RE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EO         TCGA-VR-A8EP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-Z6-A8JE         TCGA-Z6-A9VB         TCGA-Z6-AAPN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-ZR-A9CJ         TCGA-B7-5816         TCGA-B7-5818 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-B7-A5TI         TCGA-B7-A5TJ         TCGA-B7-A5TK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-B7-A5TN         TCGA-BR-4183         TCGA-BR-4184 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4267 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4368 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8058 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8284         TCGA-BR-8285         TCGA-BR-8286 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8297         TCGA-BR-8360         TCGA-BR-8361 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8363         TCGA-BR-8364         TCGA-BR-8365 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8366         TCGA-BR-8367         TCGA-BR-8368 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8369         TCGA-BR-8370         TCGA-BR-8371 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8372         TCGA-BR-8373         TCGA-BR-8380 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8381         TCGA-BR-8382         TCGA-BR-8384 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8483         TCGA-BR-8484         TCGA-BR-8485 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8486         TCGA-BR-8487         TCGA-BR-8588 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8589         TCGA-BR-8590         TCGA-BR-8591 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-8676         TCGA-BR-8677 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8678         TCGA-BR-8679         TCGA-BR-8680 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8682         TCGA-BR-8683         TCGA-BR-8686 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8687         TCGA-BR-8690         TCGA-BR-A44T 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A44U         TCGA-BR-A452         TCGA-BR-A453 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4CQ         TCGA-BR-A4CR         TCGA-BR-A4CS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J7         TCGA-BR-A4J8         TCGA-BR-A4PD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5798 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CD-5813 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8524         TCGA-CD-8525         TCGA-CD-8526 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8527         TCGA-CD-8528         TCGA-CD-8529 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8530         TCGA-CD-8531         TCGA-CD-8532 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8533         TCGA-CD-8534         TCGA-CD-8535 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8536         TCGA-CD-A486         TCGA-CD-A487 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A489         TCGA-CD-A48A         TCGA-CD-A48C 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A4MG         TCGA-CD-A4MH         TCGA-CD-A4MI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A4MJ         TCGA-CG-4300         TCGA-CG-4301 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4449         TCGA-CG-4455 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4477 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5728         TCGA-CG-5730 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6520         TCGA-D7-6522 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6822         TCGA-D7-8570         TCGA-D7-8572 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8573         TCGA-D7-8574         TCGA-D7-8575 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8576         TCGA-D7-8578         TCGA-D7-8579 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YT         TCGA-D7-A4YU         TCGA-D7-A4YV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YX         TCGA-D7-A4YY         TCGA-D7-A4Z0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6ET         TCGA-D7-A6EV         TCGA-D7-A6EX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6EY         TCGA-D7-A6EZ         TCGA-D7-A6F0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6F2         TCGA-D7-A747         TCGA-D7-A748 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A74A         TCGA-D7-A74B         TCGA-EQ-5647 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-EQ-8122         TCGA-F1-6874         TCGA-F1-6875 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-F1-A448         TCGA-F1-A72C         TCGA-FP-7735 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8211         TCGA-FP-8631         TCGA-FP-A4BE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-A4BF         TCGA-HF-7132         TCGA-HF-7133 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-7134         TCGA-HF-7136         TCGA-HF-A5NB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8243         TCGA-HU-8244         TCGA-HU-8249 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8602         TCGA-HU-8604         TCGA-HU-8608 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8610         TCGA-HU-A4G2         TCGA-HU-A4G3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4G6         TCGA-HU-A4G8         TCGA-HU-A4G9 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GC         TCGA-HU-A4GD         TCGA-HU-A4GF 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GH         TCGA-HU-A4GJ         TCGA-HU-A4GN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GP         TCGA-HU-A4GQ         TCGA-HU-A4GT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GU         TCGA-HU-A4GX         TCGA-HU-A4GY 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H0         TCGA-HU-A4H2         TCGA-HU-A4H3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H4         TCGA-HU-A4H5         TCGA-HU-A4H6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H8         TCGA-HU-A4HB         TCGA-HU-A4HD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-8462         TCGA-IN-8663 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RI         TCGA-IN-A6RJ         TCGA-IN-A6RL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RN         TCGA-IN-A6RO         TCGA-IN-A6RP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RR         TCGA-IN-A6RS         TCGA-IN-A7NR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A7NT         TCGA-IN-A7NU         TCGA-IN-AB1V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-AB1X         TCGA-IP-7968         TCGA-KB-A6F5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-KB-A6F7         TCGA-KB-A93J         TCGA-MX-A5UG 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-MX-A5UJ         TCGA-MX-A666         TCGA-R5-A7O7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A7ZE         TCGA-R5-A7ZF         TCGA-R5-A7ZI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A7ZR         TCGA-R5-A804         TCGA-R5-A805 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A7BS         TCGA-RD-A7BT         TCGA-RD-A7BW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A7C1         TCGA-RD-A8MV         TCGA-RD-A8MW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N0         TCGA-RD-A8N1         TCGA-RD-A8N2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N4         TCGA-RD-A8N5         TCGA-RD-A8N6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N9         TCGA-SW-A7EA         TCGA-SW-A7EB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8DL         TCGA-VQ-A8DT         TCGA-VQ-A8DU 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8DV         TCGA-VQ-A8DZ         TCGA-VQ-A8E2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8E7         TCGA-VQ-A8P2         TCGA-VQ-A8P3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8PE         TCGA-VQ-A8PK         TCGA-VQ-A8PM 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8PQ         TCGA-VQ-A91Q         TCGA-VQ-A91U 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A91V         TCGA-VQ-A92D         TCGA-VQ-A94T 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA64         TCGA-VQ-AA68         TCGA-VQ-AA69 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6A         TCGA-VQ-AA6B         TCGA-VQ-AA6F 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6G         TCGA-VQ-AA6I         TCGA-VQ-AA6J 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
                    vv
clus                 T0+T1  T2  T3  T4
  C16ORF74 MUTATED       0   1   0   1
  C16ORF74 WILD-TYPE    54 134 261 101
D352V4, multiclass
[1] "Remove cluster labels:" "C16ORF74 MUTATED"      
clus
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 2                550 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-S8-A6BV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5716         TCGA-CG-5727 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-FP-A8CX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-7131         TCGA-KB-A93G         TCGA-MX-A663 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GF         TCGA-2H-A9GG         TCGA-2H-A9GH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GI         TCGA-2H-A9GJ         TCGA-2H-A9GK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GL         TCGA-2H-A9GM         TCGA-2H-A9GN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GO         TCGA-2H-A9GQ         TCGA-2H-A9GR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IC-A6RE         TCGA-IG-A3I8         TCGA-IG-A3QL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A4QT         TCGA-IG-A50L         TCGA-IG-A51D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A5S3         TCGA-IG-A625 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A6QS         TCGA-IG-A7DP         TCGA-IG-A8O2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-IG-A97I         TCGA-JY-A6F8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FD         TCGA-JY-A6FE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-JY-A939 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A93C         TCGA-JY-A93D         TCGA-JY-A93E 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A93F         TCGA-KH-A6WC         TCGA-L5-A43E 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OF         TCGA-L5-A4OH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OJ         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OR         TCGA-L5-A4OS         TCGA-L5-A4OT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A88W 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88Z         TCGA-L5-A891         TCGA-L5-A893 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NI         TCGA-L5-A8NJ         TCGA-L5-A8NK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NL         TCGA-L5-A8NM         TCGA-L5-A8NN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NU         TCGA-L5-A8NV         TCGA-L5-A8NW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L7-A6VZ         TCGA-LN-A49K         TCGA-LN-A49L 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-LN-A8HZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A8I0         TCGA-LN-A8I1         TCGA-LN-A9FO 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A9FP         TCGA-LN-A9FQ         TCGA-LN-A9FR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A8W5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-S8-A6BW         TCGA-V5-A7RB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-VR-A8EO 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-X8-AAAR         TCGA-XP-A8T6         TCGA-XP-A8T7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-Z6-A9VB         TCGA-Z6-AAPN         TCGA-ZR-A9CJ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-B7-A5TI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-B7-A5TJ         TCGA-B7-A5TK         TCGA-B7-A5TN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4183         TCGA-BR-4184         TCGA-BR-4201 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4267 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4292 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4294         TCGA-BR-4357         TCGA-BR-4363 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4371         TCGA-BR-6452 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8058         TCGA-BR-8059 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8060         TCGA-BR-8077         TCGA-BR-8078 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8080         TCGA-BR-8081         TCGA-BR-8284 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8285         TCGA-BR-8286         TCGA-BR-8289 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8291         TCGA-BR-8295         TCGA-BR-8297 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8360         TCGA-BR-8361         TCGA-BR-8363 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8364         TCGA-BR-8365         TCGA-BR-8366 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8367         TCGA-BR-8368         TCGA-BR-8369 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8370         TCGA-BR-8371         TCGA-BR-8372 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8373         TCGA-BR-8380         TCGA-BR-8381 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8382         TCGA-BR-8384         TCGA-BR-8483 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8484         TCGA-BR-8485         TCGA-BR-8486 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8487         TCGA-BR-8588         TCGA-BR-8589 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8590         TCGA-BR-8591         TCGA-BR-8592 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8676         TCGA-BR-8677         TCGA-BR-8678 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8679         TCGA-BR-8680         TCGA-BR-8682 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8683         TCGA-BR-8686         TCGA-BR-8687 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8690         TCGA-BR-A44T         TCGA-BR-A44U 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A452         TCGA-BR-A453         TCGA-BR-A4CQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4CR         TCGA-BR-A4CS         TCGA-BR-A4IU 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4IV         TCGA-BR-A4IY         TCGA-BR-A4IZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J1         TCGA-BR-A4J2         TCGA-BR-A4J4 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J5         TCGA-BR-A4J6         TCGA-BR-A4J7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4PD         TCGA-BR-A4PE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4QM         TCGA-CD-5798         TCGA-CD-5799 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CD-5813 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8524         TCGA-CD-8525         TCGA-CD-8526 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8527         TCGA-CD-8528         TCGA-CD-8529 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8530         TCGA-CD-8531         TCGA-CD-8532 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8533         TCGA-CD-8534         TCGA-CD-8535 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8536         TCGA-CD-A486         TCGA-CD-A487 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A489         TCGA-CD-A48A         TCGA-CD-A48C 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A4MG         TCGA-CD-A4MH         TCGA-CD-A4MI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A4MJ         TCGA-CG-4300         TCGA-CG-4301 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4449         TCGA-CG-4455 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4477 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5728         TCGA-CG-5730 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8570         TCGA-D7-8572         TCGA-D7-8573 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8574         TCGA-D7-8575         TCGA-D7-8576 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8578         TCGA-D7-8579         TCGA-D7-A4YT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YU         TCGA-D7-A4YV         TCGA-D7-A4YX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YY         TCGA-D7-A4Z0         TCGA-D7-A6ET 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6EV         TCGA-D7-A6EX         TCGA-D7-A6EY 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6EZ         TCGA-D7-A6F0         TCGA-D7-A6F2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A747         TCGA-D7-A748         TCGA-D7-A74A 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A74B         TCGA-EQ-5647         TCGA-EQ-8122 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-F1-A448 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-F1-A72C         TCGA-FP-7735         TCGA-FP-7829 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-7916         TCGA-FP-7998         TCGA-FP-8099 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8209         TCGA-FP-8210         TCGA-FP-8211 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8631         TCGA-FP-A4BE         TCGA-FP-A4BF 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-A9TM         TCGA-HF-7132         TCGA-HF-7133 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-7134         TCGA-HF-7136         TCGA-HF-A5NB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8238         TCGA-HU-8243         TCGA-HU-8244 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GJ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GN         TCGA-HU-A4GP         TCGA-HU-A4GQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GT         TCGA-HU-A4GU         TCGA-HU-A4GX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GY         TCGA-HU-A4H0         TCGA-HU-A4H2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H3         TCGA-HU-A4H4         TCGA-HU-A4H5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H6         TCGA-HU-A4H8         TCGA-HU-A4HB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4HD         TCGA-IN-7806         TCGA-IN-7808 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RJ         TCGA-IN-A6RL         TCGA-IN-A6RN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-KB-A93J         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-MX-A666         TCGA-R5-A7O7         TCGA-R5-A7ZE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A7ZF         TCGA-R5-A7ZI         TCGA-R5-A7ZR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A804         TCGA-R5-A805         TCGA-RD-A7BS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A7BT         TCGA-RD-A7BW         TCGA-RD-A7C1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8MV         TCGA-RD-A8MW         TCGA-RD-A8N0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N1         TCGA-RD-A8N2         TCGA-RD-A8N4 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N5         TCGA-RD-A8N6         TCGA-RD-A8N9 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-SW-A7EA         TCGA-SW-A7EB         TCGA-VQ-A8DL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8DT         TCGA-VQ-A8DU         TCGA-VQ-A8DV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8DZ         TCGA-VQ-A8E2         TCGA-VQ-A8E7 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8P2         TCGA-VQ-A8P3         TCGA-VQ-A8PE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8PK         TCGA-VQ-A8PM         TCGA-VQ-A8PQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A91Q         TCGA-VQ-A91U         TCGA-VQ-A91V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A92D         TCGA-VQ-A94T         TCGA-VQ-AA64 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA68         TCGA-VQ-AA69         TCGA-VQ-AA6A 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6B         TCGA-VQ-AA6F         TCGA-VQ-AA6G 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6I         TCGA-VQ-AA6J         TCGA-VQ-AA6K 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-ZA-A8F6 
"C16ORF74 WILD-TYPE" 
                    vv
clus                  N0  N1  N2  N3
  C16ORF74 MUTATED     2   0   0   0
  C16ORF74 WILD-TYPE 193 173  89  85
D352V5, multiclass
[1] "Remove cluster labels:" "C16ORF74 MUTATED"      
clus
  C16ORF74 MUTATED C16ORF74 WILD-TYPE 
                 2                540 
        TCGA-IC-A6RF         TCGA-JY-A6FB         TCGA-JY-A938 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43I         TCGA-L5-A43J         TCGA-L5-A43M 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-S8-A6BV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5716         TCGA-CG-5727 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-FP-A8CX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-7131         TCGA-KB-A93G         TCGA-MX-A663 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GF         TCGA-2H-A9GG         TCGA-2H-A9GH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GI         TCGA-2H-A9GJ         TCGA-2H-A9GK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GL         TCGA-2H-A9GM         TCGA-2H-A9GN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-2H-A9GO         TCGA-2H-A9GQ         TCGA-2H-A9GR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IC-A6RE         TCGA-IG-A3I8         TCGA-IG-A3QL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YB 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A4QT         TCGA-IG-A50L         TCGA-IG-A51D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A5S3         TCGA-IG-A625 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IG-A6QS         TCGA-IG-A8O2         TCGA-IG-A97I 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6F8         TCGA-JY-A6FA         TCGA-JY-A6FD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A939         TCGA-JY-A93C         TCGA-JY-A93D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-JY-A93E         TCGA-JY-A93F         TCGA-KH-A6WC 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A43E         TCGA-L5-A43H         TCGA-L5-A4OF 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OJ         TCGA-L5-A4OM 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OR         TCGA-L5-A4OS 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A88W         TCGA-L5-A88Z         TCGA-L5-A891 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NH         TCGA-L5-A8NI         TCGA-L5-A8NJ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NL         TCGA-L5-A8NM 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NU         TCGA-L5-A8NV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-L7-A6VZ         TCGA-LN-A49K 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49L         TCGA-LN-A49M         TCGA-LN-A49N 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A49X         TCGA-LN-A49Y 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A1         TCGA-LN-A4A2         TCGA-LN-A4A3 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A4         TCGA-LN-A4A5         TCGA-LN-A4A6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4A8         TCGA-LN-A4A9         TCGA-LN-A4MQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A4MR         TCGA-LN-A5U5         TCGA-LN-A5U6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-LN-A8I1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A9FO         TCGA-LN-A9FP         TCGA-LN-A9FQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-LN-A9FR         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-RE-A7BO         TCGA-S8-A6BW 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RE         TCGA-V5-AASV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-Z6-A8JE         TCGA-Z6-A9VB         TCGA-Z6-AAPN 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-ZR-A9CJ         TCGA-B7-5816         TCGA-B7-5818 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-B7-A5TI         TCGA-BR-4183         TCGA-BR-4184 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4362 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-6452         TCGA-BR-6453 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8058         TCGA-BR-8059         TCGA-BR-8060 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8297         TCGA-BR-8360 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8361         TCGA-BR-8363         TCGA-BR-8364 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8365         TCGA-BR-8366         TCGA-BR-8367 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8368         TCGA-BR-8369         TCGA-BR-8370 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8371         TCGA-BR-8372         TCGA-BR-8373 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8380         TCGA-BR-8381         TCGA-BR-8382 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8384         TCGA-BR-8483         TCGA-BR-8484 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8485         TCGA-BR-8486         TCGA-BR-8487 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8588         TCGA-BR-8589         TCGA-BR-8590 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8591         TCGA-BR-8592         TCGA-BR-8676 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8677         TCGA-BR-8678         TCGA-BR-8679 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8680         TCGA-BR-8682         TCGA-BR-8683 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-8686         TCGA-BR-8687         TCGA-BR-8690 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A44T         TCGA-BR-A44U         TCGA-BR-A452 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A453         TCGA-BR-A4CQ         TCGA-BR-A4CR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4CS         TCGA-BR-A4IU         TCGA-BR-A4IV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4PD 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5798 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CD-5804 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-5813         TCGA-CD-8524         TCGA-CD-8525 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8526         TCGA-CD-8527         TCGA-CD-8528 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8529         TCGA-CD-8530         TCGA-CD-8531 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8532         TCGA-CD-8533         TCGA-CD-8534 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-8535         TCGA-CD-8536         TCGA-CD-A486 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A487         TCGA-CD-A489         TCGA-CD-A48A 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A48C         TCGA-CD-A4MG         TCGA-CD-A4MH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CD-A4MI         TCGA-CD-A4MJ         TCGA-CG-4300 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4449 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4462         TCGA-CG-4465 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4474 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5717         TCGA-CG-5718 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5728 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-6822         TCGA-D7-8570         TCGA-D7-8572 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8573         TCGA-D7-8574         TCGA-D7-8575 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-8576         TCGA-D7-8578         TCGA-D7-8579 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YT         TCGA-D7-A4YU         TCGA-D7-A4YV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A4YX         TCGA-D7-A4YY         TCGA-D7-A4Z0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6ET         TCGA-D7-A6EV         TCGA-D7-A6EX 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6EY         TCGA-D7-A6EZ         TCGA-D7-A6F0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A6F2         TCGA-D7-A747         TCGA-D7-A748 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-D7-A74A         TCGA-D7-A74B         TCGA-EQ-5647 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-EQ-8122         TCGA-F1-6874         TCGA-F1-6875 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-F1-A448         TCGA-F1-A72C         TCGA-FP-7735 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-8211         TCGA-FP-8631         TCGA-FP-A4BE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-FP-A4BF         TCGA-FP-A9TM         TCGA-HF-7132 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HF-A5NB         TCGA-HU-8238         TCGA-HU-8243 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8244         TCGA-HU-8249         TCGA-HU-8602 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-8604         TCGA-HU-8608         TCGA-HU-8610 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4G2         TCGA-HU-A4G3         TCGA-HU-A4G6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4G8         TCGA-HU-A4G9         TCGA-HU-A4GC 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GD         TCGA-HU-A4GF         TCGA-HU-A4GH 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GJ         TCGA-HU-A4GN         TCGA-HU-A4GP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GQ         TCGA-HU-A4GT         TCGA-HU-A4GU 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4GX         TCGA-HU-A4GY         TCGA-HU-A4H0 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H2         TCGA-HU-A4H3         TCGA-HU-A4H4 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4H5         TCGA-HU-A4H6         TCGA-HU-A4H8 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-HU-A4HB         TCGA-HU-A4HD         TCGA-IN-7806 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-7808         TCGA-IN-8462         TCGA-IN-8663 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RI         TCGA-IN-A6RJ         TCGA-IN-A6RL 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RN         TCGA-IN-A6RO         TCGA-IN-A6RP 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A6RR         TCGA-IN-A6RS         TCGA-IN-A7NR 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-A7NT         TCGA-IN-A7NU         TCGA-IN-AB1V 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-IN-AB1X         TCGA-IP-7968         TCGA-KB-A6F5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-KB-A6F7         TCGA-KB-A93J         TCGA-MX-A5UG 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-MX-A5UJ         TCGA-R5-A7O7         TCGA-R5-A7ZE 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A7ZF         TCGA-R5-A7ZI         TCGA-R5-A804 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-R5-A805         TCGA-RD-A7BS         TCGA-RD-A7BT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A7BW         TCGA-RD-A7C1         TCGA-RD-A8MV 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8MW         TCGA-RD-A8N0         TCGA-RD-A8N1 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N2         TCGA-RD-A8N4         TCGA-RD-A8N5 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-RD-A8N6         TCGA-RD-A8N9         TCGA-SW-A7EA 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-SW-A7EB         TCGA-VQ-A8DL         TCGA-VQ-A8DT 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8DU         TCGA-VQ-A8DV         TCGA-VQ-A8DZ 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8E2         TCGA-VQ-A8E7         TCGA-VQ-A8P2 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8P3         TCGA-VQ-A8PE         TCGA-VQ-A8PK 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A8PM         TCGA-VQ-A8PQ         TCGA-VQ-A91Q 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A91U         TCGA-VQ-A91V         TCGA-VQ-A92D 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-A94T         TCGA-VQ-AA64         TCGA-VQ-AA68 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA69         TCGA-VQ-AA6A         TCGA-VQ-AA6B 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6F         TCGA-VQ-AA6G         TCGA-VQ-AA6I 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
        TCGA-VQ-AA6J         TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" "C16ORF74 WILD-TYPE" 
D352V6, binary
                    cls
clus                   0   1
  C16ORF74 MUTATED     1   0
  C16ORF74 WILD-TYPE 481  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF74 MUTATED      1    0
  C16ORF74 WILD-TYPE  481   38
   clus
vv  C16ORF74 MUTATED C16ORF74 WILD-TYPE
  0                1                481
  1                0                 38
[1] 2 2
[1] FALSE
D352V7, binary
                    cls
clus                   0   1
  C16ORF74 MUTATED     2   1
  C16ORF74 WILD-TYPE 170 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF74 MUTATED      2    1
  C16ORF74 WILD-TYPE  170  405
        clus
vv       C16ORF74 MUTATED C16ORF74 WILD-TYPE
  FEMALE                2                170
  MALE                  1                405
[1] 2 2
[1] FALSE
D352V8, binary
                    cls
clus                   0   1
  C16ORF74 MUTATED     2   0
  C16ORF74 WILD-TYPE 414 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF74 MUTATED      2    0
  C16ORF74 WILD-TYPE  414  102
     clus
vv    C16ORF74 MUTATED C16ORF74 WILD-TYPE
  NO                 2                414
  YES                0                102
[1] 2 2
[1] FALSE
D352V9, continuous
D352V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF74 MUTATED       0                         0
  C16ORF74 WILD-TYPE   133                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF74 MUTATED                                           0     3
  C16ORF74 WILD-TYPE                                         1   354
D352V11, multiclass
                                           clus
vv                                          C16ORF74 MUTATED C16ORF74 WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V12, binary
                    cls
clus                   0   1
  C16ORF74 MUTATED     0   3
  C16ORF74 WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF74 MUTATED      0    3
  C16ORF74 WILD-TYPE   10  395
                        clus
vv                       C16ORF74 MUTATED C16ORF74 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(353) Variable = ACVR1B MUTATION ANALYSIS
D353V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED    10   4
  ACVR1B WILD-TYPE 328 212
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              14              540 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               4              212 
$`ACVR1B MUTATED`
TCGA-L5-A4OI TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7703 
       19.99         2.66        19.56         6.97        32.78        36.16 
TCGA-BR-8588 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4477 TCGA-CG-5733 
       12.79        16.14         6.58        15.95        30.97        21.07 
TCGA-HU-A4GF TCGA-IN-7806 
       25.81        36.36 

$`ACVR1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            2.66             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           36.36           122.30 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          19.775           13.495 
[1] "2.7 - 36.4 (19.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D353V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACVR1B MUTATED         1        1        1        1         4         2
  ACVR1B WILD-TYPE       9       19       45       30        80        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           0          2          1          2        0
  ACVR1B WILD-TYPE        29         82         61         37       43
                  vv
clus               STAGE IVA
  ACVR1B MUTATED           0
  ACVR1B WILD-TYPE         4
D353V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ACVR1B MUTATED       2   3   8   2
  ACVR1B WILD-TYPE    52 132 253 100
D353V4, multiclass
       clus
vv      ACVR1B MUTATED ACVR1B WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 8              253
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ACVR1B MUTATED     7   4   1   3
  ACVR1B WILD-TYPE 188 169  88  82
D353V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              7              188
  N1              4              169
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V6, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    12   0
  ACVR1B WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     12    0
  ACVR1B WILD-TYPE  470   38
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D353V7, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     5  10
  ACVR1B WILD-TYPE 167 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      5   10
  ACVR1B WILD-TYPE  167  396
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              5              167
  MALE               10              396
[1] 2 2
[1] FALSE
D353V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    14   1
  ACVR1B WILD-TYPE 402 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     14    1
  ACVR1B WILD-TYPE  402  101
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO              14              402
  YES              1              101
[1] 2 2
[1] FALSE
D353V9, continuous
D353V10, continuous
[1] "Remove cluster labels:" "ACVR1B MUTATED"        
clus
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" "ACVR1B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ACVR1B MUTATED       2                         1
  ACVR1B WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACVR1B MUTATED                                           0     9
  ACVR1B WILD-TYPE                                         1   348
D353V11, multiclass
                                           clus
vv                                          ACVR1B MUTATED ACVR1B WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V12, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     0  11
  ACVR1B WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      0   11
  ACVR1B WILD-TYPE   10  387
                        clus
vv                       ACVR1B MUTATED ACVR1B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(354) Variable = C2CD3 MUTATION ANALYSIS
D354V1, survival
                 sevent
clus2               0   1
  C2CD3 MUTATED    17  11
  C2CD3 WILD-TYPE 321 205
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             28             526 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             11             205 
$`C2CD3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A88T TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A97H TCGA-JY-A6FD 
       19.99        22.82        32.45        35.21        14.50        68.02 
TCGA-VR-AA4D TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 
       46.19        30.90         4.08        31.10         4.31         1.12 
TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4477 
       27.12        31.96         7.53        11.61         6.58        30.97 
TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-HU-A4H8 
        6.02        11.44        22.32        24.20        20.25        14.07 
TCGA-RD-A7BS TCGA-VQ-A8DL TCGA-VQ-A92D TCGA-VQ-AA6K 
       11.05         0.92        66.81        12.43 

$`C2CD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16       122.10        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        12.43        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        42.64        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  C2CD3 MUTATED C2CD3 WILD-TYPE 
           0.92            0.00 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
          68.02          122.30 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
         20.120          13.495 
[1] "0.9 - 68.0 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D354V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2CD3 MUTATED         0        1        5        0         7         4
  C2CD3 WILD-TYPE      10       19       41       31        77        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C2CD3 MUTATED           0          3          2          4        2         0
  C2CD3 WILD-TYPE        29         81         60         35       41         4
D354V3, multiclass
            clus
vv           C2CD3 MUTATED C2CD3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               0              31
  STAGE IIA              7              77
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  C2CD3 MUTATED       4   7  11   8
  C2CD3 WILD-TYPE    50 128 250  94
D354V4, multiclass
       clus
vv      C2CD3 MUTATED C2CD3 WILD-TYPE
  T0+T1             4              50
  T2                7             128
  T3               11             250
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  C2CD3 MUTATED    12   9   3   3
  C2CD3 WILD-TYPE 183 164  86  82
D354V5, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  N0            12             183
  N1             9             164
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V6, binary
                 cls
clus                0   1
  C2CD3 MUTATED    28   1
  C2CD3 WILD-TYPE 454  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     28    1
  C2CD3 WILD-TYPE  454   37
   clus
vv  C2CD3 MUTATED C2CD3 WILD-TYPE
  0            28             454
  1             1              37
[1] 2 2
[1] FALSE
D354V7, binary
                 cls
clus                0   1
  C2CD3 MUTATED    14  16
  C2CD3 WILD-TYPE 158 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     14   16
  C2CD3 WILD-TYPE  158  390
        clus
vv       C2CD3 MUTATED C2CD3 WILD-TYPE
  FEMALE            14             158
  MALE              16             390
[1] 2 2
[1] FALSE
D354V8, binary
                 cls
clus                0   1
  C2CD3 MUTATED    23   4
  C2CD3 WILD-TYPE 393  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     23    4
  C2CD3 WILD-TYPE  393   98
     clus
vv    C2CD3 MUTATED C2CD3 WILD-TYPE
  NO             23             393
  YES             4              98
[1] 2 2
[1] FALSE
D354V9, continuous
[1] "Remove cluster labels:" "C2CD3 MUTATED"         
clus
  C2CD3 MUTATED C2CD3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"C2CD3 WILD-TYPE" "C2CD3 WILD-TYPE" 
D354V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  C2CD3 MUTATED      10                         0
  C2CD3 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2CD3 MUTATED                                           0    16
  C2CD3 WILD-TYPE                                         1   341
D354V11, multiclass
                                           clus
vv                                          C2CD3 MUTATED C2CD3 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V12, binary
                 cls
clus                0   1
  C2CD3 MUTATED     0  19
  C2CD3 WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED      0   19
  C2CD3 WILD-TYPE   10  379
                        clus
vv                       C2CD3 MUTATED C2CD3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(355) Variable = MASTL MUTATION ANALYSIS
D355V1, survival
                 sevent
clus2               0   1
  MASTL MUTATED    10   6
  MASTL WILD-TYPE 328 210
  MASTL MUTATED MASTL WILD-TYPE 
             16             538 
  MASTL MUTATED MASTL WILD-TYPE 
              6             210 
$`MASTL MUTATED`
TCGA-L5-A43I TCGA-L5-A4OI TCGA-2H-A9GF TCGA-M9-A5M8 TCGA-BR-6452 TCGA-BR-6852 
       18.28        19.99        25.78        33.11        34.68        44.94 
TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5721 TCGA-CG-5728 
       14.43         0.26        31.96        13.18         6.02        65.10 
TCGA-HU-A4H4 TCGA-IN-8663 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       23.84         3.39        74.53        38.14 

$`MASTL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MASTL MUTATED MASTL WILD-TYPE 
           0.26            0.00 
  MASTL MUTATED MASTL WILD-TYPE 
          74.53          122.30 
  MASTL MUTATED MASTL WILD-TYPE 
         24.810          13.445 
[1] "0.3 - 74.5 (24.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D355V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MASTL MUTATED         0        0        2        0         3         2
  MASTL WILD-TYPE      10       20       44       31        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MASTL MUTATED           2          3          0          1        3         0
  MASTL WILD-TYPE        27         81         62         38       40         4
D355V3, multiclass
            clus
vv           MASTL MUTATED MASTL WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MASTL MUTATED       1   4   7   5
  MASTL WILD-TYPE    53 131 254  97
D355V4, multiclass
       clus
vv      MASTL MUTATED MASTL WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MASTL MUTATED     5   7   3   1
  MASTL WILD-TYPE 190 166  86  84
D355V5, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  N0             5             190
  N1             7             166
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V6, binary
                 cls
clus                0   1
  MASTL MUTATED    13   2
  MASTL WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED     13    2
  MASTL WILD-TYPE  469   36
   clus
vv  MASTL MUTATED MASTL WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D355V7, binary
                 cls
clus                0   1
  MASTL MUTATED     7  10
  MASTL WILD-TYPE 165 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      7   10
  MASTL WILD-TYPE  165  396
        clus
vv       MASTL MUTATED MASTL WILD-TYPE
  FEMALE             7             165
  MALE              10             396
[1] 2 2
[1] FALSE
D355V8, binary
                 cls
clus                0   1
  MASTL MUTATED    13   2
  MASTL WILD-TYPE 403 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED     13    2
  MASTL WILD-TYPE  403  100
     clus
vv    MASTL MUTATED MASTL WILD-TYPE
  NO             13             403
  YES             2             100
[1] 2 2
[1] FALSE
D355V9, continuous
D355V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MASTL MUTATED       3                         0
  MASTL WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MASTL MUTATED                                           0    10
  MASTL WILD-TYPE                                         1   347
D355V11, multiclass
                                           clus
vv                                          MASTL MUTATED MASTL WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V12, binary
                 cls
clus                0   1
  MASTL MUTATED     1   9
  MASTL WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      1    9
  MASTL WILD-TYPE    9  389
                        clus
vv                       MASTL MUTATED MASTL WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(356) Variable = CASP7 MUTATION ANALYSIS
D356V1, survival
                 sevent
clus2               0   1
  CASP7 MUTATED     2   3
  CASP7 WILD-TYPE 336 213
  CASP7 MUTATED CASP7 WILD-TYPE 
              5             549 
  CASP7 MUTATED CASP7 WILD-TYPE 
              3             213 
$`CASP7 MUTATED`
TCGA-L5-A4OE TCGA-BR-8361 TCGA-BR-8363 TCGA-CG-5726 TCGA-VQ-A8P2 
       24.00        31.10         0.26        28.96        38.14 

$`CASP7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CASP7 MUTATED CASP7 WILD-TYPE 
           0.26            0.00 
  CASP7 MUTATED CASP7 WILD-TYPE 
          38.14          122.30 
  CASP7 MUTATED CASP7 WILD-TYPE 
          28.96           13.51 
[1] "0.3 - 38.1 (29.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D356V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASP7 MUTATED         0        1        1        0         0         0
  CASP7 WILD-TYPE      10       19       45       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP7 MUTATED           0          1          1          1        0         0
  CASP7 WILD-TYPE        29         83         61         38       43         4
D356V3, multiclass
            clus
vv           CASP7 MUTATED CASP7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CASP7 MUTATED       1   1   1   2
  CASP7 WILD-TYPE    53 134 260 100
D356V4, multiclass
       clus
vv      CASP7 MUTATED CASP7 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CASP7 MUTATED     2   1   2   0
  CASP7 WILD-TYPE 193 172  87  85
D356V5, multiclass
    clus
vv   CASP7 MUTATED CASP7 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V6, binary
                 cls
clus                0   1
  CASP7 MUTATED     4   0
  CASP7 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      4    0
  CASP7 WILD-TYPE  478   38
   clus
vv  CASP7 MUTATED CASP7 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D356V7, binary
                 cls
clus                0   1
  CASP7 MUTATED     2   3
  CASP7 WILD-TYPE 170 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      2    3
  CASP7 WILD-TYPE  170  403
        clus
vv       CASP7 MUTATED CASP7 WILD-TYPE
  FEMALE             2             170
  MALE               3             403
[1] 2 2
[1] FALSE
D356V8, binary
                 cls
clus                0   1
  CASP7 MUTATED     3   1
  CASP7 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      3    1
  CASP7 WILD-TYPE  413  101
     clus
vv    CASP7 MUTATED CASP7 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D356V9, continuous
D356V10, continuous
[1] "Remove cluster labels:" "CASP7 MUTATED"         
clus
  CASP7 MUTATED CASP7 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OG 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" "CASP7 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CASP7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASP7 MUTATED       0                         0
  CASP7 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP7 MUTATED                                           0     4
  CASP7 WILD-TYPE                                         1   353
D356V11, multiclass
                                           clus
vv                                          CASP7 MUTATED CASP7 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V12, binary
                 cls
clus                0   1
  CASP7 MUTATED     0   2
  CASP7 WILD-TYPE  10 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      0    2
  CASP7 WILD-TYPE   10  396
                        clus
vv                       CASP7 MUTATED CASP7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             2             396
[1] 2 2
[1] FALSE

Clustering(357) Variable = HIAT1 MUTATION ANALYSIS
D357V1, survival
                 sevent
clus2               0   1
  HIAT1 MUTATED     6   4
  HIAT1 WILD-TYPE 332 212
  HIAT1 MUTATED HIAT1 WILD-TYPE 
             10             544 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              4             212 
$`HIAT1 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NR TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6566 
        4.31         8.71        19.56         6.97         9.34        32.78 
TCGA-BR-8372 TCGA-BR-8680 TCGA-VQ-A8DL TCGA-VQ-A8P2 
       31.27        31.96         0.92        38.14 

$`HIAT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HIAT1 MUTATED HIAT1 WILD-TYPE 
           0.92            0.00 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
          38.14          122.30 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
         14.450          13.565 
[1] "0.9 - 38.1 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D357V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIAT1 MUTATED         0        0        0        0         2         1
  HIAT1 WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIAT1 MUTATED           1          3          0          2        1         0
  HIAT1 WILD-TYPE        28         81         62         37       42         4
D357V3, multiclass
            clus
vv           HIAT1 MUTATED HIAT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HIAT1 MUTATED       0   0   5   5
  HIAT1 WILD-TYPE    54 135 256  97
D357V4, multiclass
       clus
vv      HIAT1 MUTATED HIAT1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HIAT1 MUTATED     4   4   1   2
  HIAT1 WILD-TYPE 191 169  88  83
D357V5, multiclass
    clus
vv   HIAT1 MUTATED HIAT1 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V6, binary
                 cls
clus                0   1
  HIAT1 MUTATED     8   1
  HIAT1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      8    1
  HIAT1 WILD-TYPE  474   37
   clus
vv  HIAT1 MUTATED HIAT1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D357V7, binary
                 cls
clus                0   1
  HIAT1 MUTATED     4   7
  HIAT1 WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      4    7
  HIAT1 WILD-TYPE  168  399
        clus
vv       HIAT1 MUTATED HIAT1 WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D357V8, binary
                 cls
clus                0   1
  HIAT1 MUTATED     8   1
  HIAT1 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      8    1
  HIAT1 WILD-TYPE  408  101
     clus
vv    HIAT1 MUTATED HIAT1 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D357V9, continuous
D357V10, continuous
[1] "Remove cluster labels:" "HIAT1 MUTATED"         
clus
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" "HIAT1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HIAT1 MUTATED       1                         0
  HIAT1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIAT1 MUTATED                                           0     9
  HIAT1 WILD-TYPE                                         1   348
D357V11, multiclass
                                           clus
vv                                          HIAT1 MUTATED HIAT1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V12, binary
                 cls
clus                0   1
  HIAT1 MUTATED     0   7
  HIAT1 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      0    7
  HIAT1 WILD-TYPE   10  391
                        clus
vv                       HIAT1 MUTATED HIAT1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(358) Variable = FAM116A MUTATION ANALYSIS
D358V1, survival
                   sevent
clus2                 0   1
  FAM116A MUTATED     7   2
  FAM116A WILD-TYPE 331 214
  FAM116A MUTATED FAM116A WILD-TYPE 
                9               545 
  FAM116A MUTATED FAM116A WILD-TYPE 
                2               214 
$`FAM116A MUTATED`
TCGA-LN-A4A8 TCGA-BR-4201 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-HF-A5NB 
       15.52        30.90        31.96        11.77        15.95        30.51 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-IN-A6RN 
        6.51        20.25        19.53 

$`FAM116A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM116A MUTATED FAM116A WILD-TYPE 
             6.51              0.00 
  FAM116A MUTATED FAM116A WILD-TYPE 
            31.96            122.30 
  FAM116A MUTATED FAM116A WILD-TYPE 
            19.53             13.51 
[1] "6.5 - 32.0 (19.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D358V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM116A MUTATED         0        0        1        1         3         0
  FAM116A WILD-TYPE      10       20       45       30        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM116A MUTATED           0          1          0          2        1
  FAM116A WILD-TYPE        29         83         62         37       42
                   vv
clus                STAGE IVA
  FAM116A MUTATED           0
  FAM116A WILD-TYPE         4
D358V3, multiclass
            clus
vv           FAM116A MUTATED FAM116A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM116A MUTATED       1   4   2   3
  FAM116A WILD-TYPE    53 131 259  99
D358V4, multiclass
       clus
vv      FAM116A MUTATED FAM116A WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM116A MUTATED     3   2   3   1
  FAM116A WILD-TYPE 192 171  86  84
D358V5, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  N0               3               192
  N1               2               171
  N2               3                86
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V6, binary
                   cls
clus                  0   1
  FAM116A MUTATED     9   1
  FAM116A WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      9    1
  FAM116A WILD-TYPE  473   37
   clus
vv  FAM116A MUTATED FAM116A WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D358V7, binary
                   cls
clus                  0   1
  FAM116A MUTATED     5   5
  FAM116A WILD-TYPE 167 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      5    5
  FAM116A WILD-TYPE  167  401
        clus
vv       FAM116A MUTATED FAM116A WILD-TYPE
  FEMALE               5               167
  MALE                 5               401
[1] 2 2
[1] FALSE
D358V8, binary
                   cls
clus                  0   1
  FAM116A MUTATED     8   1
  FAM116A WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      8    1
  FAM116A WILD-TYPE  408  101
     clus
vv    FAM116A MUTATED FAM116A WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D358V9, continuous
[1] "Remove cluster labels:" "FAM116A MUTATED"       
clus
  FAM116A MUTATED FAM116A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FAM116A WILD-TYPE" "FAM116A WILD-TYPE" "FAM116A WILD-TYPE" 
D358V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM116A MUTATED       5                         0
  FAM116A WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM116A MUTATED                                           0     2
  FAM116A WILD-TYPE                                         1   355
D358V11, multiclass
                                           clus
vv                                          FAM116A MUTATED FAM116A WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V12, binary
                   cls
clus                  0   1
  FAM116A MUTATED     0   7
  FAM116A WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      0    7
  FAM116A WILD-TYPE   10  391
                        clus
vv                       FAM116A MUTATED FAM116A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(359) Variable = ERBB3 MUTATION ANALYSIS
D359V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    20  16
  ERBB3 WILD-TYPE 318 200
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             36             518 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             16             200 
$`ERBB3 MUTATED`
TCGA-IG-A3I8 TCGA-L5-A4OJ TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A8NQ TCGA-Z6-A8JD 
       33.27        21.01         7.43        15.48        21.37         3.42 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-6706 
        6.97         9.34         9.67        34.68        39.12        18.05 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-A4QL 
       14.43        29.59         0.26         7.36        25.05        16.14 
TCGA-BR-A4QM TCGA-CD-8527 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YU TCGA-D7-A4YV 
        5.13         7.17         6.02        28.96        16.44         5.92 
TCGA-D7-A6EY TCGA-EQ-8122 TCGA-FP-7735 TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G9 
       11.44         7.99         3.48        77.29        22.32        24.20 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-KB-A93J TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A92D 
        6.58        14.07        36.95        19.04        38.14        66.81 

$`ERBB3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         4.08         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8384 
       14.04         3.32        11.80        31.27        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42         1.15        21.44        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        63.62         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.26            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          77.29          122.30 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         15.810          13.495 
[1] "0.3 - 77.3 (15.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D359V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB3 MUTATED         1        2        7        3         4         9
  ERBB3 WILD-TYPE       9       18       39       28        80        74
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB3 MUTATED           1          5          3          1        1         0
  ERBB3 WILD-TYPE        28         79         59         38       42         4
D359V3, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               7              39
  STAGE II               3              28
  STAGE IIA              4              80
  STAGE IIB              9              74
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ERBB3 MUTATED       4  10  16   7
  ERBB3 WILD-TYPE    50 125 245  95
D359V4, multiclass
       clus
vv      ERBB3 MUTATED ERBB3 WILD-TYPE
  T0+T1             4              50
  T2               10             125
  T3               16             245
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ERBB3 MUTATED    17  17   1   4
  ERBB3 WILD-TYPE 178 156  88  81
D359V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            17             178
  N1            17             156
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    37   0
  ERBB3 WILD-TYPE 445  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     37    0
  ERBB3 WILD-TYPE  445   38
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            37             445
  1             0              38
[1] 2 2
[1] FALSE
D359V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED    18  23
  ERBB3 WILD-TYPE 154 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     18   23
  ERBB3 WILD-TYPE  154  383
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE            18             154
  MALE              23             383
[1] 2 2
[1] FALSE
D359V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    31   4
  ERBB3 WILD-TYPE 385  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     31    4
  ERBB3 WILD-TYPE  385   98
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             31             385
  YES             4              98
[1] 2 2
[1] FALSE
D359V9, continuous
[1] "Remove cluster labels:" "ERBB3 MUTATED"         
clus
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              2              66 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JE 
"ERBB3 WILD-TYPE" "ERBB3 WILD-TYPE" 
D359V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB3 MUTATED       5                         1
  ERBB3 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB3 MUTATED                                           0    31
  ERBB3 WILD-TYPE                                         1   326
D359V11, multiclass
                                           clus
vv                                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                31             326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V12, binary
                 cls
clus                0   1
  ERBB3 MUTATED     0  30
  ERBB3 WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      0   30
  ERBB3 WILD-TYPE   10  368
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(360) Variable = NDST2 MUTATION ANALYSIS
D360V1, survival
                 sevent
clus2               0   1
  NDST2 MUTATED    12   3
  NDST2 WILD-TYPE 326 213
  NDST2 MUTATED NDST2 WILD-TYPE 
             15             539 
  NDST2 MUTATED NDST2 WILD-TYPE 
              3             213 
$`NDST2 MUTATED`
TCGA-2H-A9GM TCGA-JY-A6FD TCGA-VR-A8EY TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 
       13.94        68.02        33.70         2.10        19.73        26.70 
TCGA-BR-4257 TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4449 TCGA-CG-5721 TCGA-F1-A448 
        9.67        31.27        15.95        19.07         6.02        21.27 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       22.32        22.68        38.14 

$`NDST2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32         2.66        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NDST2 MUTATED NDST2 WILD-TYPE 
            2.1             0.0 
  NDST2 MUTATED NDST2 WILD-TYPE 
          68.02          122.30 
  NDST2 MUTATED NDST2 WILD-TYPE 
          21.27           13.41 
[1] "2.1 - 68.0 (21.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.6"
D360V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NDST2 MUTATED         0        0        1        2         2         4
  NDST2 WILD-TYPE      10       20       45       29        82        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NDST2 MUTATED           0          2          1          2        1         0
  NDST2 WILD-TYPE        29         82         61         37       42         4
D360V3, multiclass
            clus
vv           NDST2 MUTATED NDST2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NDST2 MUTATED       1   3   6   5
  NDST2 WILD-TYPE    53 132 255  97
D360V4, multiclass
       clus
vv      NDST2 MUTATED NDST2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NDST2 MUTATED     5   7   0   3
  NDST2 WILD-TYPE 190 166  89  82
D360V5, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  N0             5             190
  N1             7             166
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V6, binary
                 cls
clus                0   1
  NDST2 MUTATED    15   0
  NDST2 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED     15    0
  NDST2 WILD-TYPE  467   38
   clus
vv  NDST2 MUTATED NDST2 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D360V7, binary
                 cls
clus                0   1
  NDST2 MUTATED     6  10
  NDST2 WILD-TYPE 166 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      6   10
  NDST2 WILD-TYPE  166  396
        clus
vv       NDST2 MUTATED NDST2 WILD-TYPE
  FEMALE             6             166
  MALE              10             396
[1] 2 2
[1] FALSE
D360V8, binary
                 cls
clus                0   1
  NDST2 MUTATED    13   2
  NDST2 WILD-TYPE 403 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED     13    2
  NDST2 WILD-TYPE  403  100
     clus
vv    NDST2 MUTATED NDST2 WILD-TYPE
  NO             13             403
  YES             2             100
[1] 2 2
[1] FALSE
D360V9, continuous
[1] "Remove cluster labels:" "NDST2 MUTATED"         
clus
  NDST2 MUTATED NDST2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD 
"NDST2 WILD-TYPE" "NDST2 WILD-TYPE" 
D360V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NDST2 MUTATED       3                         0
  NDST2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NDST2 MUTATED                                           0     8
  NDST2 WILD-TYPE                                         1   349
D360V11, multiclass
                                           clus
vv                                          NDST2 MUTATED NDST2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V12, binary
                 cls
clus                0   1
  NDST2 MUTATED     1   7
  NDST2 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      1    7
  NDST2 WILD-TYPE    9  391
                        clus
vv                       NDST2 MUTATED NDST2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(361) Variable = RB1 MUTATION ANALYSIS
D361V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    12   5
  RB1 WILD-TYPE 326 211
  RB1 MUTATED RB1 WILD-TYPE 
           17           537 
  RB1 MUTATED RB1 WILD-TYPE 
            5           211 
$`RB1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-JY-A6FD TCGA-L5-A893 TCGA-L5-A8NN TCGA-LN-A4MQ 
       19.99        21.99        68.02         3.02         5.49        12.33 
TCGA-VR-A8EP TCGA-Z6-A8JD TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-A452 
       27.09         3.42        26.70        34.68         0.26         7.53 
TCGA-BR-A4J2 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 
       14.17        11.61         6.58         6.02       105.07 

$`RB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
       14.37         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98         0.72         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.43         6.31        12.30        11.31        12.43        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RB1 MUTATED RB1 WILD-TYPE 
         0.26          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       105.07        122.30 
  RB1 MUTATED RB1 WILD-TYPE 
        12.33         13.58 
[1] "0.3 - 105.1 (12.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D361V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RB1 MUTATED         1        1        1        1         3         4
  RB1 WILD-TYPE       9       19       45       30        81        79
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RB1 MUTATED           2          2          1          2        3         0
  RB1 WILD-TYPE        27         82         61         37       40         4
D361V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              1             9
  STAGE IA             1            19
  STAGE IB             1            45
  STAGE II             1            30
  STAGE IIA            3            81
  STAGE IIB            4            79
  STAGE III            2            27
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             3            40
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  RB1 MUTATED       2   2   9   8
  RB1 WILD-TYPE    52 133 252  94
D361V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T0+T1           2            52
  T2              2           133
  T3              9           252
  T4              8            94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RB1 MUTATED    10   7   2   2
  RB1 WILD-TYPE 185 166  87  83
D361V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          10           185
  N1           7           166
  N2           2            87
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V6, binary
               cls
clus              0   1
  RB1 MUTATED    19   1
  RB1 WILD-TYPE 463  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     19    1
  RB1 WILD-TYPE  463   37
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          19           463
  1           1            37
[1] 2 2
[1] FALSE
D361V7, binary
               cls
clus              0   1
  RB1 MUTATED    10  11
  RB1 WILD-TYPE 162 395
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     10   11
  RB1 WILD-TYPE  162  395
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          10           162
  MALE            11           395
[1] 2 2
[1] FALSE
D361V8, binary
               cls
clus              0   1
  RB1 MUTATED    18   1
  RB1 WILD-TYPE 398 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     18    1
  RB1 WILD-TYPE  398  101
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           18           398
  YES           1           101
[1] 2 2
[1] FALSE
D361V9, continuous
D361V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  RB1 MUTATED       7                         0
  RB1 WILD-TYPE   126                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RB1 MUTATED                                           0    11
  RB1 WILD-TYPE                                         1   346
D361V11, multiclass
                                           clus
vv                                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                                               7           126
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              11           346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V12, binary
               cls
clus              0   1
  RB1 MUTATED     0  13
  RB1 WILD-TYPE  10 385
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   13
  RB1 WILD-TYPE   10  385
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          13           385
[1] 2 2
[1] FALSE

Clustering(362) Variable = GNAS MUTATION ANALYSIS
D362V1, survival
                sevent
clus2              0   1
  GNAS MUTATED    32  15
  GNAS WILD-TYPE 306 201
  GNAS MUTATED GNAS WILD-TYPE 
            47            507 
  GNAS MUTATED GNAS WILD-TYPE 
            15            201 
$`GNAS MUTATED`
TCGA-IC-A6RF TCGA-S8-A6BV TCGA-CG-4460 TCGA-IG-A4QS TCGA-JY-A6FG TCGA-L5-A4OT 
       15.68        20.02        21.99         3.88        41.52         4.90 
TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L5-A8NS TCGA-Q9-A6FW 
       29.00        25.12        13.55         8.71        13.41         7.82 
TCGA-RE-A7BO TCGA-VR-AA7D TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-B7-A5TI TCGA-B7-A5TJ 
        7.00         9.17        14.37         1.32        19.56        11.01 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7958 TCGA-BR-8483 TCGA-BR-8487 
        6.97        30.90        34.68        29.56         5.39         1.12 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4465 
       31.96        16.14        13.15         6.58        12.62         9.01 
TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-8574 TCGA-EQ-8122 TCGA-FP-A4BE 
        6.02        28.96        65.10        17.19         7.99        11.08 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GY 
        6.21        77.29        52.21        22.68        29.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4HB TCGA-IN-A7NT TCGA-SW-A7EA TCGA-VQ-A8P2 
        2.10        15.68        10.62        19.04        38.14 

$`GNAS WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
        5.16        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        1.38         3.16        58.59         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
        2.10         2.66        19.73        26.70        11.70         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        1.15        21.44         5.13        13.41        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52        63.06        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.58        20.25        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GNAS MUTATED GNAS WILD-TYPE 
          0.26           0.00 
  GNAS MUTATED GNAS WILD-TYPE 
         77.29         122.30 
  GNAS MUTATED GNAS WILD-TYPE 
         13.55          13.58 
[1] "0.3 - 77.3 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D362V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNAS MUTATED         1        4        3        2         8         8
  GNAS WILD-TYPE       9       16       43       29        76        75
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNAS MUTATED           2          7          4          3        5         0
  GNAS WILD-TYPE        27         77         58         36       38         4
D362V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               1              9
  STAGE IA              4             16
  STAGE IB              3             43
  STAGE II              2             29
  STAGE IIA             8             76
  STAGE IIB             8             75
  STAGE III             2             27
  STAGE IIIA            7             77
  STAGE IIIB            4             58
  STAGE IIIC            3             36
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GNAS MUTATED       8   8  23  10
  GNAS WILD-TYPE    46 127 238  92
D362V4, multiclass
       clus
vv      GNAS MUTATED GNAS WILD-TYPE
  T0+T1            8             46
  T2               8            127
  T3              23            238
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GNAS MUTATED    17  19   5   6
  GNAS WILD-TYPE 178 154  84  79
D362V5, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  N0           17            178
  N1           19            154
  N2            5             84
  N3            6             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V6, binary
                cls
clus               0   1
  GNAS MUTATED    40   4
  GNAS WILD-TYPE 442  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     40    4
  GNAS WILD-TYPE  442   34
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0           40            442
  1            4             34
[1] 2 2
[1] FALSE
D362V7, binary
                cls
clus               0   1
  GNAS MUTATED    17  32
  GNAS WILD-TYPE 155 374
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     17   32
  GNAS WILD-TYPE  155  374
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE           17            155
  MALE             32            374
[1] 2 2
[1] FALSE
D362V8, binary
                cls
clus               0   1
  GNAS MUTATED    35  10
  GNAS WILD-TYPE 381  92
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     35   10
  GNAS WILD-TYPE  381   92
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO            35            381
  YES           10             92
[1] 2 2
[1] FALSE
D362V9, continuous
[1] "Remove cluster labels:" "GNAS MUTATED"          
clus
  GNAS MUTATED GNAS WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" 
D362V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GNAS MUTATED      10                         3
  GNAS WILD-TYPE   123                        11
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNAS MUTATED                                           0    27
  GNAS WILD-TYPE                                         1   330
D362V11, multiclass
                                           clus
vv                                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                               10            123
  BLACK OR AFRICAN AMERICAN                            3             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               27            330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V12, binary
                cls
clus               0   1
  GNAS MUTATED     1  32
  GNAS WILD-TYPE   9 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      1   32
  GNAS WILD-TYPE    9  366
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           32            366
[1] 2 2
[1] FALSE

Clustering(363) Variable = SPG11 MUTATION ANALYSIS
D363V1, survival
                 sevent
clus2               0   1
  SPG11 MUTATED    10  10
  SPG11 WILD-TYPE 328 206
  SPG11 MUTATED SPG11 WILD-TYPE 
             20             534 
  SPG11 MUTATED SPG11 WILD-TYPE 
             10             206 
$`SPG11 MUTATED`
TCGA-L5-A8NG TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-LN-A4A2 TCGA-LN-A9FO TCGA-VR-A8ER 
       35.97       122.10         7.76        12.49         0.13        12.43 
TCGA-VR-A8EY TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7722 TCGA-BR-8361 TCGA-BR-8382 
       33.70         6.97        30.90        15.32        31.10        25.05 
TCGA-CD-5803 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-8570 TCGA-D7-A4YV TCGA-D7-A6EY 
       11.21         6.58         6.02        24.72         5.92        11.44 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`SPG11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.59        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38        13.18        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        22.82         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.18        13.35        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SPG11 MUTATED SPG11 WILD-TYPE 
           0.13            0.00 
  SPG11 MUTATED SPG11 WILD-TYPE 
          122.1           122.3 
  SPG11 MUTATED SPG11 WILD-TYPE 
         13.905          13.565 
[1] "0.1 - 122.1 (13.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D363V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPG11 MUTATED         1        0        0        1         4         3
  SPG11 WILD-TYPE       9       20       46       30        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPG11 MUTATED           2          3          2          3        1         0
  SPG11 WILD-TYPE        27         81         60         36       42         4
D363V3, multiclass
            clus
vv           SPG11 MUTATED SPG11 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SPG11 MUTATED       1   3  10   7
  SPG11 WILD-TYPE    53 132 251  95
D363V4, multiclass
       clus
vv      SPG11 MUTATED SPG11 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3               10             251
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SPG11 MUTATED     7   9   2   3
  SPG11 WILD-TYPE 188 164  87  82
D363V5, multiclass
    clus
vv   SPG11 MUTATED SPG11 WILD-TYPE
  N0             7             188
  N1             9             164
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V6, binary
                 cls
clus                0   1
  SPG11 MUTATED    21   0
  SPG11 WILD-TYPE 461  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG11 MUTATED     21    0
  SPG11 WILD-TYPE  461   38
   clus
vv  SPG11 MUTATED SPG11 WILD-TYPE
  0            21             461
  1             0              38
[1] 2 2
[1] FALSE
D363V7, binary
                 cls
clus                0   1
  SPG11 MUTATED    11  11
  SPG11 WILD-TYPE 161 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG11 MUTATED     11   11
  SPG11 WILD-TYPE  161  395
        clus
vv       SPG11 MUTATED SPG11 WILD-TYPE
  FEMALE            11             161
  MALE              11             395
[1] 2 2
[1] FALSE
D363V8, binary
                 cls
clus                0   1
  SPG11 MUTATED    17   3
  SPG11 WILD-TYPE 399  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG11 MUTATED     17    3
  SPG11 WILD-TYPE  399   99
     clus
vv    SPG11 MUTATED SPG11 WILD-TYPE
  NO             17             399
  YES             3              99
[1] 2 2
[1] FALSE
D363V9, continuous
D363V10, continuous
[1] "Remove cluster labels:" "SPG11 MUTATED"         
clus
  SPG11 MUTATED SPG11 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8EU 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" "SPG11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SPG11 MUTATED       5                         0
  SPG11 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPG11 MUTATED                                           0    15
  SPG11 WILD-TYPE                                         1   342
D363V11, multiclass
                                           clus
vv                                          SPG11 MUTATED SPG11 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V12, binary
                 cls
clus                0   1
  SPG11 MUTATED     0  15
  SPG11 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG11 MUTATED      0   15
  SPG11 WILD-TYPE   10  383
                        clus
vv                       SPG11 MUTATED SPG11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(364) Variable = FAH MUTATION ANALYSIS
D364V1, survival
               sevent
clus2             0   1
  FAH MUTATED     5   3
  FAH WILD-TYPE 333 213
  FAH MUTATED FAH WILD-TYPE 
            8           546 
  FAH MUTATED FAH WILD-TYPE 
            3           213 
$`FAH MUTATED`
TCGA-2H-A9GI TCGA-L5-A4OF TCGA-B7-5816 TCGA-BR-4184 TCGA-CD-8526 TCGA-HU-A4GU 
       14.30        26.33        26.70         6.97        12.53         6.58 
TCGA-HU-A4GX TCGA-HU-A4H2 
       20.25        12.95 

$`FAH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FAH MUTATED FAH WILD-TYPE 
         6.58          0.00 
  FAH MUTATED FAH WILD-TYPE 
         26.7         122.3 
  FAH MUTATED FAH WILD-TYPE 
       13.625        13.565 
[1] "6.6 - 26.7 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D364V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAH MUTATED         0        0        0        0         0         3
  FAH WILD-TYPE      10       20       46       31        84        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAH MUTATED           1          2          1          1        0         0
  FAH WILD-TYPE        28         82         61         38       43         4
D364V3, multiclass
            clus
vv           FAH MUTATED FAH WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            0            84
  STAGE IIB            3            80
  STAGE III            1            28
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           1            38
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  FAH MUTATED       2   0   5   2
  FAH WILD-TYPE    52 135 256 100
D364V4, multiclass
       clus
vv      FAH MUTATED FAH WILD-TYPE
  T0+T1           2            52
  T2              0           135
  T3              5           256
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  FAH MUTATED     1   5   1   1
  FAH WILD-TYPE 194 168  88  84
D364V5, multiclass
    clus
vv   FAH MUTATED FAH WILD-TYPE
  N0           1           194
  N1           5           168
  N2           1            88
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V6, binary
               cls
clus              0   1
  FAH MUTATED     7   0
  FAH WILD-TYPE 475  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      7    0
  FAH WILD-TYPE  475   38
   clus
vv  FAH MUTATED FAH WILD-TYPE
  0           7           475
  1           0            38
[1] 2 2
[1] FALSE
D364V7, binary
               cls
clus              0   1
  FAH MUTATED     5   4
  FAH WILD-TYPE 167 402
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      5    4
  FAH WILD-TYPE  167  402
        clus
vv       FAH MUTATED FAH WILD-TYPE
  FEMALE           5           167
  MALE             4           402
[1] 2 2
[1] FALSE
D364V8, binary
               cls
clus              0   1
  FAH MUTATED     8   0
  FAH WILD-TYPE 408 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      8    0
  FAH WILD-TYPE  408  102
     clus
vv    FAH MUTATED FAH WILD-TYPE
  NO            8           408
  YES           0           102
[1] 2 2
[1] FALSE
D364V9, continuous
D364V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  FAH MUTATED       4                         0
  FAH WILD-TYPE   129                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAH MUTATED                                           0     4
  FAH WILD-TYPE                                         1   353
D364V11, multiclass
                                           clus
vv                                          FAH MUTATED FAH WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V12, binary
               cls
clus              0   1
  FAH MUTATED     0   7
  FAH WILD-TYPE  10 391
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      0    7
  FAH WILD-TYPE   10  391
                        clus
vv                       FAH MUTATED FAH WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           7           391
[1] 2 2
[1] FALSE

Clustering(365) Variable = CNTLN MUTATION ANALYSIS
D365V1, survival
                 sevent
clus2               0   1
  CNTLN MUTATED    29  12
  CNTLN WILD-TYPE 309 204
  CNTLN MUTATED CNTLN WILD-TYPE 
             41             513 
  CNTLN MUTATED CNTLN WILD-TYPE 
             12             204 
$`CNTLN MUTATED`
TCGA-L5-A4OI TCGA-MX-A663 TCGA-IC-A6RE TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A893 
       19.99         9.86         7.69        21.01         3.32         3.02 
TCGA-L5-A8NM TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-B7-5818 TCGA-BR-4280 
        7.76         0.13        33.11        38.40        11.70         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8368 
       34.68        15.95        32.78        44.94        31.10         4.31 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PF TCGA-CG-4465 TCGA-CG-5723 
       31.27         1.12        31.96         1.15         9.01       105.07 
TCGA-CG-5726 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-A4YV TCGA-FP-7916 TCGA-HF-7134 
       28.96        15.22        24.72         5.92        14.07        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GD TCGA-HU-A4GQ TCGA-IN-A6RR 
       30.51        26.47        22.32        22.75         0.10         6.74 
TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A91U TCGA-VQ-A91V 
       19.04         5.46        38.14         1.71        42.64 

$`CNTLN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        26.33        32.61        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.38        13.18        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18         9.57        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       15.65        20.81        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CNTLN MUTATED CNTLN WILD-TYPE 
            0.1             0.0 
  CNTLN MUTATED CNTLN WILD-TYPE 
         105.07          122.30 
  CNTLN MUTATED CNTLN WILD-TYPE 
          19.04           13.48 
[1] "0.1 - 105.1 (19.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D365V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNTLN MUTATED         3        2        5        1         8         6
  CNTLN WILD-TYPE       7       18       41       30        76        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNTLN MUTATED           1          6          2          7        2         0
  CNTLN WILD-TYPE        28         78         60         32       41         4
D365V3, multiclass
            clus
vv           CNTLN MUTATED CNTLN WILD-TYPE
  STAGE I                3               7
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               1              30
  STAGE IIA              8              76
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             6              78
  STAGE IIIB             2              60
  STAGE IIIC             7              32
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CNTLN MUTATED       6  10  15  12
  CNTLN WILD-TYPE    48 125 246  90
D365V4, multiclass
       clus
vv      CNTLN MUTATED CNTLN WILD-TYPE
  T0+T1             6              48
  T2               10             125
  T3               15             246
  T4               12              90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNTLN MUTATED    19  12   6   7
  CNTLN WILD-TYPE 176 161  83  78
D365V5, multiclass
    clus
vv   CNTLN MUTATED CNTLN WILD-TYPE
  N0            19             176
  N1            12             161
  N2             6              83
  N3             7              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V6, binary
                 cls
clus                0   1
  CNTLN MUTATED    38   2
  CNTLN WILD-TYPE 444  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     38    2
  CNTLN WILD-TYPE  444   36
   clus
vv  CNTLN MUTATED CNTLN WILD-TYPE
  0            38             444
  1             2              36
[1] 2 2
[1] FALSE
D365V7, binary
                 cls
clus                0   1
  CNTLN MUTATED    19  26
  CNTLN WILD-TYPE 153 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     19   26
  CNTLN WILD-TYPE  153  380
        clus
vv       CNTLN MUTATED CNTLN WILD-TYPE
  FEMALE            19             153
  MALE              26             380
[1] 2 2
[1] FALSE
D365V8, binary
                 cls
clus                0   1
  CNTLN MUTATED    37   3
  CNTLN WILD-TYPE 379  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     37    3
  CNTLN WILD-TYPE  379   99
     clus
vv    CNTLN MUTATED CNTLN WILD-TYPE
  NO             37             379
  YES             3              99
[1] 2 2
[1] FALSE
D365V9, continuous
D365V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNTLN MUTATED       7                         1
  CNTLN WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNTLN MUTATED                                           0    30
  CNTLN WILD-TYPE                                         1   327
D365V11, multiclass
                                           clus
vv                                          CNTLN MUTATED CNTLN WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                30             327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V12, binary
                 cls
clus                0   1
  CNTLN MUTATED     0  30
  CNTLN WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED      0   30
  CNTLN WILD-TYPE   10  368
                        clus
vv                       CNTLN MUTATED CNTLN WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(366) Variable = KIAA0748 MUTATION ANALYSIS
D366V1, survival
                    sevent
clus2                  0   1
  KIAA0748 MUTATED    12   8
  KIAA0748 WILD-TYPE 326 208
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                20                534 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 8                208 
$`KIAA0748 MUTATED`
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-L5-A4OT TCGA-V5-A7RB TCGA-Z6-A8JD TCGA-BR-4267 
       32.45         7.69         4.90         5.29         3.42         6.18 
TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8368 TCGA-CD-8535 
       15.95        19.33        44.94        32.25         4.31        12.82 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5732 TCGA-FP-A4BE TCGA-HU-A4GQ 
       12.43         6.58         8.05        69.04        11.08         0.10 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`KIAA0748 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94         8.94        16.24         4.21        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
               0.1                0.0 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
             74.53             122.30 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
            11.755             13.730 
[1] "0.1 - 74.5 (11.8)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D366V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0748 MUTATED         0        0        4        2         5         4
  KIAA0748 WILD-TYPE      10       20       42       29        79        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0748 MUTATED           0          1          0          1        3
  KIAA0748 WILD-TYPE        29         83         62         38       40
                    vv
clus                 STAGE IVA
  KIAA0748 MUTATED           0
  KIAA0748 WILD-TYPE         4
D366V3, multiclass
            clus
vv           KIAA0748 MUTATED KIAA0748 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  4                 42
  STAGE II                  2                 29
  STAGE IIA                 5                 79
  STAGE IIB                 4                 79
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0748 MUTATED       3   6   9   3
  KIAA0748 WILD-TYPE    51 129 252  99
D366V4, multiclass
       clus
vv      KIAA0748 MUTATED KIAA0748 WILD-TYPE
  T0+T1                3                 51
  T2                   6                129
  T3                   9                252
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0748 MUTATED    10   9   1   1
  KIAA0748 WILD-TYPE 185 164  88  84
D366V5, multiclass
    clus
vv   KIAA0748 MUTATED KIAA0748 WILD-TYPE
  N0               10                185
  N1                9                164
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V6, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED    18   2
  KIAA0748 WILD-TYPE 464  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED     18    2
  KIAA0748 WILD-TYPE  464   36
   clus
vv  KIAA0748 MUTATED KIAA0748 WILD-TYPE
  0               18                464
  1                2                 36
[1] 2 2
[1] FALSE
D366V7, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED     6  15
  KIAA0748 WILD-TYPE 166 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED      6   15
  KIAA0748 WILD-TYPE  166  391
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  FEMALE                6                166
  MALE                 15                391
[1] 2 2
[1] FALSE
D366V8, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED    20   1
  KIAA0748 WILD-TYPE 396 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED     20    1
  KIAA0748 WILD-TYPE  396  101
     clus
vv    KIAA0748 MUTATED KIAA0748 WILD-TYPE
  NO                20                396
  YES                1                101
[1] 2 2
[1] FALSE
D366V9, continuous
[1] "Remove cluster labels:" "KIAA0748 MUTATED"      
clus
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RC 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JE 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
D366V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0748 MUTATED       5                         1
  KIAA0748 WILD-TYPE   128                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0748 MUTATED                                           0    11
  KIAA0748 WILD-TYPE                                         1   346
D366V11, multiclass
                                           clus
vv                                          KIAA0748 MUTATED KIAA0748 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V12, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED     2  15
  KIAA0748 WILD-TYPE   8 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED      2   15
  KIAA0748 WILD-TYPE    8  383
                        clus
vv                       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               15                383
[1] 2 2
[1] FALSE

Clustering(367) Variable = ZMYM3 MUTATION ANALYSIS
D367V1, survival
                 sevent
clus2               0   1
  ZMYM3 MUTATED    13   9
  ZMYM3 WILD-TYPE 325 207
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             22             532 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              9             207 
$`ZMYM3 MUTATED`
TCGA-L5-A4OG TCGA-CG-4460 TCGA-IG-A3Y9 TCGA-KH-A6WC TCGA-L5-A8NM TCGA-L5-A8NN 
        4.70        21.99         0.85         6.28         7.76         5.49 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-B7-5816 TCGA-BR-6709 TCGA-BR-8368 TCGA-BR-8487 
        7.04        38.40        26.70        12.16         4.31         1.12 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-A6EY 
       12.59        12.43         8.05         9.01        28.96        11.44 
TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       11.08        22.68         0.10        38.14 

$`ZMYM3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
            0.1             0.0 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
           38.4           122.3 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
         10.045          13.905 
[1] "0.1 - 38.4 (10.0)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.4"
D367V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYM3 MUTATED         1        2        1        2         2         3
  ZMYM3 WILD-TYPE       9       18       45       29        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMYM3 MUTATED           1          3          2          1        2         0
  ZMYM3 WILD-TYPE        28         81         60         38       41         4
D367V3, multiclass
            clus
vv           ZMYM3 MUTATED ZMYM3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZMYM3 MUTATED       3   3   8   6
  ZMYM3 WILD-TYPE    51 132 253  96
D367V4, multiclass
       clus
vv      ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                8             253
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZMYM3 MUTATED     9   7   1   3
  ZMYM3 WILD-TYPE 186 166  88  82
D367V5, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  N0             9             186
  N1             7             166
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V6, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    18   2
  ZMYM3 WILD-TYPE 464  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     18    2
  ZMYM3 WILD-TYPE  464   36
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0            18             464
  1             2              36
[1] 2 2
[1] FALSE
D367V7, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    11  11
  ZMYM3 WILD-TYPE 161 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     11   11
  ZMYM3 WILD-TYPE  161  395
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  FEMALE            11             161
  MALE              11             395
[1] 2 2
[1] FALSE
D367V8, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    16   4
  ZMYM3 WILD-TYPE 400  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     16    4
  ZMYM3 WILD-TYPE  400   98
     clus
vv    ZMYM3 MUTATED ZMYM3 WILD-TYPE
  NO             16             400
  YES             4              98
[1] 2 2
[1] FALSE
D367V9, continuous
[1] "Remove cluster labels:" "ZMYM3 MUTATED"         
clus
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M      TCGA-LN-A49N 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A49X 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2      TCGA-LN-A4A3 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ZMYM3 WILD-TYPE" "ZMYM3 WILD-TYPE" 
D367V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZMYM3 MUTATED       4                         1
  ZMYM3 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYM3 MUTATED                                           0    13
  ZMYM3 WILD-TYPE                                         1   344
D367V11, multiclass
                                           clus
vv                                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V12, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     0  14
  ZMYM3 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      0   14
  ZMYM3 WILD-TYPE   10  384
                        clus
vv                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(368) Variable = C4ORF6 MUTATION ANALYSIS
D368V1, survival
                  sevent
clus2                0   1
  C4ORF6 MUTATED     8   1
  C4ORF6 WILD-TYPE 330 215
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
               9              545 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
               1              215 
$`C4ORF6 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5728 
        6.97        29.59         4.31        31.96         6.02        65.10 
TCGA-FP-A4BE TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.08        19.73        38.14 

$`C4ORF6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
            4.31             0.00 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
            65.1            122.3 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
           19.73            13.55 
[1] "4.3 - 65.1 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "4.4"
D368V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C4ORF6 MUTATED         1        0        3        0         1         2
  C4ORF6 WILD-TYPE       9       20       43       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF6 MUTATED           0          3          0          0        2
  C4ORF6 WILD-TYPE        29         81         62         39       41
                  vv
clus               STAGE IVA
  C4ORF6 MUTATED           0
  C4ORF6 WILD-TYPE         4
D368V3, multiclass
            clus
vv           C4ORF6 MUTATED C4ORF6 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  C4ORF6 MUTATED       1   3   3   5
  C4ORF6 WILD-TYPE    53 132 258  97
D368V4, multiclass
       clus
vv      C4ORF6 MUTATED C4ORF6 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 3              258
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  C4ORF6 MUTATED     6   4   2   0
  C4ORF6 WILD-TYPE 189 169  87  85
D368V5, multiclass
    clus
vv   C4ORF6 MUTATED C4ORF6 WILD-TYPE
  N0              6              189
  N1              4              169
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V6, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     9   1
  C4ORF6 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      9    1
  C4ORF6 WILD-TYPE  473   37
   clus
vv  C4ORF6 MUTATED C4ORF6 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D368V7, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     4   8
  C4ORF6 WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      4    8
  C4ORF6 WILD-TYPE  168  398
        clus
vv       C4ORF6 MUTATED C4ORF6 WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D368V8, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     8   2
  C4ORF6 WILD-TYPE 408 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      8    2
  C4ORF6 WILD-TYPE  408  100
     clus
vv    C4ORF6 MUTATED C4ORF6 WILD-TYPE
  NO               8              408
  YES              2              100
[1] 2 2
[1] FALSE
D368V9, continuous
D368V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  C4ORF6 MUTATED       1                         2
  C4ORF6 WILD-TYPE   132                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C4ORF6 MUTATED                                           0     6
  C4ORF6 WILD-TYPE                                         1   351
D368V11, multiclass
                                           clus
vv                                          C4ORF6 MUTATED C4ORF6 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V12, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     0   8
  C4ORF6 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      0    8
  C4ORF6 WILD-TYPE   10  390
                        clus
vv                       C4ORF6 MUTATED C4ORF6 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(369) Variable = DPP7 MUTATION ANALYSIS
D369V1, survival
                sevent
clus2              0   1
  DPP7 MUTATED     6   3
  DPP7 WILD-TYPE 332 213
  DPP7 MUTATED DPP7 WILD-TYPE 
             9            545 
  DPP7 MUTATED DPP7 WILD-TYPE 
             3            213 
$`DPP7 MUTATED`
TCGA-L5-A4OI TCGA-LN-A4A5 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8591 
       19.99        22.39        35.84        29.59         4.31        28.14 
TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-A5NB 
       28.96        11.44        30.51 

$`DPP7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DPP7 MUTATED DPP7 WILD-TYPE 
          4.31           0.00 
  DPP7 MUTATED DPP7 WILD-TYPE 
         35.84         122.30 
  DPP7 MUTATED DPP7 WILD-TYPE 
         28.14          13.51 
[1] "4.3 - 35.8 (28.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D369V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DPP7 MUTATED         0        1        2        0         1         1
  DPP7 WILD-TYPE      10       19       44       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DPP7 MUTATED           0          0          1          3        1         0
  DPP7 WILD-TYPE        29         84         61         36       42         4
D369V3, multiclass
            clus
vv           DPP7 MUTATED DPP7 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DPP7 MUTATED       1   3   2   4
  DPP7 WILD-TYPE    53 132 259  98
D369V4, multiclass
       clus
vv      DPP7 MUTATED DPP7 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DPP7 MUTATED     5   1   1   4
  DPP7 WILD-TYPE 190 172  88  81
D369V5, multiclass
    clus
vv   DPP7 MUTATED DPP7 WILD-TYPE
  N0            5            190
  N1            1            172
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V6, binary
                cls
clus               0   1
  DPP7 MUTATED    10   0
  DPP7 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED     10    0
  DPP7 WILD-TYPE  472   38
   clus
vv  DPP7 MUTATED DPP7 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D369V7, binary
                cls
clus               0   1
  DPP7 MUTATED     7   4
  DPP7 WILD-TYPE 165 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      7    4
  DPP7 WILD-TYPE  165  402
        clus
vv       DPP7 MUTATED DPP7 WILD-TYPE
  FEMALE            7            165
  MALE              4            402
[1] 2 2
[1] FALSE
D369V8, binary
                cls
clus               0   1
  DPP7 MUTATED     7   1
  DPP7 WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      7    1
  DPP7 WILD-TYPE  409  101
     clus
vv    DPP7 MUTATED DPP7 WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D369V9, continuous
[1] "Remove cluster labels:" "DPP7 MUTATED"          
clus
  DPP7 MUTATED DPP7 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A6 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
D369V10, continuous
[1] "Remove cluster labels:" "DPP7 MUTATED"          
clus
  DPP7 MUTATED DPP7 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" "DPP7 WILD-TYPE" 
    TCGA-Z6-AAPN 
"DPP7 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DPP7 MUTATED       1                         0
  DPP7 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DPP7 MUTATED                                           0     8
  DPP7 WILD-TYPE                                         1   349
D369V11, multiclass
                                           clus
vv                                          DPP7 MUTATED DPP7 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V12, binary
                cls
clus               0   1
  DPP7 MUTATED     0   8
  DPP7 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      0    8
  DPP7 WILD-TYPE   10  390
                        clus
vv                       DPP7 MUTATED DPP7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(370) Variable = DUSP9 MUTATION ANALYSIS
D370V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     5   4
  DUSP9 WILD-TYPE 333 212
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             545 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              4             212 
$`DUSP9 MUTATED`
TCGA-L5-A8NM TCGA-R6-A8WG TCGA-BR-4280 TCGA-BR-8081 TCGA-CD-8535 TCGA-HU-A4GH 
        7.76        12.69         6.61        32.25        12.82        11.77 
TCGA-IN-A6RP TCGA-RD-A8N6 TCGA-VQ-A92D 
        6.44         8.94        66.81 

$`DUSP9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA 
      115.69       116.38        71.38        57.44        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        42.64        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DUSP9 MUTATED DUSP9 WILD-TYPE 
           6.44            0.00 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          66.81          122.30 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          11.77           13.78 
[1] "6.4 - 66.8 (11.8)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.2"
D370V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DUSP9 MUTATED         0        1        1        0         0         2
  DUSP9 WILD-TYPE      10       19       45       31        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DUSP9 MUTATED           1          3          0          1        0         0
  DUSP9 WILD-TYPE        28         81         62         38       43         4
D370V3, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DUSP9 MUTATED       2   4   1   2
  DUSP9 WILD-TYPE    52 131 260 100
D370V4, multiclass
       clus
vv      DUSP9 MUTATED DUSP9 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DUSP9 MUTATED     4   3   1   1
  DUSP9 WILD-TYPE 191 170  88  84
D370V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V6, binary
                 cls
clus                0   1
  DUSP9 MUTATED     9   0
  DUSP9 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      9    0
  DUSP9 WILD-TYPE  473   38
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D370V7, binary
                 cls
clus                0   1
  DUSP9 MUTATED     5   5
  DUSP9 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      5    5
  DUSP9 WILD-TYPE  167  401
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D370V8, binary
                 cls
clus                0   1
  DUSP9 MUTATED     8   1
  DUSP9 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      8    1
  DUSP9 WILD-TYPE  408  101
     clus
vv    DUSP9 MUTATED DUSP9 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D370V9, continuous
D370V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DUSP9 MUTATED       2                         0
  DUSP9 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DUSP9 MUTATED                                           0     8
  DUSP9 WILD-TYPE                                         1   349
D370V11, multiclass
                                           clus
vv                                          DUSP9 MUTATED DUSP9 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V12, binary
                 cls
clus                0   1
  DUSP9 MUTATED     1   7
  DUSP9 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      1    7
  DUSP9 WILD-TYPE    9  391
                        clus
vv                       DUSP9 MUTATED DUSP9 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(371) Variable = BCL9L MUTATION ANALYSIS
D371V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    19  10
  BCL9L WILD-TYPE 319 206
  BCL9L MUTATED BCL9L WILD-TYPE 
             29             525 
  BCL9L MUTATED BCL9L WILD-TYPE 
             10             206 
$`BCL9L MUTATED`
TCGA-L5-A43J TCGA-IG-A4QS TCGA-L5-A4OT TCGA-LN-A9FO TCGA-S8-A6BW TCGA-BR-4280 
        4.31         3.88         4.90         0.13        20.38         6.61 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 
       29.59         6.18        31.10        25.05        28.14        31.96 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5730 
       11.77        12.62        12.03         6.02        28.96         4.01 
TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-8602 
       12.36        24.72        13.78        14.47        21.27        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-VQ-AA6K 
        0.10         6.51         6.58        19.73        12.43 

$`BCL9L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        12.20        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        12.03        15.02        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        21.37        29.98         8.98        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       16.14        27.55        17.26 

  BCL9L MUTATED BCL9L WILD-TYPE 
            0.1             0.0 
  BCL9L MUTATED BCL9L WILD-TYPE 
          31.96          122.30 
  BCL9L MUTATED BCL9L WILD-TYPE 
          12.43           13.68 
[1] "0.1 - 32.0 (12.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D371V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL9L MUTATED         0        1        4        1         3         4
  BCL9L WILD-TYPE      10       19       42       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9L MUTATED           1          4          4          5        4         0
  BCL9L WILD-TYPE        28         80         58         34       39         4
D371V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             4              58
  STAGE IIIC             5              34
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BCL9L MUTATED       1   9  11  10
  BCL9L WILD-TYPE    53 126 250  92
D371V4, multiclass
       clus
vv      BCL9L MUTATED BCL9L WILD-TYPE
  T0+T1             1              53
  T2                9             126
  T3               11             250
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BCL9L MUTATED    12   7   5   7
  BCL9L WILD-TYPE 183 166  84  78
D371V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0            12             183
  N1             7             166
  N2             5              84
  N3             7              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V6, binary
                 cls
clus                0   1
  BCL9L MUTATED    26   3
  BCL9L WILD-TYPE 456  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     26    3
  BCL9L WILD-TYPE  456   35
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            26             456
  1             3              35
[1] 2 2
[1] FALSE
D371V7, binary
                 cls
clus                0   1
  BCL9L MUTATED     9  22
  BCL9L WILD-TYPE 163 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      9   22
  BCL9L WILD-TYPE  163  384
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             9             163
  MALE              22             384
[1] 2 2
[1] FALSE
D371V8, binary
                 cls
clus                0   1
  BCL9L MUTATED    22   4
  BCL9L WILD-TYPE 394  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     22    4
  BCL9L WILD-TYPE  394   98
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO             22             394
  YES             4              98
[1] 2 2
[1] FALSE
D371V9, continuous
D371V10, continuous
[1] "Remove cluster labels:" "BCL9L MUTATED"         
clus
  BCL9L MUTATED BCL9L WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BCL9L MUTATED       8                         0
  BCL9L WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCL9L MUTATED                                           0    18
  BCL9L WILD-TYPE                                         1   339
D371V11, multiclass
                                           clus
vv                                          BCL9L MUTATED BCL9L WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V12, binary
                 cls
clus                0   1
  BCL9L MUTATED     1  22
  BCL9L WILD-TYPE   9 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      1   22
  BCL9L WILD-TYPE    9  376
                        clus
vv                       BCL9L MUTATED BCL9L WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(372) Variable = SENP3 MUTATION ANALYSIS
D372V1, survival
                 sevent
clus2               0   1
  SENP3 MUTATED     8   4
  SENP3 WILD-TYPE 330 212
  SENP3 MUTATED SENP3 WILD-TYPE 
             12             542 
  SENP3 MUTATED SENP3 WILD-TYPE 
              4             212 
$`SENP3 MUTATED`
TCGA-L5-A8NT TCGA-CG-4460 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 
       27.12        21.99         1.12        28.14         6.58         6.02 
TCGA-CG-5733 TCGA-D7-A4YT TCGA-D7-A748 TCGA-HF-A5NB TCGA-HU-A4H8 TCGA-R5-A7ZI 
       21.07        14.27         4.34        30.51        14.07        74.53 

$`SENP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29        15.65         8.38        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SENP3 MUTATED SENP3 WILD-TYPE 
           1.12            0.00 
  SENP3 MUTATED SENP3 WILD-TYPE 
          74.53          122.30 
  SENP3 MUTATED SENP3 WILD-TYPE 
          17.67           13.51 
[1] "1.1 - 74.5 (17.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D372V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SENP3 MUTATED         0        0        1        0         2         2
  SENP3 WILD-TYPE      10       20       45       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SENP3 MUTATED           0          2          0          2        5         0
  SENP3 WILD-TYPE        29         82         62         37       38         4
D372V3, multiclass
            clus
vv           SENP3 MUTATED SENP3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SENP3 MUTATED       1   2   3   8
  SENP3 WILD-TYPE    53 133 258  94
D372V4, multiclass
       clus
vv      SENP3 MUTATED SENP3 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                3             258
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SENP3 MUTATED     4   4   2   4
  SENP3 WILD-TYPE 191 169  87  81
D372V5, multiclass
    clus
vv   SENP3 MUTATED SENP3 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V6, binary
                 cls
clus                0   1
  SENP3 MUTATED    11   3
  SENP3 WILD-TYPE 471  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED     11    3
  SENP3 WILD-TYPE  471   35
   clus
vv  SENP3 MUTATED SENP3 WILD-TYPE
  0            11             471
  1             3              35
[1] 2 2
[1] FALSE
D372V7, binary
                 cls
clus                0   1
  SENP3 MUTATED     7   7
  SENP3 WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED      7    7
  SENP3 WILD-TYPE  165  399
        clus
vv       SENP3 MUTATED SENP3 WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D372V8, binary
                 cls
clus                0   1
  SENP3 MUTATED    10   3
  SENP3 WILD-TYPE 406  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED     10    3
  SENP3 WILD-TYPE  406   99
     clus
vv    SENP3 MUTATED SENP3 WILD-TYPE
  NO             10             406
  YES             3              99
[1] 2 2
[1] FALSE
D372V9, continuous
D372V10, continuous
[1] "Remove cluster labels:" "SENP3 MUTATED"         
clus
  SENP3 MUTATED SENP3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" "SENP3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SENP3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SENP3 MUTATED       2                         0
  SENP3 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SENP3 MUTATED                                           0     8
  SENP3 WILD-TYPE                                         1   349
D372V11, multiclass
                                           clus
vv                                          SENP3 MUTATED SENP3 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V12, binary
                 cls
clus                0   1
  SENP3 MUTATED     1   8
  SENP3 WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED      1    8
  SENP3 WILD-TYPE    9  390
                        clus
vv                       SENP3 MUTATED SENP3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(373) Variable = MMP3 MUTATION ANALYSIS
D373V1, survival
                sevent
clus2              0   1
  MMP3 MUTATED    10   2
  MMP3 WILD-TYPE 328 214
  MMP3 MUTATED MMP3 WILD-TYPE 
            12            542 
  MMP3 MUTATED MMP3 WILD-TYPE 
             2            214 
$`MMP3 MUTATED`
TCGA-L5-A88Z TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YY 
        7.40        34.68        29.59         6.02       105.07        13.78 
TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-8602 TCGA-IN-A6RL TCGA-R5-A7ZI TCGA-VQ-A8P2 
       11.44        30.51        22.32        13.35        74.53        38.14 

$`MMP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MMP3 MUTATED MMP3 WILD-TYPE 
          6.02           0.00 
  MMP3 MUTATED MMP3 WILD-TYPE 
        105.07         122.30 
  MMP3 MUTATED MMP3 WILD-TYPE 
        25.955         13.510 
[1] "6.0 - 105.1 (26.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.8"
D373V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP3 MUTATED         0        0        0        1         2         2
  MMP3 WILD-TYPE      10       20       46       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP3 MUTATED           0          2          2          1        2         0
  MMP3 WILD-TYPE        29         82         60         38       41         4
D373V3, multiclass
            clus
vv           MMP3 MUTATED MMP3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MMP3 MUTATED       1   2   4   6
  MMP3 WILD-TYPE    53 133 257  96
D373V4, multiclass
       clus
vv      MMP3 MUTATED MMP3 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               4            257
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MMP3 MUTATED     3   6   0   3
  MMP3 WILD-TYPE 192 167  89  82
D373V5, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  N0            3            192
  N1            6            167
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V6, binary
                cls
clus               0   1
  MMP3 MUTATED    11   1
  MMP3 WILD-TYPE 471  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED     11    1
  MMP3 WILD-TYPE  471   37
   clus
vv  MMP3 MUTATED MMP3 WILD-TYPE
  0           11            471
  1            1             37
[1] 2 2
[1] FALSE
D373V7, binary
                cls
clus               0   1
  MMP3 MUTATED     8   5
  MMP3 WILD-TYPE 164 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      8    5
  MMP3 WILD-TYPE  164  401
        clus
vv       MMP3 MUTATED MMP3 WILD-TYPE
  FEMALE            8            164
  MALE              5            401
[1] 2 2
[1] FALSE
D373V8, binary
                cls
clus               0   1
  MMP3 MUTATED     9   3
  MMP3 WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      9    3
  MMP3 WILD-TYPE  407   99
     clus
vv    MMP3 MUTATED MMP3 WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D373V9, continuous
D373V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MMP3 MUTATED       1                         0
  MMP3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MMP3 MUTATED                                           0     9
  MMP3 WILD-TYPE                                         1   348
D373V11, multiclass
                                           clus
vv                                          MMP3 MUTATED MMP3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V12, binary
                cls
clus               0   1
  MMP3 MUTATED     1   7
  MMP3 WILD-TYPE   9 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      1    7
  MMP3 WILD-TYPE    9  391
                        clus
vv                       MMP3 MUTATED MMP3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(374) Variable = RCOR3 MUTATION ANALYSIS
D374V1, survival
                 sevent
clus2               0   1
  RCOR3 MUTATED    10   6
  RCOR3 WILD-TYPE 328 210
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             16             538 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              6             210 
$`RCOR3 MUTATED`
TCGA-L5-A4OH TCGA-LN-A49U TCGA-V5-A7RE TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 
       32.61        15.35        16.44         6.97        34.68         0.26 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5726 TCGA-CG-5728 TCGA-FP-A4BE 
       28.14        31.96        16.14        28.96        65.10        11.08 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       22.32         0.10        38.14        18.41 

$`RCOR3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RCOR3 MUTATED RCOR3 WILD-TYPE 
            0.1             0.0 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
           65.1           122.3 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
         20.365          13.445 
[1] "0.1 - 65.1 (20.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D374V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RCOR3 MUTATED         1        1        3        0         3         1
  RCOR3 WILD-TYPE       9       19       43       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RCOR3 MUTATED           0          2          2          2        1         0
  RCOR3 WILD-TYPE        29         82         60         37       42         4
D374V3, multiclass
            clus
vv           RCOR3 MUTATED RCOR3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RCOR3 MUTATED       3   2   6   5
  RCOR3 WILD-TYPE    51 133 255  97
D374V4, multiclass
       clus
vv      RCOR3 MUTATED RCOR3 WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RCOR3 MUTATED     9   3   3   2
  RCOR3 WILD-TYPE 186 170  86  83
D374V5, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  N0             9             186
  N1             3             170
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V6, binary
                 cls
clus                0   1
  RCOR3 MUTATED    15   1
  RCOR3 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     15    1
  RCOR3 WILD-TYPE  467   37
   clus
vv  RCOR3 MUTATED RCOR3 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D374V7, binary
                 cls
clus                0   1
  RCOR3 MUTATED     6  11
  RCOR3 WILD-TYPE 166 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      6   11
  RCOR3 WILD-TYPE  166  395
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  FEMALE             6             166
  MALE              11             395
[1] 2 2
[1] FALSE
D374V8, binary
                 cls
clus                0   1
  RCOR3 MUTATED     9   5
  RCOR3 WILD-TYPE 407  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      9    5
  RCOR3 WILD-TYPE  407   97
     clus
vv    RCOR3 MUTATED RCOR3 WILD-TYPE
  NO              9             407
  YES             5              97
[1] 2 2
[1] FALSE
D374V9, continuous
[1] "Remove cluster labels:" "RCOR3 MUTATED"         
clus
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49V      TCGA-LN-A49W 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-V5-AASW 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
D374V10, continuous
[1] "Remove cluster labels:" "RCOR3 MUTATED"         
clus
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OM 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49V 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" "RCOR3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RCOR3 MUTATED       4                         1
  RCOR3 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RCOR3 MUTATED                                           0    10
  RCOR3 WILD-TYPE                                         1   347
D374V11, multiclass
                                           clus
vv                                          RCOR3 MUTATED RCOR3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V12, binary
                 cls
clus                0   1
  RCOR3 MUTATED     0  12
  RCOR3 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      0   12
  RCOR3 WILD-TYPE   10  386
                        clus
vv                       RCOR3 MUTATED RCOR3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(375) Variable = MBD2 MUTATION ANALYSIS
D375V1, survival
                sevent
clus2              0   1
  MBD2 MUTATED     7   4
  MBD2 WILD-TYPE 331 212
  MBD2 MUTATED MBD2 WILD-TYPE 
            11            543 
  MBD2 MUTATED MBD2 WILD-TYPE 
             4            212 
$`MBD2 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NM TCGA-R6-A8WC TCGA-VR-AA4G TCGA-BR-4184 TCGA-BR-6452 
       21.99         7.76         2.30        18.05         6.97        34.68 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-HU-A4G8 TCGA-HU-A4GT 
       31.10         0.26        31.27        22.68         6.51 

$`MBD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MBD2 MUTATED MBD2 WILD-TYPE 
          0.26           0.00 
  MBD2 MUTATED MBD2 WILD-TYPE 
         34.68         122.30 
  MBD2 MUTATED MBD2 WILD-TYPE 
         18.05          13.55 
[1] "0.3 - 34.7 (18.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D375V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD2 MUTATED         0        0        1        0         2         2
  MBD2 WILD-TYPE      10       20       45       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBD2 MUTATED           0          2          0          2        2         0
  MBD2 WILD-TYPE        29         82         62         37       41         4
D375V3, multiclass
            clus
vv           MBD2 MUTATED MBD2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MBD2 MUTATED       0   3   4   4
  MBD2 WILD-TYPE    54 132 257  98
D375V4, multiclass
       clus
vv      MBD2 MUTATED MBD2 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MBD2 MUTATED     3   4   3   1
  MBD2 WILD-TYPE 192 169  86  84
D375V5, multiclass
    clus
vv   MBD2 MUTATED MBD2 WILD-TYPE
  N0            3            192
  N1            4            169
  N2            3             86
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V6, binary
                cls
clus               0   1
  MBD2 MUTATED     9   1
  MBD2 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      9    1
  MBD2 WILD-TYPE  473   37
   clus
vv  MBD2 MUTATED MBD2 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D375V7, binary
                cls
clus               0   1
  MBD2 MUTATED     9   3
  MBD2 WILD-TYPE 163 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      9    3
  MBD2 WILD-TYPE  163  403
        clus
vv       MBD2 MUTATED MBD2 WILD-TYPE
  FEMALE            9            163
  MALE              3            403
[1] 2 2
[1] FALSE
D375V8, binary
                cls
clus               0   1
  MBD2 MUTATED    10   0
  MBD2 WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED     10    0
  MBD2 WILD-TYPE  406  102
     clus
vv    MBD2 MUTATED MBD2 WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D375V9, continuous
[1] "Remove cluster labels:" "MBD2 MUTATED"          
clus
  MBD2 MUTATED MBD2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA7B 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
D375V10, continuous
[1] "Remove cluster labels:" "MBD2 MUTATED"          
clus
  MBD2 MUTATED MBD2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" "MBD2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MBD2 MUTATED       2                         0
  MBD2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBD2 MUTATED                                           0     9
  MBD2 WILD-TYPE                                         1   348
D375V11, multiclass
                                           clus
vv                                          MBD2 MUTATED MBD2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V12, binary
                cls
clus               0   1
  MBD2 MUTATED     0   9
  MBD2 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      0    9
  MBD2 WILD-TYPE   10  389
                        clus
vv                       MBD2 MUTATED MBD2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(376) Variable = ABCB6 MUTATION ANALYSIS
D376V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED    12   6
  ABCB6 WILD-TYPE 326 210
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             18             536 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              6             210 
$`ABCB6 MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OI TCGA-2H-A9GF TCGA-2H-A9GI TCGA-IG-A3YA TCGA-LN-A9FR 
       60.39        19.99        25.78        14.30        20.78        12.26 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8360 TCGA-BR-8368 
       30.90        34.68        35.84        29.56         6.18         4.31 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A6EZ TCGA-F1-6874 TCGA-R5-A7ZI 
        1.02         6.02        21.07        20.32        14.47        74.53 

$`ABCB6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ 
        0.23        20.15         9.86        20.05        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           1.02            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
          74.53          122.30 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         20.550          13.445 
[1] "1.0 - 74.5 (20.6)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D376V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCB6 MUTATED         1        0        3        0         2         1
  ABCB6 WILD-TYPE       9       20       43       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCB6 MUTATED           2          3          1          1        3         0
  ABCB6 WILD-TYPE        27         81         61         38       40         4
D376V3, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCB6 MUTATED       1   6   7   4
  ABCB6 WILD-TYPE    53 129 254  98
D376V4, multiclass
       clus
vv      ABCB6 MUTATED ABCB6 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCB6 MUTATED     8   5   3   1
  ABCB6 WILD-TYPE 187 168  86  84
D376V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             8             187
  N1             5             168
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V6, binary
                 cls
clus                0   1
  ABCB6 MUTATED    15   2
  ABCB6 WILD-TYPE 467  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED     15    2
  ABCB6 WILD-TYPE  467   36
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0            15             467
  1             2              36
[1] 2 2
[1] FALSE
D376V7, binary
                 cls
clus                0   1
  ABCB6 MUTATED     6  12
  ABCB6 WILD-TYPE 166 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      6   12
  ABCB6 WILD-TYPE  166  394
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  FEMALE             6             166
  MALE              12             394
[1] 2 2
[1] FALSE
D376V8, binary
                 cls
clus                0   1
  ABCB6 MUTATED    16   1
  ABCB6 WILD-TYPE 400 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED     16    1
  ABCB6 WILD-TYPE  400  101
     clus
vv    ABCB6 MUTATED ABCB6 WILD-TYPE
  NO             16             400
  YES             1             101
[1] 2 2
[1] FALSE
D376V9, continuous
[1] "Remove cluster labels:" "ABCB6 MUTATED"         
clus
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YB 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
D376V10, continuous
[1] "Remove cluster labels:" "ABCB6 MUTATED"         
clus
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" "ABCB6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCB6 MUTATED       1                         0
  ABCB6 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCB6 MUTATED                                           0    12
  ABCB6 WILD-TYPE                                         1   345
D376V11, multiclass
                                           clus
vv                                          ABCB6 MUTATED ABCB6 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V12, binary
                 cls
clus                0   1
  ABCB6 MUTATED     1  10
  ABCB6 WILD-TYPE   9 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      1   10
  ABCB6 WILD-TYPE    9  388
                        clus
vv                       ABCB6 MUTATED ABCB6 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(377) Variable = BTBD11 MUTATION ANALYSIS
D377V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    22   8
  BTBD11 WILD-TYPE 316 208
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              30              524 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               8              208 
$`BTBD11 MUTATED`
TCGA-L5-A4OG TCGA-2H-A9GH TCGA-IG-A5S3 TCGA-VR-A8EZ TCGA-XP-A8T7 TCGA-B7-5816 
        4.70        31.27        23.41        18.18        41.23        26.70 
TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 
       19.56        18.35         6.18         6.61        34.68        44.94 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4IY TCGA-BR-A4QM TCGA-CD-A4MG TCGA-CG-4305 
       25.05         1.12        12.89         5.13         6.58        15.95 
TCGA-CG-4443 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-HU-8238 
       29.98         6.02         5.92        14.76        21.27         1.51 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       22.82        22.68        20.25        19.73        19.04        38.14 

$`BTBD11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.66        19.73        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        4.08         9.34         9.67         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
            1.12             0.00 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           44.94           122.30 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           19.30            13.41 
[1] "1.1 - 44.9 (19.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D377V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD11 MUTATED         1        1        2        1         6         7
  BTBD11 WILD-TYPE       9       19       44       30        78        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           1          3          1          4        1
  BTBD11 WILD-TYPE        28         81         61         35       42
                  vv
clus               STAGE IVA
  BTBD11 MUTATED           0
  BTBD11 WILD-TYPE         4
D377V3, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               7               76
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  BTBD11 MUTATED       3   7  13   7
  BTBD11 WILD-TYPE    51 128 248  95
D377V4, multiclass
       clus
vv      BTBD11 MUTATED BTBD11 WILD-TYPE
  T0+T1              3               51
  T2                 7              128
  T3                13              248
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BTBD11 MUTATED    13   8   5   4
  BTBD11 WILD-TYPE 182 165  84  81
D377V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0             13              182
  N1              8              165
  N2              5               84
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V6, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    31   0
  BTBD11 WILD-TYPE 451  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     31    0
  BTBD11 WILD-TYPE  451   38
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             31              451
  1              0               38
[1] 2 2
[1] FALSE
D377V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    16  15
  BTBD11 WILD-TYPE 156 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     16   15
  BTBD11 WILD-TYPE  156  391
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE             16              156
  MALE               15              391
[1] 2 2
[1] FALSE
D377V8, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    26   3
  BTBD11 WILD-TYPE 390  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     26    3
  BTBD11 WILD-TYPE  390   99
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO              26              390
  YES              3               99
[1] 2 2
[1] FALSE
D377V9, continuous
D377V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BTBD11 MUTATED       6                         0
  BTBD11 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD11 MUTATED                                           0    21
  BTBD11 WILD-TYPE                                         1   336
D377V11, multiclass
                                           clus
vv                                          BTBD11 MUTATED BTBD11 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 21              336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V12, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     2  22
  BTBD11 WILD-TYPE   8 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      2   22
  BTBD11 WILD-TYPE    8  376
                        clus
vv                       BTBD11 MUTATED BTBD11 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             22              376
[1] 2 2
[1] FALSE

Clustering(378) Variable = SOX7 MUTATION ANALYSIS
D378V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED    11   6
  SOX7 WILD-TYPE 327 210
  SOX7 MUTATED SOX7 WILD-TYPE 
            17            537 
  SOX7 MUTATED SOX7 WILD-TYPE 
             6            210 
$`SOX7 MUTATED`
TCGA-CG-4460 TCGA-LN-A7HW TCGA-BR-6453 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8680 
       21.99        12.00        15.95         0.26        25.05        31.96 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4G8 
        6.02        12.03        28.96        65.10        14.47        22.68 
TCGA-HU-A4GC TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-RD-A8N1 
        3.25        23.84        13.35        19.73       115.69 

$`SOX7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         1.02         0.99         0.99       105.07        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        24.26        24.20        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SOX7 MUTATED SOX7 WILD-TYPE 
          0.26           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
        115.69         122.30 
  SOX7 MUTATED SOX7 WILD-TYPE 
         19.73          13.51 
[1] "0.3 - 115.7 (19.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D378V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOX7 MUTATED         0        2        3        0         2         2
  SOX7 WILD-TYPE      10       18       43       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX7 MUTATED           0          3          2          1        4         0
  SOX7 WILD-TYPE        29         81         60         38       39         4
D378V3, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SOX7 MUTATED       2   7   4   6
  SOX7 WILD-TYPE    52 128 257  96
D378V4, multiclass
       clus
vv      SOX7 MUTATED SOX7 WILD-TYPE
  T0+T1            2             52
  T2               7            128
  T3               4            257
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SOX7 MUTATED     7   5   5   2
  SOX7 WILD-TYPE 188 168  84  83
D378V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0            7            188
  N1            5            168
  N2            5             84
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V6, binary
                cls
clus               0   1
  SOX7 MUTATED    17   3
  SOX7 WILD-TYPE 465  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     17    3
  SOX7 WILD-TYPE  465   35
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0           17            465
  1            3             35
[1] 2 2
[1] FALSE
D378V7, binary
                cls
clus               0   1
  SOX7 MUTATED     9  11
  SOX7 WILD-TYPE 163 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      9   11
  SOX7 WILD-TYPE  163  395
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  FEMALE            9            163
  MALE             11            395
[1] 2 2
[1] FALSE
D378V8, binary
                cls
clus               0   1
  SOX7 MUTATED    14   2
  SOX7 WILD-TYPE 402 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     14    2
  SOX7 WILD-TYPE  402  100
     clus
vv    SOX7 MUTATED SOX7 WILD-TYPE
  NO            14            402
  YES            2            100
[1] 2 2
[1] FALSE
D378V9, continuous
[1] "Remove cluster labels:" "SOX7 MUTATED"          
clus
  SOX7 MUTATED SOX7 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
D378V10, continuous
[1] "Remove cluster labels:" "SOX7 MUTATED"          
clus
  SOX7 MUTATED SOX7 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" "SOX7 WILD-TYPE" 
    TCGA-Z6-AAPN 
"SOX7 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SOX7 MUTATED       6                         0
  SOX7 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOX7 MUTATED                                           0     9
  SOX7 WILD-TYPE                                         1   348
D378V11, multiclass
                                           clus
vv                                          SOX7 MUTATED SOX7 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V12, binary
                cls
clus               0   1
  SOX7 MUTATED     0  15
  SOX7 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      0   15
  SOX7 WILD-TYPE   10  383
                        clus
vv                       SOX7 MUTATED SOX7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(379) Variable = HCRTR2 MUTATION ANALYSIS
D379V1, survival
                  sevent
clus2                0   1
  HCRTR2 MUTATED     7   7
  HCRTR2 WILD-TYPE 331 209
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
              14              540 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              209 
$`HCRTR2 MUTATED`
TCGA-2H-A9GJ TCGA-IG-A4P3 TCGA-LN-A49S TCGA-LN-A49Y TCGA-R6-A6XQ TCGA-VR-A8EU 
       58.55        18.64        13.15        12.46         6.35        18.31 
TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8366 TCGA-CD-A4MG TCGA-CG-4466 
        9.34        29.59         0.26         0.95         6.58        18.97 
TCGA-HF-A5NB TCGA-HU-A4GX 
       30.51        20.25 

$`HCRTR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04        38.40        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       31.10        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
            0.26             0.00 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           58.55           122.30 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
          15.730           13.565 
[1] "0.3 - 58.5 (15.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D379V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HCRTR2 MUTATED         1        0        2        0         4         2
  HCRTR2 WILD-TYPE       9       20       44       31        80        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR2 MUTATED           0          0          0          2        1
  HCRTR2 WILD-TYPE        29         84         62         37       42
                  vv
clus               STAGE IVA
  HCRTR2 MUTATED           0
  HCRTR2 WILD-TYPE         4
D379V3, multiclass
            clus
vv           HCRTR2 MUTATED HCRTR2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HCRTR2 MUTATED       2   3   4   3
  HCRTR2 WILD-TYPE    52 132 257  99
D379V4, multiclass
       clus
vv      HCRTR2 MUTATED HCRTR2 WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HCRTR2 MUTATED     8   3   1   1
  HCRTR2 WILD-TYPE 187 170  88  84
D379V5, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  N0              8              187
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V6, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED    12   1
  HCRTR2 WILD-TYPE 470  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED     12    1
  HCRTR2 WILD-TYPE  470   37
   clus
vv  HCRTR2 MUTATED HCRTR2 WILD-TYPE
  0             12              470
  1              1               37
[1] 2 2
[1] FALSE
D379V7, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   8
  HCRTR2 WILD-TYPE 166 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    8
  HCRTR2 WILD-TYPE  166  398
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  FEMALE              6              166
  MALE                8              398
[1] 2 2
[1] FALSE
D379V8, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED    10   4
  HCRTR2 WILD-TYPE 406  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED     10    4
  HCRTR2 WILD-TYPE  406   98
     clus
vv    HCRTR2 MUTATED HCRTR2 WILD-TYPE
  NO              10              406
  YES              4               98
[1] 2 2
[1] FALSE
D379V9, continuous
D379V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HCRTR2 MUTATED       4                         0
  HCRTR2 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HCRTR2 MUTATED                                           0     7
  HCRTR2 WILD-TYPE                                         1   350
D379V11, multiclass
                                           clus
vv                                          HCRTR2 MUTATED HCRTR2 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V12, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     0  10
  HCRTR2 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      0   10
  HCRTR2 WILD-TYPE   10  388
                        clus
vv                       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(380) Variable = LARP1B MUTATION ANALYSIS
D380V1, survival
                  sevent
clus2                0   1
  LARP1B MUTATED     5   9
  LARP1B WILD-TYPE 333 207
  LARP1B MUTATED LARP1B WILD-TYPE 
              14              540 
  LARP1B MUTATED LARP1B WILD-TYPE 
               9              207 
$`LARP1B MUTATED`
TCGA-L5-A4OW TCGA-R6-A6DN TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8363 TCGA-CD-A4MG 
        7.13         8.02         6.97         6.61         0.26         6.58 
TCGA-CD-A4MI TCGA-CG-5733 TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-A4G8 TCGA-HU-A4GQ 
       11.77        21.07        77.29         1.51        22.68         0.10 
TCGA-HU-A4H5 TCGA-VQ-A8P2 
       23.80        38.14 

$`LARP1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        6.21        63.06        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LARP1B MUTATED LARP1B WILD-TYPE 
             0.1              0.0 
  LARP1B MUTATED LARP1B WILD-TYPE 
           77.29           122.30 
  LARP1B MUTATED LARP1B WILD-TYPE 
           7.575           13.730 
[1] "0.1 - 77.3 (7.6)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "2"  
D380V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP1B MUTATED         0        0        2        1         1         2
  LARP1B WILD-TYPE      10       20       44       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP1B MUTATED           1          4          0          1        0
  LARP1B WILD-TYPE        28         80         62         38       43
                  vv
clus               STAGE IVA
  LARP1B MUTATED           0
  LARP1B WILD-TYPE         4
D380V3, multiclass
            clus
vv           LARP1B MUTATED LARP1B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  LARP1B MUTATED       0   6   5   2
  LARP1B WILD-TYPE    54 129 256 100
D380V4, multiclass
       clus
vv      LARP1B MUTATED LARP1B WILD-TYPE
  T0+T1              0               54
  T2                 6              129
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LARP1B MUTATED     3   7   3   0
  LARP1B WILD-TYPE 192 166  86  85
D380V5, multiclass
    clus
vv   LARP1B MUTATED LARP1B WILD-TYPE
  N0              3              192
  N1              7              166
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V6, binary
                  cls
clus                 0   1
  LARP1B MUTATED    12   0
  LARP1B WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED     12    0
  LARP1B WILD-TYPE  470   38
   clus
vv  LARP1B MUTATED LARP1B WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D380V7, binary
                  cls
clus                 0   1
  LARP1B MUTATED     5   9
  LARP1B WILD-TYPE 167 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      5    9
  LARP1B WILD-TYPE  167  397
        clus
vv       LARP1B MUTATED LARP1B WILD-TYPE
  FEMALE              5              167
  MALE                9              397
[1] 2 2
[1] FALSE
D380V8, binary
                  cls
clus                 0   1
  LARP1B MUTATED    11   2
  LARP1B WILD-TYPE 405 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED     11    2
  LARP1B WILD-TYPE  405  100
     clus
vv    LARP1B MUTATED LARP1B WILD-TYPE
  NO              11              405
  YES              2              100
[1] 2 2
[1] FALSE
D380V9, continuous
D380V10, continuous
[1] "Remove cluster labels:" "LARP1B MUTATED"        
clus
  LARP1B MUTATED LARP1B WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OX 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6L4 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LARP1B MUTATED       6                         0
  LARP1B WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP1B MUTATED                                           0     5
  LARP1B WILD-TYPE                                         1   352
D380V11, multiclass
                                           clus
vv                                          LARP1B MUTATED LARP1B WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V12, binary
                  cls
clus                 0   1
  LARP1B MUTATED     0  10
  LARP1B WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      0   10
  LARP1B WILD-TYPE   10  388
                        clus
vv                       LARP1B MUTATED LARP1B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(381) Variable = C17ORF57 MUTATION ANALYSIS
D381V1, survival
                    sevent
clus2                  0   1
  C17ORF57 MUTATED    11   2
  C17ORF57 WILD-TYPE 327 214
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                13                541 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                 2                214 
$`C17ORF57 MUTATED`
TCGA-IG-A97H TCGA-L5-A8NK TCGA-L5-A8NM TCGA-LN-A49M TCGA-B7-A5TI TCGA-BR-4184 
       14.50        13.55         7.76        12.66        19.56         6.97 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-A4GT 
       31.10         1.12        31.96         6.02        30.51         6.51 
TCGA-VQ-A8P2 
       38.14 

$`C17ORF57 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        12.92        13.48        16.47        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
              1.12               0.00 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
             38.14             122.30 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
             13.55              13.58 
[1] "1.1 - 38.1 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D381V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C17ORF57 MUTATED         0        1        0        0         5         1
  C17ORF57 WILD-TYPE      10       19       46       31        79        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF57 MUTATED           0          2          0          3        2
  C17ORF57 WILD-TYPE        29         82         62         36       41
                    vv
clus                 STAGE IVA
  C17ORF57 MUTATED           0
  C17ORF57 WILD-TYPE         4
D381V3, multiclass
            clus
vv           C17ORF57 MUTATED C17ORF57 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 5                 79
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C17ORF57 MUTATED       1   2   5   6
  C17ORF57 WILD-TYPE    53 133 256  96
D381V4, multiclass
       clus
vv      C17ORF57 MUTATED C17ORF57 WILD-TYPE
  T0+T1                1                 53
  T2                   2                133
  T3                   5                256
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C17ORF57 MUTATED     5   5   2   2
  C17ORF57 WILD-TYPE 190 168  87  83
D381V5, multiclass
    clus
vv   C17ORF57 MUTATED C17ORF57 WILD-TYPE
  N0                5                190
  N1                5                168
  N2                2                 87
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V6, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED    14   1
  C17ORF57 WILD-TYPE 468  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED     14    1
  C17ORF57 WILD-TYPE  468   37
   clus
vv  C17ORF57 MUTATED C17ORF57 WILD-TYPE
  0               14                468
  1                1                 37
[1] 2 2
[1] FALSE
D381V7, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     8   8
  C17ORF57 WILD-TYPE 164 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      8    8
  C17ORF57 WILD-TYPE  164  398
        clus
vv       C17ORF57 MUTATED C17ORF57 WILD-TYPE
  FEMALE                8                164
  MALE                  8                398
[1] 2 2
[1] FALSE
D381V8, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     8   4
  C17ORF57 WILD-TYPE 408  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      8    4
  C17ORF57 WILD-TYPE  408   98
     clus
vv    C17ORF57 MUTATED C17ORF57 WILD-TYPE
  NO                 8                408
  YES                4                 98
[1] 2 2
[1] FALSE
D381V9, continuous
[1] "Remove cluster labels:" "C17ORF57 MUTATED"      
clus
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-Z6-A8JE 
"C17ORF57 WILD-TYPE" 
D381V10, continuous
[1] "Remove cluster labels:" "C17ORF57 MUTATED"      
clus
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-JY-A6FA         TCGA-JY-A6FE 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" "C17ORF57 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C17ORF57 MUTATED       5                         0
  C17ORF57 WILD-TYPE   128                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C17ORF57 MUTATED                                           0     9
  C17ORF57 WILD-TYPE                                         1   348
D381V11, multiclass
                                           clus
vv                                          C17ORF57 MUTATED C17ORF57 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V12, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     0  11
  C17ORF57 WILD-TYPE  10 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      0   11
  C17ORF57 WILD-TYPE   10  387
                        clus
vv                       C17ORF57 MUTATED C17ORF57 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                387
[1] 2 2
[1] FALSE

Clustering(382) Variable = HAUS3 MUTATION ANALYSIS
D382V1, survival
                 sevent
clus2               0   1
  HAUS3 MUTATED     6   6
  HAUS3 WILD-TYPE 332 210
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             12             542 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              6             210 
$`HAUS3 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GO TCGA-L5-A8NM TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-8363 
       21.99        16.24         7.76        18.35        34.68         0.26 
TCGA-CD-5813 TCGA-CG-5721 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-R5-A7ZI 
       12.39         6.02         6.51         6.58        19.73        74.53 

$`HAUS3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  HAUS3 MUTATED HAUS3 WILD-TYPE 
           0.26            0.00 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          74.53          122.30 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
         14.315          13.565 
[1] "0.3 - 74.5 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D382V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAUS3 MUTATED         1        0        1        1         2         2
  HAUS3 WILD-TYPE       9       20       45       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS3 MUTATED           0          1          0          0        3         1
  HAUS3 WILD-TYPE        29         83         62         39       40         3
D382V3, multiclass
            clus
vv           HAUS3 MUTATED HAUS3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HAUS3 MUTATED       1   2   6   3
  HAUS3 WILD-TYPE    53 133 255  99
D382V4, multiclass
       clus
vv      HAUS3 MUTATED HAUS3 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HAUS3 MUTATED     4   8   1   0
  HAUS3 WILD-TYPE 191 165  88  85
D382V5, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  N0             4             191
  N1             8             165
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V6, binary
                 cls
clus                0   1
  HAUS3 MUTATED     9   3
  HAUS3 WILD-TYPE 473  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      9    3
  HAUS3 WILD-TYPE  473   35
   clus
vv  HAUS3 MUTATED HAUS3 WILD-TYPE
  0             9             473
  1             3              35
[1] 2 2
[1] FALSE
D382V7, binary
                 cls
clus                0   1
  HAUS3 MUTATED     7   6
  HAUS3 WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      7    6
  HAUS3 WILD-TYPE  165  400
        clus
vv       HAUS3 MUTATED HAUS3 WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D382V8, binary
                 cls
clus                0   1
  HAUS3 MUTATED    13   0
  HAUS3 WILD-TYPE 403 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED     13    0
  HAUS3 WILD-TYPE  403  102
     clus
vv    HAUS3 MUTATED HAUS3 WILD-TYPE
  NO             13             403
  YES             0             102
[1] 2 2
[1] FALSE
D382V9, continuous
D382V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HAUS3 MUTATED       3                         1
  HAUS3 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAUS3 MUTATED                                           0     6
  HAUS3 WILD-TYPE                                         1   351
D382V11, multiclass
                                           clus
vv                                          HAUS3 MUTATED HAUS3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V12, binary
                 cls
clus                0   1
  HAUS3 MUTATED     1   8
  HAUS3 WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      1    8
  HAUS3 WILD-TYPE    9  390
                        clus
vv                       HAUS3 MUTATED HAUS3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(383) Variable = EHMT2 MUTATION ANALYSIS
D383V1, survival
                 sevent
clus2               0   1
  EHMT2 MUTATED    16   6
  EHMT2 WILD-TYPE 322 210
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             22             532 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              6             210 
$`EHMT2 MUTATED`
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NR TCGA-R6-A6XQ TCGA-BR-4184 TCGA-BR-4201 
        3.75        13.48         8.71         6.35         6.97        30.90 
TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 TCGA-CD-8525 TCGA-CG-5721 
       36.16        29.59        31.10        28.14        12.59         6.02 
TCGA-D7-8578 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GX 
       21.14        30.51        22.68        24.20         8.98        20.25 
TCGA-HU-A4H2 TCGA-R5-A7ZF TCGA-VQ-A8PK TCGA-VQ-AA68 
       12.95         8.52        17.85        43.66 

$`EHMT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.26         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.58         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM 
       43.36        37.41        38.14        37.22        22.19         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EHMT2 MUTATED EHMT2 WILD-TYPE 
           3.75            0.00 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
          43.66          122.30 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
          19.05           13.53 
[1] "3.8 - 43.7 (19.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D383V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EHMT2 MUTATED         0        2        1        0         1         2
  EHMT2 WILD-TYPE      10       18       45       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EHMT2 MUTATED           2          2          2          5        2         0
  EHMT2 WILD-TYPE        27         82         60         34       41         4
D383V3, multiclass
            clus
vv           EHMT2 MUTATED EHMT2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             5              34
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EHMT2 MUTATED       2   3   8   8
  EHMT2 WILD-TYPE    52 132 253  94
D383V4, multiclass
       clus
vv      EHMT2 MUTATED EHMT2 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                8             253
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EHMT2 MUTATED     4   9   2   5
  EHMT2 WILD-TYPE 191 164  87  80
D383V5, multiclass
    clus
vv   EHMT2 MUTATED EHMT2 WILD-TYPE
  N0             4             191
  N1             9             164
  N2             2              87
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V6, binary
                 cls
clus                0   1
  EHMT2 MUTATED    20   1
  EHMT2 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     20    1
  EHMT2 WILD-TYPE  462   37
   clus
vv  EHMT2 MUTATED EHMT2 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D383V7, binary
                 cls
clus                0   1
  EHMT2 MUTATED    13  10
  EHMT2 WILD-TYPE 159 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     13   10
  EHMT2 WILD-TYPE  159  396
        clus
vv       EHMT2 MUTATED EHMT2 WILD-TYPE
  FEMALE            13             159
  MALE              10             396
[1] 2 2
[1] FALSE
D383V8, binary
                 cls
clus                0   1
  EHMT2 MUTATED    18   3
  EHMT2 WILD-TYPE 398  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     18    3
  EHMT2 WILD-TYPE  398   99
     clus
vv    EHMT2 MUTATED EHMT2 WILD-TYPE
  NO             18             398
  YES             3              99
[1] 2 2
[1] FALSE
D383V9, continuous
D383V10, continuous
[1] "Remove cluster labels:" "EHMT2 MUTATED"         
clus
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EHMT2 MUTATED       6                         1
  EHMT2 WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EHMT2 MUTATED                                           0    13
  EHMT2 WILD-TYPE                                         1   344
D383V11, multiclass
                                           clus
vv                                          EHMT2 MUTATED EHMT2 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V12, binary
                 cls
clus                0   1
  EHMT2 MUTATED     0  16
  EHMT2 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      0   16
  EHMT2 WILD-TYPE   10  382
                        clus
vv                       EHMT2 MUTATED EHMT2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(384) Variable = PLEKHA5 MUTATION ANALYSIS
D384V1, survival
                   sevent
clus2                 0   1
  PLEKHA5 MUTATED    16   5
  PLEKHA5 WILD-TYPE 322 211
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               21               533 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
                5               211 
$`PLEKHA5 MUTATED`
TCGA-L5-A4OI TCGA-LN-A4A4 TCGA-LN-A7HY TCGA-LN-A9FR TCGA-BR-4184 TCGA-BR-4257 
       19.99        12.59        12.03        12.26         6.97         9.67 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ 
        0.26        31.27        27.12        28.14        16.14        12.62 
TCGA-CG-4305 TCGA-CG-5723 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4H4 
       15.95       105.07        11.44        14.47        29.98        23.84 
TCGA-HU-A4H8 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       14.07        37.41        38.14 

$`PLEKHA5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
             0.26              0.00 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
           105.07            122.30 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
            15.95             13.51 
[1] "0.3 - 105.1 (15.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D384V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA5 MUTATED         1        0        4        2         1         2
  PLEKHA5 WILD-TYPE       9       20       42       29        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA5 MUTATED           2          2          3          3        1
  PLEKHA5 WILD-TYPE        27         82         59         36       42
                   vv
clus                STAGE IVA
  PLEKHA5 MUTATED           0
  PLEKHA5 WILD-TYPE         4
D384V3, multiclass
            clus
vv           PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 2                29
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                2                27
  STAGE IIIA               2                82
  STAGE IIIB               3                59
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PLEKHA5 MUTATED       2   8   7   4
  PLEKHA5 WILD-TYPE    52 127 254  98
D384V4, multiclass
       clus
vv      PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  T0+T1               2                52
  T2                  8               127
  T3                  7               254
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PLEKHA5 MUTATED     3  12   1   5
  PLEKHA5 WILD-TYPE 192 161  88  80
D384V5, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  N0               3               192
  N1              12               161
  N2               1                88
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V6, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED    19   1
  PLEKHA5 WILD-TYPE 463  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED     19    1
  PLEKHA5 WILD-TYPE  463   37
   clus
vv  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  0              19               463
  1               1                37
[1] 2 2
[1] FALSE
D384V7, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     6  17
  PLEKHA5 WILD-TYPE 166 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      6   17
  PLEKHA5 WILD-TYPE  166  389
        clus
vv       PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  FEMALE               6               166
  MALE                17               389
[1] 2 2
[1] FALSE
D384V8, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED    19   3
  PLEKHA5 WILD-TYPE 397  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED     19    3
  PLEKHA5 WILD-TYPE  397   99
     clus
vv    PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  NO               19               397
  YES               3                99
[1] 2 2
[1] FALSE
D384V9, continuous
[1] "Remove cluster labels:" "PLEKHA5 MUTATED"       
clus
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A5        TCGA-LN-A4A6 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-V5-A7RB 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-V5-AASW 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
D384V10, continuous
[1] "Remove cluster labels:" "PLEKHA5 MUTATED"       
clus
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" "PLEKHA5 WILD-TYPE" 
       TCGA-Z6-AAPN 
"PLEKHA5 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHA5 MUTATED       7                         1
  PLEKHA5 WILD-TYPE   126                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHA5 MUTATED                                           0    13
  PLEKHA5 WILD-TYPE                                         1   344
D384V11, multiclass
                                           clus
vv                                          PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V12, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     0  18
  PLEKHA5 WILD-TYPE  10 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      0   18
  PLEKHA5 WILD-TYPE   10  380
                        clus
vv                       PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(385) Variable = ALG10 MUTATION ANALYSIS
D385V1, survival
                 sevent
clus2               0   1
  ALG10 MUTATED     8   8
  ALG10 WILD-TYPE 330 208
  ALG10 MUTATED ALG10 WILD-TYPE 
             16             538 
  ALG10 MUTATED ALG10 WILD-TYPE 
              8             208 
$`ALG10 MUTATED`
TCGA-L5-A4OF TCGA-LN-A4A3 TCGA-VR-AA4G TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4201 
       26.33        12.76        18.05         6.61         6.97        30.90 
TCGA-BR-6452 TCGA-BR-6455 TCGA-CD-A4MI TCGA-CG-5726 TCGA-D7-6818 TCGA-D7-A4YY 
       34.68        13.87        11.77        28.96        12.36        13.78 
TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-VQ-AA6A 
       22.32         6.58        29.00        38.93 

$`ALG10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.47         9.44         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57         6.61        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ALG10 MUTATED ALG10 WILD-TYPE 
           6.58            0.00 
  ALG10 MUTATED ALG10 WILD-TYPE 
          38.93          122.30 
  ALG10 MUTATED ALG10 WILD-TYPE 
          15.96           13.51 
[1] "6.6 - 38.9 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D385V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALG10 MUTATED         0        1        0        0         1         5
  ALG10 WILD-TYPE      10       19       46       31        83        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALG10 MUTATED           1          5          1          2        0         0
  ALG10 WILD-TYPE        28         79         61         37       43         4
D385V3, multiclass
            clus
vv           ALG10 MUTATED ALG10 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ALG10 MUTATED       2   3   8   4
  ALG10 WILD-TYPE    52 132 253  98
D385V4, multiclass
       clus
vv      ALG10 MUTATED ALG10 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ALG10 MUTATED     4   7   1   4
  ALG10 WILD-TYPE 191 166  88  81
D385V5, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  N0             4             191
  N1             7             166
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V6, binary
                 cls
clus                0   1
  ALG10 MUTATED    15   0
  ALG10 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED     15    0
  ALG10 WILD-TYPE  467   38
   clus
vv  ALG10 MUTATED ALG10 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D385V7, binary
                 cls
clus                0   1
  ALG10 MUTATED     6  11
  ALG10 WILD-TYPE 166 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      6   11
  ALG10 WILD-TYPE  166  395
        clus
vv       ALG10 MUTATED ALG10 WILD-TYPE
  FEMALE             6             166
  MALE              11             395
[1] 2 2
[1] FALSE
D385V8, binary
                 cls
clus                0   1
  ALG10 MUTATED    11   4
  ALG10 WILD-TYPE 405  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED     11    4
  ALG10 WILD-TYPE  405   98
     clus
vv    ALG10 MUTATED ALG10 WILD-TYPE
  NO             11             405
  YES             4              98
[1] 2 2
[1] FALSE
D385V9, continuous
[1] "Remove cluster labels:" "ALG10 MUTATED"         
clus
  ALG10 MUTATED ALG10 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
D385V10, continuous
[1] "Remove cluster labels:" "ALG10 MUTATED"         
clus
  ALG10 MUTATED ALG10 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A6 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" "ALG10 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALG10 MUTATED       5                         0
  ALG10 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALG10 MUTATED                                           0    11
  ALG10 WILD-TYPE                                         1   346
D385V11, multiclass
                                           clus
vv                                          ALG10 MUTATED ALG10 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V12, binary
                 cls
clus                0   1
  ALG10 MUTATED     0  13
  ALG10 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      0   13
  ALG10 WILD-TYPE   10  385
                        clus
vv                       ALG10 MUTATED ALG10 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(386) Variable = NAA16 MUTATION ANALYSIS
D386V1, survival
                 sevent
clus2               0   1
  NAA16 MUTATED    10   5
  NAA16 WILD-TYPE 328 211
  NAA16 MUTATED NAA16 WILD-TYPE 
             15             539 
  NAA16 MUTATED NAA16 WILD-TYPE 
              5             211 
$`NAA16 MUTATED`
TCGA-L5-A88T TCGA-IC-A6RE TCGA-L5-A4OX TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-VR-A8ER 
       22.82         7.69         7.43        12.33         7.82        12.43 
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 
       26.70         9.67        34.68        31.96        16.14         1.02 
TCGA-CG-4449 TCGA-CG-5723 TCGA-VQ-A8P2 
       19.07       105.07        38.14 

$`NAA16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26        33.11         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        22.82         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NAA16 MUTATED NAA16 WILD-TYPE 
           1.02            0.00 
  NAA16 MUTATED NAA16 WILD-TYPE 
         105.07          122.30 
  NAA16 MUTATED NAA16 WILD-TYPE 
          16.14           13.55 
[1] "1.0 - 105.1 (16.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D386V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA16 MUTATED         0        0        0        2         1         5
  NAA16 WILD-TYPE      10       20       46       29        83        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA16 MUTATED           1          1          2          0        2         0
  NAA16 WILD-TYPE        28         83         60         39       41         4
D386V3, multiclass
            clus
vv           NAA16 MUTATED NAA16 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NAA16 MUTATED       1   5   4   4
  NAA16 WILD-TYPE    53 130 257  98
D386V4, multiclass
       clus
vv      NAA16 MUTATED NAA16 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                4             257
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NAA16 MUTATED     2   8   3   1
  NAA16 WILD-TYPE 193 165  86  84
D386V5, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  N0             2             193
  N1             8             165
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V6, binary
                 cls
clus                0   1
  NAA16 MUTATED    13   2
  NAA16 WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED     13    2
  NAA16 WILD-TYPE  469   36
   clus
vv  NAA16 MUTATED NAA16 WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D386V7, binary
                 cls
clus                0   1
  NAA16 MUTATED     4  11
  NAA16 WILD-TYPE 168 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      4   11
  NAA16 WILD-TYPE  168  395
        clus
vv       NAA16 MUTATED NAA16 WILD-TYPE
  FEMALE             4             168
  MALE              11             395
[1] 2 2
[1] FALSE
D386V8, binary
                 cls
clus                0   1
  NAA16 MUTATED    11   3
  NAA16 WILD-TYPE 405  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED     11    3
  NAA16 WILD-TYPE  405   99
     clus
vv    NAA16 MUTATED NAA16 WILD-TYPE
  NO             11             405
  YES             3              99
[1] 2 2
[1] FALSE
D386V9, continuous
[1] "Remove cluster labels:" "NAA16 MUTATED"         
clus
  NAA16 MUTATED NAA16 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NAA16 WILD-TYPE" "NAA16 WILD-TYPE" 
D386V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAA16 MUTATED       2                         0
  NAA16 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAA16 MUTATED                                           0     9
  NAA16 WILD-TYPE                                         1   348
D386V11, multiclass
                                           clus
vv                                          NAA16 MUTATED NAA16 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V12, binary
                 cls
clus                0   1
  NAA16 MUTATED     0   8
  NAA16 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      0    8
  NAA16 WILD-TYPE   10  390
                        clus
vv                       NAA16 MUTATED NAA16 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(387) Variable = C6ORF150 MUTATION ANALYSIS
D387V1, survival
                    sevent
clus2                  0   1
  C6ORF150 MUTATED     6   1
  C6ORF150 WILD-TYPE 332 215
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 7                547 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 1                215 
$`C6ORF150 MUTATED`
TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-8487 TCGA-BR-8680 TCGA-HU-A4GU TCGA-IN-A7NT 
        9.44         9.67         1.12        31.96         6.58        10.62 
TCGA-SW-A7EA 
       19.04 

$`C6ORF150 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
              1.12               0.00 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
             31.96             122.30 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
              9.67              13.68 
[1] "1.1 - 32.0 (9.7)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "2"  
D387V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C6ORF150 MUTATED         0        0        1        0         1         3
  C6ORF150 WILD-TYPE      10       20       45       31        83        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF150 MUTATED           0          1          0          0        1
  C6ORF150 WILD-TYPE        29         83         62         39       42
                    vv
clus                 STAGE IVA
  C6ORF150 MUTATED           0
  C6ORF150 WILD-TYPE         4
D387V3, multiclass
            clus
vv           C6ORF150 MUTATED C6ORF150 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C6ORF150 MUTATED       0   1   3   3
  C6ORF150 WILD-TYPE    54 134 258  99
D387V4, multiclass
       clus
vv      C6ORF150 MUTATED C6ORF150 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   3                258
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C6ORF150 MUTATED     3   2   1   0
  C6ORF150 WILD-TYPE 192 171  88  85
D387V5, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V6, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     7   1
  C6ORF150 WILD-TYPE 475  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      7    1
  C6ORF150 WILD-TYPE  475   37
   clus
vv  C6ORF150 MUTATED C6ORF150 WILD-TYPE
  0                7                475
  1                1                 37
[1] 2 2
[1] FALSE
D387V7, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     5   3
  C6ORF150 WILD-TYPE 167 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      5    3
  C6ORF150 WILD-TYPE  167  403
        clus
vv       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  FEMALE                5                167
  MALE                  3                403
[1] 2 2
[1] FALSE
D387V8, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     7   0
  C6ORF150 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      7    0
  C6ORF150 WILD-TYPE  409  102
     clus
vv    C6ORF150 MUTATED C6ORF150 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D387V9, continuous
D387V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C6ORF150 MUTATED       2                         0
  C6ORF150 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6ORF150 MUTATED                                           0     6
  C6ORF150 WILD-TYPE                                         1   351
D387V11, multiclass
                                           clus
vv                                          C6ORF150 MUTATED C6ORF150 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V12, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     0   8
  C6ORF150 WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      0    8
  C6ORF150 WILD-TYPE   10  390
                        clus
vv                       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(388) Variable = SLC7A10 MUTATION ANALYSIS
D388V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     4   0
  SLC7A10 WILD-TYPE 334 216
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                4               550 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                0               216 
$`SLC7A10 MUTATED`
TCGA-CD-8536 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-7132 
       12.43         6.02        11.08        77.29 

$`SLC7A10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
             6.02              0.00 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            77.29            122.30 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
           11.755            13.630 
[1] "6.0 - 77.3 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr="     "3400000"
D388V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC7A10 MUTATED         0        0        0        2         1         1
  SLC7A10 WILD-TYPE      10       20       46       29        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          1        1
  SLC7A10 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  SLC7A10 MUTATED           0
  SLC7A10 WILD-TYPE         4
D388V3, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 2                29
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC7A10 MUTATED       0   1   2   3
  SLC7A10 WILD-TYPE    54 134 259  99
D388V4, multiclass
       clus
vv      SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC7A10 MUTATED     3   2   0   1
  SLC7A10 WILD-TYPE 192 171  89  84
D388V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               3               192
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V6, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     6   0
  SLC7A10 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      6    0
  SLC7A10 WILD-TYPE  476   38
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D388V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     1   5
  SLC7A10 WILD-TYPE 171 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      1    5
  SLC7A10 WILD-TYPE  171  401
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               1               171
  MALE                 5               401
[1] 2 2
[1] FALSE
D388V8, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     4   2
  SLC7A10 WILD-TYPE 412 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      4    2
  SLC7A10 WILD-TYPE  412  100
     clus
vv    SLC7A10 MUTATED SLC7A10 WILD-TYPE
  NO                4               412
  YES               2               100
[1] 2 2
[1] FALSE
D388V9, continuous
D388V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC7A10 MUTATED       1                         1
  SLC7A10 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC7A10 MUTATED                                           0     2
  SLC7A10 WILD-TYPE                                         1   355
D388V11, multiclass
                                           clus
vv                                          SLC7A10 MUTATED SLC7A10 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V12, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     0   4
  SLC7A10 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      0    4
  SLC7A10 WILD-TYPE   10  394
                        clus
vv                       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(389) Variable = KIF21A MUTATION ANALYSIS
D389V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    14   8
  KIF21A WILD-TYPE 324 208
  KIF21A MUTATED KIF21A WILD-TYPE 
              22              532 
  KIF21A MUTATED KIF21A WILD-TYPE 
               8              208 
$`KIF21A MUTATED`
TCGA-L5-A4OI TCGA-IG-A97H TCGA-L5-A4ON TCGA-L5-A8NQ TCGA-RE-A7BO TCGA-VR-AA7B 
       19.99        14.50        18.35        21.37         7.00        11.24 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-8531 
        6.97        34.68        29.59         0.26        31.96        12.59 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4305 TCGA-HU-8238 TCGA-HU-A4G8 TCGA-HU-A4GQ 
        6.58        11.77        15.95         1.51        22.68         0.10 
TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       20.25        23.84        19.73        38.14 

$`KIF21A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       77.29        63.06        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KIF21A MUTATED KIF21A WILD-TYPE 
             0.1              0.0 
  KIF21A MUTATED KIF21A WILD-TYPE 
           38.14           122.30 
  KIF21A MUTATED KIF21A WILD-TYPE 
           17.15            13.51 
[1] "0.1 - 38.1 (17.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D389V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF21A MUTATED         0        0        1        1         4         6
  KIF21A WILD-TYPE      10       20       45       30        80        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21A MUTATED           0          6          0          3        2
  KIF21A WILD-TYPE        29         78         62         36       41
                  vv
clus               STAGE IVA
  KIF21A MUTATED           0
  KIF21A WILD-TYPE         4
D389V3, multiclass
            clus
vv           KIF21A MUTATED KIF21A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               6               77
  STAGE III               0               29
  STAGE IIIA              6               78
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KIF21A MUTATED       2   4  11   7
  KIF21A WILD-TYPE    52 131 250  95
D389V4, multiclass
       clus
vv      KIF21A MUTATED KIF21A WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                11              250
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KIF21A MUTATED     7   8   6   2
  KIF21A WILD-TYPE 188 165  83  83
D389V5, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  N0              7              188
  N1              8              165
  N2              6               83
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V6, binary
                  cls
clus                 0   1
  KIF21A MUTATED    19   2
  KIF21A WILD-TYPE 463  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     19    2
  KIF21A WILD-TYPE  463   36
   clus
vv  KIF21A MUTATED KIF21A WILD-TYPE
  0             19              463
  1              2               36
[1] 2 2
[1] FALSE
D389V7, binary
                  cls
clus                 0   1
  KIF21A MUTATED    11  13
  KIF21A WILD-TYPE 161 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     11   13
  KIF21A WILD-TYPE  161  393
        clus
vv       KIF21A MUTATED KIF21A WILD-TYPE
  FEMALE             11              161
  MALE               13              393
[1] 2 2
[1] FALSE
D389V8, binary
                  cls
clus                 0   1
  KIF21A MUTATED    19   2
  KIF21A WILD-TYPE 397 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     19    2
  KIF21A WILD-TYPE  397  100
     clus
vv    KIF21A MUTATED KIF21A WILD-TYPE
  NO              19              397
  YES              2              100
[1] 2 2
[1] FALSE
D389V9, continuous
[1] "Remove cluster labels:" "KIF21A MUTATED"        
clus
  KIF21A MUTATED KIF21A WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KIF21A WILD-TYPE" "KIF21A WILD-TYPE" "KIF21A WILD-TYPE" 
D389V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF21A MUTATED      10                         0
  KIF21A WILD-TYPE   123                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF21A MUTATED                                           0    13
  KIF21A WILD-TYPE                                         1   344
D389V11, multiclass
                                           clus
vv                                          KIF21A MUTATED KIF21A WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V12, binary
                  cls
clus                 0   1
  KIF21A MUTATED     0  18
  KIF21A WILD-TYPE  10 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED      0   18
  KIF21A WILD-TYPE   10  380
                        clus
vv                       KIF21A MUTATED KIF21A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(390) Variable = GPR82 MUTATION ANALYSIS
D390V1, survival
                 sevent
clus2               0   1
  GPR82 MUTATED     7   2
  GPR82 WILD-TYPE 331 214
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             545 
  GPR82 MUTATED GPR82 WILD-TYPE 
              2             214 
$`GPR82 MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-5728 
       34.68        25.05        31.96         6.58        12.62        65.10 
TCGA-HF-7132 TCGA-HU-A4GH TCGA-HU-A4GU 
       77.29        11.77         6.58 

$`GPR82 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GPR82 MUTATED GPR82 WILD-TYPE 
           6.58            0.00 
  GPR82 MUTATED GPR82 WILD-TYPE 
          77.29          122.30 
  GPR82 MUTATED GPR82 WILD-TYPE 
          25.05           13.55 
[1] "6.6 - 77.3 (25.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.6"
D390V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR82 MUTATED         0        1        2        1         2         1
  GPR82 WILD-TYPE      10       19       44       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR82 MUTATED           0          0          0          1        1         0
  GPR82 WILD-TYPE        29         84         62         38       42         4
D390V3, multiclass
            clus
vv           GPR82 MUTATED GPR82 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GPR82 MUTATED       1   3   3   2
  GPR82 WILD-TYPE    53 132 258 100
D390V4, multiclass
       clus
vv      GPR82 MUTATED GPR82 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GPR82 MUTATED     5   2   1   1
  GPR82 WILD-TYPE 190 171  88  84
D390V5, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  N0             5             190
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V6, binary
                 cls
clus                0   1
  GPR82 MUTATED     8   1
  GPR82 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      8    1
  GPR82 WILD-TYPE  474   37
   clus
vv  GPR82 MUTATED GPR82 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D390V7, binary
                 cls
clus                0   1
  GPR82 MUTATED     3   6
  GPR82 WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      3    6
  GPR82 WILD-TYPE  169  400
        clus
vv       GPR82 MUTATED GPR82 WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D390V8, binary
                 cls
clus                0   1
  GPR82 MUTATED     7   1
  GPR82 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      7    1
  GPR82 WILD-TYPE  409  101
     clus
vv    GPR82 MUTATED GPR82 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D390V9, continuous
D390V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPR82 MUTATED       5                         0
  GPR82 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR82 MUTATED                                           0     2
  GPR82 WILD-TYPE                                         1   355
D390V11, multiclass
                                           clus
vv                                          GPR82 MUTATED GPR82 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V12, binary
                 cls
clus                0   1
  GPR82 MUTATED     0   7
  GPR82 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      0    7
  GPR82 WILD-TYPE   10  391
                        clus
vv                       GPR82 MUTATED GPR82 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(391) Variable = C14ORF50 MUTATION ANALYSIS
D391V1, survival
                    sevent
clus2                  0   1
  C14ORF50 MUTATED     3   5
  C14ORF50 WILD-TYPE 335 211
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                546 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 5                211 
$`C14ORF50 MUTATED`
TCGA-BR-4201 TCGA-BR-6709 TCGA-BR-8363 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5728 
       30.90        12.16         0.26        31.96         1.02        65.10 
TCGA-D7-A4YV TCGA-HU-A4GT 
        5.92         6.51 

$`C14ORF50 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
              0.26               0.00 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
              65.1              122.3 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
             9.335             13.630 
[1] "0.3 - 65.1 (9.3)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D391V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C14ORF50 MUTATED         0        0        2        0         1         1
  C14ORF50 WILD-TYPE      10       20       44       31        83        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF50 MUTATED           0          0          1          0        2
  C14ORF50 WILD-TYPE        29         84         61         39       41
                    vv
clus                 STAGE IVA
  C14ORF50 MUTATED           0
  C14ORF50 WILD-TYPE         4
D391V3, multiclass
            clus
vv           C14ORF50 MUTATED C14ORF50 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C14ORF50 MUTATED       0   3   4   1
  C14ORF50 WILD-TYPE    54 132 257 101
D391V4, multiclass
       clus
vv      C14ORF50 MUTATED C14ORF50 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   4                257
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C14ORF50 MUTATED     3   1   2   1
  C14ORF50 WILD-TYPE 192 172  87  84
D391V5, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  N0                3                192
  N1                1                172
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V6, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   2
  C14ORF50 WILD-TYPE 476  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    2
  C14ORF50 WILD-TYPE  476   36
   clus
vv  C14ORF50 MUTATED C14ORF50 WILD-TYPE
  0                6                476
  1                2                 36
[1] 2 2
[1] FALSE
D391V7, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   2
  C14ORF50 WILD-TYPE 166 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    2
  C14ORF50 WILD-TYPE  166  404
        clus
vv       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  FEMALE                6                166
  MALE                  2                404
[1] 2 2
[1] FALSE
D391V8, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   0
  C14ORF50 WILD-TYPE 410 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    0
  C14ORF50 WILD-TYPE  410  102
     clus
vv    C14ORF50 MUTATED C14ORF50 WILD-TYPE
  NO                 6                410
  YES                0                102
[1] 2 2
[1] FALSE
D391V9, continuous
D391V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C14ORF50 MUTATED       2                         0
  C14ORF50 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF50 MUTATED                                           0     4
  C14ORF50 WILD-TYPE                                         1   353
D391V11, multiclass
                                           clus
vv                                          C14ORF50 MUTATED C14ORF50 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V12, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     0   6
  C14ORF50 WILD-TYPE  10 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      0    6
  C14ORF50 WILD-TYPE   10  392
                        clus
vv                       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                6                392
[1] 2 2
[1] FALSE

Clustering(392) Variable = ELOVL2 MUTATION ANALYSIS
D392V1, survival
                  sevent
clus2                0   1
  ELOVL2 MUTATED     6   2
  ELOVL2 WILD-TYPE 332 214
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               8              546 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               2              214 
$`ELOVL2 MUTATED`
TCGA-L5-A4OI TCGA-VR-A8EO TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-CD-8535 
       19.99        25.81         6.97        34.68         0.26        12.82 
TCGA-D7-A4YY TCGA-HU-A4G2 
       13.78        24.30 

$`ELOVL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
            0.26             0.00 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
           34.68           122.30 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
          16.885           13.530 
[1] "0.3 - 34.7 (16.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D392V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELOVL2 MUTATED         0        0        1        0         2         1
  ELOVL2 WILD-TYPE      10       20       45       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELOVL2 MUTATED           0          3          1          1        0
  ELOVL2 WILD-TYPE        29         81         61         38       43
                  vv
clus               STAGE IVA
  ELOVL2 MUTATED           0
  ELOVL2 WILD-TYPE         4
D392V3, multiclass
            clus
vv           ELOVL2 MUTATED ELOVL2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ELOVL2 MUTATED       0   1   8   0
  ELOVL2 WILD-TYPE    54 134 253 102
D392V4, multiclass
       clus
vv      ELOVL2 MUTATED ELOVL2 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 8              253
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ELOVL2 MUTATED     3   4   0   2
  ELOVL2 WILD-TYPE 192 169  89  83
D392V5, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V6, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     7   0
  ELOVL2 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      7    0
  ELOVL2 WILD-TYPE  475   38
   clus
vv  ELOVL2 MUTATED ELOVL2 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D392V7, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     2   7
  ELOVL2 WILD-TYPE 170 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      2    7
  ELOVL2 WILD-TYPE  170  399
        clus
vv       ELOVL2 MUTATED ELOVL2 WILD-TYPE
  FEMALE              2              170
  MALE                7              399
[1] 2 2
[1] FALSE
D392V8, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     6   3
  ELOVL2 WILD-TYPE 410  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      6    3
  ELOVL2 WILD-TYPE  410   99
     clus
vv    ELOVL2 MUTATED ELOVL2 WILD-TYPE
  NO               6              410
  YES              3               99
[1] 2 2
[1] FALSE
D392V9, continuous
[1] "Remove cluster labels:" "ELOVL2 MUTATED"        
clus
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EP 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
D392V10, continuous
[1] "Remove cluster labels:" "ELOVL2 MUTATED"        
clus
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" "ELOVL2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ELOVL2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ELOVL2 MUTATED       2                         0
  ELOVL2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELOVL2 MUTATED                                           0     6
  ELOVL2 WILD-TYPE                                         1   351
D392V11, multiclass
                                           clus
vv                                          ELOVL2 MUTATED ELOVL2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V12, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     0   6
  ELOVL2 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      0    6
  ELOVL2 WILD-TYPE   10  392
                        clus
vv                       ELOVL2 MUTATED ELOVL2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(393) Variable = GPC4 MUTATION ANALYSIS
D393V1, survival
                sevent
clus2              0   1
  GPC4 MUTATED     7   1
  GPC4 WILD-TYPE 331 215
  GPC4 MUTATED GPC4 WILD-TYPE 
             8            546 
  GPC4 MUTATED GPC4 WILD-TYPE 
             1            215 
$`GPC4 MUTATED`
TCGA-L5-A8NM TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8486 TCGA-CG-4437 
        7.76        36.16        29.59         4.31        20.22         8.05 
TCGA-F1-A448 TCGA-FP-A4BE 
       21.27        11.08 

$`GPC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GPC4 MUTATED GPC4 WILD-TYPE 
          4.31           0.00 
  GPC4 MUTATED GPC4 WILD-TYPE 
         36.16         122.30 
  GPC4 MUTATED GPC4 WILD-TYPE 
        15.650         13.565 
[1] "4.3 - 36.2 (15.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3.1"
D393V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPC4 MUTATED         0        2        1        1         1         2
  GPC4 WILD-TYPE      10       18       45       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPC4 MUTATED           0          0          1          0        0         0
  GPC4 WILD-TYPE        29         84         61         39       43         4
D393V3, multiclass
            clus
vv           GPC4 MUTATED GPC4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GPC4 MUTATED       3   3   2   1
  GPC4 WILD-TYPE    51 132 259 101
D393V4, multiclass
       clus
vv      GPC4 MUTATED GPC4 WILD-TYPE
  T0+T1            3             51
  T2               3            132
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GPC4 MUTATED     5   2   0   1
  GPC4 WILD-TYPE 190 171  89  84
D393V5, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  N0            5            190
  N1            2            171
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V6, binary
                cls
clus               0   1
  GPC4 MUTATED     9   0
  GPC4 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      9    0
  GPC4 WILD-TYPE  473   38
   clus
vv  GPC4 MUTATED GPC4 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D393V7, binary
                cls
clus               0   1
  GPC4 MUTATED     5   4
  GPC4 WILD-TYPE 167 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      5    4
  GPC4 WILD-TYPE  167  402
        clus
vv       GPC4 MUTATED GPC4 WILD-TYPE
  FEMALE            5            167
  MALE              4            402
[1] 2 2
[1] FALSE
D393V8, binary
                cls
clus               0   1
  GPC4 MUTATED     6   2
  GPC4 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      6    2
  GPC4 WILD-TYPE  410  100
     clus
vv    GPC4 MUTATED GPC4 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D393V9, continuous
D393V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GPC4 MUTATED       0                         1
  GPC4 WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPC4 MUTATED                                           0     7
  GPC4 WILD-TYPE                                         1   350
D393V11, multiclass
                                           clus
vv                                          GPC4 MUTATED GPC4 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V12, binary
                cls
clus               0   1
  GPC4 MUTATED     1   6
  GPC4 WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      1    6
  GPC4 WILD-TYPE    9  392
                        clus
vv                       GPC4 MUTATED GPC4 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(394) Variable = FOXN3 MUTATION ANALYSIS
D394V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED     9   4
  FOXN3 WILD-TYPE 329 212
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             13             541 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              4             212 
$`FOXN3 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GL TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 
       19.99         5.92        26.70         6.97        34.68        32.78 
TCGA-BR-7707 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GT 
       35.84         6.18         6.58         6.02         5.92         6.51 
TCGA-MX-A5UJ 
       19.73 

$`FOXN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FOXN3 MUTATED FOXN3 WILD-TYPE 
           5.92            0.00 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          35.84          122.30 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
           6.97           13.58 
[1] "5.9 - 35.8 (7.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D394V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOXN3 MUTATED         0        0        1        0         5         3
  FOXN3 WILD-TYPE      10       20       45       31        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXN3 MUTATED           1          2          0          1        1         0
  FOXN3 WILD-TYPE        28         82         62         38       42         4
D394V3, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FOXN3 MUTATED       0   1  10   3
  FOXN3 WILD-TYPE    54 134 251  99
D394V4, multiclass
       clus
vv      FOXN3 MUTATED FOXN3 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3               10             251
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FOXN3 MUTATED     8   4   1   1
  FOXN3 WILD-TYPE 187 169  88  84
D394V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0             8             187
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V6, binary
                 cls
clus                0   1
  FOXN3 MUTATED    13   0
  FOXN3 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     13    0
  FOXN3 WILD-TYPE  469   38
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D394V7, binary
                 cls
clus                0   1
  FOXN3 MUTATED     8   7
  FOXN3 WILD-TYPE 164 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      8    7
  FOXN3 WILD-TYPE  164  399
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  FEMALE             8             164
  MALE               7             399
[1] 2 2
[1] FALSE
D394V8, binary
                 cls
clus                0   1
  FOXN3 MUTATED    14   0
  FOXN3 WILD-TYPE 402 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     14    0
  FOXN3 WILD-TYPE  402  102
     clus
vv    FOXN3 MUTATED FOXN3 WILD-TYPE
  NO             14             402
  YES             0             102
[1] 2 2
[1] FALSE
D394V9, continuous
D394V10, continuous
[1] "Remove cluster labels:" "FOXN3 MUTATED"         
clus
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" "FOXN3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"FOXN3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FOXN3 MUTATED       2                         0
  FOXN3 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FOXN3 MUTATED                                           0    11
  FOXN3 WILD-TYPE                                         1   346
D394V11, multiclass
                                           clus
vv                                          FOXN3 MUTATED FOXN3 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V12, binary
                 cls
clus                0   1
  FOXN3 MUTATED     0  12
  FOXN3 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      0   12
  FOXN3 WILD-TYPE   10  386
                        clus
vv                       FOXN3 MUTATED FOXN3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(395) Variable = SETDB2 MUTATION ANALYSIS
D395V1, survival
                  sevent
clus2                0   1
  SETDB2 MUTATED     9   6
  SETDB2 WILD-TYPE 329 210
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              15              539 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               6              210 
$`SETDB2 MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A4QS TCGA-JY-A6FH TCGA-B7-5816 
       14.30         4.21        35.21         3.88        47.38        26.70 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8591 
        6.97        30.90        34.68        31.10         4.31        28.14 
TCGA-CG-4305 TCGA-CG-4443 TCGA-VQ-AA64 
       15.95        29.98        18.41 

$`SETDB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
        8.94        16.24        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SETDB2 MUTATED SETDB2 WILD-TYPE 
            3.88             0.00 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
           47.38           122.30 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
           26.70            13.48 
[1] "3.9 - 47.4 (26.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D395V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETDB2 MUTATED         0        1        2        1         2         2
  SETDB2 WILD-TYPE      10       19       44       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SETDB2 MUTATED           2          1          2          2        0
  SETDB2 WILD-TYPE        27         83         60         37       43
                  vv
clus               STAGE IVA
  SETDB2 MUTATED           0
  SETDB2 WILD-TYPE         4
D395V3, multiclass
            clus
vv           SETDB2 MUTATED SETDB2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SETDB2 MUTATED       1   6   6   3
  SETDB2 WILD-TYPE    53 129 255  99
D395V4, multiclass
       clus
vv      SETDB2 MUTATED SETDB2 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 6              255
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SETDB2 MUTATED     6   5   3   1
  SETDB2 WILD-TYPE 189 168  86  84
D395V5, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  N0              6              189
  N1              5              168
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V6, binary
                  cls
clus                 0   1
  SETDB2 MUTATED    16   0
  SETDB2 WILD-TYPE 466  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED     16    0
  SETDB2 WILD-TYPE  466   38
   clus
vv  SETDB2 MUTATED SETDB2 WILD-TYPE
  0             16              466
  1              0               38
[1] 2 2
[1] FALSE
D395V7, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     6  11
  SETDB2 WILD-TYPE 166 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      6   11
  SETDB2 WILD-TYPE  166  395
        clus
vv       SETDB2 MUTATED SETDB2 WILD-TYPE
  FEMALE              6              166
  MALE               11              395
[1] 2 2
[1] FALSE
D395V8, binary
                  cls
clus                 0   1
  SETDB2 MUTATED    13   1
  SETDB2 WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED     13    1
  SETDB2 WILD-TYPE  403  101
     clus
vv    SETDB2 MUTATED SETDB2 WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D395V9, continuous
[1] "Remove cluster labels:" "SETDB2 MUTATED"        
clus
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YB 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
D395V10, continuous
[1] "Remove cluster labels:" "SETDB2 MUTATED"        
clus
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" "SETDB2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SETDB2 MUTATED       0                         0
  SETDB2 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SETDB2 MUTATED                                           0    12
  SETDB2 WILD-TYPE                                         1   345
D395V11, multiclass
                                           clus
vv                                          SETDB2 MUTATED SETDB2 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V12, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     0  10
  SETDB2 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      0   10
  SETDB2 WILD-TYPE   10  388
                        clus
vv                       SETDB2 MUTATED SETDB2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(396) Variable = CTNNA1 MUTATION ANALYSIS
D396V1, survival
                  sevent
clus2                0   1
  CTNNA1 MUTATED    13   7
  CTNNA1 WILD-TYPE 325 209
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              20              534 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               7              209 
$`CTNNA1 MUTATED`
TCGA-L5-A8NT TCGA-L5-A8NE TCGA-L5-A8NM TCGA-LN-A49M TCGA-LN-A49X TCGA-R6-A6DQ 
       27.12        55.50         7.76        12.66        12.62         7.59 
TCGA-R6-A6L6 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5717 TCGA-CG-5720 
        7.04        31.10        31.96        16.14         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HU-8602 TCGA-HU-A4H3 
        6.02       105.07        14.27         5.92        22.32        29.00 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`CTNNA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       30.97        36.00         1.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
            0.99             0.00 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
          105.07           122.30 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
          15.205           13.530 
[1] "1.0 - 105.1 (15.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D396V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNNA1 MUTATED         0        0        1        2         2         5
  CTNNA1 WILD-TYPE      10       20       45       29        82        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA1 MUTATED           0          3          1          3        2
  CTNNA1 WILD-TYPE        29         81         61         36       41
                  vv
clus               STAGE IVA
  CTNNA1 MUTATED           0
  CTNNA1 WILD-TYPE         4
D396V3, multiclass
            clus
vv           CTNNA1 MUTATED CTNNA1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CTNNA1 MUTATED       0   7   5   7
  CTNNA1 WILD-TYPE    54 128 256  95
D396V4, multiclass
       clus
vv      CTNNA1 MUTATED CTNNA1 WILD-TYPE
  T0+T1              0               54
  T2                 7              128
  T3                 5              256
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CTNNA1 MUTATED     5   8   3   4
  CTNNA1 WILD-TYPE 190 165  86  81
D396V5, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  N0              5              190
  N1              8              165
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V6, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED    19   1
  CTNNA1 WILD-TYPE 463  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED     19    1
  CTNNA1 WILD-TYPE  463   37
   clus
vv  CTNNA1 MUTATED CTNNA1 WILD-TYPE
  0             19              463
  1              1               37
[1] 2 2
[1] FALSE
D396V7, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     9  13
  CTNNA1 WILD-TYPE 163 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      9   13
  CTNNA1 WILD-TYPE  163  393
        clus
vv       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  FEMALE              9              163
  MALE               13              393
[1] 2 2
[1] FALSE
D396V8, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED    14   4
  CTNNA1 WILD-TYPE 402  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED     14    4
  CTNNA1 WILD-TYPE  402   98
     clus
vv    CTNNA1 MUTATED CTNNA1 WILD-TYPE
  NO              14              402
  YES              4               98
[1] 2 2
[1] FALSE
D396V9, continuous
[1] "Remove cluster labels:" "CTNNA1 MUTATED"        
clus
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
D396V10, continuous
[1] "Remove cluster labels:" "CTNNA1 MUTATED"        
clus
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NF 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" "CTNNA1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNNA1 MUTATED       5                         0
  CTNNA1 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNA1 MUTATED                                           0    13
  CTNNA1 WILD-TYPE                                         1   344
D396V11, multiclass
                                           clus
vv                                          CTNNA1 MUTATED CTNNA1 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V12, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     0  14
  CTNNA1 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      0   14
  CTNNA1 WILD-TYPE   10  384
                        clus
vv                       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(397) Variable = UBE2Q1 MUTATION ANALYSIS
D397V1, survival
                  sevent
clus2                0   1
  UBE2Q1 MUTATED     2   3
  UBE2Q1 WILD-TYPE 336 213
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               5              549 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               3              213 
$`UBE2Q1 MUTATED`
TCGA-BR-4184 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4438 TCGA-CG-5721 
        6.97        16.14         6.58        54.08         6.02 

$`UBE2Q1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
            6.02             0.00 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
           54.08           122.30 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
            6.97            13.58 
[1] "6.0 - 54.1 (7.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D397V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBE2Q1 MUTATED         0        0        0        0         1         0
  UBE2Q1 WILD-TYPE      10       20       46       31        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBE2Q1 MUTATED           0          1          1          0        3
  UBE2Q1 WILD-TYPE        29         83         61         39       40
                  vv
clus               STAGE IVA
  UBE2Q1 MUTATED           0
  UBE2Q1 WILD-TYPE         4
D397V3, multiclass
            clus
vv           UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  UBE2Q1 MUTATED       0   0   3   3
  UBE2Q1 WILD-TYPE    54 135 258  99
D397V4, multiclass
       clus
vv      UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 3              258
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  UBE2Q1 MUTATED     1   3   2   1
  UBE2Q1 WILD-TYPE 194 170  87  84
D397V5, multiclass
    clus
vv   UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  N0              1              194
  N1              3              170
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V6, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     6   0
  UBE2Q1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      6    0
  UBE2Q1 WILD-TYPE  476   38
   clus
vv  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D397V7, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     3   4
  UBE2Q1 WILD-TYPE 169 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      3    4
  UBE2Q1 WILD-TYPE  169  402
        clus
vv       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  FEMALE              3              169
  MALE                4              402
[1] 2 2
[1] FALSE
D397V8, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     4   0
  UBE2Q1 WILD-TYPE 412 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      4    0
  UBE2Q1 WILD-TYPE  412  102
     clus
vv    UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  NO               4              412
  YES              0              102
[1] 2 2
[1] FALSE
D397V9, continuous
D397V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UBE2Q1 MUTATED       1                         0
  UBE2Q1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBE2Q1 MUTATED                                           0     4
  UBE2Q1 WILD-TYPE                                         1   353
D397V11, multiclass
                                           clus
vv                                          UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V12, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     0   5
  UBE2Q1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      0    5
  UBE2Q1 WILD-TYPE   10  393
                        clus
vv                       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(398) Variable = MAP2K7 MUTATION ANALYSIS
D398V1, survival
                  sevent
clus2                0   1
  MAP2K7 MUTATED    15   8
  MAP2K7 WILD-TYPE 323 208
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              23              531 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
               8              208 
$`MAP2K7 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7959 TCGA-BR-8360 TCGA-BR-8368 
        6.97        34.68        35.84        33.21         6.18         4.31 
TCGA-BR-8591 TCGA-BR-A4J7 TCGA-CD-A4MI TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5733 
       28.14        32.52        11.77        36.00        12.03        21.07 
TCGA-D7-A748 TCGA-FP-A4BE TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8610 TCGA-KB-A6F5 
        4.34        11.08        52.21         1.51         0.76         5.56 
TCGA-MX-A5UJ TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A8N1 TCGA-VQ-A8P2 
       19.73         6.08        11.05       115.69        38.14 

$`MAP2K7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34         0.66        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        6.21        77.29        63.06        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       24.39        28.96        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
            0.76             0.00 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
          115.69           122.30 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
           12.03            13.58 
[1] "0.8 - 115.7 (12.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D398V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP2K7 MUTATED         0        3        3        1         3         1
  MAP2K7 WILD-TYPE      10       17       43       30        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K7 MUTATED           1          8          1          1        3
  MAP2K7 WILD-TYPE        28         76         61         38       40
                  vv
clus               STAGE IVA
  MAP2K7 MUTATED           0
  MAP2K7 WILD-TYPE         4
D398V3, multiclass
            clus
vv           MAP2K7 MUTATED MAP2K7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                3               17
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              8               76
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAP2K7 MUTATED       4   5  12   6
  MAP2K7 WILD-TYPE    50 130 249  96
D398V4, multiclass
       clus
vv      MAP2K7 MUTATED MAP2K7 WILD-TYPE
  T0+T1              4               50
  T2                 5              130
  T3                12              249
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP2K7 MUTATED     9   6   6   3
  MAP2K7 WILD-TYPE 186 167  83  82
D398V5, multiclass
    clus
vv   MAP2K7 MUTATED MAP2K7 WILD-TYPE
  N0              9              186
  N1              6              167
  N2              6               83
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V6, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    24   2
  MAP2K7 WILD-TYPE 458  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     24    2
  MAP2K7 WILD-TYPE  458   36
   clus
vv  MAP2K7 MUTATED MAP2K7 WILD-TYPE
  0             24              458
  1              2               36
[1] 2 2
[1] FALSE
D398V7, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    10  17
  MAP2K7 WILD-TYPE 162 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     10   17
  MAP2K7 WILD-TYPE  162  389
        clus
vv       MAP2K7 MUTATED MAP2K7 WILD-TYPE
  FEMALE             10              162
  MALE               17              389
[1] 2 2
[1] FALSE
D398V8, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    18   6
  MAP2K7 WILD-TYPE 398  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     18    6
  MAP2K7 WILD-TYPE  398   96
     clus
vv    MAP2K7 MUTATED MAP2K7 WILD-TYPE
  NO              18              398
  YES              6               96
[1] 2 2
[1] FALSE
D398V9, continuous
D398V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP2K7 MUTATED       5                         2
  MAP2K7 WILD-TYPE   128                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP2K7 MUTATED                                           0    14
  MAP2K7 WILD-TYPE                                         1   343
D398V11, multiclass
                                           clus
vv                                          MAP2K7 MUTATED MAP2K7 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V12, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED     0  20
  MAP2K7 WILD-TYPE  10 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED      0   20
  MAP2K7 WILD-TYPE   10  378
                        clus
vv                       MAP2K7 MUTATED MAP2K7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             20              378
[1] 2 2
[1] FALSE

Clustering(399) Variable = SH3RF1 MUTATION ANALYSIS
D399V1, survival
                  sevent
clus2                0   1
  SH3RF1 MUTATED     8   6
  SH3RF1 WILD-TYPE 330 210
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              14              540 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
               6              210 
$`SH3RF1 MUTATED`
TCGA-JY-A6FE TCGA-L5-A43H TCGA-R6-A6XG TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 
        3.68         0.30        38.40        30.90        35.84        29.59 
TCGA-BR-8363 TCGA-BR-8487 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GQ 
        0.26         1.12       105.07        11.44        22.32         0.10 
TCGA-HU-A4H4 TCGA-VQ-A8P2 
       23.84        38.14 

$`SH3RF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
             0.1              0.0 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
          105.07           122.30 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
           23.08            13.53 
[1] "0.1 - 105.1 (23.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D399V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH3RF1 MUTATED         0        0        2        1         1         3
  SH3RF1 WILD-TYPE      10       20       44       30        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3RF1 MUTATED           2          1          1          1        0
  SH3RF1 WILD-TYPE        27         83         61         38       43
                  vv
clus               STAGE IVA
  SH3RF1 MUTATED           0
  SH3RF1 WILD-TYPE         4
D399V3, multiclass
            clus
vv           SH3RF1 MUTATED SH3RF1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SH3RF1 MUTATED       0   5   4   4
  SH3RF1 WILD-TYPE    54 130 257  98
D399V4, multiclass
       clus
vv      SH3RF1 MUTATED SH3RF1 WILD-TYPE
  T0+T1              0               54
  T2                 5              130
  T3                 4              257
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SH3RF1 MUTATED     5   4   2   1
  SH3RF1 WILD-TYPE 190 169  87  84
D399V5, multiclass
    clus
vv   SH3RF1 MUTATED SH3RF1 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V6, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED    14   0
  SH3RF1 WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED     14    0
  SH3RF1 WILD-TYPE  468   38
   clus
vv  SH3RF1 MUTATED SH3RF1 WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D399V7, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED     9   6
  SH3RF1 WILD-TYPE 163 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED      9    6
  SH3RF1 WILD-TYPE  163  400
        clus
vv       SH3RF1 MUTATED SH3RF1 WILD-TYPE
  FEMALE              9              163
  MALE                6              400
[1] 2 2
[1] FALSE
D399V8, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED    13   1
  SH3RF1 WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED     13    1
  SH3RF1 WILD-TYPE  403  101
     clus
vv    SH3RF1 MUTATED SH3RF1 WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D399V9, continuous
D399V10, continuous
[1] "Remove cluster labels:" "SH3RF1 MUTATED"        
clus
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" "SH3RF1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SH3RF1 MUTATED       3                         0
  SH3RF1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3RF1 MUTATED                                           0    11
  SH3RF1 WILD-TYPE                                         1   346
D399V11, multiclass
                                           clus
vv                                          SH3RF1 MUTATED SH3RF1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V12, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED     0  11
  SH3RF1 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED      0   11
  SH3RF1 WILD-TYPE   10  387
                        clus
vv                       SH3RF1 MUTATED SH3RF1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(400) Variable = GPR161 MUTATION ANALYSIS
D400V1, survival
                  sevent
clus2                0   1
  GPR161 MUTATED    12   5
  GPR161 WILD-TYPE 326 211
  GPR161 MUTATED GPR161 WILD-TYPE 
              17              537 
  GPR161 MUTATED GPR161 WILD-TYPE 
               5              211 
$`GPR161 MUTATED`
TCGA-LN-A5U7 TCGA-Q9-A6FW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-AA4G TCGA-XP-A8T6 
       25.25         7.82         8.98        27.09        18.05        25.08 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-CD-5804 TCGA-CD-8536 TCGA-CG-5726 
        6.97        30.90         9.67        12.10        12.43        28.96 
TCGA-CG-5728 TCGA-FP-8211 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       65.10        13.58        14.07        19.73        38.14 

$`GPR161 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       16.44        15.35         9.27        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GPR161 MUTATED GPR161 WILD-TYPE 
            6.97             0.00 
  GPR161 MUTATED GPR161 WILD-TYPE 
            65.1            122.3 
  GPR161 MUTATED GPR161 WILD-TYPE 
           18.05            13.51 
[1] "7.0 - 65.1 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D400V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR161 MUTATED         0        1        2        1         1         2
  GPR161 WILD-TYPE      10       19       44       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR161 MUTATED           0          4          2          0        0
  GPR161 WILD-TYPE        29         80         60         39       43
                  vv
clus               STAGE IVA
  GPR161 MUTATED           0
  GPR161 WILD-TYPE         4
D400V3, multiclass
            clus
vv           GPR161 MUTATED GPR161 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR161 MUTATED       2   5   8   1
  GPR161 WILD-TYPE    52 130 253 101
D400V4, multiclass
       clus
vv      GPR161 MUTATED GPR161 WILD-TYPE
  T0+T1              2               52
  T2                 5              130
  T3                 8              253
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR161 MUTATED     4   6   4   0
  GPR161 WILD-TYPE 191 167  85  85
D400V5, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  N0              4              191
  N1              6              167
  N2              4               85
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V6, binary
                  cls
clus                 0   1
  GPR161 MUTATED    14   0
  GPR161 WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED     14    0
  GPR161 WILD-TYPE  468   38
   clus
vv  GPR161 MUTATED GPR161 WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D400V7, binary
                  cls
clus                 0   1
  GPR161 MUTATED     6  12
  GPR161 WILD-TYPE 166 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      6   12
  GPR161 WILD-TYPE  166  394
        clus
vv       GPR161 MUTATED GPR161 WILD-TYPE
  FEMALE              6              166
  MALE               12              394
[1] 2 2
[1] FALSE
D400V8, binary
                  cls
clus                 0   1
  GPR161 MUTATED    12   2
  GPR161 WILD-TYPE 404 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED     12    2
  GPR161 WILD-TYPE  404  100
     clus
vv    GPR161 MUTATED GPR161 WILD-TYPE
  NO              12              404
  YES              2              100
[1] 2 2
[1] FALSE
D400V9, continuous
D400V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR161 MUTATED       4                         1
  GPR161 WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR161 MUTATED                                           0    11
  GPR161 WILD-TYPE                                         1   346
D400V11, multiclass
                                           clus
vv                                          GPR161 MUTATED GPR161 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V12, binary
                  cls
clus                 0   1
  GPR161 MUTATED     1  12
  GPR161 WILD-TYPE   9 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      1   12
  GPR161 WILD-TYPE    9  386
                        clus
vv                       GPR161 MUTATED GPR161 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(401) Variable = KANK4 MUTATION ANALYSIS
D401V1, survival
                 sevent
clus2               0   1
  KANK4 MUTATED     9   9
  KANK4 WILD-TYPE 329 207
  KANK4 MUTATED KANK4 WILD-TYPE 
             18             536 
  KANK4 MUTATED KANK4 WILD-TYPE 
              9             207 
$`KANK4 MUTATED`
TCGA-2H-A9GF TCGA-L5-A8NL TCGA-R6-A6L4 TCGA-V5-AASX TCGA-BR-4280 TCGA-BR-6452 
       25.78        13.22        16.31         8.98         6.61        34.68 
TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8687 TCGA-BR-A4QL TCGA-CD-A48C 
       35.84         1.12        28.14         8.22        16.14        11.61 
TCGA-CG-5726 TCGA-D7-A6EY TCGA-HU-A4GX TCGA-IN-A7NU TCGA-SW-A7EA TCGA-VQ-A8PE 
       28.96        11.44        20.25        11.70        19.04        22.19 

$`KANK4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KANK4 MUTATED KANK4 WILD-TYPE 
           1.12            0.00 
  KANK4 MUTATED KANK4 WILD-TYPE 
          35.84          122.30 
  KANK4 MUTATED KANK4 WILD-TYPE 
         16.225          13.530 
[1] "1.1 - 35.8 (16.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D401V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KANK4 MUTATED         0        1        2        0         2         1
  KANK4 WILD-TYPE      10       19       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KANK4 MUTATED           3          0          4          3        0         0
  KANK4 WILD-TYPE        26         84         58         36       43         4
D401V3, multiclass
            clus
vv           KANK4 MUTATED KANK4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              3              26
  STAGE IIIA             0              84
  STAGE IIIB             4              58
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KANK4 MUTATED       1   3   9   3
  KANK4 WILD-TYPE    53 132 252  99
D401V4, multiclass
       clus
vv      KANK4 MUTATED KANK4 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                9             252
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KANK4 MUTATED     5   5   2   5
  KANK4 WILD-TYPE 190 168  87  80
D401V5, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  N0             5             190
  N1             5             168
  N2             2              87
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V6, binary
                 cls
clus                0   1
  KANK4 MUTATED    17   0
  KANK4 WILD-TYPE 465  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     17    0
  KANK4 WILD-TYPE  465   38
   clus
vv  KANK4 MUTATED KANK4 WILD-TYPE
  0            17             465
  1             0              38
[1] 2 2
[1] FALSE
D401V7, binary
                 cls
clus                0   1
  KANK4 MUTATED    11   8
  KANK4 WILD-TYPE 161 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     11    8
  KANK4 WILD-TYPE  161  398
        clus
vv       KANK4 MUTATED KANK4 WILD-TYPE
  FEMALE            11             161
  MALE               8             398
[1] 2 2
[1] FALSE
D401V8, binary
                 cls
clus                0   1
  KANK4 MUTATED    15   0
  KANK4 WILD-TYPE 401 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     15    0
  KANK4 WILD-TYPE  401  102
     clus
vv    KANK4 MUTATED KANK4 WILD-TYPE
  NO             15             401
  YES             0             102
[1] 2 2
[1] FALSE
D401V9, continuous
[1] "Remove cluster labels:" "KANK4 MUTATED"         
clus
  KANK4 MUTATED KANK4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
D401V10, continuous
[1] "Remove cluster labels:" "KANK4 MUTATED"         
clus
  KANK4 MUTATED KANK4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" "KANK4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"KANK4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KANK4 MUTATED       2                         0
  KANK4 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KANK4 MUTATED                                           0    15
  KANK4 WILD-TYPE                                         1   342
D401V11, multiclass
                                           clus
vv                                          KANK4 MUTATED KANK4 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V12, binary
                 cls
clus                0   1
  KANK4 MUTATED     0  15
  KANK4 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      0   15
  KANK4 WILD-TYPE   10  383
                        clus
vv                       KANK4 MUTATED KANK4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(402) Variable = ZC3H4 MUTATION ANALYSIS
D402V1, survival
                 sevent
clus2               0   1
  ZC3H4 MUTATED    12   9
  ZC3H4 WILD-TYPE 326 207
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             21             533 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              9             207 
$`ZC3H4 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OW TCGA-L5-A8NH TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 
       21.99         7.13        12.92         9.34        34.68        32.25 
TCGA-BR-8368 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5726 TCGA-CG-5728 
        4.31        16.14         6.58        15.95        28.96        65.10 
TCGA-D7-6815 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-IN-8462 
       15.98        11.44        14.47        22.82        22.68        18.81 
TCGA-IN-8663 TCGA-IP-7968 TCGA-VQ-A8P2 
        3.39         2.53        38.14 

$`ZC3H4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        15.02         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       33.40        36.36         3.45        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
           2.53            0.00 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
           65.1           122.3 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
          15.98           13.51 
[1] "2.5 - 65.1 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D402V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H4 MUTATED         0        1        3        1         3         6
  ZC3H4 WILD-TYPE      10       19       43       30        81        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZC3H4 MUTATED           0          2          3          0        2         0
  ZC3H4 WILD-TYPE        29         82         59         39       41         4
D402V3, multiclass
            clus
vv           ZC3H4 MUTATED ZC3H4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZC3H4 MUTATED       2   8   7   4
  ZC3H4 WILD-TYPE    52 127 254  98
D402V4, multiclass
       clus
vv      ZC3H4 MUTATED ZC3H4 WILD-TYPE
  T0+T1             2              52
  T2                8             127
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZC3H4 MUTATED    10   7   3   2
  ZC3H4 WILD-TYPE 185 166  86  83
D402V5, multiclass
    clus
vv   ZC3H4 MUTATED ZC3H4 WILD-TYPE
  N0            10             185
  N1             7             166
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V6, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    19   2
  ZC3H4 WILD-TYPE 463  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     19    2
  ZC3H4 WILD-TYPE  463   36
   clus
vv  ZC3H4 MUTATED ZC3H4 WILD-TYPE
  0            19             463
  1             2              36
[1] 2 2
[1] FALSE
D402V7, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    12  10
  ZC3H4 WILD-TYPE 160 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     12   10
  ZC3H4 WILD-TYPE  160  396
        clus
vv       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  FEMALE            12             160
  MALE              10             396
[1] 2 2
[1] FALSE
D402V8, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    16   1
  ZC3H4 WILD-TYPE 400 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     16    1
  ZC3H4 WILD-TYPE  400  101
     clus
vv    ZC3H4 MUTATED ZC3H4 WILD-TYPE
  NO             16             400
  YES             1             101
[1] 2 2
[1] FALSE
D402V9, continuous
D402V10, continuous
[1] "Remove cluster labels:" "ZC3H4 MUTATED"         
clus
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ZC3H4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H4 MUTATED       3                         0
  ZC3H4 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H4 MUTATED                                           0    14
  ZC3H4 WILD-TYPE                                         1   343
D402V11, multiclass
                                           clus
vv                                          ZC3H4 MUTATED ZC3H4 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V12, binary
                 cls
clus                0   1
  ZC3H4 MUTATED     0  15
  ZC3H4 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      0   15
  ZC3H4 WILD-TYPE   10  383
                        clus
vv                       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(403) Variable = KYNU MUTATION ANALYSIS
D403V1, survival
                sevent
clus2              0   1
  KYNU MUTATED    11   1
  KYNU WILD-TYPE 327 215
  KYNU MUTATED KYNU WILD-TYPE 
            12            542 
  KYNU MUTATED KYNU WILD-TYPE 
             1            215 
$`KYNU MUTATED`
TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8368 TCGA-BR-8680 
       14.37         1.32        44.94        29.56         4.31        31.96 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4HD 
        9.01         6.02       105.07        30.51        23.84        33.40 

$`KYNU WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       41.23         3.42         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KYNU MUTATED KYNU WILD-TYPE 
          1.32           0.00 
  KYNU MUTATED KYNU WILD-TYPE 
        105.07         122.30 
  KYNU MUTATED KYNU WILD-TYPE 
         26.70          13.51 
[1] "1.3 - 105.1 (26.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "6.6"
D403V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KYNU MUTATED         0        0        2        1         1         2
  KYNU WILD-TYPE      10       20       44       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KYNU MUTATED           0          3          1          1        3         0
  KYNU WILD-TYPE        29         81         61         38       40         4
D403V3, multiclass
            clus
vv           KYNU MUTATED KYNU WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  KYNU MUTATED       1   4   3   6
  KYNU WILD-TYPE    53 131 258  96
D403V4, multiclass
       clus
vv      KYNU MUTATED KYNU WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               3            258
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KYNU MUTATED     5   4   3   2
  KYNU WILD-TYPE 190 169  86  83
D403V5, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  N0            5            190
  N1            4            169
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V6, binary
                cls
clus               0   1
  KYNU MUTATED    12   2
  KYNU WILD-TYPE 470  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED     12    2
  KYNU WILD-TYPE  470   36
   clus
vv  KYNU MUTATED KYNU WILD-TYPE
  0           12            470
  1            2             36
[1] 2 2
[1] FALSE
D403V7, binary
                cls
clus               0   1
  KYNU MUTATED     6   8
  KYNU WILD-TYPE 166 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      6    8
  KYNU WILD-TYPE  166  398
        clus
vv       KYNU MUTATED KYNU WILD-TYPE
  FEMALE            6            166
  MALE              8            398
[1] 2 2
[1] FALSE
D403V8, binary
                cls
clus               0   1
  KYNU MUTATED     9   2
  KYNU WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      9    2
  KYNU WILD-TYPE  407  100
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D403V9, continuous
[1] "Remove cluster labels:" "KYNU MUTATED"          
clus
  KYNU MUTATED KYNU WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
D403V10, continuous
[1] "Remove cluster labels:" "KYNU MUTATED"          
clus
  KYNU MUTATED KYNU WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-Z6-AAPN 
"KYNU WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KYNU MUTATED       3                         1
  KYNU WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KYNU MUTATED                                           0     5
  KYNU WILD-TYPE                                         1   352
D403V11, multiclass
                                           clus
vv                                          KYNU MUTATED KYNU WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V12, binary
                cls
clus               0   1
  KYNU MUTATED     1   8
  KYNU WILD-TYPE   9 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      1    8
  KYNU WILD-TYPE    9  390
                        clus
vv                       KYNU MUTATED KYNU WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(404) Variable = MIA2 MUTATION ANALYSIS
D404V1, survival
                sevent
clus2              0   1
  MIA2 MUTATED     6   3
  MIA2 WILD-TYPE 332 213
  MIA2 MUTATED MIA2 WILD-TYPE 
             9            545 
  MIA2 MUTATED MIA2 WILD-TYPE 
             3            213 
$`MIA2 MUTATED`
TCGA-L5-A88Z TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-A4MG 
        7.40        32.78        28.73        31.96         7.53         6.58 
TCGA-HF-A5NB TCGA-HU-A4GX TCGA-VQ-A8P2 
       30.51        20.25        38.14 

$`MIA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MIA2 MUTATED MIA2 WILD-TYPE 
          6.58           0.00 
  MIA2 MUTATED MIA2 WILD-TYPE 
         38.14         122.30 
  MIA2 MUTATED MIA2 WILD-TYPE 
         28.73          13.51 
[1] "6.6 - 38.1 (28.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D404V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MIA2 MUTATED         0        0        0        0         3         0
  MIA2 WILD-TYPE      10       20       46       31        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIA2 MUTATED           0          2          1          2        1         0
  MIA2 WILD-TYPE        29         82         61         37       42         4
D404V3, multiclass
            clus
vv           MIA2 MUTATED MIA2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MIA2 MUTATED       2   0   3   5
  MIA2 WILD-TYPE    52 135 258  97
D404V4, multiclass
       clus
vv      MIA2 MUTATED MIA2 WILD-TYPE
  T0+T1            2             52
  T2               0            135
  T3               3            258
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MIA2 MUTATED     2   4   2   2
  MIA2 WILD-TYPE 193 169  87  83
D404V5, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  N0            2            193
  N1            4            169
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V6, binary
                cls
clus               0   1
  MIA2 MUTATED    10   1
  MIA2 WILD-TYPE 472  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED     10    1
  MIA2 WILD-TYPE  472   37
   clus
vv  MIA2 MUTATED MIA2 WILD-TYPE
  0           10            472
  1            1             37
[1] 2 2
[1] FALSE
D404V7, binary
                cls
clus               0   1
  MIA2 MUTATED     6   5
  MIA2 WILD-TYPE 166 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      6    5
  MIA2 WILD-TYPE  166  401
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  FEMALE            6            166
  MALE              5            401
[1] 2 2
[1] FALSE
D404V8, binary
                cls
clus               0   1
  MIA2 MUTATED     7   2
  MIA2 WILD-TYPE 409 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      7    2
  MIA2 WILD-TYPE  409  100
     clus
vv    MIA2 MUTATED MIA2 WILD-TYPE
  NO             7            409
  YES            2            100
[1] 2 2
[1] FALSE
D404V9, continuous
D404V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MIA2 MUTATED       4                         0
  MIA2 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MIA2 MUTATED                                           0     6
  MIA2 WILD-TYPE                                         1   351
D404V11, multiclass
                                           clus
vv                                          MIA2 MUTATED MIA2 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V12, binary
                cls
clus               0   1
  MIA2 MUTATED     0   8
  MIA2 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      0    8
  MIA2 WILD-TYPE   10  390
                        clus
vv                       MIA2 MUTATED MIA2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(405) Variable = PHF1 MUTATION ANALYSIS
D405V1, survival
                sevent
clus2              0   1
  PHF1 MUTATED     4   5
  PHF1 WILD-TYPE 334 211
  PHF1 MUTATED PHF1 WILD-TYPE 
             9            545 
  PHF1 MUTATED PHF1 WILD-TYPE 
             5            211 
$`PHF1 MUTATED`
TCGA-L5-A43J TCGA-2H-A9GI TCGA-L5-A8NM TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4306 
        4.31        14.30         7.76         6.58        15.95         1.02 
TCGA-HU-A4GN TCGA-HU-A4H8 TCGA-VQ-A8P2 
       29.98        14.07        38.14 

$`PHF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PHF1 MUTATED PHF1 WILD-TYPE 
          1.02           0.00 
  PHF1 MUTATED PHF1 WILD-TYPE 
         38.14         122.30 
  PHF1 MUTATED PHF1 WILD-TYPE 
         14.07          13.55 
[1] "1.0 - 38.1 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D405V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHF1 MUTATED         0        0        1        1         2         2
  PHF1 WILD-TYPE      10       20       45       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF1 MUTATED           1          1          0          0        1         0
  PHF1 WILD-TYPE        28         83         62         39       42         4
D405V3, multiclass
            clus
vv           PHF1 MUTATED PHF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PHF1 MUTATED       1   3   4   1
  PHF1 WILD-TYPE    53 132 257 101
D405V4, multiclass
       clus
vv      PHF1 MUTATED PHF1 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               4            257
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PHF1 MUTATED     2   6   1   0
  PHF1 WILD-TYPE 193 167  88  85
D405V5, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  N0            2            193
  N1            6            167
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V6, binary
                cls
clus               0   1
  PHF1 MUTATED     7   1
  PHF1 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      7    1
  PHF1 WILD-TYPE  475   37
   clus
vv  PHF1 MUTATED PHF1 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D405V7, binary
                cls
clus               0   1
  PHF1 MUTATED     1   8
  PHF1 WILD-TYPE 171 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      1    8
  PHF1 WILD-TYPE  171  398
        clus
vv       PHF1 MUTATED PHF1 WILD-TYPE
  FEMALE            1            171
  MALE              8            398
[1] 2 2
[1] FALSE
D405V8, binary
                cls
clus               0   1
  PHF1 MUTATED     6   1
  PHF1 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      6    1
  PHF1 WILD-TYPE  410  101
     clus
vv    PHF1 MUTATED PHF1 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D405V9, continuous
D405V10, continuous
[1] "Remove cluster labels:" "PHF1 MUTATED"          
clus
  PHF1 MUTATED PHF1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" "PHF1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PHF1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PHF1 MUTATED       3                         0
  PHF1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHF1 MUTATED                                           0     3
  PHF1 WILD-TYPE                                         1   354
D405V11, multiclass
                                           clus
vv                                          PHF1 MUTATED PHF1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V12, binary
                cls
clus               0   1
  PHF1 MUTATED     0   3
  PHF1 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      0    3
  PHF1 WILD-TYPE   10  395
                        clus
vv                       PHF1 MUTATED PHF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(406) Variable = TMEFF2 MUTATION ANALYSIS
D406V1, survival
                  sevent
clus2                0   1
  TMEFF2 MUTATED     9   3
  TMEFF2 WILD-TYPE 329 213
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
              12              542 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
               3              213 
$`TMEFF2 MUTATED`
TCGA-L5-A8NM TCGA-L7-A56G TCGA-LN-A4A2 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8361 
        7.76        10.85        12.49        34.68        44.94        31.10 
TCGA-BR-8372 TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4H4 TCGA-VQ-A91U 
       31.27        12.43         6.02       105.07        23.84         1.71 

$`TMEFF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
            1.71             0.00 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
          105.07           122.30 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
          18.165           13.565 
[1] "1.7 - 105.1 (18.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D406V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEFF2 MUTATED         0        0        0        2         3         2
  TMEFF2 WILD-TYPE      10       20       46       29        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEFF2 MUTATED           0          1          0          2        2
  TMEFF2 WILD-TYPE        29         83         62         37       41
                  vv
clus               STAGE IVA
  TMEFF2 MUTATED           0
  TMEFF2 WILD-TYPE         4
D406V3, multiclass
            clus
vv           TMEFF2 MUTATED TMEFF2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                2               29
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TMEFF2 MUTATED       0   3   5   4
  TMEFF2 WILD-TYPE    54 132 256  98
D406V4, multiclass
       clus
vv      TMEFF2 MUTATED TMEFF2 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TMEFF2 MUTATED     4   4   3   1
  TMEFF2 WILD-TYPE 191 169  86  84
D406V5, multiclass
    clus
vv   TMEFF2 MUTATED TMEFF2 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V6, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED    12   0
  TMEFF2 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED     12    0
  TMEFF2 WILD-TYPE  470   38
   clus
vv  TMEFF2 MUTATED TMEFF2 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D406V7, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED     6   7
  TMEFF2 WILD-TYPE 166 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED      6    7
  TMEFF2 WILD-TYPE  166  399
        clus
vv       TMEFF2 MUTATED TMEFF2 WILD-TYPE
  FEMALE              6              166
  MALE                7              399
[1] 2 2
[1] FALSE
D406V8, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED    10   2
  TMEFF2 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED     10    2
  TMEFF2 WILD-TYPE  406  100
     clus
vv    TMEFF2 MUTATED TMEFF2 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D406V9, continuous
[1] "Remove cluster labels:" "TMEFF2 MUTATED"        
clus
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" "TMEFF2 WILD-TYPE" 
D406V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TMEFF2 MUTATED       4                         1
  TMEFF2 WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEFF2 MUTATED                                           0     6
  TMEFF2 WILD-TYPE                                         1   351
D406V11, multiclass
                                           clus
vv                                          TMEFF2 MUTATED TMEFF2 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V12, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED     0   9
  TMEFF2 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED      0    9
  TMEFF2 WILD-TYPE   10  389
                        clus
vv                       TMEFF2 MUTATED TMEFF2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(407) Variable = FAM83E MUTATION ANALYSIS
D407V1, survival
                  sevent
clus2                0   1
  FAM83E MUTATED    10   3
  FAM83E WILD-TYPE 328 213
  FAM83E MUTATED FAM83E WILD-TYPE 
              13              541 
  FAM83E MUTATED FAM83E WILD-TYPE 
               3              213 
$`FAM83E MUTATED`
TCGA-L5-A4OI TCGA-IG-A3YC TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-A4QL 
       19.99        20.12        44.94         6.18         1.12        16.14 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HU-A4GU TCGA-HU-A4GX 
        6.58         6.02        11.44        11.08         6.58        20.25 
TCGA-MX-A5UJ 
       19.73 

$`FAM83E WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FAM83E MUTATED FAM83E WILD-TYPE 
            1.12             0.00 
  FAM83E MUTATED FAM83E WILD-TYPE 
           44.94           122.30 
  FAM83E MUTATED FAM83E WILD-TYPE 
           11.44            13.58 
[1] "1.1 - 44.9 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D407V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM83E MUTATED         0        0        1        0         5         1
  FAM83E WILD-TYPE      10       20       45       31        79        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM83E MUTATED           0          2          2          2        1
  FAM83E WILD-TYPE        29         82         60         37       42
                  vv
clus               STAGE IVA
  FAM83E MUTATED           0
  FAM83E WILD-TYPE         4
D407V3, multiclass
            clus
vv           FAM83E MUTATED FAM83E WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM83E MUTATED       1   1  11   2
  FAM83E WILD-TYPE    53 134 250 100
D407V4, multiclass
       clus
vv      FAM83E MUTATED FAM83E WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                11              250
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM83E MUTATED     6   3   2   3
  FAM83E WILD-TYPE 189 170  87  82
D407V5, multiclass
    clus
vv   FAM83E MUTATED FAM83E WILD-TYPE
  N0              6              189
  N1              3              170
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V6, binary
                  cls
clus                 0   1
  FAM83E MUTATED    14   0
  FAM83E WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED     14    0
  FAM83E WILD-TYPE  468   38
   clus
vv  FAM83E MUTATED FAM83E WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D407V7, binary
                  cls
clus                 0   1
  FAM83E MUTATED     7   8
  FAM83E WILD-TYPE 165 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED      7    8
  FAM83E WILD-TYPE  165  398
        clus
vv       FAM83E MUTATED FAM83E WILD-TYPE
  FEMALE              7              165
  MALE                8              398
[1] 2 2
[1] FALSE
D407V8, binary
                  cls
clus                 0   1
  FAM83E MUTATED    12   1
  FAM83E WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED     12    1
  FAM83E WILD-TYPE  404  101
     clus
vv    FAM83E MUTATED FAM83E WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D407V9, continuous
[1] "Remove cluster labels:" "FAM83E MUTATED"        
clus
  FAM83E MUTATED FAM83E WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
D407V10, continuous
[1] "Remove cluster labels:" "FAM83E MUTATED"        
clus
  FAM83E MUTATED FAM83E WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A4P3       TCGA-IG-A4QT 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS       TCGA-IG-A8O2 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" "FAM83E WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM83E MUTATED       3                         1
  FAM83E WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM83E MUTATED                                           0     9
  FAM83E WILD-TYPE                                         1   348
D407V11, multiclass
                                           clus
vv                                          FAM83E MUTATED FAM83E WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V12, binary
                  cls
clus                 0   1
  FAM83E MUTATED     0  12
  FAM83E WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED      0   12
  FAM83E WILD-TYPE   10  386
                        clus
vv                       FAM83E MUTATED FAM83E WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(408) Variable = PPP3CA MUTATION ANALYSIS
D408V1, survival
                  sevent
clus2                0   1
  PPP3CA MUTATED     9   4
  PPP3CA WILD-TYPE 329 212
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              13              541 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               4              212 
$`PPP3CA MUTATED`
TCGA-CG-4460 TCGA-VR-A8EZ TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-7958 TCGA-CD-8536 
       21.99        18.18         6.97        35.84        29.56        12.43 
TCGA-CG-4465 TCGA-CG-5721 TCGA-FP-7998 TCGA-HU-8249 TCGA-HU-A4H4 TCGA-SW-A7EA 
        9.01         6.02        22.29        28.96        23.84        19.04 
TCGA-VQ-A8P2 
       38.14 

$`PPP3CA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       18.15        15.32        28.73         3.45         9.07        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PPP3CA MUTATED PPP3CA WILD-TYPE 
            6.02             0.00 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           38.14           122.30 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           21.99            13.51 
[1] "6.0 - 38.1 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D408V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP3CA MUTATED         0        0        2        1         0         1
  PPP3CA WILD-TYPE      10       20       44       30        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP3CA MUTATED           0          3          1          2        3
  PPP3CA WILD-TYPE        29         81         61         37       40
                  vv
clus               STAGE IVA
  PPP3CA MUTATED           0
  PPP3CA WILD-TYPE         4
D408V3, multiclass
            clus
vv           PPP3CA MUTATED PPP3CA WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PPP3CA MUTATED       0   3   4   6
  PPP3CA WILD-TYPE    54 132 257  96
D408V4, multiclass
       clus
vv      PPP3CA MUTATED PPP3CA WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 4              257
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PPP3CA MUTATED     4   4   2   3
  PPP3CA WILD-TYPE 191 169  87  82
D408V5, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  N0              4              191
  N1              4              169
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V6, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     9   2
  PPP3CA WILD-TYPE 473  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      9    2
  PPP3CA WILD-TYPE  473   36
   clus
vv  PPP3CA MUTATED PPP3CA WILD-TYPE
  0              9              473
  1              2               36
[1] 2 2
[1] FALSE
D408V7, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     5   8
  PPP3CA WILD-TYPE 167 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      5    8
  PPP3CA WILD-TYPE  167  398
        clus
vv       PPP3CA MUTATED PPP3CA WILD-TYPE
  FEMALE              5              167
  MALE                8              398
[1] 2 2
[1] FALSE
D408V8, binary
                  cls
clus                 0   1
  PPP3CA MUTATED    11   1
  PPP3CA WILD-TYPE 405 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED     11    1
  PPP3CA WILD-TYPE  405  101
     clus
vv    PPP3CA MUTATED PPP3CA WILD-TYPE
  NO              11              405
  YES              1              101
[1] 2 2
[1] FALSE
D408V9, continuous
[1] "Remove cluster labels:" "PPP3CA MUTATED"        
clus
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
D408V10, continuous
[1] "Remove cluster labels:" "PPP3CA MUTATED"        
clus
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-Z6-AAPN 
"PPP3CA WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PPP3CA MUTATED       3                         0
  PPP3CA WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP3CA MUTATED                                           0     7
  PPP3CA WILD-TYPE                                         1   350
D408V11, multiclass
                                           clus
vv                                          PPP3CA MUTATED PPP3CA WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V12, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     1   7
  PPP3CA WILD-TYPE   9 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      1    7
  PPP3CA WILD-TYPE    9  391
                        clus
vv                       PPP3CA MUTATED PPP3CA WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(409) Variable = RASAL2 MUTATION ANALYSIS
D409V1, survival
                  sevent
clus2                0   1
  RASAL2 MUTATED    16   6
  RASAL2 WILD-TYPE 322 210
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              22              532 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               6              210 
$`RASAL2 MUTATED`
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-LN-A49U TCGA-BR-4188 TCGA-BR-4256 
       13.22         7.76        13.41        15.35         7.43         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8487 
        9.67        34.68        30.90        29.59        32.25         1.12 
TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5723 TCGA-D7-5579 TCGA-D7-A6EY 
       31.96         9.01        18.97       105.07        20.91        11.44 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-VQ-A8P2 
       21.27        11.08        29.98        38.14 

$`RASAL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
            1.12             0.00 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
          105.07           122.30 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           17.16            13.53 
[1] "1.1 - 105.1 (17.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D409V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASAL2 MUTATED         0        0        1        1         5         5
  RASAL2 WILD-TYPE      10       20       45       30        79        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASAL2 MUTATED           1          3          2          0        2
  RASAL2 WILD-TYPE        28         81         60         39       41
                  vv
clus               STAGE IVA
  RASAL2 MUTATED           0
  RASAL2 WILD-TYPE         4
D409V3, multiclass
            clus
vv           RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               5               79
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RASAL2 MUTATED       0   4  10   6
  RASAL2 WILD-TYPE    54 131 251  96
D409V4, multiclass
       clus
vv      RASAL2 MUTATED RASAL2 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                10              251
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RASAL2 MUTATED     9   7   3   3
  RASAL2 WILD-TYPE 186 166  86  82
D409V5, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  N0              9              186
  N1              7              166
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V6, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    21   2
  RASAL2 WILD-TYPE 461  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     21    2
  RASAL2 WILD-TYPE  461   36
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0             21              461
  1              2               36
[1] 2 2
[1] FALSE
D409V7, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    10  13
  RASAL2 WILD-TYPE 162 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     10   13
  RASAL2 WILD-TYPE  162  393
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  FEMALE             10              162
  MALE               13              393
[1] 2 2
[1] FALSE
D409V8, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    16   5
  RASAL2 WILD-TYPE 400  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     16    5
  RASAL2 WILD-TYPE  400   97
     clus
vv    RASAL2 MUTATED RASAL2 WILD-TYPE
  NO              16              400
  YES              5               97
[1] 2 2
[1] FALSE
D409V9, continuous
[1] "Remove cluster labels:" "RASAL2 MUTATED"        
clus
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49V       TCGA-LN-A49W 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
D409V10, continuous
[1] "Remove cluster labels:" "RASAL2 MUTATED"        
clus
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49V 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RASAL2 MUTATED       3                         1
  RASAL2 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASAL2 MUTATED                                           0    16
  RASAL2 WILD-TYPE                                         1   341
D409V11, multiclass
                                           clus
vv                                          RASAL2 MUTATED RASAL2 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V12, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     1  15
  RASAL2 WILD-TYPE   9 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      1   15
  RASAL2 WILD-TYPE    9  383
                        clus
vv                       RASAL2 MUTATED RASAL2 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(410) Variable = RRS1 MUTATION ANALYSIS
D410V1, survival
                sevent
clus2              0   1
  RRS1 MUTATED     5   3
  RRS1 WILD-TYPE 333 213
  RRS1 MUTATED RRS1 WILD-TYPE 
             8            546 
  RRS1 MUTATED RRS1 WILD-TYPE 
             3            213 
$`RRS1 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OR TCGA-VR-A8EX TCGA-Z6-A9VB TCGA-BR-7707 TCGA-BR-8487 
       21.99         3.16        28.11         1.32        35.84         1.12 
TCGA-D7-5578 TCGA-D7-A4YT 
       12.66        14.27 

$`RRS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RRS1 MUTATED RRS1 WILD-TYPE 
          1.12           0.00 
  RRS1 MUTATED RRS1 WILD-TYPE 
         35.84         122.30 
  RRS1 MUTATED RRS1 WILD-TYPE 
        13.465         13.565 
[1] "1.1 - 35.8 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D410V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRS1 MUTATED         0        1        1        0         1         1
  RRS1 WILD-TYPE      10       19       45       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRS1 MUTATED           0          4          0          0        1         1
  RRS1 WILD-TYPE        29         80         62         39       42         3
D410V3, multiclass
            clus
vv           RRS1 MUTATED RRS1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RRS1 MUTATED       2   2   3   3
  RRS1 WILD-TYPE    52 133 258  99
D410V4, multiclass
       clus
vv      RRS1 MUTATED RRS1 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RRS1 MUTATED     5   3   1   1
  RRS1 WILD-TYPE 190 170  88  84
D410V5, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  N0            5            190
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V6, binary
                cls
clus               0   1
  RRS1 MUTATED     7   2
  RRS1 WILD-TYPE 475  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      7    2
  RRS1 WILD-TYPE  475   36
   clus
vv  RRS1 MUTATED RRS1 WILD-TYPE
  0            7            475
  1            2             36
[1] 2 2
[1] FALSE
D410V7, binary
                cls
clus               0   1
  RRS1 MUTATED     4   6
  RRS1 WILD-TYPE 168 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    6
  RRS1 WILD-TYPE  168  400
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  FEMALE            4            168
  MALE              6            400
[1] 2 2
[1] FALSE
D410V8, binary
                cls
clus               0   1
  RRS1 MUTATED     9   0
  RRS1 WILD-TYPE 407 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      9    0
  RRS1 WILD-TYPE  407  102
     clus
vv    RRS1 MUTATED RRS1 WILD-TYPE
  NO             9            407
  YES            0            102
[1] 2 2
[1] FALSE
D410V9, continuous
[1] "Remove cluster labels:" "RRS1 MUTATED"          
clus
  RRS1 MUTATED RRS1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
D410V10, continuous
[1] "Remove cluster labels:" "RRS1 MUTATED"          
clus
  RRS1 MUTATED RRS1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EZ 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" "RRS1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"RRS1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RRS1 MUTATED       0                         0
  RRS1 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRS1 MUTATED                                           0     8
  RRS1 WILD-TYPE                                         1   349
D410V11, multiclass
                                           clus
vv                                          RRS1 MUTATED RRS1 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V12, binary
                cls
clus               0   1
  RRS1 MUTATED     0   7
  RRS1 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      0    7
  RRS1 WILD-TYPE   10  391
                        clus
vv                       RRS1 MUTATED RRS1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(411) Variable = RBM6 MUTATION ANALYSIS
D411V1, survival
                sevent
clus2              0   1
  RBM6 MUTATED    12   9
  RBM6 WILD-TYPE 326 207
  RBM6 MUTATED RBM6 WILD-TYPE 
            21            533 
  RBM6 MUTATED RBM6 WILD-TYPE 
             9            207 
$`RBM6 MUTATED`
TCGA-L5-A8NS TCGA-L7-A56G TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
       13.41        10.85         2.66         6.97        30.90        34.68 
TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 
       44.94         8.05         2.20         0.95        26.33        11.80 
TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5728 
       25.05        28.14        31.96         6.58        15.95        65.10 
TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-VQ-A8P2 
       22.68        23.84        38.14 

$`RBM6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         1.32        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        29.59         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19        17.52         4.31        14.04         3.32 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RBM6 MUTATED RBM6 WILD-TYPE 
          0.95           0.00 
  RBM6 MUTATED RBM6 WILD-TYPE 
          65.1          122.3 
  RBM6 MUTATED RBM6 WILD-TYPE 
         22.68          13.51 
[1] "0.9 - 65.1 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D411V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM6 MUTATED         1        0        2        1         5         4
  RBM6 WILD-TYPE       9       20       44       30        79        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM6 MUTATED           0          3          2          3        2         0
  RBM6 WILD-TYPE        29         81         60         36       41         4
D411V3, multiclass
            clus
vv           RBM6 MUTATED RBM6 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RBM6 MUTATED       2   5  10   8
  RBM6 WILD-TYPE    52 130 251  94
D411V4, multiclass
       clus
vv      RBM6 MUTATED RBM6 WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3              10            251
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RBM6 MUTATED    10   5   3   5
  RBM6 WILD-TYPE 185 168  86  80
D411V5, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  N0           10            185
  N1            5            168
  N2            3             86
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V6, binary
                cls
clus               0   1
  RBM6 MUTATED    22   1
  RBM6 WILD-TYPE 460  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     22    1
  RBM6 WILD-TYPE  460   37
   clus
vv  RBM6 MUTATED RBM6 WILD-TYPE
  0           22            460
  1            1             37
[1] 2 2
[1] FALSE
D411V7, binary
                cls
clus               0   1
  RBM6 MUTATED    13  13
  RBM6 WILD-TYPE 159 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     13   13
  RBM6 WILD-TYPE  159  393
        clus
vv       RBM6 MUTATED RBM6 WILD-TYPE
  FEMALE           13            159
  MALE             13            393
[1] 2 2
[1] FALSE
D411V8, binary
                cls
clus               0   1
  RBM6 MUTATED    18   3
  RBM6 WILD-TYPE 398  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     18    3
  RBM6 WILD-TYPE  398   99
     clus
vv    RBM6 MUTATED RBM6 WILD-TYPE
  NO            18            398
  YES            3             99
[1] 2 2
[1] FALSE
D411V9, continuous
D411V10, continuous
[1] "Remove cluster labels:" "RBM6 MUTATED"          
clus
  RBM6 MUTATED RBM6 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NW     TCGA-LN-A49O 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" "RBM6 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RBM6 MUTATED       4                         2
  RBM6 WILD-TYPE   129                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBM6 MUTATED                                           0    17
  RBM6 WILD-TYPE                                         1   340
D411V11, multiclass
                                           clus
vv                                          RBM6 MUTATED RBM6 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V12, binary
                cls
clus               0   1
  RBM6 MUTATED     0  21
  RBM6 WILD-TYPE  10 377
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED      0   21
  RBM6 WILD-TYPE   10  377
                        clus
vv                       RBM6 MUTATED RBM6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           21            377
[1] 2 2
[1] FALSE

Clustering(412) Variable = AXIN2 MUTATION ANALYSIS
D412V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED    10  11
  AXIN2 WILD-TYPE 328 205
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             21             533 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             11             205 
$`AXIN2 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OT TCGA-S8-A6BW TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8078 
       21.99         4.90        20.38        34.68         9.07        29.59 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG 
       31.10         1.12        34.98        16.14        12.43         6.58 
TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-MX-A5UJ 
       15.95         9.01       105.07         5.92        11.44        19.73 
TCGA-R5-A7ZE TCGA-RD-A7BW TCGA-RD-A8N6 
       18.21         5.13         8.94 

$`AXIN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         3.45        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  AXIN2 MUTATED AXIN2 WILD-TYPE 
           1.12            0.00 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
         105.07          122.30 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          15.95           13.55 
[1] "1.1 - 105.1 (15.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D412V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AXIN2 MUTATED         0        0        2        3         3         3
  AXIN2 WILD-TYPE      10       20       44       28        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AXIN2 MUTATED           0          4          2          1        4         0
  AXIN2 WILD-TYPE        29         80         60         38       39         4
D412V3, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AXIN2 MUTATED       0   5  11   6
  AXIN2 WILD-TYPE    54 130 250  96
D412V4, multiclass
       clus
vv      AXIN2 MUTATED AXIN2 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3               11             250
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AXIN2 MUTATED     8   6   4   4
  AXIN2 WILD-TYPE 187 167  85  81
D412V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0             8             187
  N1             6             167
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V6, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   4
  AXIN2 WILD-TYPE 465  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    4
  AXIN2 WILD-TYPE  465   34
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            17             465
  1             4              34
[1] 2 2
[1] FALSE
D412V7, binary
                 cls
clus                0   1
  AXIN2 MUTATED    14   8
  AXIN2 WILD-TYPE 158 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     14    8
  AXIN2 WILD-TYPE  158  398
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  FEMALE            14             158
  MALE               8             398
[1] 2 2
[1] FALSE
D412V8, binary
                 cls
clus                0   1
  AXIN2 MUTATED    20   1
  AXIN2 WILD-TYPE 396 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     20    1
  AXIN2 WILD-TYPE  396  101
     clus
vv    AXIN2 MUTATED AXIN2 WILD-TYPE
  NO             20             396
  YES             1             101
[1] 2 2
[1] FALSE
D412V9, continuous
D412V10, continuous
[1] "Remove cluster labels:" "AXIN2 MUTATED"         
clus
  AXIN2 MUTATED AXIN2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" "AXIN2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"AXIN2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AXIN2 MUTATED       2                         0
  AXIN2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AXIN2 MUTATED                                           0    16
  AXIN2 WILD-TYPE                                         1   341
D412V11, multiclass
                                           clus
vv                                          AXIN2 MUTATED AXIN2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V12, binary
                 cls
clus                0   1
  AXIN2 MUTATED     0  17
  AXIN2 WILD-TYPE  10 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED      0   17
  AXIN2 WILD-TYPE   10  381
                        clus
vv                       AXIN2 MUTATED AXIN2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(413) Variable = TFE3 MUTATION ANALYSIS
D413V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED     5   4
  TFE3 WILD-TYPE 333 212
  TFE3 MUTATED TFE3 WILD-TYPE 
             9            545 
  TFE3 MUTATED TFE3 WILD-TYPE 
             4            212 
$`TFE3 MUTATED`
TCGA-2H-A9GJ TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4QL 
       58.55        32.78        44.94         1.12         1.48        16.14 
TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-HU-A4GU 
        6.58        22.68         6.58 

$`TFE3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TFE3 MUTATED TFE3 WILD-TYPE 
          1.12           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         58.55         122.30 
  TFE3 MUTATED TFE3 WILD-TYPE 
         16.14          13.55 
[1] "1.1 - 58.5 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D413V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TFE3 MUTATED         1        0        0        0         4         2
  TFE3 WILD-TYPE       9       20       46       31        80        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TFE3 MUTATED           0          0          1          1        0         0
  TFE3 WILD-TYPE        29         84         61         38       43         4
D413V3, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TFE3 MUTATED       2   0   7   1
  TFE3 WILD-TYPE    52 135 254 101
D413V4, multiclass
       clus
vv      TFE3 MUTATED TFE3 WILD-TYPE
  T0+T1            2             52
  T2               0            135
  T3               7            254
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TFE3 MUTATED     5   2   0   2
  TFE3 WILD-TYPE 190 171  89  83
D413V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0            5            190
  N1            2            171
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V6, binary
                cls
clus               0   1
  TFE3 MUTATED    10   0
  TFE3 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED     10    0
  TFE3 WILD-TYPE  472   38
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D413V7, binary
                cls
clus               0   1
  TFE3 MUTATED     6   4
  TFE3 WILD-TYPE 166 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      6    4
  TFE3 WILD-TYPE  166  402
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  FEMALE            6            166
  MALE              4            402
[1] 2 2
[1] FALSE
D413V8, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 407 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  407  102
     clus
vv    TFE3 MUTATED TFE3 WILD-TYPE
  NO             9            407
  YES            0            102
[1] 2 2
[1] FALSE
D413V9, continuous
D413V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TFE3 MUTATED       3                         0
  TFE3 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TFE3 MUTATED                                           0     6
  TFE3 WILD-TYPE                                         1   351
D413V11, multiclass
                                           clus
vv                                          TFE3 MUTATED TFE3 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V12, binary
                cls
clus               0   1
  TFE3 MUTATED     0   9
  TFE3 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      0    9
  TFE3 WILD-TYPE   10  389
                        clus
vv                       TFE3 MUTATED TFE3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(414) Variable = RPL22 MUTATION ANALYSIS
D414V1, survival
                 sevent
clus2               0   1
  RPL22 MUTATED     6   2
  RPL22 WILD-TYPE 332 214
  RPL22 MUTATED RPL22 WILD-TYPE 
              8             546 
  RPL22 MUTATED RPL22 WILD-TYPE 
              2             214 
$`RPL22 MUTATED`
TCGA-BR-6852 TCGA-BR-8592 TCGA-BR-8680 TCGA-CG-5728 TCGA-EQ-8122 TCGA-HF-A5NB 
       44.94         6.28        31.96        65.10         7.99        30.51 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`RPL22 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       28.14         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RPL22 MUTATED RPL22 WILD-TYPE 
           6.28            0.00 
  RPL22 MUTATED RPL22 WILD-TYPE 
           65.1           122.3 
  RPL22 MUTATED RPL22 WILD-TYPE 
         31.235          13.510 
[1] "6.3 - 65.1 (31.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D414V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RPL22 MUTATED         0        0        2        0         1         1
  RPL22 WILD-TYPE      10       20       44       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPL22 MUTATED           0          1          1          1        1         0
  RPL22 WILD-TYPE        29         83         61         38       42         4
D414V3, multiclass
            clus
vv           RPL22 MUTATED RPL22 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RPL22 MUTATED       1   1   2   4
  RPL22 WILD-TYPE    53 134 259  98
D414V4, multiclass
       clus
vv      RPL22 MUTATED RPL22 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                2             259
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RPL22 MUTATED     2   5   1   1
  RPL22 WILD-TYPE 193 168  88  84
D414V5, multiclass
    clus
vv   RPL22 MUTATED RPL22 WILD-TYPE
  N0             2             193
  N1             5             168
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V6, binary
                 cls
clus                0   1
  RPL22 MUTATED     7   1
  RPL22 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      7    1
  RPL22 WILD-TYPE  475   37
   clus
vv  RPL22 MUTATED RPL22 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D414V7, binary
                 cls
clus                0   1
  RPL22 MUTATED     6   3
  RPL22 WILD-TYPE 166 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      6    3
  RPL22 WILD-TYPE  166  403
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  FEMALE             6             166
  MALE               3             403
[1] 2 2
[1] FALSE
D414V8, binary
                 cls
clus                0   1
  RPL22 MUTATED     4   3
  RPL22 WILD-TYPE 412  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      4    3
  RPL22 WILD-TYPE  412   99
     clus
vv    RPL22 MUTATED RPL22 WILD-TYPE
  NO              4             412
  YES             3              99
[1] 2 2
[1] FALSE
D414V9, continuous
D414V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RPL22 MUTATED       2                         0
  RPL22 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPL22 MUTATED                                           0     5
  RPL22 WILD-TYPE                                         1   352
D414V11, multiclass
                                           clus
vv                                          RPL22 MUTATED RPL22 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V12, binary
                 cls
clus                0   1
  RPL22 MUTATED     0   6
  RPL22 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      0    6
  RPL22 WILD-TYPE   10  392
                        clus
vv                       RPL22 MUTATED RPL22 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(415) Variable = CDC5L MUTATION ANALYSIS
D415V1, survival
                 sevent
clus2               0   1
  CDC5L MUTATED     9   5
  CDC5L WILD-TYPE 329 211
  CDC5L MUTATED CDC5L WILD-TYPE 
             14             540 
  CDC5L MUTATED CDC5L WILD-TYPE 
              5             211 
$`CDC5L MUTATED`
TCGA-2H-A9GF TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6801 
       25.78        26.70         6.97        30.90        34.68        40.21 
TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MI TCGA-FP-A4BE TCGA-HU-A4H8 
       35.84         1.12        31.96        11.77        11.08        14.07 
TCGA-IN-7808 TCGA-MX-A666 
        3.45        14.04 

$`CDC5L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CDC5L MUTATED CDC5L WILD-TYPE 
           1.12            0.00 
  CDC5L MUTATED CDC5L WILD-TYPE 
          40.21          122.30 
  CDC5L MUTATED CDC5L WILD-TYPE 
         19.925          13.510 
[1] "1.1 - 40.2 (19.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D415V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC5L MUTATED         0        0        2        0         5         2
  CDC5L WILD-TYPE      10       20       44       31        79        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC5L MUTATED           1          2          0          0        1         0
  CDC5L WILD-TYPE        28         82         62         39       42         4
D415V3, multiclass
            clus
vv           CDC5L MUTATED CDC5L WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CDC5L MUTATED       1   3   9   3
  CDC5L WILD-TYPE    53 132 252  99
D415V4, multiclass
       clus
vv      CDC5L MUTATED CDC5L WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                9             252
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CDC5L MUTATED     7   5   1   1
  CDC5L WILD-TYPE 188 168  88  84
D415V5, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  N0             7             188
  N1             5             168
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V6, binary
                 cls
clus                0   1
  CDC5L MUTATED    12   2
  CDC5L WILD-TYPE 470  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     12    2
  CDC5L WILD-TYPE  470   36
   clus
vv  CDC5L MUTATED CDC5L WILD-TYPE
  0            12             470
  1             2              36
[1] 2 2
[1] FALSE
D415V7, binary
                 cls
clus                0   1
  CDC5L MUTATED     6  11
  CDC5L WILD-TYPE 166 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      6   11
  CDC5L WILD-TYPE  166  395
        clus
vv       CDC5L MUTATED CDC5L WILD-TYPE
  FEMALE             6             166
  MALE              11             395
[1] 2 2
[1] FALSE
D415V8, binary
                 cls
clus                0   1
  CDC5L MUTATED    14   1
  CDC5L WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     14    1
  CDC5L WILD-TYPE  402  101
     clus
vv    CDC5L MUTATED CDC5L WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D415V9, continuous
D415V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDC5L MUTATED       3                         1
  CDC5L WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC5L MUTATED                                           0    12
  CDC5L WILD-TYPE                                         1   345
D415V11, multiclass
                                           clus
vv                                          CDC5L MUTATED CDC5L WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V12, binary
                 cls
clus                0   1
  CDC5L MUTATED     0  16
  CDC5L WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      0   16
  CDC5L WILD-TYPE   10  382
                        clus
vv                       CDC5L MUTATED CDC5L WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(416) Variable = SYNCRIP MUTATION ANALYSIS
D416V1, survival
                   sevent
clus2                 0   1
  SYNCRIP MUTATED    10   7
  SYNCRIP WILD-TYPE 328 209
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               17               537 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                7               209 
$`SYNCRIP MUTATED`
TCGA-CG-4460 TCGA-L5-A8NL TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 
       21.99        13.22         2.66        26.70        19.56         6.97 
TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8295 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A486 
       34.68        18.15         2.20         1.12        31.96         6.31 
TCGA-CD-A4MG TCGA-CG-5728 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-VQ-A8PE 
        6.58        65.10        30.51         6.51        22.19 

$`SYNCRIP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        3.42         2.10         1.32        19.73        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        37.22        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             1.12              0.00 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             65.1             122.3 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            18.15             13.55 
[1] "1.1 - 65.1 (18.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D416V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYNCRIP MUTATED         0        0        1        0         6         2
  SYNCRIP WILD-TYPE      10       20       45       31        78        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNCRIP MUTATED           1          1          1          2        3
  SYNCRIP WILD-TYPE        28         83         61         37       40
                   vv
clus                STAGE IVA
  SYNCRIP MUTATED           0
  SYNCRIP WILD-TYPE         4
D416V3, multiclass
            clus
vv           SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                6                78
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SYNCRIP MUTATED       0   1   9   7
  SYNCRIP WILD-TYPE    54 134 252  95
D416V4, multiclass
       clus
vv      SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  9               252
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SYNCRIP MUTATED     9   4   1   3
  SYNCRIP WILD-TYPE 186 169  88  82
D416V5, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  N0               9               186
  N1               4               169
  N2               1                88
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V6, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    14   2
  SYNCRIP WILD-TYPE 468  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     14    2
  SYNCRIP WILD-TYPE  468   36
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0              14               468
  1               2                36
[1] 2 2
[1] FALSE
D416V7, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     8   9
  SYNCRIP WILD-TYPE 164 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      8    9
  SYNCRIP WILD-TYPE  164  397
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  FEMALE               8               164
  MALE                 9               397
[1] 2 2
[1] FALSE
D416V8, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    14   1
  SYNCRIP WILD-TYPE 402 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     14    1
  SYNCRIP WILD-TYPE  402  101
     clus
vv    SYNCRIP MUTATED SYNCRIP WILD-TYPE
  NO               14               402
  YES               1               101
[1] 2 2
[1] FALSE
D416V9, continuous
D416V10, continuous
[1] "Remove cluster labels:" "SYNCRIP MUTATED"       
clus
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" "SYNCRIP WILD-TYPE" 
       TCGA-XP-A8T8 
"SYNCRIP WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SYNCRIP MUTATED       4                         0
  SYNCRIP WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYNCRIP MUTATED                                           0    10
  SYNCRIP WILD-TYPE                                         1   347
D416V11, multiclass
                                           clus
vv                                          SYNCRIP MUTATED SYNCRIP WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V12, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     0  12
  SYNCRIP WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      0   12
  SYNCRIP WILD-TYPE   10  386
                        clus
vv                       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(417) Variable = CRYGA MUTATION ANALYSIS
D417V1, survival
                 sevent
clus2               0   1
  CRYGA MUTATED     8   3
  CRYGA WILD-TYPE 330 213
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             543 
  CRYGA MUTATED CRYGA WILD-TYPE 
              3             213 
$`CRYGA MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5721 
       34.68        29.59         6.18        31.96        11.77         6.02 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-R5-A7ZI TCGA-RD-A7C1 
        0.10         6.58        29.00        74.53        16.67 

$`CRYGA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CRYGA MUTATED CRYGA WILD-TYPE 
            0.1             0.0 
  CRYGA MUTATED CRYGA WILD-TYPE 
          74.53          122.30 
  CRYGA MUTATED CRYGA WILD-TYPE 
          16.67           13.55 
[1] "0.1 - 74.5 (16.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D417V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYGA MUTATED         0        0        1        0         2         2
  CRYGA WILD-TYPE      10       20       45       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRYGA MUTATED           0          1          0          2        3         0
  CRYGA WILD-TYPE        29         83         62         37       40         4
D417V3, multiclass
            clus
vv           CRYGA MUTATED CRYGA WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CRYGA MUTATED       0   1   4   6
  CRYGA WILD-TYPE    54 134 257  96
D417V4, multiclass
       clus
vv      CRYGA MUTATED CRYGA WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CRYGA MUTATED     4   4   2   1
  CRYGA WILD-TYPE 191 169  87  84
D417V5, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V6, binary
                 cls
clus                0   1
  CRYGA MUTATED     9   2
  CRYGA WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      9    2
  CRYGA WILD-TYPE  473   36
   clus
vv  CRYGA MUTATED CRYGA WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D417V7, binary
                 cls
clus                0   1
  CRYGA MUTATED     4   7
  CRYGA WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      4    7
  CRYGA WILD-TYPE  168  399
        clus
vv       CRYGA MUTATED CRYGA WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D417V8, binary
                 cls
clus                0   1
  CRYGA MUTATED    10   0
  CRYGA WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED     10    0
  CRYGA WILD-TYPE  406  102
     clus
vv    CRYGA MUTATED CRYGA WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D417V9, continuous
D417V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CRYGA MUTATED       5                         0
  CRYGA WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYGA MUTATED                                           0     5
  CRYGA WILD-TYPE                                         1   352
D417V11, multiclass
                                           clus
vv                                          CRYGA MUTATED CRYGA WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V12, binary
                 cls
clus                0   1
  CRYGA MUTATED     1   9
  CRYGA WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      1    9
  CRYGA WILD-TYPE    9  389
                        clus
vv                       CRYGA MUTATED CRYGA WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(418) Variable = SF3B2 MUTATION ANALYSIS
D418V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED    11   8
  SF3B2 WILD-TYPE 327 208
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             19             535 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              8             208 
$`SF3B2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GN TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-4184 
        4.31        19.99         8.94         7.76        26.70         6.97 
TCGA-BR-6565 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-CG-4477 
        9.17         6.18         1.12        12.79        31.96        30.97 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN 
        6.02        28.96        13.78        26.47        22.68        29.98 
TCGA-HU-A4GQ 
        0.10 

$`SF3B2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 
       12.03         0.00         9.01        18.97         7.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SF3B2 MUTATED SF3B2 WILD-TYPE 
            0.1             0.0 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          31.96          122.30 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          12.79           13.58 
[1] "0.1 - 32.0 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D418V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SF3B2 MUTATED         0        1        2        0         3         6
  SF3B2 WILD-TYPE      10       19       44       31        81        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF3B2 MUTATED           1          1          1          2        2         0
  SF3B2 WILD-TYPE        28         83         61         37       41         4
D418V3, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SF3B2 MUTATED       1   4   8   6
  SF3B2 WILD-TYPE    53 131 253  96
D418V4, multiclass
       clus
vv      SF3B2 MUTATED SF3B2 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                8             253
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SF3B2 MUTATED     9   6   2   2
  SF3B2 WILD-TYPE 186 167  87  83
D418V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             9             186
  N1             6             167
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V6, binary
                 cls
clus                0   1
  SF3B2 MUTATED    15   1
  SF3B2 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     15    1
  SF3B2 WILD-TYPE  467   37
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D418V7, binary
                 cls
clus                0   1
  SF3B2 MUTATED     8  12
  SF3B2 WILD-TYPE 164 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      8   12
  SF3B2 WILD-TYPE  164  394
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  FEMALE             8             164
  MALE              12             394
[1] 2 2
[1] FALSE
D418V8, binary
                 cls
clus                0   1
  SF3B2 MUTATED    15   2
  SF3B2 WILD-TYPE 401 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     15    2
  SF3B2 WILD-TYPE  401  100
     clus
vv    SF3B2 MUTATED SF3B2 WILD-TYPE
  NO             15             401
  YES             2             100
[1] 2 2
[1] FALSE
D418V9, continuous
D418V10, continuous
[1] "Remove cluster labels:" "SF3B2 MUTATED"         
clus
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL      TCGA-IG-A3Y9 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" "SF3B2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SF3B2 MUTATED       4                         0
  SF3B2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SF3B2 MUTATED                                           0    12
  SF3B2 WILD-TYPE                                         1   345
D418V11, multiclass
                                           clus
vv                                          SF3B2 MUTATED SF3B2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V12, binary
                 cls
clus                0   1
  SF3B2 MUTATED     0  13
  SF3B2 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      0   13
  SF3B2 WILD-TYPE   10  385
                        clus
vv                       SF3B2 MUTATED SF3B2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(419) Variable = FAM113B MUTATION ANALYSIS
D419V1, survival
                   sevent
clus2                 0   1
  FAM113B MUTATED     9   6
  FAM113B WILD-TYPE 329 210
  FAM113B MUTATED FAM113B WILD-TYPE 
               15               539 
  FAM113B MUTATED FAM113B WILD-TYPE 
                6               210 
$`FAM113B MUTATED`
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8361 
        7.04        38.40        30.90        35.84        14.43        31.10 
TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY 
       31.27        31.96         6.02       105.07        21.07        11.44 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-IN-A6RL 
       14.47        11.08        13.35 

$`FAM113B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM113B MUTATED FAM113B WILD-TYPE 
             6.02              0.00 
  FAM113B MUTATED FAM113B WILD-TYPE 
           105.07            122.30 
  FAM113B MUTATED FAM113B WILD-TYPE 
            21.07             13.51 
[1] "6.0 - 105.1 (21.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D419V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM113B MUTATED         0        0        2        1         1         1
  FAM113B WILD-TYPE      10       20       44       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM113B MUTATED           1          3          1          2        2
  FAM113B WILD-TYPE        28         81         61         37       41
                   vv
clus                STAGE IVA
  FAM113B MUTATED           0
  FAM113B WILD-TYPE         4
D419V3, multiclass
            clus
vv           FAM113B MUTATED FAM113B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               3                81
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM113B MUTATED       0   6   2   7
  FAM113B WILD-TYPE    54 129 259  95
D419V4, multiclass
       clus
vv      FAM113B MUTATED FAM113B WILD-TYPE
  T0+T1               0                54
  T2                  6               129
  T3                  2               259
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM113B MUTATED     5   4   3   2
  FAM113B WILD-TYPE 190 169  86  83
D419V5, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  N0               5               190
  N1               4               169
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V6, binary
                   cls
clus                  0   1
  FAM113B MUTATED    14   1
  FAM113B WILD-TYPE 468  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED     14    1
  FAM113B WILD-TYPE  468   37
   clus
vv  FAM113B MUTATED FAM113B WILD-TYPE
  0              14               468
  1               1                37
[1] 2 2
[1] FALSE
D419V7, binary
                   cls
clus                  0   1
  FAM113B MUTATED     6  11
  FAM113B WILD-TYPE 166 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      6   11
  FAM113B WILD-TYPE  166  395
        clus
vv       FAM113B MUTATED FAM113B WILD-TYPE
  FEMALE               6               166
  MALE                11               395
[1] 2 2
[1] FALSE
D419V8, binary
                   cls
clus                  0   1
  FAM113B MUTATED    15   1
  FAM113B WILD-TYPE 401 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED     15    1
  FAM113B WILD-TYPE  401  101
     clus
vv    FAM113B MUTATED FAM113B WILD-TYPE
  NO               15               401
  YES               1               101
[1] 2 2
[1] FALSE
D419V9, continuous
D419V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM113B MUTATED       1                         1
  FAM113B WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM113B MUTATED                                           0    12
  FAM113B WILD-TYPE                                         1   345
D419V11, multiclass
                                           clus
vv                                          FAM113B MUTATED FAM113B WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V12, binary
                   cls
clus                  0   1
  FAM113B MUTATED     0  14
  FAM113B WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      0   14
  FAM113B WILD-TYPE   10  384
                        clus
vv                       FAM113B MUTATED FAM113B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(420) Variable = PTPN4 MUTATION ANALYSIS
D420V1, survival
                 sevent
clus2               0   1
  PTPN4 MUTATED     6   8
  PTPN4 WILD-TYPE 332 208
  PTPN4 MUTATED PTPN4 WILD-TYPE 
             14             540 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              8             208 
$`PTPN4 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GR TCGA-L5-A8NH TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-XP-A8T6 
       21.99        32.45        12.92        12.23        13.38        25.08 
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4QL TCGA-D7-A6EY 
        6.97         9.67        29.59        31.96        16.14        11.44 
TCGA-FP-A4BE TCGA-VQ-AA6J 
       11.08        27.55 

$`PTPN4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 

  PTPN4 MUTATED PTPN4 WILD-TYPE 
           6.97            0.00 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
          32.45          122.30 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
         14.760          13.565 
[1] "7.0 - 32.5 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D420V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN4 MUTATED         0        0        0        0         4         3
  PTPN4 WILD-TYPE      10       20       46       31        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN4 MUTATED           0          2          3          0        4         0
  PTPN4 WILD-TYPE        29         82         59         39       39         4
D420V3, multiclass
            clus
vv           PTPN4 MUTATED PTPN4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             0              39
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPN4 MUTATED       1   3   5   7
  PTPN4 WILD-TYPE    53 132 256  95
D420V4, multiclass
       clus
vv      PTPN4 MUTATED PTPN4 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                5             256
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPN4 MUTATED     8   3   3   2
  PTPN4 WILD-TYPE 187 170  86  83
D420V5, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  N0             8             187
  N1             3             170
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V6, binary
                 cls
clus                0   1
  PTPN4 MUTATED    13   3
  PTPN4 WILD-TYPE 469  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED     13    3
  PTPN4 WILD-TYPE  469   35
   clus
vv  PTPN4 MUTATED PTPN4 WILD-TYPE
  0            13             469
  1             3              35
[1] 2 2
[1] FALSE
D420V7, binary
                 cls
clus                0   1
  PTPN4 MUTATED     7  10
  PTPN4 WILD-TYPE 165 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      7   10
  PTPN4 WILD-TYPE  165  396
        clus
vv       PTPN4 MUTATED PTPN4 WILD-TYPE
  FEMALE             7             165
  MALE              10             396
[1] 2 2
[1] FALSE
D420V8, binary
                 cls
clus                0   1
  PTPN4 MUTATED    12   2
  PTPN4 WILD-TYPE 404 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED     12    2
  PTPN4 WILD-TYPE  404  100
     clus
vv    PTPN4 MUTATED PTPN4 WILD-TYPE
  NO             12             404
  YES             2             100
[1] 2 2
[1] FALSE
D420V9, continuous
[1] "Remove cluster labels:" "PTPN4 MUTATED"         
clus
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PTPN4 WILD-TYPE" "PTPN4 WILD-TYPE" 
D420V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPN4 MUTATED       3                         3
  PTPN4 WILD-TYPE   130                        11
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN4 MUTATED                                           0     9
  PTPN4 WILD-TYPE                                         1   348
D420V11, multiclass
                                           clus
vv                                          PTPN4 MUTATED PTPN4 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             3              11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V12, binary
                 cls
clus                0   1
  PTPN4 MUTATED     1  12
  PTPN4 WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      1   12
  PTPN4 WILD-TYPE    9  386
                        clus
vv                       PTPN4 MUTATED PTPN4 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(421) Variable = RNF111 MUTATION ANALYSIS
D421V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED    11   5
  RNF111 WILD-TYPE 327 211
  RNF111 MUTATED RNF111 WILD-TYPE 
              16              538 
  RNF111 MUTATED RNF111 WILD-TYPE 
               5              211 
$`RNF111 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GG TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-V5-AASX 
       19.99        20.05         0.13        12.03        12.85         8.98 
TCGA-VR-A8EP TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8680 TCGA-CG-4465 
       27.09         6.97         6.61        32.78        31.96         9.01 
TCGA-CG-5721 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-VQ-A8P2 
        6.02        16.44         5.92        38.14 

$`RNF111 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91        14.27        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RNF111 MUTATED RNF111 WILD-TYPE 
            0.13             0.00 
  RNF111 MUTATED RNF111 WILD-TYPE 
           38.14           122.30 
  RNF111 MUTATED RNF111 WILD-TYPE 
           12.44            13.63 
[1] "0.1 - 38.1 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D421V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF111 MUTATED         0        0        0        0         4         1
  RNF111 WILD-TYPE      10       20       46       31        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           2          2          2          1        3
  RNF111 WILD-TYPE        27         82         60         38       40
                  vv
clus               STAGE IVA
  RNF111 MUTATED           0
  RNF111 WILD-TYPE         4
D421V3, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RNF111 MUTATED       0   3   9   4
  RNF111 WILD-TYPE    54 132 252  98
D421V4, multiclass
       clus
vv      RNF111 MUTATED RNF111 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 9              252
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RNF111 MUTATED     4   7   2   3
  RNF111 WILD-TYPE 191 166  87  82
D421V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0              4              191
  N1              7              166
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V6, binary
                  cls
clus                 0   1
  RNF111 MUTATED    12   2
  RNF111 WILD-TYPE 470  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     12    2
  RNF111 WILD-TYPE  470   36
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0             12              470
  1              2               36
[1] 2 2
[1] FALSE
D421V7, binary
                  cls
clus                 0   1
  RNF111 MUTATED     7  11
  RNF111 WILD-TYPE 165 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      7   11
  RNF111 WILD-TYPE  165  395
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  FEMALE              7              165
  MALE               11              395
[1] 2 2
[1] FALSE
D421V8, binary
                  cls
clus                 0   1
  RNF111 MUTATED    12   2
  RNF111 WILD-TYPE 404 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     12    2
  RNF111 WILD-TYPE  404  100
     clus
vv    RNF111 MUTATED RNF111 WILD-TYPE
  NO              12              404
  YES              2              100
[1] 2 2
[1] FALSE
D421V9, continuous
[1] "Remove cluster labels:" "RNF111 MUTATED"        
clus
  RNF111 MUTATED RNF111 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-VR-A8EO       TCGA-VR-A8EQ 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
D421V10, continuous
[1] "Remove cluster labels:" "RNF111 MUTATED"        
clus
  RNF111 MUTATED RNF111 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8ER       TCGA-VR-A8EU 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" "RNF111 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RNF111 MUTATED       4                         0
  RNF111 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF111 MUTATED                                           0    11
  RNF111 WILD-TYPE                                         1   346
D421V11, multiclass
                                           clus
vv                                          RNF111 MUTATED RNF111 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V12, binary
                  cls
clus                 0   1
  RNF111 MUTATED     0  12
  RNF111 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      0   12
  RNF111 WILD-TYPE   10  386
                        clus
vv                       RNF111 MUTATED RNF111 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(422) Variable = LAT2 MUTATION ANALYSIS
D422V1, survival
                sevent
clus2              0   1
  LAT2 MUTATED     6   5
  LAT2 WILD-TYPE 332 211
  LAT2 MUTATED LAT2 WILD-TYPE 
            11            543 
  LAT2 MUTATED LAT2 WILD-TYPE 
             5            211 
$`LAT2 MUTATED`
TCGA-L5-A43J TCGA-JY-A939 TCGA-Q9-A6FW TCGA-BR-4184 TCGA-CD-A4MI TCGA-CG-5728 
        4.31        21.70         7.82         6.97        11.77        65.10 
TCGA-CG-5730 TCGA-D7-A6EY TCGA-IN-A6RI TCGA-IN-A6RR TCGA-VQ-A8P2 
        4.01        11.44        18.38         6.74        38.14 

$`LAT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02        28.96        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  LAT2 MUTATED LAT2 WILD-TYPE 
          4.01           0.00 
  LAT2 MUTATED LAT2 WILD-TYPE 
          65.1          122.3 
  LAT2 MUTATED LAT2 WILD-TYPE 
         11.44          13.68 
[1] "4.0 - 65.1 (11.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D422V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LAT2 MUTATED         1        0        1        0         0         2
  LAT2 WILD-TYPE       9       20       45       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAT2 MUTATED           0          4          2          0        1         0
  LAT2 WILD-TYPE        29         80         60         39       42         4
D422V3, multiclass
            clus
vv           LAT2 MUTATED LAT2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  LAT2 MUTATED       2   2   6   1
  LAT2 WILD-TYPE    52 133 255 101
D422V4, multiclass
       clus
vv      LAT2 MUTATED LAT2 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               6            255
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  LAT2 MUTATED     3   6   1   1
  LAT2 WILD-TYPE 192 167  88  84
D422V5, multiclass
    clus
vv   LAT2 MUTATED LAT2 WILD-TYPE
  N0            3            192
  N1            6            167
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V6, binary
                cls
clus               0   1
  LAT2 MUTATED     8   1
  LAT2 WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      8    1
  LAT2 WILD-TYPE  474   37
   clus
vv  LAT2 MUTATED LAT2 WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D422V7, binary
                cls
clus               0   1
  LAT2 MUTATED     3   8
  LAT2 WILD-TYPE 169 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      3    8
  LAT2 WILD-TYPE  169  398
        clus
vv       LAT2 MUTATED LAT2 WILD-TYPE
  FEMALE            3            169
  MALE              8            398
[1] 2 2
[1] FALSE
D422V8, binary
                cls
clus               0   1
  LAT2 MUTATED     7   1
  LAT2 WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      7    1
  LAT2 WILD-TYPE  409  101
     clus
vv    LAT2 MUTATED LAT2 WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D422V9, continuous
D422V10, continuous
[1] "Remove cluster labels:" "LAT2 MUTATED"          
clus
  LAT2 MUTATED LAT2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-R6-A6DN     TCGA-R6-A6L4 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" "LAT2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  LAT2 MUTATED       1                         0
  LAT2 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LAT2 MUTATED                                           0     8
  LAT2 WILD-TYPE                                         1   349
D422V11, multiclass
                                           clus
vv                                          LAT2 MUTATED LAT2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V12, binary
                cls
clus               0   1
  LAT2 MUTATED     0   6
  LAT2 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      0    6
  LAT2 WILD-TYPE   10  392
                        clus
vv                       LAT2 MUTATED LAT2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(423) Variable = ENTPD2 MUTATION ANALYSIS
D423V1, survival
                  sevent
clus2                0   1
  ENTPD2 MUTATED     4   2
  ENTPD2 WILD-TYPE 334 214
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               6              548 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               2              214 
$`ENTPD2 MUTATED`
TCGA-L5-A4OO TCGA-B7-5816 TCGA-CD-A4MI TCGA-D7-A4YV TCGA-HU-A4G9 TCGA-VQ-A91V 
        3.32        26.70        11.77         5.92        24.20        42.64 

$`ENTPD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
            3.32             0.00 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           42.64           122.30 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
          17.985           13.565 
[1] "3.3 - 42.6 (18.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D423V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ENTPD2 MUTATED         0        1        0        0         0         2
  ENTPD2 WILD-TYPE      10       19       46       31        84        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD2 MUTATED           0          2          0          1        0
  ENTPD2 WILD-TYPE        29         82         62         38       43
                  vv
clus               STAGE IVA
  ENTPD2 MUTATED           0
  ENTPD2 WILD-TYPE         4
D423V3, multiclass
            clus
vv           ENTPD2 MUTATED ENTPD2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ENTPD2 MUTATED       1   0   4   1
  ENTPD2 WILD-TYPE    53 135 257 101
D423V4, multiclass
       clus
vv      ENTPD2 MUTATED ENTPD2 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 4              257
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ENTPD2 MUTATED     2   3   1   1
  ENTPD2 WILD-TYPE 193 170  88  84
D423V5, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V6, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     7   0
  ENTPD2 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      7    0
  ENTPD2 WILD-TYPE  475   38
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D423V7, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   3
  ENTPD2 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    3
  ENTPD2 WILD-TYPE  168  403
        clus
vv       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D423V8, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   1
  ENTPD2 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    1
  ENTPD2 WILD-TYPE  412  101
     clus
vv    ENTPD2 MUTATED ENTPD2 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D423V9, continuous
D423V10, continuous
[1] "Remove cluster labels:" "ENTPD2 MUTATED"        
clus
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ENTPD2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ENTPD2 MUTATED       2                         0
  ENTPD2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ENTPD2 MUTATED                                           0     4
  ENTPD2 WILD-TYPE                                         1   353
D423V11, multiclass
                                           clus
vv                                          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V12, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     0   5
  ENTPD2 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      0    5
  ENTPD2 WILD-TYPE   10  393
                        clus
vv                       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(424) Variable = CUL2 MUTATION ANALYSIS
D424V1, survival
                sevent
clus2              0   1
  CUL2 MUTATED     7   2
  CUL2 WILD-TYPE 331 214
  CUL2 MUTATED CUL2 WILD-TYPE 
             9            545 
  CUL2 MUTATED CUL2 WILD-TYPE 
             2            214 
$`CUL2 MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-HU-8602 
       19.99         6.97        34.68        44.94        32.25        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-SW-A7EA 
        0.10        20.25        19.04 

$`CUL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CUL2 MUTATED CUL2 WILD-TYPE 
           0.1            0.0 
  CUL2 MUTATED CUL2 WILD-TYPE 
         44.94         122.30 
  CUL2 MUTATED CUL2 WILD-TYPE 
         20.25          13.51 
[1] "0.1 - 44.9 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D424V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUL2 MUTATED         0        0        2        0         2         2
  CUL2 WILD-TYPE      10       20       44       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUL2 MUTATED           0          1          0          3        0         0
  CUL2 WILD-TYPE        29         83         62         36       43         4
D424V3, multiclass
            clus
vv           CUL2 MUTATED CUL2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CUL2 MUTATED       0   2   4   4
  CUL2 WILD-TYPE    54 133 257  98
D424V4, multiclass
       clus
vv      CUL2 MUTATED CUL2 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUL2 MUTATED     6   1   2   1
  CUL2 WILD-TYPE 189 172  87  84
D424V5, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  N0            6            189
  N1            1            172
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V6, binary
                cls
clus               0   1
  CUL2 MUTATED     8   0
  CUL2 WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      8    0
  CUL2 WILD-TYPE  474   38
   clus
vv  CUL2 MUTATED CUL2 WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D424V7, binary
                cls
clus               0   1
  CUL2 MUTATED     7   3
  CUL2 WILD-TYPE 165 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      7    3
  CUL2 WILD-TYPE  165  403
        clus
vv       CUL2 MUTATED CUL2 WILD-TYPE
  FEMALE            7            165
  MALE              3            403
[1] 2 2
[1] FALSE
D424V8, binary
                cls
clus               0   1
  CUL2 MUTATED    10   0
  CUL2 WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     10    0
  CUL2 WILD-TYPE  406  102
     clus
vv    CUL2 MUTATED CUL2 WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D424V9, continuous
D424V10, continuous
[1] "Remove cluster labels:" "CUL2 MUTATED"          
clus
  CUL2 MUTATED CUL2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" "CUL2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"CUL2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUL2 MUTATED       3                         0
  CUL2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUL2 MUTATED                                           0     7
  CUL2 WILD-TYPE                                         1   350
D424V11, multiclass
                                           clus
vv                                          CUL2 MUTATED CUL2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V12, binary
                cls
clus               0   1
  CUL2 MUTATED     0   9
  CUL2 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      0    9
  CUL2 WILD-TYPE   10  389
                        clus
vv                       CUL2 MUTATED CUL2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(425) Variable = CROT MUTATION ANALYSIS
D425V1, survival
                sevent
clus2              0   1
  CROT MUTATED    12   4
  CROT WILD-TYPE 326 212
  CROT MUTATED CROT WILD-TYPE 
            16            538 
  CROT MUTATED CROT WILD-TYPE 
             4            212 
$`CROT MUTATED`
TCGA-IG-A97H TCGA-JY-A93D TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 
       14.50        31.56         6.97        34.68        32.25         4.31 
TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A6EZ 
       27.12        31.96        12.30         6.58         6.02        20.32 
TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-VQ-A8P2 
       22.32         6.58        14.07        38.14 

$`CROT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CROT MUTATED CROT WILD-TYPE 
          4.31           0.00 
  CROT MUTATED CROT WILD-TYPE 
         38.14         122.30 
  CROT MUTATED CROT WILD-TYPE 
         17.41          13.51 
[1] "4.3 - 38.1 (17.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D425V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CROT MUTATED         0        0        2        0         3         3
  CROT WILD-TYPE      10       20       44       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CROT MUTATED           0          3          1          1        3         0
  CROT WILD-TYPE        29         81         61         38       40         4
D425V3, multiclass
            clus
vv           CROT MUTATED CROT WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CROT MUTATED       1   2   6   7
  CROT WILD-TYPE    53 133 255  95
D425V4, multiclass
       clus
vv      CROT MUTATED CROT WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               6            255
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CROT MUTATED     6   7   2   1
  CROT WILD-TYPE 189 166  87  84
D425V5, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  N0            6            189
  N1            7            166
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V6, binary
                cls
clus               0   1
  CROT MUTATED    14   2
  CROT WILD-TYPE 468  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     14    2
  CROT WILD-TYPE  468   36
   clus
vv  CROT MUTATED CROT WILD-TYPE
  0           14            468
  1            2             36
[1] 2 2
[1] FALSE
D425V7, binary
                cls
clus               0   1
  CROT MUTATED     5  12
  CROT WILD-TYPE 167 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      5   12
  CROT WILD-TYPE  167  394
        clus
vv       CROT MUTATED CROT WILD-TYPE
  FEMALE            5            167
  MALE             12            394
[1] 2 2
[1] FALSE
D425V8, binary
                cls
clus               0   1
  CROT MUTATED    12   3
  CROT WILD-TYPE 404  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     12    3
  CROT WILD-TYPE  404   99
     clus
vv    CROT MUTATED CROT WILD-TYPE
  NO            12            404
  YES            3             99
[1] 2 2
[1] FALSE
D425V9, continuous
D425V10, continuous
[1] "Remove cluster labels:" "CROT MUTATED"          
clus
  CROT MUTATED CROT WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" "CROT WILD-TYPE" 
    TCGA-Z6-AAPN 
"CROT WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CROT MUTATED       7                         0
  CROT WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CROT MUTATED                                           0     9
  CROT WILD-TYPE                                         1   348
D425V11, multiclass
                                           clus
vv                                          CROT MUTATED CROT WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V12, binary
                cls
clus               0   1
  CROT MUTATED     0  14
  CROT WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      0   14
  CROT WILD-TYPE   10  384
                        clus
vv                       CROT MUTATED CROT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(426) Variable = PDS5B MUTATION ANALYSIS
D426V1, survival
                 sevent
clus2               0   1
  PDS5B MUTATED    16   9
  PDS5B WILD-TYPE 322 207
  PDS5B MUTATED PDS5B WILD-TYPE 
             25             529 
  PDS5B MUTATED PDS5B WILD-TYPE 
              9             207 
$`PDS5B MUTATED`
TCGA-CG-4460 TCGA-IG-A3Y9 TCGA-L5-A8NQ TCGA-LN-A4A1 TCGA-VR-A8EO TCGA-VR-A8EZ 
       21.99         0.85        21.37        12.59        25.81        18.18 
TCGA-VR-AA7D TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 
        9.17        14.37         2.10        26.70         6.97         9.34 
TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A4YY TCGA-HU-8602 
        6.18        31.96         6.58       105.07        13.78        22.32 
TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-R5-A7ZI TCGA-SW-A7EA 
       24.20         0.10         6.58        21.17        74.53        19.04 
TCGA-VQ-A8P2 
       38.14 

$`PDS5B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PDS5B MUTATED PDS5B WILD-TYPE 
            0.1             0.0 
  PDS5B MUTATED PDS5B WILD-TYPE 
         105.07          122.30 
  PDS5B MUTATED PDS5B WILD-TYPE 
          18.18           13.51 
[1] "0.1 - 105.1 (18.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D426V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDS5B MUTATED         0        2        1        1         5         4
  PDS5B WILD-TYPE      10       18       45       30        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDS5B MUTATED           0          5          1          3        4         0
  PDS5B WILD-TYPE        29         79         61         36       39         4
D426V3, multiclass
            clus
vv           PDS5B MUTATED PDS5B WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PDS5B MUTATED       3   3  11   9
  PDS5B WILD-TYPE    51 132 250  93
D426V4, multiclass
       clus
vv      PDS5B MUTATED PDS5B WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3               11             250
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PDS5B MUTATED    11   9   4   3
  PDS5B WILD-TYPE 184 164  85  82
D426V5, multiclass
    clus
vv   PDS5B MUTATED PDS5B WILD-TYPE
  N0            11             184
  N1             9             164
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V6, binary
                 cls
clus                0   1
  PDS5B MUTATED    23   3
  PDS5B WILD-TYPE 459  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED     23    3
  PDS5B WILD-TYPE  459   35
   clus
vv  PDS5B MUTATED PDS5B WILD-TYPE
  0            23             459
  1             3              35
[1] 2 2
[1] FALSE
D426V7, binary
                 cls
clus                0   1
  PDS5B MUTATED     8  19
  PDS5B WILD-TYPE 164 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED      8   19
  PDS5B WILD-TYPE  164  387
        clus
vv       PDS5B MUTATED PDS5B WILD-TYPE
  FEMALE             8             164
  MALE              19             387
[1] 2 2
[1] FALSE
D426V8, binary
                 cls
clus                0   1
  PDS5B MUTATED    20   6
  PDS5B WILD-TYPE 396  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED     20    6
  PDS5B WILD-TYPE  396   96
     clus
vv    PDS5B MUTATED PDS5B WILD-TYPE
  NO             20             396
  YES             6              96
[1] 2 2
[1] FALSE
D426V9, continuous
D426V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDS5B MUTATED       9                         1
  PDS5B WILD-TYPE   124                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDS5B MUTATED                                           0    14
  PDS5B WILD-TYPE                                         1   343
D426V11, multiclass
                                           clus
vv                                          PDS5B MUTATED PDS5B WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V12, binary
                 cls
clus                0   1
  PDS5B MUTATED     2  18
  PDS5B WILD-TYPE   8 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED      2   18
  PDS5B WILD-TYPE    8  380
                        clus
vv                       PDS5B MUTATED PDS5B WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(427) Variable = MTMR6 MUTATION ANALYSIS
D427V1, survival
                 sevent
clus2               0   1
  MTMR6 MUTATED     8   4
  MTMR6 WILD-TYPE 330 212
  MTMR6 MUTATED MTMR6 WILD-TYPE 
             12             542 
  MTMR6 MUTATED MTMR6 WILD-TYPE 
              4             212 
$`MTMR6 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6F8 TCGA-L5-A4OJ TCGA-R6-A6DQ TCGA-BR-6452 TCGA-BR-6566 
       19.99       122.10        21.01         7.59        34.68        32.78 
TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-A48A TCGA-CG-5725 TCGA-CG-5726 TCGA-KB-A6F7 
        0.26        31.96        12.43        15.02        28.96        63.62 

$`MTMR6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MTMR6 MUTATED MTMR6 WILD-TYPE 
           0.26            0.00 
  MTMR6 MUTATED MTMR6 WILD-TYPE 
          122.1           122.3 
  MTMR6 MUTATED MTMR6 WILD-TYPE 
         24.985          13.495 
[1] "0.3 - 122.1 (25.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D427V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTMR6 MUTATED         2        1        3        0         3         0
  MTMR6 WILD-TYPE       8       19       43       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTMR6 MUTATED           0          0          0          1        2         0
  MTMR6 WILD-TYPE        29         84         62         38       41         4
D427V3, multiclass
            clus
vv           MTMR6 MUTATED MTMR6 WILD-TYPE
  STAGE I                2               8
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MTMR6 MUTATED       4   2   4   2
  MTMR6 WILD-TYPE    50 133 257 100
D427V4, multiclass
       clus
vv      MTMR6 MUTATED MTMR6 WILD-TYPE
  T0+T1             4              50
  T2                2             133
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MTMR6 MUTATED     8   1   2   1
  MTMR6 WILD-TYPE 187 172  87  84
D427V5, multiclass
    clus
vv   MTMR6 MUTATED MTMR6 WILD-TYPE
  N0             8             187
  N1             1             172
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V6, binary
                 cls
clus                0   1
  MTMR6 MUTATED    10   1
  MTMR6 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR6 MUTATED     10    1
  MTMR6 WILD-TYPE  472   37
   clus
vv  MTMR6 MUTATED MTMR6 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D427V7, binary
                 cls
clus                0   1
  MTMR6 MUTATED     7   6
  MTMR6 WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR6 MUTATED      7    6
  MTMR6 WILD-TYPE  165  400
        clus
vv       MTMR6 MUTATED MTMR6 WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D427V8, binary
                 cls
clus                0   1
  MTMR6 MUTATED     8   2
  MTMR6 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR6 MUTATED      8    2
  MTMR6 WILD-TYPE  408  100
     clus
vv    MTMR6 MUTATED MTMR6 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D427V9, continuous
D427V10, continuous
[1] "Remove cluster labels:" "MTMR6 MUTATED"         
clus
  MTMR6 MUTATED MTMR6 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" "MTMR6 WILD-TYPE" 
     TCGA-Z6-AAPN 
"MTMR6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTMR6 MUTATED       2                         0
  MTMR6 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTMR6 MUTATED                                           0     8
  MTMR6 WILD-TYPE                                         1   349
D427V11, multiclass
                                           clus
vv                                          MTMR6 MUTATED MTMR6 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V12, binary
                 cls
clus                0   1
  MTMR6 MUTATED     0   7
  MTMR6 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR6 MUTATED      0    7
  MTMR6 WILD-TYPE   10  391
                        clus
vv                       MTMR6 MUTATED MTMR6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(428) Variable = SYCP2L MUTATION ANALYSIS
D428V1, survival
                  sevent
clus2                0   1
  SYCP2L MUTATED    10   6
  SYCP2L WILD-TYPE 328 210
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              16              538 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
               6              210 
$`SYCP2L MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NQ TCGA-LN-A4A9 TCGA-VR-A8EU TCGA-B7-5818 TCGA-BR-6452 
       19.99        21.37        11.54        18.31        11.70        34.68 
TCGA-BR-8382 TCGA-BR-8588 TCGA-BR-A4J5 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8536 
       25.05        12.79        28.34        16.14        12.30        12.43 
TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-A4G8 TCGA-MX-A666 
       15.95         1.02        22.68        14.04 

$`SYCP2L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SYCP2L MUTATED SYCP2L WILD-TYPE 
            1.02             0.00 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
           34.68           122.30 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
          16.045           13.510 
[1] "1.0 - 34.7 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D428V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYCP2L MUTATED         0        0        1        2         4         2
  SYCP2L WILD-TYPE      10       20       45       29        80        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYCP2L MUTATED           0          1          1          2        3
  SYCP2L WILD-TYPE        29         83         61         37       40
                  vv
clus               STAGE IVA
  SYCP2L MUTATED           0
  SYCP2L WILD-TYPE         4
D428V3, multiclass
            clus
vv           SYCP2L MUTATED SYCP2L WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SYCP2L MUTATED       1   5   6   4
  SYCP2L WILD-TYPE    53 130 255  98
D428V4, multiclass
       clus
vv      SYCP2L MUTATED SYCP2L WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 6              255
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SYCP2L MUTATED     7   5   1   3
  SYCP2L WILD-TYPE 188 168  88  82
D428V5, multiclass
    clus
vv   SYCP2L MUTATED SYCP2L WILD-TYPE
  N0              7              188
  N1              5              168
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V6, binary
                  cls
clus                 0   1
  SYCP2L MUTATED    12   3
  SYCP2L WILD-TYPE 470  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED     12    3
  SYCP2L WILD-TYPE  470   35
   clus
vv  SYCP2L MUTATED SYCP2L WILD-TYPE
  0             12              470
  1              3               35
[1] 2 2
[1] FALSE
D428V7, binary
                  cls
clus                 0   1
  SYCP2L MUTATED     6  11
  SYCP2L WILD-TYPE 166 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED      6   11
  SYCP2L WILD-TYPE  166  395
        clus
vv       SYCP2L MUTATED SYCP2L WILD-TYPE
  FEMALE              6              166
  MALE               11              395
[1] 2 2
[1] FALSE
D428V8, binary
                  cls
clus                 0   1
  SYCP2L MUTATED    13   2
  SYCP2L WILD-TYPE 403 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED     13    2
  SYCP2L WILD-TYPE  403  100
     clus
vv    SYCP2L MUTATED SYCP2L WILD-TYPE
  NO              13              403
  YES              2              100
[1] 2 2
[1] FALSE
D428V9, continuous
[1] "Remove cluster labels:" "SYCP2L MUTATED"        
clus
  SYCP2L MUTATED SYCP2L WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EW 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SYCP2L WILD-TYPE" "SYCP2L WILD-TYPE" 
D428V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SYCP2L MUTATED       5                         0
  SYCP2L WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYCP2L MUTATED                                           0    10
  SYCP2L WILD-TYPE                                         1   347
D428V11, multiclass
                                           clus
vv                                          SYCP2L MUTATED SYCP2L WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V12, binary
                  cls
clus                 0   1
  SYCP2L MUTATED     0  12
  SYCP2L WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED      0   12
  SYCP2L WILD-TYPE   10  386
                        clus
vv                       SYCP2L MUTATED SYCP2L WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(429) Variable = NUB1 MUTATION ANALYSIS
D429V1, survival
                sevent
clus2              0   1
  NUB1 MUTATED     8   4
  NUB1 WILD-TYPE 330 212
  NUB1 MUTATED NUB1 WILD-TYPE 
            12            542 
  NUB1 MUTATED NUB1 WILD-TYPE 
             4            212 
$`NUB1 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GH TCGA-2H-A9GN TCGA-IG-A6QS TCGA-JY-A93F TCGA-L5-A4OH 
       19.99        31.27         8.94         9.96        24.03        32.61 
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-R5-A7ZI 
       34.68        36.16         1.12        31.96         6.58        74.53 

$`NUB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.22         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NUB1 MUTATED NUB1 WILD-TYPE 
          1.12           0.00 
  NUB1 MUTATED NUB1 WILD-TYPE 
         74.53         122.30 
  NUB1 MUTATED NUB1 WILD-TYPE 
         27.65          13.51 
[1] "1.1 - 74.5 (27.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D429V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUB1 MUTATED         1        1        1        0         3         2
  NUB1 WILD-TYPE       9       19       45       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUB1 MUTATED           1          0          0          1        2         0
  NUB1 WILD-TYPE        28         84         62         38       41         4
D429V3, multiclass
            clus
vv           NUB1 MUTATED NUB1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NUB1 MUTATED       3   2   5   2
  NUB1 WILD-TYPE    51 133 256 100
D429V4, multiclass
       clus
vv      NUB1 MUTATED NUB1 WILD-TYPE
  T0+T1            3             51
  T2               2            133
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NUB1 MUTATED     6   4   1   1
  NUB1 WILD-TYPE 189 169  88  84
D429V5, multiclass
    clus
vv   NUB1 MUTATED NUB1 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V6, binary
                cls
clus               0   1
  NUB1 MUTATED     9   2
  NUB1 WILD-TYPE 473  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUB1 MUTATED      9    2
  NUB1 WILD-TYPE  473   36
   clus
vv  NUB1 MUTATED NUB1 WILD-TYPE
  0            9            473
  1            2             36
[1] 2 2
[1] FALSE
D429V7, binary
                cls
clus               0   1
  NUB1 MUTATED     4   8
  NUB1 WILD-TYPE 168 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUB1 MUTATED      4    8
  NUB1 WILD-TYPE  168  398
        clus
vv       NUB1 MUTATED NUB1 WILD-TYPE
  FEMALE            4            168
  MALE              8            398
[1] 2 2
[1] FALSE
D429V8, binary
                cls
clus               0   1
  NUB1 MUTATED    12   0
  NUB1 WILD-TYPE 404 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUB1 MUTATED     12    0
  NUB1 WILD-TYPE  404  102
     clus
vv    NUB1 MUTATED NUB1 WILD-TYPE
  NO            12            404
  YES            0            102
[1] 2 2
[1] FALSE
D429V9, continuous
D429V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NUB1 MUTATED       2                         0
  NUB1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUB1 MUTATED                                           0     8
  NUB1 WILD-TYPE                                         1   349
D429V11, multiclass
                                           clus
vv                                          NUB1 MUTATED NUB1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V12, binary
                cls
clus               0   1
  NUB1 MUTATED     1   6
  NUB1 WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUB1 MUTATED      1    6
  NUB1 WILD-TYPE    9  392
                        clus
vv                       NUB1 MUTATED NUB1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(430) Variable = ZFHX3 MUTATION ANALYSIS
D430V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    24  19
  ZFHX3 WILD-TYPE 314 197
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             43             511 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             19             197 
$`ZFHX3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A6QS TCGA-JY-A6FE TCGA-LN-A8HZ 
        4.31        19.99        21.99         9.96         3.68        12.33 
TCGA-R6-A6L4 TCGA-RE-A7BO TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 
       16.31         7.00         2.10        26.70         6.97        30.90 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 
        9.67        34.68        32.78        35.84        14.43        29.59 
TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8526 TCGA-CD-A48C 
       31.10        25.05         1.12        31.96        12.53        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        6.58        11.77         1.02         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 
       65.10        21.07         7.99        19.53        17.06        77.29 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H4 
       28.96        22.32         0.10         6.51        20.25        23.84 
TCGA-VQ-A8P2 
       38.14 

$`ZFHX3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        0.53        17.03         0.79        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.59         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
        0.99        12.03        15.02         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8604 
       30.51        26.47         1.51         5.92        24.39        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
            0.1             0.0 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         105.07          122.30 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          19.53           13.48 
[1] "0.1 - 105.1 (19.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D430V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFHX3 MUTATED         0        1        2        2         7        10
  ZFHX3 WILD-TYPE      10       19       44       29        77        73
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFHX3 MUTATED           2          8          0          5        5         0
  ZFHX3 WILD-TYPE        27         76         62         34       38         4
D430V3, multiclass
            clus
vv           ZFHX3 MUTATED ZFHX3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              7              77
  STAGE IIB             10              73
  STAGE III              2              27
  STAGE IIIA             8              76
  STAGE IIIB             0              62
  STAGE IIIC             5              34
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZFHX3 MUTATED       3   9  18  14
  ZFHX3 WILD-TYPE    51 126 243  88
D430V4, multiclass
       clus
vv      ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T0+T1             3              51
  T2                9             126
  T3               18             243
  T4               14              88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZFHX3 MUTATED    15  16   9   2
  ZFHX3 WILD-TYPE 180 157  80  83
D430V5, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  N0            15             180
  N1            16             157
  N2             9              80
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V6, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    37   3
  ZFHX3 WILD-TYPE 445  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     37    3
  ZFHX3 WILD-TYPE  445   35
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0            37             445
  1             3              35
[1] 2 2
[1] FALSE
D430V7, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    24  22
  ZFHX3 WILD-TYPE 148 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     24   22
  ZFHX3 WILD-TYPE  148  384
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  FEMALE            24             148
  MALE              22             384
[1] 2 2
[1] FALSE
D430V8, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    34   5
  ZFHX3 WILD-TYPE 382  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     34    5
  ZFHX3 WILD-TYPE  382   97
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO             34             382
  YES             5              97
[1] 2 2
[1] FALSE
D430V9, continuous
[1] "Remove cluster labels:" "ZFHX3 MUTATED"         
clus
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
     TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JD 
"ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" "ZFHX3 WILD-TYPE" 
D430V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZFHX3 MUTATED      12                         0
  ZFHX3 WILD-TYPE   121                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFHX3 MUTATED                                           0    26
  ZFHX3 WILD-TYPE                                         1   331
D430V11, multiclass
                                           clus
vv                                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                                12             121
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                26             331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V12, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     0  34
  ZFHX3 WILD-TYPE  10 364
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      0   34
  ZFHX3 WILD-TYPE   10  364
                        clus
vv                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            34             364
[1] 2 2
[1] FALSE

Clustering(431) Variable = EVI5 MUTATION ANALYSIS
D431V1, survival
                sevent
clus2              0   1
  EVI5 MUTATED    11   1
  EVI5 WILD-TYPE 327 215
  EVI5 MUTATED EVI5 WILD-TYPE 
            12            542 
  EVI5 MUTATED EVI5 WILD-TYPE 
             1            215 
$`EVI5 MUTATED`
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-R6-A6XG TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-7958 
       16.47         7.76        38.40        26.70        44.94        29.56 
TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8572 TCGA-HU-A4GH 
        6.18        31.96         6.02        65.10        16.80        11.77 

$`EVI5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EVI5 MUTATED EVI5 WILD-TYPE 
          6.02           0.00 
  EVI5 MUTATED EVI5 WILD-TYPE 
          65.1          122.3 
  EVI5 MUTATED EVI5 WILD-TYPE 
         21.75          13.51 
[1] "6.0 - 65.1 (21.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "6.3"
D431V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EVI5 MUTATED         0        1        1        0         2         3
  EVI5 WILD-TYPE      10       19       45       31        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EVI5 MUTATED           1          0          1          0        2         0
  EVI5 WILD-TYPE        28         84         61         39       41         4
D431V3, multiclass
            clus
vv           EVI5 MUTATED EVI5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  EVI5 MUTATED       1   3   3   4
  EVI5 WILD-TYPE    53 132 258  98
D431V4, multiclass
       clus
vv      EVI5 MUTATED EVI5 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               3            258
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EVI5 MUTATED     6   4   2   0
  EVI5 WILD-TYPE 189 169  87  85
D431V5, multiclass
    clus
vv   EVI5 MUTATED EVI5 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V6, binary
                cls
clus               0   1
  EVI5 MUTATED    11   1
  EVI5 WILD-TYPE 471  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED     11    1
  EVI5 WILD-TYPE  471   37
   clus
vv  EVI5 MUTATED EVI5 WILD-TYPE
  0           11            471
  1            1             37
[1] 2 2
[1] FALSE
D431V7, binary
                cls
clus               0   1
  EVI5 MUTATED     5   8
  EVI5 WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      5    8
  EVI5 WILD-TYPE  167  398
        clus
vv       EVI5 MUTATED EVI5 WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D431V8, binary
                cls
clus               0   1
  EVI5 MUTATED    11   0
  EVI5 WILD-TYPE 405 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED     11    0
  EVI5 WILD-TYPE  405  102
     clus
vv    EVI5 MUTATED EVI5 WILD-TYPE
  NO            11            405
  YES            0            102
[1] 2 2
[1] FALSE
D431V9, continuous
D431V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EVI5 MUTATED       2                         0
  EVI5 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EVI5 MUTATED                                           0     9
  EVI5 WILD-TYPE                                         1   348
D431V11, multiclass
                                           clus
vv                                          EVI5 MUTATED EVI5 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V12, binary
                cls
clus               0   1
  EVI5 MUTATED     0   9
  EVI5 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      0    9
  EVI5 WILD-TYPE   10  389
                        clus
vv                       EVI5 MUTATED EVI5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(432) Variable = TIMP3 MUTATION ANALYSIS
D432V1, survival
                 sevent
clus2               0   1
  TIMP3 MUTATED     8   1
  TIMP3 WILD-TYPE 330 215
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              9             545 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              1             215 
$`TIMP3 MUTATED`
TCGA-M9-A5M8 TCGA-RE-A7BO TCGA-B7-A5TI TCGA-BR-8487 TCGA-BR-A4J4 TCGA-HU-A4G9 
       33.11         7.00        19.56         1.12         0.53        24.20 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P3 
        6.51         6.58        37.22 

$`TIMP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        38.14        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TIMP3 MUTATED TIMP3 WILD-TYPE 
           0.53            0.00 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
          37.22          122.30 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
           7.00           13.58 
[1] "0.5 - 37.2 (7.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.9"
D432V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIMP3 MUTATED         0        1        0        0         3         2
  TIMP3 WILD-TYPE      10       19       46       31        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIMP3 MUTATED           0          2          1          1        0         0
  TIMP3 WILD-TYPE        29         82         61         38       43         4
D432V3, multiclass
            clus
vv           TIMP3 MUTATED TIMP3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TIMP3 MUTATED       2   0   6   3
  TIMP3 WILD-TYPE    52 135 255  99
D432V4, multiclass
       clus
vv      TIMP3 MUTATED TIMP3 WILD-TYPE
  T0+T1             2              52
  T2                0             135
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TIMP3 MUTATED     4   4   1   1
  TIMP3 WILD-TYPE 191 169  88  84
D432V5, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V6, binary
                 cls
clus                0   1
  TIMP3 MUTATED    10   0
  TIMP3 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED     10    0
  TIMP3 WILD-TYPE  472   38
   clus
vv  TIMP3 MUTATED TIMP3 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D432V7, binary
                 cls
clus                0   1
  TIMP3 MUTATED     4   7
  TIMP3 WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      4    7
  TIMP3 WILD-TYPE  168  399
        clus
vv       TIMP3 MUTATED TIMP3 WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D432V8, binary
                 cls
clus                0   1
  TIMP3 MUTATED     7   2
  TIMP3 WILD-TYPE 409 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      7    2
  TIMP3 WILD-TYPE  409  100
     clus
vv    TIMP3 MUTATED TIMP3 WILD-TYPE
  NO              7             409
  YES             2             100
[1] 2 2
[1] FALSE
D432V9, continuous
D432V10, continuous
[1] "Remove cluster labels:" "TIMP3 MUTATED"         
clus
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-V5-A7RB      TCGA-V5-A7RC 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" "TIMP3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TIMP3 MUTATED       4                         0
  TIMP3 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIMP3 MUTATED                                           0     5
  TIMP3 WILD-TYPE                                         1   352
D432V11, multiclass
                                           clus
vv                                          TIMP3 MUTATED TIMP3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V12, binary
                 cls
clus                0   1
  TIMP3 MUTATED     0   8
  TIMP3 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      0    8
  TIMP3 WILD-TYPE   10  390
                        clus
vv                       TIMP3 MUTATED TIMP3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(433) Variable = EIF4EBP2 MUTATION ANALYSIS
D433V1, survival
                    sevent
clus2                  0   1
  EIF4EBP2 MUTATED     4   3
  EIF4EBP2 WILD-TYPE 334 213
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 7                547 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 3                213 
$`EIF4EBP2 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OH TCGA-R6-A6L6 TCGA-BR-6452 TCGA-CD-8527 TCGA-HJ-7597 
       19.99        32.61         7.04        34.68         7.17        26.47 
TCGA-MX-A5UJ 
       19.73 

$`EIF4EBP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
              7.04               0.00 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
             34.68             122.30 
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
             19.99              13.51 
[1] "7.0 - 34.7 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D433V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4EBP2 MUTATED         1        0        1        1         1         0
  EIF4EBP2 WILD-TYPE       9       20       45       30        83        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4EBP2 MUTATED           0          1          0          1        0
  EIF4EBP2 WILD-TYPE        29         83         62         38       43
                    vv
clus                 STAGE IVA
  EIF4EBP2 MUTATED           0
  EIF4EBP2 WILD-TYPE         4
D433V3, multiclass
            clus
vv           EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 1                 83
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  EIF4EBP2 MUTATED       1   2   3   0
  EIF4EBP2 WILD-TYPE    53 133 258 102
D433V4, multiclass
       clus
vv      EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  T0+T1                1                 53
  T2                   2                133
  T3                   3                258
  T4                   0                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  EIF4EBP2 MUTATED     3   1   1   1
  EIF4EBP2 WILD-TYPE 192 172  88  84
D433V5, multiclass
    clus
vv   EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  N0                3                192
  N1                1                172
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V6, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     4   0
  EIF4EBP2 WILD-TYPE 478  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      4    0
  EIF4EBP2 WILD-TYPE  478   38
   clus
vv  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  0                4                478
  1                0                 38
[1] 2 2
[1] FALSE
D433V7, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     4   3
  EIF4EBP2 WILD-TYPE 168 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      4    3
  EIF4EBP2 WILD-TYPE  168  403
        clus
vv       EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  FEMALE                4                168
  MALE                  3                403
[1] 2 2
[1] FALSE
D433V8, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     7   0
  EIF4EBP2 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      7    0
  EIF4EBP2 WILD-TYPE  409  102
     clus
vv    EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D433V9, continuous
D433V10, continuous
[1] "Remove cluster labels:" "EIF4EBP2 MUTATED"      
clus
  EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OT 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" "EIF4EBP2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  EIF4EBP2 MUTATED       1                         0
  EIF4EBP2 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4EBP2 MUTATED                                           0     6
  EIF4EBP2 WILD-TYPE                                         1   351
D433V11, multiclass
                                           clus
vv                                          EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V12, binary
                    cls
clus                   0   1
  EIF4EBP2 MUTATED     0   5
  EIF4EBP2 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EIF4EBP2 MUTATED      0    5
  EIF4EBP2 WILD-TYPE   10  393
                        clus
vv                       EIF4EBP2 MUTATED EIF4EBP2 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(434) Variable = HOXB7 MUTATION ANALYSIS
D434V1, survival
                 sevent
clus2               0   1
  HOXB7 MUTATED     7   2
  HOXB7 WILD-TYPE 331 214
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              9             545 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              2             214 
$`HOXB7 MUTATED`
TCGA-L5-A8NG TCGA-LN-A49W TCGA-Z6-A8JD TCGA-BR-8081 TCGA-HU-A4GT TCGA-MX-A5UJ 
       35.97        13.25         3.42        32.25         6.51        19.73 
TCGA-VQ-A8P2 TCGA-VQ-AA6I TCGA-VQ-AA6K 
       38.14        16.14        12.43 

$`HOXB7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        54.12        26.04        27.55        17.26 

  HOXB7 MUTATED HOXB7 WILD-TYPE 
           3.42            0.00 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
          38.14          122.30 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
          16.14           13.55 
[1] "3.4 - 38.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D434V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOXB7 MUTATED         0        0        0        0         1         2
  HOXB7 WILD-TYPE      10       20       46       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOXB7 MUTATED           2          2          1          1        0         0
  HOXB7 WILD-TYPE        27         82         61         38       43         4
D434V3, multiclass
            clus
vv           HOXB7 MUTATED HOXB7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HOXB7 MUTATED       0   0   6   3
  HOXB7 WILD-TYPE    54 135 255  99
D434V4, multiclass
       clus
vv      HOXB7 MUTATED HOXB7 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HOXB7 MUTATED     3   3   1   2
  HOXB7 WILD-TYPE 192 170  88  83
D434V5, multiclass
    clus
vv   HOXB7 MUTATED HOXB7 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V6, binary
                 cls
clus                0   1
  HOXB7 MUTATED     9   0
  HOXB7 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      9    0
  HOXB7 WILD-TYPE  473   38
   clus
vv  HOXB7 MUTATED HOXB7 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D434V7, binary
                 cls
clus                0   1
  HOXB7 MUTATED     3   6
  HOXB7 WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      3    6
  HOXB7 WILD-TYPE  169  400
        clus
vv       HOXB7 MUTATED HOXB7 WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D434V8, binary
                 cls
clus                0   1
  HOXB7 MUTATED     6   3
  HOXB7 WILD-TYPE 410  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      6    3
  HOXB7 WILD-TYPE  410   99
     clus
vv    HOXB7 MUTATED HOXB7 WILD-TYPE
  NO              6             410
  YES             3              99
[1] 2 2
[1] FALSE
D434V9, continuous
[1] "Remove cluster labels:" "HOXB7 MUTATED"         
clus
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JE 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
D434V10, continuous
[1] "Remove cluster labels:" "HOXB7 MUTATED"         
clus
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" "HOXB7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOXB7 MUTATED       2                         0
  HOXB7 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOXB7 MUTATED                                           0     7
  HOXB7 WILD-TYPE                                         1   350
D434V11, multiclass
                                           clus
vv                                          HOXB7 MUTATED HOXB7 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V12, binary
                 cls
clus                0   1
  HOXB7 MUTATED     0   4
  HOXB7 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      0    4
  HOXB7 WILD-TYPE   10  394
                        clus
vv                       HOXB7 MUTATED HOXB7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(435) Variable = CYP4B1 MUTATION ANALYSIS
D435V1, survival
                  sevent
clus2                0   1
  CYP4B1 MUTATED     7   3
  CYP4B1 WILD-TYPE 331 213
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
              10              544 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
               3              213 
$`CYP4B1 MUTATED`
TCGA-S8-A6BV TCGA-BR-8059 TCGA-BR-8680 TCGA-BR-A4CS TCGA-D7-A4YV TCGA-HF-A5NB 
       20.02        14.43        31.96         1.48         5.92        30.51 
TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-AA6J 
       24.20         6.51        29.00        27.55 

$`CYP4B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        17.26 

  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
            1.48             0.00 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
           31.96           122.30 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
           22.11            13.51 
[1] "1.5 - 32.0 (22.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D435V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP4B1 MUTATED         0        1        0        0         1         1
  CYP4B1 WILD-TYPE      10       19       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4B1 MUTATED           1          1          1          3        2
  CYP4B1 WILD-TYPE        28         83         61         36       41
                  vv
clus               STAGE IVA
  CYP4B1 MUTATED           0
  CYP4B1 WILD-TYPE         4
D435V3, multiclass
            clus
vv           CYP4B1 MUTATED CYP4B1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CYP4B1 MUTATED       1   0   3   7
  CYP4B1 WILD-TYPE    53 135 258  95
D435V4, multiclass
       clus
vv      CYP4B1 MUTATED CYP4B1 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 3              258
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CYP4B1 MUTATED     2   3   3   3
  CYP4B1 WILD-TYPE 193 170  86  82
D435V5, multiclass
    clus
vv   CYP4B1 MUTATED CYP4B1 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V6, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     9   1
  CYP4B1 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      9    1
  CYP4B1 WILD-TYPE  473   37
   clus
vv  CYP4B1 MUTATED CYP4B1 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D435V7, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     6   5
  CYP4B1 WILD-TYPE 166 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      6    5
  CYP4B1 WILD-TYPE  166  401
        clus
vv       CYP4B1 MUTATED CYP4B1 WILD-TYPE
  FEMALE              6              166
  MALE                5              401
[1] 2 2
[1] FALSE
D435V8, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     8   1
  CYP4B1 WILD-TYPE 408 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      8    1
  CYP4B1 WILD-TYPE  408  101
     clus
vv    CYP4B1 MUTATED CYP4B1 WILD-TYPE
  NO               8              408
  YES              1              101
[1] 2 2
[1] FALSE
D435V9, continuous
D435V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CYP4B1 MUTATED       4                         1
  CYP4B1 WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP4B1 MUTATED                                           0     5
  CYP4B1 WILD-TYPE                                         1   352
D435V11, multiclass
                                           clus
vv                                          CYP4B1 MUTATED CYP4B1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V12, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     0   9
  CYP4B1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      0    9
  CYP4B1 WILD-TYPE   10  389
                        clus
vv                       CYP4B1 MUTATED CYP4B1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(436) Variable = PTOV1 MUTATION ANALYSIS
D436V1, survival
                 sevent
clus2               0   1
  PTOV1 MUTATED     8   5
  PTOV1 WILD-TYPE 330 211
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             13             541 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              5             211 
$`PTOV1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8080 
       19.99         7.76         6.61        32.78        30.90         9.60 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8686 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-HU-A4GT 
        4.31        31.27        20.88         6.58        12.62         6.51 
TCGA-HU-A4H3 
       29.00 

$`PTOV1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PTOV1 MUTATED PTOV1 WILD-TYPE 
           4.31            0.00 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
          32.78          122.30 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
          12.62           13.58 
[1] "4.3 - 32.8 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D436V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTOV1 MUTATED         0        0        2        0         3         1
  PTOV1 WILD-TYPE      10       20       44       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTOV1 MUTATED           1          1          1          4        0         0
  PTOV1 WILD-TYPE        28         83         61         35       43         4
D436V3, multiclass
            clus
vv           PTOV1 MUTATED PTOV1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTOV1 MUTATED       0   4   5   4
  PTOV1 WILD-TYPE    54 131 256  98
D436V4, multiclass
       clus
vv      PTOV1 MUTATED PTOV1 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTOV1 MUTATED     5   3   1   4
  PTOV1 WILD-TYPE 190 170  88  81
D436V5, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V6, binary
                 cls
clus                0   1
  PTOV1 MUTATED    12   0
  PTOV1 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED     12    0
  PTOV1 WILD-TYPE  470   38
   clus
vv  PTOV1 MUTATED PTOV1 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D436V7, binary
                 cls
clus                0   1
  PTOV1 MUTATED     7   6
  PTOV1 WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      7    6
  PTOV1 WILD-TYPE  165  400
        clus
vv       PTOV1 MUTATED PTOV1 WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D436V8, binary
                 cls
clus                0   1
  PTOV1 MUTATED    12   0
  PTOV1 WILD-TYPE 404 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED     12    0
  PTOV1 WILD-TYPE  404  102
     clus
vv    PTOV1 MUTATED PTOV1 WILD-TYPE
  NO             12             404
  YES             0             102
[1] 2 2
[1] FALSE
D436V9, continuous
D436V10, continuous
[1] "Remove cluster labels:" "PTOV1 MUTATED"         
clus
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" "PTOV1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"PTOV1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTOV1 MUTATED       5                         0
  PTOV1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTOV1 MUTATED                                           0     8
  PTOV1 WILD-TYPE                                         1   349
D436V11, multiclass
                                           clus
vv                                          PTOV1 MUTATED PTOV1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V12, binary
                 cls
clus                0   1
  PTOV1 MUTATED     0  11
  PTOV1 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      0   11
  PTOV1 WILD-TYPE   10  387
                        clus
vv                       PTOV1 MUTATED PTOV1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(437) Variable = NOBOX MUTATION ANALYSIS
D437V1, survival
                 sevent
clus2               0   1
  NOBOX MUTATED     6   3
  NOBOX WILD-TYPE 332 213
  NOBOX MUTATED NOBOX WILD-TYPE 
              9             545 
  NOBOX MUTATED NOBOX WILD-TYPE 
              3             213 
$`NOBOX MUTATED`
TCGA-IG-A3I8 TCGA-XP-A8T8 TCGA-BR-7958 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI 
       33.27        14.37        29.56         6.18        31.96        11.77 
TCGA-CG-4306 TCGA-D7-A6EZ TCGA-VQ-A8P2 
        1.02        20.32        38.14 

$`NOBOX WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NOBOX MUTATED NOBOX WILD-TYPE 
           1.02            0.00 
  NOBOX MUTATED NOBOX WILD-TYPE 
          38.14          122.30 
  NOBOX MUTATED NOBOX WILD-TYPE 
          20.32           13.51 
[1] "1.0 - 38.1 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D437V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOBOX MUTATED         0        0        1        0         2         1
  NOBOX WILD-TYPE      10       20       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOBOX MUTATED           0          3          1          0        3         0
  NOBOX WILD-TYPE        29         81         61         39       40         4
D437V3, multiclass
            clus
vv           NOBOX MUTATED NOBOX WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NOBOX MUTATED       1   1   5   4
  NOBOX WILD-TYPE    53 134 256  98
D437V4, multiclass
       clus
vv      NOBOX MUTATED NOBOX WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NOBOX MUTATED     4   3   4   0
  NOBOX WILD-TYPE 191 170  85  85
D437V5, multiclass
    clus
vv   NOBOX MUTATED NOBOX WILD-TYPE
  N0             4             191
  N1             3             170
  N2             4              85
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V6, binary
                 cls
clus                0   1
  NOBOX MUTATED    10   2
  NOBOX WILD-TYPE 472  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED     10    2
  NOBOX WILD-TYPE  472   36
   clus
vv  NOBOX MUTATED NOBOX WILD-TYPE
  0            10             472
  1             2              36
[1] 2 2
[1] FALSE
D437V7, binary
                 cls
clus                0   1
  NOBOX MUTATED     3   9
  NOBOX WILD-TYPE 169 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      3    9
  NOBOX WILD-TYPE  169  397
        clus
vv       NOBOX MUTATED NOBOX WILD-TYPE
  FEMALE             3             169
  MALE               9             397
[1] 2 2
[1] FALSE
D437V8, binary
                 cls
clus                0   1
  NOBOX MUTATED     6   2
  NOBOX WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      6    2
  NOBOX WILD-TYPE  410  100
     clus
vv    NOBOX MUTATED NOBOX WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D437V9, continuous
[1] "Remove cluster labels:" "NOBOX MUTATED"         
clus
  NOBOX MUTATED NOBOX WILD-TYPE 
              2              66 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
D437V10, continuous
[1] "Remove cluster labels:" "NOBOX MUTATED"         
clus
  NOBOX MUTATED NOBOX WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-Z6-AAPN 
"NOBOX WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NOBOX MUTATED       2                         1
  NOBOX WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOBOX MUTATED                                           0     7
  NOBOX WILD-TYPE                                         1   350
D437V11, multiclass
                                           clus
vv                                          NOBOX MUTATED NOBOX WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V12, binary
                 cls
clus                0   1
  NOBOX MUTATED     1   8
  NOBOX WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      1    8
  NOBOX WILD-TYPE    9  390
                        clus
vv                       NOBOX MUTATED NOBOX WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(438) Variable = SORBS2 MUTATION ANALYSIS
D438V1, survival
                  sevent
clus2                0   1
  SORBS2 MUTATED    18   7
  SORBS2 WILD-TYPE 320 209
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              25              529 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               7              209 
$`SORBS2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-CG-4460 TCGA-JY-A6FG TCGA-L5-A4ON TCGA-L5-A8NM 
        4.31        19.99        21.99        41.52        18.35         7.76 
TCGA-LN-A8HZ TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
       12.33        34.68        31.27         1.12        31.96         6.02 
TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A747 TCGA-F1-6874 TCGA-HU-8602 
       28.96        13.78        11.31         8.38        14.47        22.32 
TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-VQ-A8E7 
       24.20         6.58        20.25        45.67        74.53        37.41 
TCGA-VQ-A8P2 
       38.14 

$`SORBS2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
        5.46        13.25        13.02        43.36        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
            1.12             0.00 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           74.53           122.30 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           20.25            13.41 
[1] "1.1 - 74.5 (20.2)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D438V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SORBS2 MUTATED         0        2        1        0         3         6
  SORBS2 WILD-TYPE      10       18       45       31        81        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SORBS2 MUTATED           1          2          1          3        7
  SORBS2 WILD-TYPE        28         82         61         36       36
                  vv
clus               STAGE IVA
  SORBS2 MUTATED           0
  SORBS2 WILD-TYPE         4
D438V3, multiclass
            clus
vv           SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               6               77
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                7               36
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SORBS2 MUTATED       3   3  11   9
  SORBS2 WILD-TYPE    51 132 250  93
D438V4, multiclass
       clus
vv      SORBS2 MUTATED SORBS2 WILD-TYPE
  T0+T1              3               51
  T2                 3              132
  T3                11              250
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SORBS2 MUTATED     8  11   4   3
  SORBS2 WILD-TYPE 187 162  85  82
D438V5, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  N0              8              187
  N1             11              162
  N2              4               85
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V6, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    19   5
  SORBS2 WILD-TYPE 463  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     19    5
  SORBS2 WILD-TYPE  463   33
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0             19              463
  1              5               33
[1] 2 2
[1] FALSE
D438V7, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    11  16
  SORBS2 WILD-TYPE 161 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     11   16
  SORBS2 WILD-TYPE  161  390
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE             11              161
  MALE               16              390
[1] 2 2
[1] FALSE
D438V8, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    19   3
  SORBS2 WILD-TYPE 397  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     19    3
  SORBS2 WILD-TYPE  397   99
     clus
vv    SORBS2 MUTATED SORBS2 WILD-TYPE
  NO              19              397
  YES              3               99
[1] 2 2
[1] FALSE
D438V9, continuous
D438V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SORBS2 MUTATED       6                         0
  SORBS2 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SORBS2 MUTATED                                           0    18
  SORBS2 WILD-TYPE                                         1   339
D438V11, multiclass
                                           clus
vv                                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V12, binary
                  cls
clus                 0   1
  SORBS2 MUTATED     2  15
  SORBS2 WILD-TYPE   8 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2   15
  SORBS2 WILD-TYPE    8  383
                        clus
vv                       SORBS2 MUTATED SORBS2 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(439) Variable = DNAH5 MUTATION ANALYSIS
D439V1, survival
                 sevent
clus2               0   1
  DNAH5 MUTATED    61  37
  DNAH5 WILD-TYPE 277 179
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             98             456 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             37             179 
$`DNAH5 MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-CG-4460 TCGA-EQ-A4SO 
       15.68         4.31        24.00        19.99        21.99        16.24 
TCGA-KB-A93G TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A8O2 
       20.15        16.24         7.69        17.03        23.41         4.67 
TCGA-IG-A97I TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       12.16         3.68        31.56        25.22        24.03         6.28 
TCGA-L5-A4OJ TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NM TCGA-L5-A8NN 
       21.01         4.90         7.13        55.50         7.76         5.49 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A4A1 TCGA-LN-A4A6 TCGA-LN-A7HY TCGA-LN-A9FO 
       10.85        10.36        12.59        12.85        12.03         0.13 
TCGA-R6-A6DN TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EQ 
        8.02         9.30        15.78         2.30         3.42        22.82 
TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4188 
       52.27         2.10        26.70        11.70        11.01         7.43 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7196 
        6.61        34.68        19.33        32.78        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
       36.16        35.84        18.15        14.43        11.44         8.05 
TCGA-BR-8286 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8373 TCGA-BR-8382 
       29.42         7.40         6.18         0.26        14.79        25.05 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A44U 
        9.21         1.12        27.12        28.14        31.96        13.87 
TCGA-BR-A4IY TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-A48C 
       12.89        13.41        13.15        13.18        12.10        11.61 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5733 
       15.95         1.02        14.01         0.99         6.02        21.07 
TCGA-D7-6525 TCGA-D7-A4Z0 TCGA-D7-A6EZ TCGA-F1-6874 TCGA-FP-A4BE TCGA-HF-7132 
       13.35        14.76        20.32        14.47        11.08        77.29 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GC TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-IN-A6RL 
       26.47        22.32         3.25        12.95        14.07        13.35 
TCGA-IN-A6RS TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-VQ-A8DT TCGA-VQ-A8P2 
       12.59        19.73        45.67         4.60        48.79        38.14 
TCGA-VQ-A8P3 TCGA-VQ-AA6J 
       37.22        27.55 

$`DNAH5 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T 
       60.39        34.85        18.28         8.94         4.70        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
        0.36        35.97        27.12         5.16        20.02        47.05 
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       22.98        79.07         0.23         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.53         0.79        12.82         9.96        14.86        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       23.18         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       58.59        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.04        38.40         6.35        53.95         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TI 
       14.37         3.42         1.32         2.66        19.73        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 
        9.47         9.44         6.61         6.97         4.64        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        9.57        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 
        8.98        40.21        30.90        31.20         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8361 
       32.25         0.56         2.66        19.96         2.20        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        31.27         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       25.18        20.22        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5802 
        1.15        21.44        16.14         5.13        13.02        13.35 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       30.51         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        2.10        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        19.53         6.44         6.74         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE 
        5.46        13.25        13.02        43.36        37.41        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 

  DNAH5 MUTATED DNAH5 WILD-TYPE 
           0.13            0.00 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
          77.29          122.30 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
          13.94           13.53 
[1] "0.1 - 77.3 (13.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D439V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH5 MUTATED         1        4       10        6        10        16
  DNAH5 WILD-TYPE       9       16       36       25        74        67
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH5 MUTATED           6         13          9          9       11         2
  DNAH5 WILD-TYPE        23         71         53         30       32         2
D439V3, multiclass
            clus
vv           DNAH5 MUTATED DNAH5 WILD-TYPE
  STAGE I                1               9
  STAGE IA               4              16
  STAGE IB              10              36
  STAGE II               6              25
  STAGE IIA             10              74
  STAGE IIB             16              67
  STAGE III              6              23
  STAGE IIIA            13              71
  STAGE IIIB             9              53
  STAGE IIIC             9              30
  STAGE IV              11              32
  STAGE IVA              2               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DNAH5 MUTATED       8  25  42  25
  DNAH5 WILD-TYPE    46 110 219  77
D439V4, multiclass
       clus
vv      DNAH5 MUTATED DNAH5 WILD-TYPE
  T0+T1             8              46
  T2               25             110
  T3               42             219
  T4               25              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DNAH5 MUTATED    34  35  16  13
  DNAH5 WILD-TYPE 161 138  73  72
D439V5, multiclass
    clus
vv   DNAH5 MUTATED DNAH5 WILD-TYPE
  N0            34             161
  N1            35             138
  N2            16              73
  N3            13              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V6, binary
                 cls
clus                0   1
  DNAH5 MUTATED    83  10
  DNAH5 WILD-TYPE 399  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED     83   10
  DNAH5 WILD-TYPE  399   28
   clus
vv  DNAH5 MUTATED DNAH5 WILD-TYPE
  0            83             399
  1            10              28
[1] 2 2
[1] FALSE
D439V7, binary
                 cls
clus                0   1
  DNAH5 MUTATED    32  74
  DNAH5 WILD-TYPE 140 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED     32   74
  DNAH5 WILD-TYPE  140  332
        clus
vv       DNAH5 MUTATED DNAH5 WILD-TYPE
  FEMALE            32             140
  MALE              74             332
[1] 2 2
[1] FALSE
D439V8, binary
                 cls
clus                0   1
  DNAH5 MUTATED    79  14
  DNAH5 WILD-TYPE 337  88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED     79   14
  DNAH5 WILD-TYPE  337   88
     clus
vv    DNAH5 MUTATED DNAH5 WILD-TYPE
  NO             79             337
  YES            14              88
[1] 2 2
[1] FALSE
D439V9, continuous
D439V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DNAH5 MUTATED      16                         5
  DNAH5 WILD-TYPE   117                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAH5 MUTATED                                           0    72
  DNAH5 WILD-TYPE                                         1   285
D439V11, multiclass
                                           clus
vv                                          DNAH5 MUTATED DNAH5 WILD-TYPE
  ASIAN                                                16             117
  BLACK OR AFRICAN AMERICAN                             5               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                72             285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V12, binary
                 cls
clus                0   1
  DNAH5 MUTATED     2  73
  DNAH5 WILD-TYPE   8 325
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      2   73
  DNAH5 WILD-TYPE    8  325
                        clus
vv                       DNAH5 MUTATED DNAH5 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            73             325
[1] 2 2
[1] FALSE

Clustering(440) Variable = CLMN MUTATION ANALYSIS
D440V1, survival
                sevent
clus2              0   1
  CLMN MUTATED     6   8
  CLMN WILD-TYPE 332 208
  CLMN MUTATED CLMN WILD-TYPE 
            14            540 
  CLMN MUTATED CLMN WILD-TYPE 
             8            208 
$`CLMN MUTATED`
TCGA-IC-A6RF TCGA-2H-A9GN TCGA-R6-A6L6 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 
       15.68         8.94         7.04         6.97         9.34         9.67 
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A4YV 
       32.78        35.84        25.05        31.96         6.58         5.92 
TCGA-HU-A4G8 TCGA-HU-A4GX 
       22.68        20.25 

$`CLMN WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         4.08         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CLMN MUTATED CLMN WILD-TYPE 
          5.92           0.00 
  CLMN MUTATED CLMN WILD-TYPE 
         35.84         122.30 
  CLMN MUTATED CLMN WILD-TYPE 
        12.675         13.565 
[1] "5.9 - 35.8 (12.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D440V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLMN MUTATED         0        1        2        0         2         3
  CLMN WILD-TYPE      10       19       44       31        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLMN MUTATED           1          1          0          2        1         0
  CLMN WILD-TYPE        28         83         62         37       42         4
D440V3, multiclass
            clus
vv           CLMN MUTATED CLMN WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CLMN MUTATED       1   2   6   4
  CLMN WILD-TYPE    53 133 255  98
D440V4, multiclass
       clus
vv      CLMN MUTATED CLMN WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               6            255
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CLMN MUTATED     6   5   2   1
  CLMN WILD-TYPE 189 168  87  84
D440V5, multiclass
    clus
vv   CLMN MUTATED CLMN WILD-TYPE
  N0            6            189
  N1            5            168
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V6, binary
                cls
clus               0   1
  CLMN MUTATED    14   1
  CLMN WILD-TYPE 468  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED     14    1
  CLMN WILD-TYPE  468   37
   clus
vv  CLMN MUTATED CLMN WILD-TYPE
  0           14            468
  1            1             37
[1] 2 2
[1] FALSE
D440V7, binary
                cls
clus               0   1
  CLMN MUTATED     9   8
  CLMN WILD-TYPE 163 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED      9    8
  CLMN WILD-TYPE  163  398
        clus
vv       CLMN MUTATED CLMN WILD-TYPE
  FEMALE            9            163
  MALE              8            398
[1] 2 2
[1] FALSE
D440V8, binary
                cls
clus               0   1
  CLMN MUTATED    15   0
  CLMN WILD-TYPE 401 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED     15    0
  CLMN WILD-TYPE  401  102
     clus
vv    CLMN MUTATED CLMN WILD-TYPE
  NO            15            401
  YES            0            102
[1] 2 2
[1] FALSE
D440V9, continuous
D440V10, continuous
[1] "Remove cluster labels:" "CLMN MUTATED"          
clus
  CLMN MUTATED CLMN WILD-TYPE 
             1             97 
    TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE     TCGA-L5-A4OG 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" "CLMN WILD-TYPE" 
    TCGA-Z6-AAPN 
"CLMN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CLMN MUTATED       4                         0
  CLMN WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLMN MUTATED                                           0    11
  CLMN WILD-TYPE                                         1   346
D440V11, multiclass
                                           clus
vv                                          CLMN MUTATED CLMN WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V12, binary
                cls
clus               0   1
  CLMN MUTATED     0  15
  CLMN WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED      0   15
  CLMN WILD-TYPE   10  383
                        clus
vv                       CLMN MUTATED CLMN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(441) Variable = CBLN3 MUTATION ANALYSIS
D441V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     2   4
  CBLN3 WILD-TYPE 336 212
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             548 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              4             212 
$`CBLN3 MUTATED`
TCGA-CG-4460 TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-8576 TCGA-VQ-A8P2 
       21.99         4.31        16.14        28.96        14.66        38.14 

$`CBLN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CBLN3 MUTATED CBLN3 WILD-TYPE 
           4.31            0.00 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
          38.14          122.30 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
         19.065          13.510 
[1] "4.3 - 38.1 (19.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D441V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBLN3 MUTATED         0        1        2        0         0         0
  CBLN3 WILD-TYPE      10       19       44       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBLN3 MUTATED           0          1          2          0        1         0
  CBLN3 WILD-TYPE        29         83         60         39       42         4
D441V3, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CBLN3 MUTATED       1   2   2   2
  CBLN3 WILD-TYPE    53 133 259 100
D441V4, multiclass
       clus
vv      CBLN3 MUTATED CBLN3 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CBLN3 MUTATED     3   2   0   2
  CBLN3 WILD-TYPE 192 171  89  83
D441V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V6, binary
                 cls
clus                0   1
  CBLN3 MUTATED     6   1
  CBLN3 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      6    1
  CBLN3 WILD-TYPE  476   37
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D441V7, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   3
  CBLN3 WILD-TYPE 168 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    3
  CBLN3 WILD-TYPE  168  403
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  FEMALE             4             168
  MALE               3             403
[1] 2 2
[1] FALSE
D441V8, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   1
  CBLN3 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    1
  CBLN3 WILD-TYPE  412  101
     clus
vv    CBLN3 MUTATED CBLN3 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D441V9, continuous
D441V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBLN3 MUTATED       0                         0
  CBLN3 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBLN3 MUTATED                                           0     4
  CBLN3 WILD-TYPE                                         1   353
D441V11, multiclass
                                           clus
vv                                          CBLN3 MUTATED CBLN3 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V12, binary
                 cls
clus                0   1
  CBLN3 MUTATED     0   3
  CBLN3 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      0    3
  CBLN3 WILD-TYPE   10  395
                        clus
vv                       CBLN3 MUTATED CBLN3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(442) Variable = JHDM1D MUTATION ANALYSIS
D442V1, survival
                  sevent
clus2                0   1
  JHDM1D MUTATED     6   4
  JHDM1D WILD-TYPE 332 212
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              10              544 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               4              212 
$`JHDM1D MUTATED`
TCGA-LN-A4A9 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-8535 TCGA-CD-A4MG 
       11.54         6.97        34.68         4.31        12.82         6.58 
TCGA-CG-4305 TCGA-D7-A4YV TCGA-F1-6874 TCGA-VQ-A8P2 
       15.95         5.92        14.47        38.14 

$`JHDM1D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  JHDM1D MUTATED JHDM1D WILD-TYPE 
            4.31             0.00 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
           38.14           122.30 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
           12.18            13.63 
[1] "4.3 - 38.1 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D442V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JHDM1D MUTATED         0        0        3        1         3         1
  JHDM1D WILD-TYPE      10       20       43       30        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JHDM1D MUTATED           0          3          0          0        0
  JHDM1D WILD-TYPE        29         81         62         39       43
                  vv
clus               STAGE IVA
  JHDM1D MUTATED           0
  JHDM1D WILD-TYPE         4
D442V3, multiclass
            clus
vv           JHDM1D MUTATED JHDM1D WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  JHDM1D MUTATED       0   5   5   1
  JHDM1D WILD-TYPE    54 130 256 101
D442V4, multiclass
       clus
vv      JHDM1D MUTATED JHDM1D WILD-TYPE
  T0+T1              0               54
  T2                 5              130
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  JHDM1D MUTATED     6   5   0   0
  JHDM1D WILD-TYPE 189 168  89  85
D442V5, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  N0              6              189
  N1              5              168
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V6, binary
                  cls
clus                 0   1
  JHDM1D MUTATED    10   0
  JHDM1D WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED     10    0
  JHDM1D WILD-TYPE  472   38
   clus
vv  JHDM1D MUTATED JHDM1D WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D442V7, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     3   8
  JHDM1D WILD-TYPE 169 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      3    8
  JHDM1D WILD-TYPE  169  398
        clus
vv       JHDM1D MUTATED JHDM1D WILD-TYPE
  FEMALE              3              169
  MALE                8              398
[1] 2 2
[1] FALSE
D442V8, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     9   1
  JHDM1D WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      9    1
  JHDM1D WILD-TYPE  407  101
     clus
vv    JHDM1D MUTATED JHDM1D WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D442V9, continuous
[1] "Remove cluster labels:" "JHDM1D MUTATED"        
clus
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
D442V10, continuous
[1] "Remove cluster labels:" "JHDM1D MUTATED"        
clus
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" "JHDM1D WILD-TYPE" 
      TCGA-Z6-AAPN 
"JHDM1D WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  JHDM1D MUTATED       3                         0
  JHDM1D WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JHDM1D MUTATED                                           0     6
  JHDM1D WILD-TYPE                                         1   351
D442V11, multiclass
                                           clus
vv                                          JHDM1D MUTATED JHDM1D WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V12, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     0   8
  JHDM1D WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      0    8
  JHDM1D WILD-TYPE   10  390
                        clus
vv                       JHDM1D MUTATED JHDM1D WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(443) Variable = FAM123C MUTATION ANALYSIS
D443V1, survival
                   sevent
clus2                 0   1
  FAM123C MUTATED    13   4
  FAM123C WILD-TYPE 325 212
  FAM123C MUTATED FAM123C WILD-TYPE 
               17               537 
  FAM123C MUTATED FAM123C WILD-TYPE 
                4               212 
$`FAM123C MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-V5-AASX TCGA-XP-A8T8 TCGA-BR-6452 TCGA-BR-6852 
       19.99         5.16         8.98        14.37        34.68        44.94 
TCGA-BR-7196 TCGA-BR-8360 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-A4YV 
       21.90         6.18         1.02         9.01         6.02         5.92 
TCGA-D7-A4YY TCGA-F1-6874 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-A4GX 
       13.78        14.47        52.21        30.51        20.25 

$`FAM123C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        30.90        31.20         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FAM123C MUTATED FAM123C WILD-TYPE 
             1.02              0.00 
  FAM123C MUTATED FAM123C WILD-TYPE 
            52.21            122.30 
  FAM123C MUTATED FAM123C WILD-TYPE 
            14.37             13.51 
[1] "1.0 - 52.2 (14.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D443V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM123C MUTATED         0        1        1        0         3         2
  FAM123C WILD-TYPE      10       19       45       31        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM123C MUTATED           0          0          2          3        4
  FAM123C WILD-TYPE        29         84         60         36       39
                   vv
clus                STAGE IVA
  FAM123C MUTATED           0
  FAM123C WILD-TYPE         4
D443V3, multiclass
            clus
vv           FAM123C MUTATED FAM123C WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               2                60
  STAGE IIIC               3                36
  STAGE IV                 4                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM123C MUTATED       2   1   9   4
  FAM123C WILD-TYPE    52 134 252  98
D443V4, multiclass
       clus
vv      FAM123C MUTATED FAM123C WILD-TYPE
  T0+T1               2                52
  T2                  1               134
  T3                  9               252
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM123C MUTATED     5   3   3   5
  FAM123C WILD-TYPE 190 170  86  80
D443V5, multiclass
    clus
vv   FAM123C MUTATED FAM123C WILD-TYPE
  N0               5               190
  N1               3               170
  N2               3                86
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V6, binary
                   cls
clus                  0   1
  FAM123C MUTATED    12   3
  FAM123C WILD-TYPE 470  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED     12    3
  FAM123C WILD-TYPE  470   35
   clus
vv  FAM123C MUTATED FAM123C WILD-TYPE
  0              12               470
  1               3                35
[1] 2 2
[1] FALSE
D443V7, binary
                   cls
clus                  0   1
  FAM123C MUTATED     7  10
  FAM123C WILD-TYPE 165 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED      7   10
  FAM123C WILD-TYPE  165  396
        clus
vv       FAM123C MUTATED FAM123C WILD-TYPE
  FEMALE               7               165
  MALE                10               396
[1] 2 2
[1] FALSE
D443V8, binary
                   cls
clus                  0   1
  FAM123C MUTATED    11   3
  FAM123C WILD-TYPE 405  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED     11    3
  FAM123C WILD-TYPE  405   99
     clus
vv    FAM123C MUTATED FAM123C WILD-TYPE
  NO               11               405
  YES               3                99
[1] 2 2
[1] FALSE
D443V9, continuous
[1] "Remove cluster labels:" "FAM123C MUTATED"       
clus
  FAM123C MUTATED FAM123C WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-VR-A8EO        TCGA-VR-A8EP 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FAM123C WILD-TYPE" "FAM123C WILD-TYPE" 
D443V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM123C MUTATED       1                         1
  FAM123C WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM123C MUTATED                                           0    10
  FAM123C WILD-TYPE                                         1   347
D443V11, multiclass
                                           clus
vv                                          FAM123C MUTATED FAM123C WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V12, binary
                   cls
clus                  0   1
  FAM123C MUTATED     1  10
  FAM123C WILD-TYPE   9 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED      1   10
  FAM123C WILD-TYPE    9  388
                        clus
vv                       FAM123C MUTATED FAM123C WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(444) Variable = GLIPR1L2 MUTATION ANALYSIS
D444V1, survival
                    sevent
clus2                  0   1
  GLIPR1L2 MUTATED     5   9
  GLIPR1L2 WILD-TYPE 333 207
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                14                540 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                 9                207 
$`GLIPR1L2 MUTATED`
TCGA-L5-A4OQ TCGA-XP-A8T6 TCGA-BR-4201 TCGA-BR-6566 TCGA-CD-5801 TCGA-CD-8536 
        1.38        25.08        30.90        32.78        13.18        12.43 
TCGA-CG-4465 TCGA-CG-5718 TCGA-D7-6527 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GQ 
        9.01        36.00        10.26        21.27        11.08         0.10 
TCGA-IN-7808 TCGA-VQ-A8P2 
        3.45        38.14 

$`GLIPR1L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        0.00        18.97         7.07        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
               0.1                0.0 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
             38.14             122.30 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
            12.805             13.630 
[1] "0.1 - 38.1 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D444V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLIPR1L2 MUTATED         0        0        1        3         2         1
  GLIPR1L2 WILD-TYPE      10       20       45       28        82        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLIPR1L2 MUTATED           0          3          1          1        1
  GLIPR1L2 WILD-TYPE        29         81         61         38       42
                    vv
clus                 STAGE IVA
  GLIPR1L2 MUTATED           0
  GLIPR1L2 WILD-TYPE         4
D444V3, multiclass
            clus
vv           GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  3                 28
  STAGE IIA                 2                 82
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  GLIPR1L2 MUTATED       0   6   6   3
  GLIPR1L2 WILD-TYPE    54 129 255  99
D444V4, multiclass
       clus
vv      GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  T0+T1                0                 54
  T2                   6                129
  T3                   6                255
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  GLIPR1L2 MUTATED     4   5   2   3
  GLIPR1L2 WILD-TYPE 191 168  87  82
D444V5, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  N0                4                191
  N1                5                168
  N2                2                 87
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V6, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED    12   2
  GLIPR1L2 WILD-TYPE 470  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED     12    2
  GLIPR1L2 WILD-TYPE  470   36
   clus
vv  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  0               12                470
  1                2                 36
[1] 2 2
[1] FALSE
D444V7, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     4  11
  GLIPR1L2 WILD-TYPE 168 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      4   11
  GLIPR1L2 WILD-TYPE  168  395
        clus
vv       GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  FEMALE                4                168
  MALE                 11                395
[1] 2 2
[1] FALSE
D444V8, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     9   4
  GLIPR1L2 WILD-TYPE 407  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      9    4
  GLIPR1L2 WILD-TYPE  407   98
     clus
vv    GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  NO                 9                407
  YES                4                 98
[1] 2 2
[1] FALSE
D444V9, continuous
[1] "Remove cluster labels:" "GLIPR1L2 MUTATED"      
clus
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-Z6-A8JE 
"GLIPR1L2 WILD-TYPE" 
D444V10, continuous
[1] "Remove cluster labels:" "GLIPR1L2 MUTATED"      
clus
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" "GLIPR1L2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  GLIPR1L2 MUTATED       3                         2
  GLIPR1L2 WILD-TYPE   130                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLIPR1L2 MUTATED                                           0     7
  GLIPR1L2 WILD-TYPE                                         1   350
D444V11, multiclass
                                           clus
vv                                          GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V12, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     2   8
  GLIPR1L2 WILD-TYPE   8 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      2    8
  GLIPR1L2 WILD-TYPE    8  390
                        clus
vv                       GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(445) Variable = TBC1D26 MUTATION ANALYSIS
D445V1, survival
                   sevent
clus2                 0   1
  TBC1D26 MUTATED     6   2
  TBC1D26 WILD-TYPE 332 214
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
                8               546 
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
                2               214 
$`TBC1D26 MUTATED`
TCGA-LN-A49R TCGA-LN-A49Y TCGA-V5-A7RB TCGA-BR-7707 TCGA-BR-8365 TCGA-BR-8591 
       13.38        12.46         5.29        35.84        17.52        28.14 
TCGA-HU-8604 TCGA-VQ-A8P2 
       22.82        38.14 

$`TBC1D26 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
             5.29              0.00 
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
            38.14            122.30 
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
            20.17             13.53 
[1] "5.3 - 38.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D445V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D26 MUTATED         0        0        1        0         3         0
  TBC1D26 WILD-TYPE      10       20       45       31        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D26 MUTATED           1          1          0          1        0
  TBC1D26 WILD-TYPE        28         83         62         38       43
                   vv
clus                STAGE IVA
  TBC1D26 MUTATED           0
  TBC1D26 WILD-TYPE         4
D445V3, multiclass
            clus
vv           TBC1D26 MUTATED TBC1D26 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TBC1D26 MUTATED       1   1   4   2
  TBC1D26 WILD-TYPE    53 134 257 100
D445V4, multiclass
       clus
vv      TBC1D26 MUTATED TBC1D26 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TBC1D26 MUTATED     4   3   0   1
  TBC1D26 WILD-TYPE 191 170  89  84
D445V5, multiclass
    clus
vv   TBC1D26 MUTATED TBC1D26 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V6, binary
                   cls
clus                  0   1
  TBC1D26 MUTATED     7   0
  TBC1D26 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D26 MUTATED      7    0
  TBC1D26 WILD-TYPE  475   38
   clus
vv  TBC1D26 MUTATED TBC1D26 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D445V7, binary
                   cls
clus                  0   1
  TBC1D26 MUTATED     3   5
  TBC1D26 WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D26 MUTATED      3    5
  TBC1D26 WILD-TYPE  169  401
        clus
vv       TBC1D26 MUTATED TBC1D26 WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D445V8, binary
                   cls
clus                  0   1
  TBC1D26 MUTATED     6   2
  TBC1D26 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D26 MUTATED      6    2
  TBC1D26 WILD-TYPE  410  100
     clus
vv    TBC1D26 MUTATED TBC1D26 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D445V9, continuous
D445V10, continuous
[1] "Remove cluster labels:" "TBC1D26 MUTATED"       
clus
  TBC1D26 MUTATED TBC1D26 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49S        TCGA-LN-A49U 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RC 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" "TBC1D26 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D26 MUTATED       3                         0
  TBC1D26 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D26 MUTATED                                           0     4
  TBC1D26 WILD-TYPE                                         1   353
D445V11, multiclass
                                           clus
vv                                          TBC1D26 MUTATED TBC1D26 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V12, binary
                   cls
clus                  0   1
  TBC1D26 MUTATED     1   6
  TBC1D26 WILD-TYPE   9 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D26 MUTATED      1    6
  TBC1D26 WILD-TYPE    9  392
                        clus
vv                       TBC1D26 MUTATED TBC1D26 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(446) Variable = BTNL3 MUTATION ANALYSIS
D446V1, survival
                 sevent
clus2               0   1
  BTNL3 MUTATED     3   2
  BTNL3 WILD-TYPE 335 214
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              5             549 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              2             214 
$`BTNL3 MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8373 TCGA-CG-5723 TCGA-CG-5726 
        6.97        32.25        14.79       105.07        28.96 

$`BTNL3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BTNL3 MUTATED BTNL3 WILD-TYPE 
           6.97            0.00 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
         105.07          122.30 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          28.96           13.51 
[1] "7.0 - 105.1 (29.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D446V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTNL3 MUTATED         0        1        0        1         0         2
  BTNL3 WILD-TYPE      10       19       46       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTNL3 MUTATED           0          2          0          0        0         0
  BTNL3 WILD-TYPE        29         82         62         39       43         4
D446V3, multiclass
            clus
vv           BTNL3 MUTATED BTNL3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BTNL3 MUTATED       1   1   1   3
  BTNL3 WILD-TYPE    53 134 260  99
D446V4, multiclass
       clus
vv      BTNL3 MUTATED BTNL3 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                1             260
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BTNL3 MUTATED     3   3   0   0
  BTNL3 WILD-TYPE 192 170  89  85
D446V5, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V6, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   0
  BTNL3 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    0
  BTNL3 WILD-TYPE  477   38
   clus
vv  BTNL3 MUTATED BTNL3 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D446V7, binary
                 cls
clus                0   1
  BTNL3 MUTATED     2   4
  BTNL3 WILD-TYPE 170 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      2    4
  BTNL3 WILD-TYPE  170  402
        clus
vv       BTNL3 MUTATED BTNL3 WILD-TYPE
  FEMALE             2             170
  MALE               4             402
[1] 2 2
[1] FALSE
D446V8, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   0
  BTNL3 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    0
  BTNL3 WILD-TYPE  411  102
     clus
vv    BTNL3 MUTATED BTNL3 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D446V9, continuous
D446V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BTNL3 MUTATED       0                         0
  BTNL3 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTNL3 MUTATED                                           0     4
  BTNL3 WILD-TYPE                                         1   353
D446V11, multiclass
                                           clus
vv                                          BTNL3 MUTATED BTNL3 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V12, binary
                 cls
clus                0   1
  BTNL3 MUTATED     0   4
  BTNL3 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      0    4
  BTNL3 WILD-TYPE   10  394
                        clus
vv                       BTNL3 MUTATED BTNL3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(447) Variable = MYO9B MUTATION ANALYSIS
D447V1, survival
                 sevent
clus2               0   1
  MYO9B MUTATED    15  13
  MYO9B WILD-TYPE 323 203
  MYO9B MUTATED MYO9B WILD-TYPE 
             28             526 
  MYO9B MUTATED MYO9B WILD-TYPE 
             13             203 
$`MYO9B MUTATED`
TCGA-2H-A9GG TCGA-IG-A50L TCGA-JY-A939 TCGA-L5-A8NM TCGA-LN-A49S TCGA-LN-A4A9 
       20.05         0.53        21.70         7.76        13.15        11.54 
TCGA-LN-A7HW TCGA-R6-A6XQ TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-8081 
       12.00         6.35         6.97         9.67        35.24        32.25 
TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 
        0.26        25.05        31.96         1.02         6.02        28.96 
TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-HJ-7597 TCGA-HU-A4G8 
       21.07        15.22         5.92        36.43        26.47        22.68 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-7806 TCGA-VQ-A8P2 
        6.58        14.07        36.36        38.14 

$`MYO9B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91        14.27        16.44        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       23.80        21.17        15.68        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MYO9B MUTATED MYO9B WILD-TYPE 
           0.26            0.00 
  MYO9B MUTATED MYO9B WILD-TYPE 
          38.14          122.30 
  MYO9B MUTATED MYO9B WILD-TYPE 
         14.645          13.530 
[1] "0.3 - 38.1 (14.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D447V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYO9B MUTATED         0        1        4        1         3         8
  MYO9B WILD-TYPE      10       19       42       30        81        75
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO9B MUTATED           1          4          0          1        3         0
  MYO9B WILD-TYPE        28         80         62         38       40         4
D447V3, multiclass
            clus
vv           MYO9B MUTATED MYO9B WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              8              75
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYO9B MUTATED       3   7  11   5
  MYO9B WILD-TYPE    51 128 250  97
D447V4, multiclass
       clus
vv      MYO9B MUTATED MYO9B WILD-TYPE
  T0+T1             3              51
  T2                7             128
  T3               11             250
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYO9B MUTATED     9  13   3   1
  MYO9B WILD-TYPE 186 160  86  84
D447V5, multiclass
    clus
vv   MYO9B MUTATED MYO9B WILD-TYPE
  N0             9             186
  N1            13             160
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V6, binary
                 cls
clus                0   1
  MYO9B MUTATED    23   2
  MYO9B WILD-TYPE 459  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     23    2
  MYO9B WILD-TYPE  459   36
   clus
vv  MYO9B MUTATED MYO9B WILD-TYPE
  0            23             459
  1             2              36
[1] 2 2
[1] FALSE
D447V7, binary
                 cls
clus                0   1
  MYO9B MUTATED    11  17
  MYO9B WILD-TYPE 161 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     11   17
  MYO9B WILD-TYPE  161  389
        clus
vv       MYO9B MUTATED MYO9B WILD-TYPE
  FEMALE            11             161
  MALE              17             389
[1] 2 2
[1] FALSE
D447V8, binary
                 cls
clus                0   1
  MYO9B MUTATED    23   2
  MYO9B WILD-TYPE 393 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     23    2
  MYO9B WILD-TYPE  393  100
     clus
vv    MYO9B MUTATED MYO9B WILD-TYPE
  NO             23             393
  YES             2             100
[1] 2 2
[1] FALSE
D447V9, continuous
D447V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYO9B MUTATED       8                         0
  MYO9B WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYO9B MUTATED                                           0    15
  MYO9B WILD-TYPE                                         1   342
D447V11, multiclass
                                           clus
vv                                          MYO9B MUTATED MYO9B WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V12, binary
                 cls
clus                0   1
  MYO9B MUTATED     0  20
  MYO9B WILD-TYPE  10 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED      0   20
  MYO9B WILD-TYPE   10  378
                        clus
vv                       MYO9B MUTATED MYO9B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(448) Variable = KDM3B MUTATION ANALYSIS
D448V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED    20   7
  KDM3B WILD-TYPE 318 209
  KDM3B MUTATED KDM3B WILD-TYPE 
             27             527 
  KDM3B MUTATED KDM3B WILD-TYPE 
              7             209 
$`KDM3B MUTATED`
TCGA-CG-4460 TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-JY-A6FD 
       21.99        25.78        58.55         7.69         0.79        68.02 
TCGA-JY-A93F TCGA-L5-A4OH TCGA-LN-A49X TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-6452 
       24.03        32.61        12.62        11.01         6.97        34.68 
TCGA-BR-6453 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-5803 TCGA-CD-A4MJ 
       15.95        31.10        31.96        20.42        11.21        12.62 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-HU-A4GH 
       15.95         6.02       105.07        65.10        13.78        11.77 
TCGA-HU-A4GQ TCGA-R5-A7ZI TCGA-VQ-A8P2 
        0.10        74.53        38.14 

$`KDM3B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        25.22         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       19.56         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57         6.61        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KDM3B MUTATED KDM3B WILD-TYPE 
            0.1             0.0 
  KDM3B MUTATED KDM3B WILD-TYPE 
         105.07          122.30 
  KDM3B MUTATED KDM3B WILD-TYPE 
          20.42           13.48 
[1] "0.1 - 105.1 (20.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D448V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KDM3B MUTATED         2        1        5        3         4         2
  KDM3B WILD-TYPE       8       19       41       28        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM3B MUTATED           1          2          1          2        4         0
  KDM3B WILD-TYPE        28         82         61         37       39         4
D448V3, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                2               8
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               3              28
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KDM3B MUTATED       4   7   8   8
  KDM3B WILD-TYPE    50 128 253  94
D448V4, multiclass
       clus
vv      KDM3B MUTATED KDM3B WILD-TYPE
  T0+T1             4              50
  T2                7             128
  T3                8             253
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KDM3B MUTATED    12  10   3   1
  KDM3B WILD-TYPE 183 163  86  84
D448V5, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  N0            12             183
  N1            10             163
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V6, binary
                 cls
clus                0   1
  KDM3B MUTATED    24   3
  KDM3B WILD-TYPE 458  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     24    3
  KDM3B WILD-TYPE  458   35
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            24             458
  1             3              35
[1] 2 2
[1] FALSE
D448V7, binary
                 cls
clus                0   1
  KDM3B MUTATED    10  18
  KDM3B WILD-TYPE 162 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     10   18
  KDM3B WILD-TYPE  162  388
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  FEMALE            10             162
  MALE              18             388
[1] 2 2
[1] FALSE
D448V8, binary
                 cls
clus                0   1
  KDM3B MUTATED    23   3
  KDM3B WILD-TYPE 393  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     23    3
  KDM3B WILD-TYPE  393   99
     clus
vv    KDM3B MUTATED KDM3B WILD-TYPE
  NO             23             393
  YES             3              99
[1] 2 2
[1] FALSE
D448V9, continuous
[1] "Remove cluster labels:" "KDM3B MUTATED"         
clus
  KDM3B MUTATED KDM3B WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KDM3B WILD-TYPE" "KDM3B WILD-TYPE" "KDM3B WILD-TYPE" 
D448V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KDM3B MUTATED       7                         0
  KDM3B WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KDM3B MUTATED                                           0    14
  KDM3B WILD-TYPE                                         1   343
D448V11, multiclass
                                           clus
vv                                          KDM3B MUTATED KDM3B WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V12, binary
                 cls
clus                0   1
  KDM3B MUTATED     1  16
  KDM3B WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      1   16
  KDM3B WILD-TYPE    9  382
                        clus
vv                       KDM3B MUTATED KDM3B WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(449) Variable = USP35 MUTATION ANALYSIS
D449V1, survival
                 sevent
clus2               0   1
  USP35 MUTATED     7   5
  USP35 WILD-TYPE 331 211
  USP35 MUTATED USP35 WILD-TYPE 
             12             542 
  USP35 MUTATED USP35 WILD-TYPE 
              5             211 
$`USP35 MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-RE-A7BO TCGA-Z6-AAPN TCGA-BR-6452 TCGA-BR-6566 
       18.28         4.31         7.00         2.66        34.68        32.78 
TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-8535 TCGA-CD-A48C TCGA-HF-A5NB TCGA-HU-A4GQ 
       29.59        31.10        12.82        11.61        30.51         0.10 

$`USP35 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  USP35 MUTATED USP35 WILD-TYPE 
            0.1             0.0 
  USP35 MUTATED USP35 WILD-TYPE 
          34.68          122.30 
  USP35 MUTATED USP35 WILD-TYPE 
         15.550          13.565 
[1] "0.1 - 34.7 (15.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D449V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP35 MUTATED         0        0        0        0         3         4
  USP35 WILD-TYPE      10       20       46       31        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP35 MUTATED           0          2          0          3        0         0
  USP35 WILD-TYPE        29         82         62         36       43         4
D449V3, multiclass
            clus
vv           USP35 MUTATED USP35 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP35 MUTATED       1   0   7   4
  USP35 WILD-TYPE    53 135 254  98
D449V4, multiclass
       clus
vv      USP35 MUTATED USP35 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP35 MUTATED     5   4   2   1
  USP35 WILD-TYPE 190 169  87  84
D449V5, multiclass
    clus
vv   USP35 MUTATED USP35 WILD-TYPE
  N0             5             190
  N1             4             169
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V6, binary
                 cls
clus                0   1
  USP35 MUTATED    10   0
  USP35 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED     10    0
  USP35 WILD-TYPE  472   38
   clus
vv  USP35 MUTATED USP35 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D449V7, binary
                 cls
clus                0   1
  USP35 MUTATED     7   5
  USP35 WILD-TYPE 165 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      7    5
  USP35 WILD-TYPE  165  401
        clus
vv       USP35 MUTATED USP35 WILD-TYPE
  FEMALE             7             165
  MALE               5             401
[1] 2 2
[1] FALSE
D449V8, binary
                 cls
clus                0   1
  USP35 MUTATED     9   2
  USP35 WILD-TYPE 407 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      9    2
  USP35 WILD-TYPE  407  100
     clus
vv    USP35 MUTATED USP35 WILD-TYPE
  NO              9             407
  YES             2             100
[1] 2 2
[1] FALSE
D449V9, continuous
D449V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP35 MUTATED       3                         0
  USP35 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP35 MUTATED                                           0     8
  USP35 WILD-TYPE                                         1   349
D449V11, multiclass
                                           clus
vv                                          USP35 MUTATED USP35 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V12, binary
                 cls
clus                0   1
  USP35 MUTATED     0   9
  USP35 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      0    9
  USP35 WILD-TYPE   10  389
                        clus
vv                       USP35 MUTATED USP35 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(450) Variable = ARAF MUTATION ANALYSIS
D450V1, survival
                sevent
clus2              0   1
  ARAF MUTATED    10   2
  ARAF WILD-TYPE 328 214
  ARAF MUTATED ARAF WILD-TYPE 
            12            542 
  ARAF MUTATED ARAF WILD-TYPE 
             2            214 
$`ARAF MUTATED`
TCGA-L5-A8NT TCGA-L5-A4OJ TCGA-LN-A49W TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 
       27.12        21.01        13.25        34.68         6.18         1.12 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4YV TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-SW-A7EA 
        6.58         6.02         5.92        63.62        19.73        19.04 

$`ARAF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
       13.51         2.53         5.56        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ARAF MUTATED ARAF WILD-TYPE 
          1.12           0.00 
  ARAF MUTATED ARAF WILD-TYPE 
         63.62         122.30 
  ARAF MUTATED ARAF WILD-TYPE 
        16.145         13.565 
[1] "1.1 - 63.6 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D450V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARAF MUTATED         1        0        3        0         5         2
  ARAF WILD-TYPE       9       20       43       31        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARAF MUTATED           1          1          0          0        1         0
  ARAF WILD-TYPE        28         83         62         39       42         4
D450V3, multiclass
            clus
vv           ARAF MUTATED ARAF WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ARAF MUTATED       2   2   9   1
  ARAF WILD-TYPE    52 133 252 101
D450V4, multiclass
       clus
vv      ARAF MUTATED ARAF WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               9            252
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ARAF MUTATED     9   5   1   0
  ARAF WILD-TYPE 186 168  88  85
D450V5, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  N0            9            186
  N1            5            168
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V6, binary
                cls
clus               0   1
  ARAF MUTATED    15   0
  ARAF WILD-TYPE 467  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED     15    0
  ARAF WILD-TYPE  467   38
   clus
vv  ARAF MUTATED ARAF WILD-TYPE
  0           15            467
  1            0             38
[1] 2 2
[1] FALSE
D450V7, binary
                cls
clus               0   1
  ARAF MUTATED     8   7
  ARAF WILD-TYPE 164 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      8    7
  ARAF WILD-TYPE  164  399
        clus
vv       ARAF MUTATED ARAF WILD-TYPE
  FEMALE            8            164
  MALE              7            399
[1] 2 2
[1] FALSE
D450V8, binary
                cls
clus               0   1
  ARAF MUTATED     9   3
  ARAF WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      9    3
  ARAF WILD-TYPE  407   99
     clus
vv    ARAF MUTATED ARAF WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D450V9, continuous
[1] "Remove cluster labels:" "ARAF MUTATED"          
clus
  ARAF MUTATED ARAF WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
D450V10, continuous
[1] "Remove cluster labels:" "ARAF MUTATED"          
clus
  ARAF MUTATED ARAF WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" "ARAF WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARAF MUTATED       2                         0
  ARAF WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARAF MUTATED                                           0    10
  ARAF WILD-TYPE                                         1   347
D450V11, multiclass
                                           clus
vv                                          ARAF MUTATED ARAF WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V12, binary
                cls
clus               0   1
  ARAF MUTATED     0   9
  ARAF WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      0    9
  ARAF WILD-TYPE   10  389
                        clus
vv                       ARAF MUTATED ARAF WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(451) Variable = YLPM1 MUTATION ANALYSIS
D451V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    21   6
  YLPM1 WILD-TYPE 317 210
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             27             527 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              6             210 
$`YLPM1 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-2H-A9GJ TCGA-L5-A8NM TCGA-LN-A4A8 TCGA-LN-A7HX 
       34.85        19.99        58.55         7.76        15.52        12.23 
TCGA-LN-A9FO TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 
        0.13         9.47         6.97         9.34        34.68        44.94 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4305 
       29.59        32.25         6.18        25.05        31.96        15.95 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6822 TCGA-HF-A5NB TCGA-HU-A4GT 
        6.02       105.07        21.07        12.33        30.51         6.51 
TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-VQ-A8P2 
       20.25        74.53        38.14 

$`YLPM1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44         0.69         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           0.13            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         105.07          122.30 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          20.25           13.48 
[1] "0.1 - 105.1 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D451V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YLPM1 MUTATED         2        0        1        2         7         5
  YLPM1 WILD-TYPE       8       20       45       29        77        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YLPM1 MUTATED           0          4          0          4        4         0
  YLPM1 WILD-TYPE        29         80         62         35       39         4
D451V3, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              7              77
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  YLPM1 MUTATED       3   8   7  12
  YLPM1 WILD-TYPE    51 127 254  90
D451V4, multiclass
       clus
vv      YLPM1 MUTATED YLPM1 WILD-TYPE
  T0+T1             3              51
  T2                8             127
  T3                7             254
  T4               12              90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  YLPM1 MUTATED    13   9   4   3
  YLPM1 WILD-TYPE 182 164  85  82
D451V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0            13             182
  N1             9             164
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V6, binary
                 cls
clus                0   1
  YLPM1 MUTATED    26   2
  YLPM1 WILD-TYPE 456  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     26    2
  YLPM1 WILD-TYPE  456   36
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            26             456
  1             2              36
[1] 2 2
[1] FALSE
D451V7, binary
                 cls
clus                0   1
  YLPM1 MUTATED    13  18
  YLPM1 WILD-TYPE 159 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     13   18
  YLPM1 WILD-TYPE  159  388
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  FEMALE            13             159
  MALE              18             388
[1] 2 2
[1] FALSE
D451V8, binary
                 cls
clus                0   1
  YLPM1 MUTATED    26   3
  YLPM1 WILD-TYPE 390  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     26    3
  YLPM1 WILD-TYPE  390   99
     clus
vv    YLPM1 MUTATED YLPM1 WILD-TYPE
  NO             26             390
  YES             3              99
[1] 2 2
[1] FALSE
D451V9, continuous
[1] "Remove cluster labels:" "YLPM1 MUTATED"         
clus
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
D451V10, continuous
[1] "Remove cluster labels:" "YLPM1 MUTATED"         
clus
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" "YLPM1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YLPM1 MUTATED       6                         1
  YLPM1 WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YLPM1 MUTATED                                           0    18
  YLPM1 WILD-TYPE                                         1   339
D451V11, multiclass
                                           clus
vv                                          YLPM1 MUTATED YLPM1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V12, binary
                 cls
clus                0   1
  YLPM1 MUTATED     1  20
  YLPM1 WILD-TYPE   9 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED      1   20
  YLPM1 WILD-TYPE    9  378
                        clus
vv                       YLPM1 MUTATED YLPM1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(452) Variable = TXLNG MUTATION ANALYSIS
D452V1, survival
                 sevent
clus2               0   1
  TXLNG MUTATED     2   6
  TXLNG WILD-TYPE 336 210
  TXLNG MUTATED TXLNG WILD-TYPE 
              8             546 
  TXLNG MUTATED TXLNG WILD-TYPE 
              6             210 
$`TXLNG MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-A44U TCGA-BR-A4QL 
       31.27        14.30        34.68        29.59        13.87        16.14 
TCGA-CD-A4MG TCGA-D7-A4YV 
        6.58         5.92 

$`TXLNG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       20.05        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TXLNG MUTATED TXLNG WILD-TYPE 
           5.92            0.00 
  TXLNG MUTATED TXLNG WILD-TYPE 
          34.68          122.30 
  TXLNG MUTATED TXLNG WILD-TYPE 
          15.22           13.51 
[1] "5.9 - 34.7 (15.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D452V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TXLNG MUTATED         0        0        0        0         2         3
  TXLNG WILD-TYPE      10       20       46       31        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TXLNG MUTATED           1          1          2          0        0         0
  TXLNG WILD-TYPE        28         83         60         39       43         4
D452V3, multiclass
            clus
vv           TXLNG MUTATED TXLNG WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TXLNG MUTATED       1   0   6   2
  TXLNG WILD-TYPE    53 135 255 100
D452V4, multiclass
       clus
vv      TXLNG MUTATED TXLNG WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TXLNG MUTATED     4   3   0   2
  TXLNG WILD-TYPE 191 170  89  83
D452V5, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  N0             4             191
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V6, binary
                 cls
clus                0   1
  TXLNG MUTATED     9   0
  TXLNG WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      9    0
  TXLNG WILD-TYPE  473   38
   clus
vv  TXLNG MUTATED TXLNG WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D452V7, binary
                 cls
clus                0   1
  TXLNG MUTATED     5   4
  TXLNG WILD-TYPE 167 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      5    4
  TXLNG WILD-TYPE  167  402
        clus
vv       TXLNG MUTATED TXLNG WILD-TYPE
  FEMALE             5             167
  MALE               4             402
[1] 2 2
[1] FALSE
D452V8, binary
                 cls
clus                0   1
  TXLNG MUTATED     8   0
  TXLNG WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      8    0
  TXLNG WILD-TYPE  408  102
     clus
vv    TXLNG MUTATED TXLNG WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D452V9, continuous
D452V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TXLNG MUTATED       1                         0
  TXLNG WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TXLNG MUTATED                                           0     6
  TXLNG WILD-TYPE                                         1   351
D452V11, multiclass
                                           clus
vv                                          TXLNG MUTATED TXLNG WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V12, binary
                 cls
clus                0   1
  TXLNG MUTATED     0   7
  TXLNG WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      0    7
  TXLNG WILD-TYPE   10  391
                        clus
vv                       TXLNG MUTATED TXLNG WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(453) Variable = PIK3R3 MUTATION ANALYSIS
D453V1, survival
                  sevent
clus2                0   1
  PIK3R3 MUTATED     5   4
  PIK3R3 WILD-TYPE 333 212
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               9              545 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               4              212 
$`PIK3R3 MUTATED`
TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-BR-4256 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 
        7.82         7.04         9.34        28.14        31.96        13.18 
TCGA-CG-4477 TCGA-HJ-7597 TCGA-HU-A4G8 
       30.97        26.47        22.68 

$`PIK3R3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97         7.07         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
            7.04             0.00 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           31.96           122.30 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           22.68            13.55 
[1] "7.0 - 32.0 (22.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D453V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3R3 MUTATED         0        0        3        0         0         1
  PIK3R3 WILD-TYPE      10       20       43       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R3 MUTATED           0          1          1          1        1
  PIK3R3 WILD-TYPE        29         83         61         38       42
                  vv
clus               STAGE IVA
  PIK3R3 MUTATED           0
  PIK3R3 WILD-TYPE         4
D453V3, multiclass
            clus
vv           PIK3R3 MUTATED PIK3R3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PIK3R3 MUTATED       0   3   3   2
  PIK3R3 WILD-TYPE    54 132 258 100
D453V4, multiclass
       clus
vv      PIK3R3 MUTATED PIK3R3 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3R3 MUTATED     3   3   2   1
  PIK3R3 WILD-TYPE 192 170  87  84
D453V5, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  N0              3              192
  N1              3              170
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V6, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     7   1
  PIK3R3 WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      7    1
  PIK3R3 WILD-TYPE  475   37
   clus
vv  PIK3R3 MUTATED PIK3R3 WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D453V7, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     4   6
  PIK3R3 WILD-TYPE 168 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      4    6
  PIK3R3 WILD-TYPE  168  400
        clus
vv       PIK3R3 MUTATED PIK3R3 WILD-TYPE
  FEMALE              4              168
  MALE                6              400
[1] 2 2
[1] FALSE
D453V8, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     9   1
  PIK3R3 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      9    1
  PIK3R3 WILD-TYPE  407  101
     clus
vv    PIK3R3 MUTATED PIK3R3 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D453V9, continuous
D453V10, continuous
[1] "Remove cluster labels:" "PIK3R3 MUTATED"        
clus
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-R6-A6DN 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" "PIK3R3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PIK3R3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3R3 MUTATED       3                         0
  PIK3R3 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3R3 MUTATED                                           0     6
  PIK3R3 WILD-TYPE                                         1   351
D453V11, multiclass
                                           clus
vv                                          PIK3R3 MUTATED PIK3R3 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V12, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     0   9
  PIK3R3 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      0    9
  PIK3R3 WILD-TYPE   10  389
                        clus
vv                       PIK3R3 MUTATED PIK3R3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(454) Variable = UBR3 MUTATION ANALYSIS
D454V1, survival
                sevent
clus2              0   1
  UBR3 MUTATED    10   4
  UBR3 WILD-TYPE 328 212
  UBR3 MUTATED UBR3 WILD-TYPE 
            14            540 
  UBR3 MUTATED UBR3 WILD-TYPE 
             4            212 
$`UBR3 MUTATED`
TCGA-2H-A9GG TCGA-2H-A9GR TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A8NK TCGA-LN-A7HV 
       20.05        32.45        41.52         6.28        13.55        10.52 
TCGA-BR-4201 TCGA-BR-8372 TCGA-CG-4437 TCGA-CG-5721 TCGA-HF-7132 TCGA-HF-A5NB 
       30.90        31.27         8.05         6.02        77.29        30.51 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`UBR3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  UBR3 MUTATED UBR3 WILD-TYPE 
          6.02           0.00 
  UBR3 MUTATED UBR3 WILD-TYPE 
         77.29         122.30 
  UBR3 MUTATED UBR3 WILD-TYPE 
        25.280         13.495 
[1] "6.0 - 77.3 (25.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D454V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBR3 MUTATED         0        1        0        2         3         0
  UBR3 WILD-TYPE      10       19       46       29        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR3 MUTATED           2          2          0          2        1         0
  UBR3 WILD-TYPE        27         82         62         37       42         4
D454V3, multiclass
            clus
vv           UBR3 MUTATED UBR3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  UBR3 MUTATED       1   4   5   4
  UBR3 WILD-TYPE    53 131 256  98
D454V4, multiclass
       clus
vv      UBR3 MUTATED UBR3 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  UBR3 MUTATED     4   6   1   2
  UBR3 WILD-TYPE 191 167  88  83
D454V5, multiclass
    clus
vv   UBR3 MUTATED UBR3 WILD-TYPE
  N0            4            191
  N1            6            167
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V6, binary
                cls
clus               0   1
  UBR3 MUTATED    14   0
  UBR3 WILD-TYPE 468  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR3 MUTATED     14    0
  UBR3 WILD-TYPE  468   38
   clus
vv  UBR3 MUTATED UBR3 WILD-TYPE
  0           14            468
  1            0             38
[1] 2 2
[1] FALSE
D454V7, binary
                cls
clus               0   1
  UBR3 MUTATED     4  10
  UBR3 WILD-TYPE 168 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR3 MUTATED      4   10
  UBR3 WILD-TYPE  168  396
        clus
vv       UBR3 MUTATED UBR3 WILD-TYPE
  FEMALE            4            168
  MALE             10            396
[1] 2 2
[1] FALSE
D454V8, binary
                cls
clus               0   1
  UBR3 MUTATED     8   5
  UBR3 WILD-TYPE 408  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR3 MUTATED      8    5
  UBR3 WILD-TYPE  408   97
     clus
vv    UBR3 MUTATED UBR3 WILD-TYPE
  NO             8            408
  YES            5             97
[1] 2 2
[1] FALSE
D454V9, continuous
[1] "Remove cluster labels:" "UBR3 MUTATED"          
clus
  UBR3 MUTATED UBR3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HW 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"UBR3 WILD-TYPE" "UBR3 WILD-TYPE" 
D454V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UBR3 MUTATED       1                         0
  UBR3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBR3 MUTATED                                           0     7
  UBR3 WILD-TYPE                                         1   350
D454V11, multiclass
                                           clus
vv                                          UBR3 MUTATED UBR3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V12, binary
                cls
clus               0   1
  UBR3 MUTATED     0   5
  UBR3 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR3 MUTATED      0    5
  UBR3 WILD-TYPE   10  393
                        clus
vv                       UBR3 MUTATED UBR3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(455) Variable = RELT MUTATION ANALYSIS
D455V1, survival
                sevent
clus2              0   1
  RELT MUTATED     6   2
  RELT WILD-TYPE 332 214
  RELT MUTATED RELT WILD-TYPE 
             8            546 
  RELT MUTATED RELT WILD-TYPE 
             2            214 
$`RELT MUTATED`
TCGA-JY-A6FD TCGA-BR-8078 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HF-7134 TCGA-HU-A4GQ 
       68.02        29.59         1.12        11.44        52.21         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU 
        6.51         6.58 

$`RELT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX 
       25.81        11.77        21.37        29.98         8.98        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RELT MUTATED RELT WILD-TYPE 
           0.1            0.0 
  RELT MUTATED RELT WILD-TYPE 
         68.02         122.30 
  RELT MUTATED RELT WILD-TYPE 
          9.01          13.63 
[1] "0.1 - 68.0 (9.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D455V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RELT MUTATED         0        1        0        0         3         2
  RELT WILD-TYPE      10       19       46       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELT MUTATED           0          0          1          1        0         0
  RELT WILD-TYPE        29         84         61         38       43         4
D455V3, multiclass
            clus
vv           RELT MUTATED RELT WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RELT MUTATED       1   0   5   2
  RELT WILD-TYPE    53 135 256 100
D455V4, multiclass
       clus
vv      RELT MUTATED RELT WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RELT MUTATED     5   1   1   1
  RELT WILD-TYPE 190 172  88  84
D455V5, multiclass
    clus
vv   RELT MUTATED RELT WILD-TYPE
  N0            5            190
  N1            1            172
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V6, binary
                cls
clus               0   1
  RELT MUTATED     8   0
  RELT WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      8    0
  RELT WILD-TYPE  474   38
   clus
vv  RELT MUTATED RELT WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D455V7, binary
                cls
clus               0   1
  RELT MUTATED     5   3
  RELT WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      5    3
  RELT WILD-TYPE  167  403
        clus
vv       RELT MUTATED RELT WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D455V8, binary
                cls
clus               0   1
  RELT MUTATED     8   0
  RELT WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      8    0
  RELT WILD-TYPE  408  102
     clus
vv    RELT MUTATED RELT WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D455V9, continuous
D455V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RELT MUTATED       4                         0
  RELT WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RELT MUTATED                                           0     3
  RELT WILD-TYPE                                         1   354
D455V11, multiclass
                                           clus
vv                                          RELT MUTATED RELT WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V12, binary
                cls
clus               0   1
  RELT MUTATED     0   6
  RELT WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      0    6
  RELT WILD-TYPE   10  392
                        clus
vv                       RELT MUTATED RELT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(456) Variable = TUBE1 MUTATION ANALYSIS
D456V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     7   3
  TUBE1 WILD-TYPE 331 213
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             10             544 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              3             213 
$`TUBE1 MUTATED`
TCGA-L5-A4OU TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-8680 
       29.00         6.97        30.90        31.10        28.14        31.96 
TCGA-BR-A4QL TCGA-D7-8572 TCGA-F1-A448 TCGA-IN-A6RN 
       16.14        16.80        21.27        19.53 

$`TUBE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           6.97            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
          31.96          122.30 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         24.705          13.445 
[1] "7.0 - 32.0 (24.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D456V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TUBE1 MUTATED         0        0        0        0         2         1
  TUBE1 WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TUBE1 MUTATED           0          1          2          2        1         0
  TUBE1 WILD-TYPE        29         83         60         37       42         4
D456V3, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TUBE1 MUTATED       1   2   4   3
  TUBE1 WILD-TYPE    53 133 257  99
D456V4, multiclass
       clus
vv      TUBE1 MUTATED TUBE1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TUBE1 MUTATED     1   1   4   3
  TUBE1 WILD-TYPE 194 172  85  82
D456V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V6, binary
                 cls
clus                0   1
  TUBE1 MUTATED     8   1
  TUBE1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      8    1
  TUBE1 WILD-TYPE  474   37
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D456V7, binary
                 cls
clus                0   1
  TUBE1 MUTATED     4   6
  TUBE1 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      4    6
  TUBE1 WILD-TYPE  168  400
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D456V8, binary
                 cls
clus                0   1
  TUBE1 MUTATED     9   1
  TUBE1 WILD-TYPE 407 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      9    1
  TUBE1 WILD-TYPE  407  101
     clus
vv    TUBE1 MUTATED TUBE1 WILD-TYPE
  NO              9             407
  YES             1             101
[1] 2 2
[1] FALSE
D456V9, continuous
D456V10, continuous
[1] "Remove cluster labels:" "TUBE1 MUTATED"         
clus
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OW      TCGA-L5-A4OX 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" "TUBE1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"TUBE1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TUBE1 MUTATED       1                         0
  TUBE1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TUBE1 MUTATED                                           0     9
  TUBE1 WILD-TYPE                                         1   348
D456V11, multiclass
                                           clus
vv                                          TUBE1 MUTATED TUBE1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V12, binary
                 cls
clus                0   1
  TUBE1 MUTATED     1   8
  TUBE1 WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      1    8
  TUBE1 WILD-TYPE    9  390
                        clus
vv                       TUBE1 MUTATED TUBE1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(457) Variable = TRIP11 MUTATION ANALYSIS
D457V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED    14   4
  TRIP11 WILD-TYPE 324 212
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              18              536 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               4              212 
$`TRIP11 MUTATED`
TCGA-L5-A4OE TCGA-IG-A6QS TCGA-LN-A7HW TCGA-LN-A9FP TCGA-Z6-A9VB TCGA-BR-7703 
       24.00         9.96        12.00        12.03         1.32        36.16 
TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-5800 TCGA-CG-4466 
       35.24        29.59         4.31        31.96        13.15        18.97 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.02        65.10        21.07         0.10         6.58        38.14 

$`TRIP11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
             0.1              0.0 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
            65.1            122.3 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
          16.060           13.565 
[1] "0.1 - 65.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D457V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP11 MUTATED         0        1        3        2         2         3
  TRIP11 WILD-TYPE      10       19       43       29        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           0          3          1          1        2
  TRIP11 WILD-TYPE        29         81         61         38       41
                  vv
clus               STAGE IVA
  TRIP11 MUTATED           0
  TRIP11 WILD-TYPE         4
D457V3, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TRIP11 MUTATED       1   7   5   5
  TRIP11 WILD-TYPE    53 128 256  97
D457V4, multiclass
       clus
vv      TRIP11 MUTATED TRIP11 WILD-TYPE
  T0+T1              1               53
  T2                 7              128
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TRIP11 MUTATED     9   5   4   0
  TRIP11 WILD-TYPE 186 168  85  85
D457V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0              9              186
  N1              5              168
  N2              4               85
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V6, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    16   1
  TRIP11 WILD-TYPE 466  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     16    1
  TRIP11 WILD-TYPE  466   37
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             16              466
  1              1               37
[1] 2 2
[1] FALSE
D457V7, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     8  10
  TRIP11 WILD-TYPE 164 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      8   10
  TRIP11 WILD-TYPE  164  396
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE              8              164
  MALE               10              396
[1] 2 2
[1] FALSE
D457V8, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    15   2
  TRIP11 WILD-TYPE 401 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     15    2
  TRIP11 WILD-TYPE  401  100
     clus
vv    TRIP11 MUTATED TRIP11 WILD-TYPE
  NO              15              401
  YES              2              100
[1] 2 2
[1] FALSE
D457V9, continuous
[1] "Remove cluster labels:" "TRIP11 MUTATED"        
clus
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
D457V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIP11 MUTATED       6                         0
  TRIP11 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP11 MUTATED                                           0     8
  TRIP11 WILD-TYPE                                         1   349
D457V11, multiclass
                                           clus
vv                                          TRIP11 MUTATED TRIP11 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V12, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     0  12
  TRIP11 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      0   12
  TRIP11 WILD-TYPE   10  386
                        clus
vv                       TRIP11 MUTATED TRIP11 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(458) Variable = ADCY10 MUTATION ANALYSIS
D458V1, survival
                  sevent
clus2                0   1
  ADCY10 MUTATED    12  11
  ADCY10 WILD-TYPE 326 205
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              23              531 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              11              205 
$`ADCY10 MUTATED`
TCGA-L5-A43I TCGA-CG-4460 TCGA-2H-A9GH TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A6QS 
       18.28        21.99        31.27         5.92        33.27         9.96 
TCGA-L5-A8NV TCGA-LN-A9FP TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-A44T TCGA-BR-A4QL 
       52.57        12.03        34.68        25.05        34.13        16.14 
TCGA-CD-8524 TCGA-CD-8536 TCGA-D7-5577 TCGA-FP-8211 TCGA-HU-A4GH TCGA-HU-A4GQ 
       12.76        12.43        25.71        13.58        11.77         0.10 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-VQ-A8DL 
        6.51        29.00        19.73        45.67         0.92 

$`ADCY10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       22.75        25.81        21.37        29.98         8.98         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44         8.94        35.61        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ADCY10 MUTATED ADCY10 WILD-TYPE 
             0.1              0.0 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
           52.57           122.30 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
           18.28            13.51 
[1] "0.1 - 52.6 (18.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D458V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADCY10 MUTATED         0        1        2        2         7         3
  ADCY10 WILD-TYPE      10       19       44       29        77        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADCY10 MUTATED           1          4          1          3        2
  ADCY10 WILD-TYPE        28         80         61         36       41
                  vv
clus               STAGE IVA
  ADCY10 MUTATED           0
  ADCY10 WILD-TYPE         4
D458V3, multiclass
            clus
vv           ADCY10 MUTATED ADCY10 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                2               29
  STAGE IIA               7               77
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ADCY10 MUTATED       3   5  14   5
  ADCY10 WILD-TYPE    51 130 247  97
D458V4, multiclass
       clus
vv      ADCY10 MUTATED ADCY10 WILD-TYPE
  T0+T1              3               51
  T2                 5              130
  T3                14              247
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ADCY10 MUTATED    13   7   2   4
  ADCY10 WILD-TYPE 182 166  87  81
D458V5, multiclass
    clus
vv   ADCY10 MUTATED ADCY10 WILD-TYPE
  N0             13              182
  N1              7              166
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V6, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    22   2
  ADCY10 WILD-TYPE 460  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     22    2
  ADCY10 WILD-TYPE  460   36
   clus
vv  ADCY10 MUTATED ADCY10 WILD-TYPE
  0             22              460
  1              2               36
[1] 2 2
[1] FALSE
D458V7, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    16  11
  ADCY10 WILD-TYPE 156 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     16   11
  ADCY10 WILD-TYPE  156  395
        clus
vv       ADCY10 MUTATED ADCY10 WILD-TYPE
  FEMALE             16              156
  MALE               11              395
[1] 2 2
[1] FALSE
D458V8, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    19   4
  ADCY10 WILD-TYPE 397  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     19    4
  ADCY10 WILD-TYPE  397   98
     clus
vv    ADCY10 MUTATED ADCY10 WILD-TYPE
  NO              19              397
  YES              4               98
[1] 2 2
[1] FALSE
D458V9, continuous
[1] "Remove cluster labels:" "ADCY10 MUTATED"        
clus
  ADCY10 MUTATED ADCY10 WILD-TYPE 
               1               67 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YB 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
D458V10, continuous
[1] "Remove cluster labels:" "ADCY10 MUTATED"        
clus
  ADCY10 MUTATED ADCY10 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43J       TCGA-L5-A4OE       TCGA-L5-A4OG 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A8O2 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" "ADCY10 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ADCY10 MUTATED       7                         0
  ADCY10 WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADCY10 MUTATED                                           0    15
  ADCY10 WILD-TYPE                                         1   342
D458V11, multiclass
                                           clus
vv                                          ADCY10 MUTATED ADCY10 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V12, binary
                  cls
clus                 0   1
  ADCY10 MUTATED     1  18
  ADCY10 WILD-TYPE   9 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED      1   18
  ADCY10 WILD-TYPE    9  380
                        clus
vv                       ADCY10 MUTATED ADCY10 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(459) Variable = INTS12 MUTATION ANALYSIS
D459V1, survival
                  sevent
clus2                0   1
  INTS12 MUTATED     2   2
  INTS12 WILD-TYPE 336 214
  INTS12 MUTATED INTS12 WILD-TYPE 
               4              550 
  INTS12 MUTATED INTS12 WILD-TYPE 
               2              214 
$`INTS12 MUTATED`
TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8360 TCGA-BR-A4QL 
       34.68        14.43         6.18        16.14 

$`INTS12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  INTS12 MUTATED INTS12 WILD-TYPE 
            6.18             0.00 
  INTS12 MUTATED INTS12 WILD-TYPE 
           34.68           122.30 
  INTS12 MUTATED INTS12 WILD-TYPE 
          15.285           13.530 
[1] "6.2 - 34.7 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D459V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INTS12 MUTATED         0        0        0        0         2         0
  INTS12 WILD-TYPE      10       20       46       31        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INTS12 MUTATED           1          0          1          0        1
  INTS12 WILD-TYPE        28         84         61         39       42
                  vv
clus               STAGE IVA
  INTS12 MUTATED           0
  INTS12 WILD-TYPE         4
D459V3, multiclass
            clus
vv           INTS12 MUTATED INTS12 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  INTS12 MUTATED       0   0   3   2
  INTS12 WILD-TYPE    54 135 258 100
D459V4, multiclass
       clus
vv      INTS12 MUTATED INTS12 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  INTS12 MUTATED     2   2   1   1
  INTS12 WILD-TYPE 193 171  88  84
D459V5, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V6, binary
                  cls
clus                 0   1
  INTS12 MUTATED     6   0
  INTS12 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      6    0
  INTS12 WILD-TYPE  476   38
   clus
vv  INTS12 MUTATED INTS12 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D459V7, binary
                  cls
clus                 0   1
  INTS12 MUTATED     4   2
  INTS12 WILD-TYPE 168 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      4    2
  INTS12 WILD-TYPE  168  404
        clus
vv       INTS12 MUTATED INTS12 WILD-TYPE
  FEMALE              4              168
  MALE                2              404
[1] 2 2
[1] FALSE
D459V8, binary
                  cls
clus                 0   1
  INTS12 MUTATED     4   0
  INTS12 WILD-TYPE 412 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      4    0
  INTS12 WILD-TYPE  412  102
     clus
vv    INTS12 MUTATED INTS12 WILD-TYPE
  NO               4              412
  YES              0              102
[1] 2 2
[1] FALSE
D459V9, continuous
D459V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INTS12 MUTATED       0                         0
  INTS12 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INTS12 MUTATED                                           0     6
  INTS12 WILD-TYPE                                         1   351
D459V11, multiclass
                                           clus
vv                                          INTS12 MUTATED INTS12 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V12, binary
                  cls
clus                 0   1
  INTS12 MUTATED     0   6
  INTS12 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      0    6
  INTS12 WILD-TYPE   10  392
                        clus
vv                       INTS12 MUTATED INTS12 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(460) Variable = TNFRSF9 MUTATION ANALYSIS
D460V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     6   5
  TNFRSF9 WILD-TYPE 332 211
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               11               543 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                5               211 
$`TNFRSF9 MUTATED`
TCGA-V5-A7RC TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-8680 
        3.42         6.97        30.90        35.84        28.14        31.96 
TCGA-BR-A4QI TCGA-CG-4441 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4H3 
       21.44        14.01         6.02        11.44        29.00 

$`TNFRSF9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
             3.42              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            35.84            122.30 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            21.44             13.51 
[1] "3.4 - 35.8 (21.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D460V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFRSF9 MUTATED         0        0        1        0         1         0
  TNFRSF9 WILD-TYPE      10       20       45       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           0          3          1          2        2
  TNFRSF9 WILD-TYPE        29         81         61         37       41
                   vv
clus                STAGE IVA
  TNFRSF9 MUTATED           0
  TNFRSF9 WILD-TYPE         4
D460V3, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TNFRSF9 MUTATED       0   2   4   4
  TNFRSF9 WILD-TYPE    54 133 257  98
D460V4, multiclass
       clus
vv      TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  4               257
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TNFRSF9 MUTATED     2   2   3   3
  TNFRSF9 WILD-TYPE 193 171  86  82
D460V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               2               193
  N1               2               171
  N2               3                86
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V6, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      8    1
  TNFRSF9 WILD-TYPE  474   37
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D460V7, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     4   7
  TNFRSF9 WILD-TYPE 168 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      4    7
  TNFRSF9 WILD-TYPE  168  399
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  FEMALE               4               168
  MALE                 7               399
[1] 2 2
[1] FALSE
D460V8, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      8    1
  TNFRSF9 WILD-TYPE  408  101
     clus
vv    TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D460V9, continuous
[1] "Remove cluster labels:" "TNFRSF9 MUTATED"       
clus
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RE        TCGA-V5-AASV 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
D460V10, continuous
[1] "Remove cluster labels:" "TNFRSF9 MUTATED"       
clus
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" "TNFRSF9 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TNFRSF9 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFRSF9 MUTATED       2                         1
  TNFRSF9 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFRSF9 MUTATED                                           0     6
  TNFRSF9 WILD-TYPE                                         1   351
D460V11, multiclass
                                           clus
vv                                          TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V12, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     0   9
  TNFRSF9 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      0    9
  TNFRSF9 WILD-TYPE   10  389
                        clus
vv                       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(461) Variable = DYX1C1 MUTATION ANALYSIS
D461V1, survival
                  sevent
clus2                0   1
  DYX1C1 MUTATED     9   3
  DYX1C1 WILD-TYPE 329 213
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              12              542 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
               3              213 
$`DYX1C1 MUTATED`
TCGA-JY-A6FE TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8369 TCGA-BR-8680 
        3.68         6.97        34.68         8.05        14.04        31.96 
TCGA-BR-A4J8 TCGA-CG-5723 TCGA-D7-A4YY TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GN 
       13.51       105.07        13.78        24.20        11.77        29.98 

$`DYX1C1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
            3.68             0.00 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
          105.07           122.30 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
           13.91            13.53 
[1] "3.7 - 105.1 (13.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D461V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYX1C1 MUTATED         0        2        0        1         2         0
  DYX1C1 WILD-TYPE      10       18       46       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYX1C1 MUTATED           1          1          3          1        1
  DYX1C1 WILD-TYPE        28         83         59         38       42
                  vv
clus               STAGE IVA
  DYX1C1 MUTATED           0
  DYX1C1 WILD-TYPE         4
D461V3, multiclass
            clus
vv           DYX1C1 MUTATED DYX1C1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DYX1C1 MUTATED       3   2   6   2
  DYX1C1 WILD-TYPE    51 133 255 100
D461V4, multiclass
       clus
vv      DYX1C1 MUTATED DYX1C1 WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                 6              255
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DYX1C1 MUTATED     3   4   1   4
  DYX1C1 WILD-TYPE 192 169  88  81
D461V5, multiclass
    clus
vv   DYX1C1 MUTATED DYX1C1 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              1               88
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V6, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED    11   1
  DYX1C1 WILD-TYPE 471  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED     11    1
  DYX1C1 WILD-TYPE  471   37
   clus
vv  DYX1C1 MUTATED DYX1C1 WILD-TYPE
  0             11              471
  1              1               37
[1] 2 2
[1] FALSE
D461V7, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED     6   7
  DYX1C1 WILD-TYPE 166 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED      6    7
  DYX1C1 WILD-TYPE  166  399
        clus
vv       DYX1C1 MUTATED DYX1C1 WILD-TYPE
  FEMALE              6              166
  MALE                7              399
[1] 2 2
[1] FALSE
D461V8, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED    11   1
  DYX1C1 WILD-TYPE 405 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED     11    1
  DYX1C1 WILD-TYPE  405  101
     clus
vv    DYX1C1 MUTATED DYX1C1 WILD-TYPE
  NO              11              405
  YES              1              101
[1] 2 2
[1] FALSE
D461V9, continuous
D461V10, continuous
[1] "Remove cluster labels:" "DYX1C1 MUTATED"        
clus
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" "DYX1C1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"DYX1C1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DYX1C1 MUTATED       4                         0
  DYX1C1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYX1C1 MUTATED                                           0     8
  DYX1C1 WILD-TYPE                                         1   349
D461V11, multiclass
                                           clus
vv                                          DYX1C1 MUTATED DYX1C1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V12, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED     0  11
  DYX1C1 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED      0   11
  DYX1C1 WILD-TYPE   10  387
                        clus
vv                       DYX1C1 MUTATED DYX1C1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(462) Variable = KIAA1522 MUTATION ANALYSIS
D462V1, survival
                    sevent
clus2                  0   1
  KIAA1522 MUTATED     7   5
  KIAA1522 WILD-TYPE 331 211
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                12                542 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                 5                211 
$`KIAA1522 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NQ TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-A4QL TCGA-CD-A4MG 
       21.99        21.37        26.70        32.78        16.14         6.58 
TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-VQ-A94T 
        6.02        65.10        22.32        29.98        19.73        11.24 

$`KIAA1522 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
              6.02               0.00 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
              65.1              122.3 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
            21.680             13.495 
[1] "6.0 - 65.1 (21.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D462V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1522 MUTATED         0        0        1        0         4         3
  KIAA1522 WILD-TYPE      10       20       45       31        80        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1522 MUTATED           0          1          2          0        2
  KIAA1522 WILD-TYPE        29         83         60         39       41
                    vv
clus                 STAGE IVA
  KIAA1522 MUTATED           0
  KIAA1522 WILD-TYPE         4
D462V3, multiclass
            clus
vv           KIAA1522 MUTATED KIAA1522 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 4                 80
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                2                 60
  STAGE IIIC                0                 39
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1522 MUTATED       0   3   5   5
  KIAA1522 WILD-TYPE    54 132 256  97
D462V4, multiclass
       clus
vv      KIAA1522 MUTATED KIAA1522 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   5                256
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1522 MUTATED     7   3   2   1
  KIAA1522 WILD-TYPE 188 170  87  84
D462V5, multiclass
    clus
vv   KIAA1522 MUTATED KIAA1522 WILD-TYPE
  N0                7                188
  N1                3                170
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V6, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED    12   1
  KIAA1522 WILD-TYPE 470  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED     12    1
  KIAA1522 WILD-TYPE  470   37
   clus
vv  KIAA1522 MUTATED KIAA1522 WILD-TYPE
  0               12                470
  1                1                 37
[1] 2 2
[1] FALSE
D462V7, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     7   6
  KIAA1522 WILD-TYPE 165 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      7    6
  KIAA1522 WILD-TYPE  165  400
        clus
vv       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  FEMALE                7                165
  MALE                  6                400
[1] 2 2
[1] FALSE
D462V8, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED    12   0
  KIAA1522 WILD-TYPE 404 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED     12    0
  KIAA1522 WILD-TYPE  404  102
     clus
vv    KIAA1522 MUTATED KIAA1522 WILD-TYPE
  NO                12                404
  YES                0                102
[1] 2 2
[1] FALSE
D462V9, continuous
D462V10, continuous
[1] "Remove cluster labels:" "KIAA1522 MUTATED"      
clus
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" "KIAA1522 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KIAA1522 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1522 MUTATED       3                         0
  KIAA1522 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1522 MUTATED                                           0     6
  KIAA1522 WILD-TYPE                                         1   351
D462V11, multiclass
                                           clus
vv                                          KIAA1522 MUTATED KIAA1522 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V12, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     0   8
  KIAA1522 WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      0    8
  KIAA1522 WILD-TYPE   10  390
                        clus
vv                       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(463) Variable = WDR5 MUTATION ANALYSIS
D463V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     1   3
  WDR5 WILD-TYPE 337 213
  WDR5 MUTATED WDR5 WILD-TYPE 
             4            550 
  WDR5 MUTATED WDR5 WILD-TYPE 
             3            213 
$`WDR5 MUTATED`
TCGA-R6-A8W5 TCGA-BR-4256 TCGA-BR-7703 TCGA-CG-5718 
       15.78         9.34        36.16        36.00 

$`WDR5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  WDR5 MUTATED WDR5 WILD-TYPE 
          9.34           0.00 
  WDR5 MUTATED WDR5 WILD-TYPE 
         36.16         122.30 
  WDR5 MUTATED WDR5 WILD-TYPE 
         25.89          13.53 
[1] "9.3 - 36.2 (25.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D463V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR5 MUTATED         0        1        0        1         0         0
  WDR5 WILD-TYPE      10       19       46       30        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR5 MUTATED           0          0          0          0        1         1
  WDR5 WILD-TYPE        29         84         62         39       42         3
D463V3, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WDR5 MUTATED       1   1   2   1
  WDR5 WILD-TYPE    53 134 259 101
D463V4, multiclass
       clus
vv      WDR5 MUTATED WDR5 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WDR5 MUTATED     1   3   1   0
  WDR5 WILD-TYPE 194 170  88  85
D463V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            1            194
  N1            3            170
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V6, binary
                cls
clus               0   1
  WDR5 MUTATED     4   1
  WDR5 WILD-TYPE 478  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      4    1
  WDR5 WILD-TYPE  478   37
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            4            478
  1            1             37
[1] 2 2
[1] FALSE
D463V7, binary
                cls
clus               0   1
  WDR5 MUTATED     3   3
  WDR5 WILD-TYPE 169 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      3    3
  WDR5 WILD-TYPE  169  403
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            3            169
  MALE              3            403
[1] 2 2
[1] FALSE
D463V8, binary
                cls
clus               0   1
  WDR5 MUTATED     4   0
  WDR5 WILD-TYPE 412 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      4    0
  WDR5 WILD-TYPE  412  102
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             4            412
  YES            0            102
[1] 2 2
[1] FALSE
D463V9, continuous
D463V10, continuous
[1] "Remove cluster labels:" "WDR5 MUTATED"          
clus
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" "WDR5 WILD-TYPE" 
    TCGA-Z6-AAPN 
"WDR5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WDR5 MUTATED       0                         0
  WDR5 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR5 MUTATED                                           0     5
  WDR5 WILD-TYPE                                         1   352
D463V11, multiclass
                                           clus
vv                                          WDR5 MUTATED WDR5 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V12, binary
                cls
clus               0   1
  WDR5 MUTATED     0   5
  WDR5 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      0    5
  WDR5 WILD-TYPE   10  393
                        clus
vv                       WDR5 MUTATED WDR5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(464) Variable = GCDH MUTATION ANALYSIS
D464V1, survival
                sevent
clus2              0   1
  GCDH MUTATED     5   2
  GCDH WILD-TYPE 333 214
  GCDH MUTATED GCDH WILD-TYPE 
             7            547 
  GCDH MUTATED GCDH WILD-TYPE 
             2            214 
$`GCDH MUTATED`
TCGA-LN-A49Y TCGA-BR-6452 TCGA-BR-8361 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HJ-7597 
       12.46        34.68        31.10       105.07        11.44        26.47 
TCGA-VQ-A8P2 
       38.14 

$`GCDH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GCDH MUTATED GCDH WILD-TYPE 
         11.44           0.00 
  GCDH MUTATED GCDH WILD-TYPE 
        105.07         122.30 
  GCDH MUTATED GCDH WILD-TYPE 
         31.10          13.51 
[1] "11.4 - 105.1 (31.1)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "2.5"
D464V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCDH MUTATED         0        0        2        1         2         0
  GCDH WILD-TYPE      10       20       44       30        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCDH MUTATED           0          1          1          1        0         0
  GCDH WILD-TYPE        29         83         61         38       43         4
D464V3, multiclass
            clus
vv           GCDH MUTATED GCDH WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GCDH MUTATED       0   3   3   2
  GCDH WILD-TYPE    54 132 258 100
D464V4, multiclass
       clus
vv      GCDH MUTATED GCDH WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GCDH MUTATED     4   2   1   1
  GCDH WILD-TYPE 191 171  88  84
D464V5, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  N0            4            191
  N1            2            171
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V6, binary
                cls
clus               0   1
  GCDH MUTATED     7   0
  GCDH WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      7    0
  GCDH WILD-TYPE  475   38
   clus
vv  GCDH MUTATED GCDH WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D464V7, binary
                cls
clus               0   1
  GCDH MUTATED     4   4
  GCDH WILD-TYPE 168 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      4    4
  GCDH WILD-TYPE  168  402
        clus
vv       GCDH MUTATED GCDH WILD-TYPE
  FEMALE            4            168
  MALE              4            402
[1] 2 2
[1] FALSE
D464V8, binary
                cls
clus               0   1
  GCDH MUTATED     6   1
  GCDH WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      6    1
  GCDH WILD-TYPE  410  101
     clus
vv    GCDH MUTATED GCDH WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D464V9, continuous
[1] "Remove cluster labels:" "GCDH MUTATED"          
clus
  GCDH MUTATED GCDH WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A4A1     TCGA-LN-A4A2 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GCDH WILD-TYPE" "GCDH WILD-TYPE" "GCDH WILD-TYPE" 
D464V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GCDH MUTATED       1                         0
  GCDH WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCDH MUTATED                                           0     5
  GCDH WILD-TYPE                                         1   352
D464V11, multiclass
                                           clus
vv                                          GCDH MUTATED GCDH WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V12, binary
                cls
clus               0   1
  GCDH MUTATED     0   5
  GCDH WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      0    5
  GCDH WILD-TYPE   10  393
                        clus
vv                       GCDH MUTATED GCDH WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(465) Variable = CREBBP MUTATION ANALYSIS
D465V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    25  20
  CREBBP WILD-TYPE 313 196
  CREBBP MUTATED CREBBP WILD-TYPE 
              45              509 
  CREBBP MUTATED CREBBP WILD-TYPE 
              20              196 
$`CREBBP MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GQ TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A4OJ 
       19.99        21.99         4.21         3.68         0.30        21.01 
TCGA-L5-A8NM TCGA-LN-A49K TCGA-LN-A49W TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6Y2 
        7.76         5.92        13.25         0.13        12.03         9.30 
TCGA-VR-AA7D TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 
        9.17        26.70        30.90         9.34        34.68        32.78 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 
       32.25         0.26         4.31        25.05         1.12        31.96 
TCGA-BR-8690 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-5733 TCGA-D7-6817 
       10.68        16.14         6.58        12.62        21.07        12.79 
TCGA-D7-8575 TCGA-D7-A6EY TCGA-F1-6874 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB 
       18.21        11.44        14.47        11.08        77.29        30.51 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       26.47        22.68        29.98         6.58        20.25         2.10 
TCGA-IN-A6RR TCGA-MX-A5UJ TCGA-VQ-AA6I 
        6.74        19.73        16.14 

$`CREBBP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       24.79        32.58         9.86        20.88         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10         6.51         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.13             0.00 
  CREBBP MUTATED CREBBP WILD-TYPE 
           77.29           122.30 
  CREBBP MUTATED CREBBP WILD-TYPE 
           13.25            13.58 
[1] "0.1 - 77.3 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D465V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CREBBP MUTATED         1        0        5        1         9         6
  CREBBP WILD-TYPE       9       20       41       30        75        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREBBP MUTATED           4          6          4          6        3
  CREBBP WILD-TYPE        25         78         58         33       40
                  vv
clus               STAGE IVA
  CREBBP MUTATED           0
  CREBBP WILD-TYPE         4
D465V3, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                5               41
  STAGE II                1               30
  STAGE IIA               9               75
  STAGE IIB               6               77
  STAGE III               4               25
  STAGE IIIA              6               78
  STAGE IIIB              4               58
  STAGE IIIC              6               33
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CREBBP MUTATED       1  13  21  11
  CREBBP WILD-TYPE    53 122 240  91
D465V4, multiclass
       clus
vv      CREBBP MUTATED CREBBP WILD-TYPE
  T0+T1              1               53
  T2                13              122
  T3                21              240
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CREBBP MUTATED    18  12   6  10
  CREBBP WILD-TYPE 177 161  83  75
D465V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             18              177
  N1             12              161
  N2              6               83
  N3             10               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V6, binary
                  cls
clus                 0   1
  CREBBP MUTATED    43   2
  CREBBP WILD-TYPE 439  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     43    2
  CREBBP WILD-TYPE  439   36
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             43              439
  1              2               36
[1] 2 2
[1] FALSE
D465V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED    24  24
  CREBBP WILD-TYPE 148 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     24   24
  CREBBP WILD-TYPE  148  382
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             24              148
  MALE               24              382
[1] 2 2
[1] FALSE
D465V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    39   7
  CREBBP WILD-TYPE 377  95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     39    7
  CREBBP WILD-TYPE  377   95
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              39              377
  YES              7               95
[1] 2 2
[1] FALSE
D465V9, continuous
D465V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CREBBP MUTATED      12                         1
  CREBBP WILD-TYPE   121                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CREBBP MUTATED                                           0    29
  CREBBP WILD-TYPE                                         1   328
D465V11, multiclass
                                           clus
vv                                          CREBBP MUTATED CREBBP WILD-TYPE
  ASIAN                                                 12              121
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 29              328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V12, binary
                  cls
clus                 0   1
  CREBBP MUTATED     1  34
  CREBBP WILD-TYPE   9 364
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      1   34
  CREBBP WILD-TYPE    9  364
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             34              364
[1] 2 2
[1] FALSE

Clustering(466) Variable = IDH2 MUTATION ANALYSIS
D466V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED     7   1
  IDH2 WILD-TYPE 331 215
  IDH2 MUTATED IDH2 WILD-TYPE 
             8            546 
  IDH2 MUTATED IDH2 WILD-TYPE 
             1            215 
$`IDH2 MUTATED`
TCGA-JY-A6F8 TCGA-L5-A43C TCGA-VR-A8EU TCGA-XP-A8T8 TCGA-BR-A4IY TCGA-CG-5723 
      122.10         3.16        18.31        14.37        12.89       105.07 
TCGA-HU-A4G9 TCGA-HU-A4GT 
       24.20         6.51 

$`IDH2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        27.55        28.57         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  IDH2 MUTATED IDH2 WILD-TYPE 
          3.16           0.00 
  IDH2 MUTATED IDH2 WILD-TYPE 
         122.1          122.3 
  IDH2 MUTATED IDH2 WILD-TYPE 
         16.34          13.53 
[1] "3.2 - 122.1 (16.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4.9"
D466V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDH2 MUTATED         1        1        0        1         1         2
  IDH2 WILD-TYPE       9       19       46       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH2 MUTATED           0          0          0          0        1         0
  IDH2 WILD-TYPE        29         84         62         39       42         4
D466V3, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IDH2 MUTATED       4   1   1   1
  IDH2 WILD-TYPE    50 134 260 101
D466V4, multiclass
       clus
vv      IDH2 MUTATED IDH2 WILD-TYPE
  T0+T1            4             50
  T2               1            134
  T3               1            260
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IDH2 MUTATED     4   3   0   0
  IDH2 WILD-TYPE 191 170  89  85
D466V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0            4            191
  N1            3            170
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V6, binary
                cls
clus               0   1
  IDH2 MUTATED     6   1
  IDH2 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      6    1
  IDH2 WILD-TYPE  476   37
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D466V7, binary
                cls
clus               0   1
  IDH2 MUTATED     2   6
  IDH2 WILD-TYPE 170 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      2    6
  IDH2 WILD-TYPE  170  400
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE            2            170
  MALE              6            400
[1] 2 2
[1] FALSE
D466V8, binary
                cls
clus               0   1
  IDH2 MUTATED     6   2
  IDH2 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      6    2
  IDH2 WILD-TYPE  410  100
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D466V9, continuous
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
D466V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IDH2 MUTATED       3                         1
  IDH2 WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IDH2 MUTATED                                           0     3
  IDH2 WILD-TYPE                                         1   354
D466V11, multiclass
                                           clus
vv                                          IDH2 MUTATED IDH2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V12, binary
                cls
clus               0   1
  IDH2 MUTATED     1   3
  IDH2 WILD-TYPE   9 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      1    3
  IDH2 WILD-TYPE    9  395
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(467) Variable = POP1 MUTATION ANALYSIS
D467V1, survival
                sevent
clus2              0   1
  POP1 MUTATED    14   5
  POP1 WILD-TYPE 324 211
  POP1 MUTATED POP1 WILD-TYPE 
            19            535 
  POP1 MUTATED POP1 WILD-TYPE 
             5            211 
$`POP1 MUTATED`
TCGA-L5-A4OG TCGA-CG-4460 TCGA-L5-A88S TCGA-LN-A49R TCGA-BR-4191 TCGA-BR-6852 
        4.70        21.99        15.48        13.38        18.35        44.94 
TCGA-BR-7197 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 
        9.21        14.43        32.25        31.10        31.27        31.96 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-IN-7808 TCGA-SW-A7EA 
        6.58         6.02        11.08        29.98         3.45        19.04 
TCGA-VQ-A8P2 
       38.14 

$`POP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       40.21        30.90        31.20        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  POP1 MUTATED POP1 WILD-TYPE 
          3.45           0.00 
  POP1 MUTATED POP1 WILD-TYPE 
         44.94         122.30 
  POP1 MUTATED POP1 WILD-TYPE 
         18.35          13.51 
[1] "3.5 - 44.9 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D467V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POP1 MUTATED         1        0        3        1         4         1
  POP1 WILD-TYPE       9       20       43       30        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POP1 MUTATED           2          1          0          2        3         0
  POP1 WILD-TYPE        27         83         62         37       40         4
D467V3, multiclass
            clus
vv           POP1 MUTATED POP1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             2             27
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  POP1 MUTATED       1   3   8   8
  POP1 WILD-TYPE    53 132 253  94
D467V4, multiclass
       clus
vv      POP1 MUTATED POP1 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               8            253
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  POP1 MUTATED     9   7   2   2
  POP1 WILD-TYPE 186 166  87  83
D467V5, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  N0            9            186
  N1            7            166
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V6, binary
                cls
clus               0   1
  POP1 MUTATED    17   3
  POP1 WILD-TYPE 465  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED     17    3
  POP1 WILD-TYPE  465   35
   clus
vv  POP1 MUTATED POP1 WILD-TYPE
  0           17            465
  1            3             35
[1] 2 2
[1] FALSE
D467V7, binary
                cls
clus               0   1
  POP1 MUTATED     7  15
  POP1 WILD-TYPE 165 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      7   15
  POP1 WILD-TYPE  165  391
        clus
vv       POP1 MUTATED POP1 WILD-TYPE
  FEMALE            7            165
  MALE             15            391
[1] 2 2
[1] FALSE
D467V8, binary
                cls
clus               0   1
  POP1 MUTATED    16   3
  POP1 WILD-TYPE 400  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED     16    3
  POP1 WILD-TYPE  400   99
     clus
vv    POP1 MUTATED POP1 WILD-TYPE
  NO            16            400
  YES            3             99
[1] 2 2
[1] FALSE
D467V9, continuous
[1] "Remove cluster labels:" "POP1 MUTATED"          
clus
  POP1 MUTATED POP1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"POP1 WILD-TYPE" "POP1 WILD-TYPE" "POP1 WILD-TYPE" 
D467V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  POP1 MUTATED       4                         1
  POP1 WILD-TYPE   129                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POP1 MUTATED                                           0    14
  POP1 WILD-TYPE                                         1   343
D467V11, multiclass
                                           clus
vv                                          POP1 MUTATED POP1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V12, binary
                cls
clus               0   1
  POP1 MUTATED     0  16
  POP1 WILD-TYPE  10 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      0   16
  POP1 WILD-TYPE   10  382
                        clus
vv                       POP1 MUTATED POP1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           16            382
[1] 2 2
[1] FALSE

Clustering(468) Variable = NTAN1 MUTATION ANALYSIS
D468V1, survival
                 sevent
clus2               0   1
  NTAN1 MUTATED     5   2
  NTAN1 WILD-TYPE 333 214
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              7             547 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              2             214 
$`NTAN1 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-CG-5721 
        4.31        19.99        30.90        34.68        35.84         6.02 
TCGA-HF-A5NB 
       30.51 

$`NTAN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NTAN1 MUTATED NTAN1 WILD-TYPE 
           4.31            0.00 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          35.84          122.30 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          30.51           13.51 
[1] "4.3 - 35.8 (30.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D468V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NTAN1 MUTATED         0        0        1        0         1         1
  NTAN1 WILD-TYPE      10       20       45       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTAN1 MUTATED           0          0          0          2        1         0
  NTAN1 WILD-TYPE        29         84         62         37       42         4
D468V3, multiclass
            clus
vv           NTAN1 MUTATED NTAN1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NTAN1 MUTATED       0   2   3   2
  NTAN1 WILD-TYPE    54 133 258 100
D468V4, multiclass
       clus
vv      NTAN1 MUTATED NTAN1 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NTAN1 MUTATED     3   1   0   2
  NTAN1 WILD-TYPE 192 172  89  83
D468V5, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  N0             3             192
  N1             1             172
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V6, binary
                 cls
clus                0   1
  NTAN1 MUTATED     5   0
  NTAN1 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      5    0
  NTAN1 WILD-TYPE  477   38
   clus
vv  NTAN1 MUTATED NTAN1 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D468V7, binary
                 cls
clus                0   1
  NTAN1 MUTATED     4   3
  NTAN1 WILD-TYPE 168 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      4    3
  NTAN1 WILD-TYPE  168  403
        clus
vv       NTAN1 MUTATED NTAN1 WILD-TYPE
  FEMALE             4             168
  MALE               3             403
[1] 2 2
[1] FALSE
D468V8, binary
                 cls
clus                0   1
  NTAN1 MUTATED     5   1
  NTAN1 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      5    1
  NTAN1 WILD-TYPE  411  101
     clus
vv    NTAN1 MUTATED NTAN1 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D468V9, continuous
D468V10, continuous
[1] "Remove cluster labels:" "NTAN1 MUTATED"         
clus
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL      TCGA-IG-A3Y9 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" "NTAN1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NTAN1 MUTATED       0                         0
  NTAN1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NTAN1 MUTATED                                           0     5
  NTAN1 WILD-TYPE                                         1   352
D468V11, multiclass
                                           clus
vv                                          NTAN1 MUTATED NTAN1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V12, binary
                 cls
clus                0   1
  NTAN1 MUTATED     0   3
  NTAN1 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      0    3
  NTAN1 WILD-TYPE   10  395
                        clus
vv                       NTAN1 MUTATED NTAN1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(469) Variable = ZNF776 MUTATION ANALYSIS
D469V1, survival
                  sevent
clus2                0   1
  ZNF776 MUTATED     7   2
  ZNF776 WILD-TYPE 331 214
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               9              545 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               2              214 
$`ZNF776 MUTATED`
TCGA-JY-A938 TCGA-L5-A8NK TCGA-BR-4256 TCGA-BR-6452 TCGA-CG-5723 TCGA-CG-5728 
       34.85        13.55         9.34        34.68       105.07        65.10 
TCGA-D7-A6EY TCGA-SW-A7EA TCGA-VQ-A8P2 
       11.44        19.04        38.14 

$`ZNF776 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZNF776 MUTATED ZNF776 WILD-TYPE 
            9.34             0.00 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
          105.07           122.30 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
           34.68            13.51 
[1] "9.3 - 105.1 (34.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.1"
D469V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF776 MUTATED         0        0        2        1         2         1
  ZNF776 WILD-TYPE      10       20       44       30        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF776 MUTATED           0          1          1          0        0
  ZNF776 WILD-TYPE        29         83         61         39       43
                  vv
clus               STAGE IVA
  ZNF776 MUTATED           0
  ZNF776 WILD-TYPE         4
D469V3, multiclass
            clus
vv           ZNF776 MUTATED ZNF776 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF776 MUTATED       0   3   5   1
  ZNF776 WILD-TYPE    54 132 256 101
D469V4, multiclass
       clus
vv      ZNF776 MUTATED ZNF776 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF776 MUTATED     5   3   0   1
  ZNF776 WILD-TYPE 190 170  89  84
D469V5, multiclass
    clus
vv   ZNF776 MUTATED ZNF776 WILD-TYPE
  N0              5              190
  N1              3              170
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V6, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     9   0
  ZNF776 WILD-TYPE 473  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      9    0
  ZNF776 WILD-TYPE  473   38
   clus
vv  ZNF776 MUTATED ZNF776 WILD-TYPE
  0              9              473
  1              0               38
[1] 2 2
[1] FALSE
D469V7, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     6   4
  ZNF776 WILD-TYPE 166 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      6    4
  ZNF776 WILD-TYPE  166  402
        clus
vv       ZNF776 MUTATED ZNF776 WILD-TYPE
  FEMALE              6              166
  MALE                4              402
[1] 2 2
[1] FALSE
D469V8, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     6   1
  ZNF776 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      6    1
  ZNF776 WILD-TYPE  410  101
     clus
vv    ZNF776 MUTATED ZNF776 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D469V9, continuous
D469V10, continuous
[1] "Remove cluster labels:" "ZNF776 MUTATED"        
clus
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" "ZNF776 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZNF776 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF776 MUTATED       0                         0
  ZNF776 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF776 MUTATED                                           0     8
  ZNF776 WILD-TYPE                                         1   349
D469V11, multiclass
                                           clus
vv                                          ZNF776 MUTATED ZNF776 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V12, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     0   5
  ZNF776 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      0    5
  ZNF776 WILD-TYPE   10  393
                        clus
vv                       ZNF776 MUTATED ZNF776 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(470) Variable = USP15 MUTATION ANALYSIS
D470V1, survival
                 sevent
clus2               0   1
  USP15 MUTATED     7   1
  USP15 WILD-TYPE 331 215
  USP15 MUTATED USP15 WILD-TYPE 
              8             546 
  USP15 MUTATED USP15 WILD-TYPE 
              1             215 
$`USP15 MUTATED`
TCGA-L5-A4OX TCGA-L7-A6VZ TCGA-B7-5816 TCGA-BR-8081 TCGA-CG-5721 TCGA-CG-5723 
        7.43        10.36        26.70        32.25         6.02       105.07 
TCGA-HF-A5NB TCGA-HU-A4GT 
       30.51         6.51 

$`USP15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  USP15 MUTATED USP15 WILD-TYPE 
           6.02            0.00 
  USP15 MUTATED USP15 WILD-TYPE 
         105.07          122.30 
  USP15 MUTATED USP15 WILD-TYPE 
         18.530          13.565 
[1] "6.0 - 105.1 (18.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "4.2"
D470V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP15 MUTATED         0        0        1        1         1         3
  USP15 WILD-TYPE      10       20       45       30        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP15 MUTATED           0          0          0          2        1         0
  USP15 WILD-TYPE        29         84         62         37       42         4
D470V3, multiclass
            clus
vv           USP15 MUTATED USP15 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP15 MUTATED       0   3   2   4
  USP15 WILD-TYPE    54 132 259  98
D470V4, multiclass
       clus
vv      USP15 MUTATED USP15 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                2             259
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP15 MUTATED     4   3   0   2
  USP15 WILD-TYPE 191 170  89  83
D470V5, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V6, binary
                 cls
clus                0   1
  USP15 MUTATED     8   0
  USP15 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      8    0
  USP15 WILD-TYPE  474   38
   clus
vv  USP15 MUTATED USP15 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D470V7, binary
                 cls
clus                0   1
  USP15 MUTATED     4   5
  USP15 WILD-TYPE 168 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      4    5
  USP15 WILD-TYPE  168  401
        clus
vv       USP15 MUTATED USP15 WILD-TYPE
  FEMALE             4             168
  MALE               5             401
[1] 2 2
[1] FALSE
D470V8, binary
                 cls
clus                0   1
  USP15 MUTATED     6   2
  USP15 WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      6    2
  USP15 WILD-TYPE  410  100
     clus
vv    USP15 MUTATED USP15 WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D470V9, continuous
D470V10, continuous
[1] "Remove cluster labels:" "USP15 MUTATED"         
clus
  USP15 MUTATED USP15 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" "USP15 WILD-TYPE" 
     TCGA-Z6-AAPN 
"USP15 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP15 MUTATED       1                         0
  USP15 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP15 MUTATED                                           0     4
  USP15 WILD-TYPE                                         1   353
D470V11, multiclass
                                           clus
vv                                          USP15 MUTATED USP15 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V12, binary
                 cls
clus                0   1
  USP15 MUTATED     0   4
  USP15 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      0    4
  USP15 WILD-TYPE   10  394
                        clus
vv                       USP15 MUTATED USP15 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(471) Variable = IGFBP1 MUTATION ANALYSIS
D471V1, survival
                  sevent
clus2                0   1
  IGFBP1 MUTATED     7   4
  IGFBP1 WILD-TYPE 331 212
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              543 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
               4              212 
$`IGFBP1 MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8286 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4QL 
       26.70        35.84        29.42         0.26        31.96        16.14 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5718 TCGA-CG-5721 TCGA-SW-A7EA 
       12.43         6.58        36.00         6.02        19.04 

$`IGFBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
            0.26             0.00 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
            36.0            122.3 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
           19.04            13.51 
[1] "0.3 - 36.0 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D471V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGFBP1 MUTATED         0        0        3        3         1         1
  IGFBP1 WILD-TYPE      10       20       43       28        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP1 MUTATED           0          0          1          0        2
  IGFBP1 WILD-TYPE        29         84         61         39       41
                  vv
clus               STAGE IVA
  IGFBP1 MUTATED           0
  IGFBP1 WILD-TYPE         4
D471V3, multiclass
            clus
vv           IGFBP1 MUTATED IGFBP1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  IGFBP1 MUTATED       0   4   4   3
  IGFBP1 WILD-TYPE    54 131 257  99
D471V4, multiclass
       clus
vv      IGFBP1 MUTATED IGFBP1 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  IGFBP1 MUTATED     7   2   1   1
  IGFBP1 WILD-TYPE 188 171  88  84
D471V5, multiclass
    clus
vv   IGFBP1 MUTATED IGFBP1 WILD-TYPE
  N0              7              188
  N1              2              171
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V6, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED    10   1
  IGFBP1 WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED     10    1
  IGFBP1 WILD-TYPE  472   37
   clus
vv  IGFBP1 MUTATED IGFBP1 WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D471V7, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED     6   5
  IGFBP1 WILD-TYPE 166 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED      6    5
  IGFBP1 WILD-TYPE  166  401
        clus
vv       IGFBP1 MUTATED IGFBP1 WILD-TYPE
  FEMALE              6              166
  MALE                5              401
[1] 2 2
[1] FALSE
D471V8, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED    11   0
  IGFBP1 WILD-TYPE 405 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED     11    0
  IGFBP1 WILD-TYPE  405  102
     clus
vv    IGFBP1 MUTATED IGFBP1 WILD-TYPE
  NO              11              405
  YES              0              102
[1] 2 2
[1] FALSE
D471V9, continuous
D471V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGFBP1 MUTATED       3                         0
  IGFBP1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGFBP1 MUTATED                                           0     6
  IGFBP1 WILD-TYPE                                         1   351
D471V11, multiclass
                                           clus
vv                                          IGFBP1 MUTATED IGFBP1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V12, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED     0   9
  IGFBP1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED      0    9
  IGFBP1 WILD-TYPE   10  389
                        clus
vv                       IGFBP1 MUTATED IGFBP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(472) Variable = GON4L MUTATION ANALYSIS
D472V1, survival
                 sevent
clus2               0   1
  GON4L MUTATED    11   8
  GON4L WILD-TYPE 327 208
  GON4L MUTATED GON4L WILD-TYPE 
             19             535 
  GON4L MUTATED GON4L WILD-TYPE 
              8             208 
$`GON4L MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NM TCGA-LN-A8I0 TCGA-LN-A9FR 
       34.85         4.31        19.99         7.76        13.38        12.26 
TCGA-V5-A7RB TCGA-VR-AA7D TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 
        5.29         9.17        26.70        30.90        34.68        29.59 
TCGA-BR-8372 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5733 TCGA-D7-A6EY TCGA-HU-A4H3 
       31.27        11.77        12.62        21.07        11.44        29.00 
TCGA-VQ-A8P2 
       38.14 

$`GON4L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GON4L MUTATED GON4L WILD-TYPE 
           4.31            0.00 
  GON4L MUTATED GON4L WILD-TYPE 
          38.14          122.30 
  GON4L MUTATED GON4L WILD-TYPE 
          19.99           13.55 
[1] "4.3 - 38.1 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D472V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GON4L MUTATED         1        0        1        0         2         6
  GON4L WILD-TYPE       9       20       45       31        82        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GON4L MUTATED           0          3          1          4        0         0
  GON4L WILD-TYPE        29         81         61         35       43         4
D472V3, multiclass
            clus
vv           GON4L MUTATED GON4L WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GON4L MUTATED       2   6   7   5
  GON4L WILD-TYPE    52 129 254  97
D472V4, multiclass
       clus
vv      GON4L MUTATED GON4L WILD-TYPE
  T0+T1             2              52
  T2                6             129
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GON4L MUTATED     7   6   1   5
  GON4L WILD-TYPE 188 167  88  80
D472V5, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  N0             7             188
  N1             6             167
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V6, binary
                 cls
clus                0   1
  GON4L MUTATED    16   0
  GON4L WILD-TYPE 466  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     16    0
  GON4L WILD-TYPE  466   38
   clus
vv  GON4L MUTATED GON4L WILD-TYPE
  0            16             466
  1             0              38
[1] 2 2
[1] FALSE
D472V7, binary
                 cls
clus                0   1
  GON4L MUTATED     8  12
  GON4L WILD-TYPE 164 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      8   12
  GON4L WILD-TYPE  164  394
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  FEMALE             8             164
  MALE              12             394
[1] 2 2
[1] FALSE
D472V8, binary
                 cls
clus                0   1
  GON4L MUTATED    15   3
  GON4L WILD-TYPE 401  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     15    3
  GON4L WILD-TYPE  401   99
     clus
vv    GON4L MUTATED GON4L WILD-TYPE
  NO             15             401
  YES             3              99
[1] 2 2
[1] FALSE
D472V9, continuous
[1] "Remove cluster labels:" "GON4L MUTATED"         
clus
  GON4L MUTATED GON4L WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" "GON4L WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"GON4L WILD-TYPE" "GON4L WILD-TYPE" 
D472V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GON4L MUTATED       5                         1
  GON4L WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GON4L MUTATED                                           0    11
  GON4L WILD-TYPE                                         1   346
D472V11, multiclass
                                           clus
vv                                          GON4L MUTATED GON4L WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V12, binary
                 cls
clus                0   1
  GON4L MUTATED     1  12
  GON4L WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      1   12
  GON4L WILD-TYPE    9  386
                        clus
vv                       GON4L MUTATED GON4L WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(473) Variable = C19ORF26 MUTATION ANALYSIS
D473V1, survival
                    sevent
clus2                  0   1
  C19ORF26 MUTATED     3   3
  C19ORF26 WILD-TYPE 335 213
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 6                548 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 3                213 
$`C19ORF26 MUTATED`
TCGA-BR-6452 TCGA-BR-8059 TCGA-CD-A4MI TCGA-CG-5721 TCGA-MX-A5UJ TCGA-R5-A7ZE 
       34.68        14.43        11.77         6.02        19.73        18.21 

$`C19ORF26 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
              6.02               0.00 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
             34.68             122.30 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
             16.32              13.53 
[1] "6.0 - 34.7 (16.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D473V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF26 MUTATED         1        0        2        0         1         0
  C19ORF26 WILD-TYPE       9       20       44       31        83        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF26 MUTATED           1          3          0          0        1
  C19ORF26 WILD-TYPE        28         81         62         39       42
                    vv
clus                 STAGE IVA
  C19ORF26 MUTATED           0
  C19ORF26 WILD-TYPE         4
D473V3, multiclass
            clus
vv           C19ORF26 MUTATED C19ORF26 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 0                 83
  STAGE III                 1                 28
  STAGE IIIA                3                 81
  STAGE IIIB                0                 62
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C19ORF26 MUTATED       1   2   4   2
  C19ORF26 WILD-TYPE    53 133 257 100
D473V4, multiclass
       clus
vv      C19ORF26 MUTATED C19ORF26 WILD-TYPE
  T0+T1                1                 53
  T2                   2                133
  T3                   4                257
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C19ORF26 MUTATED     3   4   2   0
  C19ORF26 WILD-TYPE 192 169  87  85
D473V5, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  N0                3                192
  N1                4                169
  N2                2                 87
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V6, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     9   0
  C19ORF26 WILD-TYPE 473  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      9    0
  C19ORF26 WILD-TYPE  473   38
   clus
vv  C19ORF26 MUTATED C19ORF26 WILD-TYPE
  0                9                473
  1                0                 38
[1] 2 2
[1] FALSE
D473V7, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     5   5
  C19ORF26 WILD-TYPE 167 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      5    5
  C19ORF26 WILD-TYPE  167  401
        clus
vv       C19ORF26 MUTATED C19ORF26 WILD-TYPE
  FEMALE                5                167
  MALE                  5                401
[1] 2 2
[1] FALSE
D473V8, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     8   0
  C19ORF26 WILD-TYPE 408 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      8    0
  C19ORF26 WILD-TYPE  408  102
     clus
vv    C19ORF26 MUTATED C19ORF26 WILD-TYPE
  NO                 8                408
  YES                0                102
[1] 2 2
[1] FALSE
D473V9, continuous
D473V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF26 MUTATED       1                         1
  C19ORF26 WILD-TYPE   132                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF26 MUTATED                                           0     6
  C19ORF26 WILD-TYPE                                         1   351
D473V11, multiclass
                                           clus
vv                                          C19ORF26 MUTATED C19ORF26 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V12, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     0   8
  C19ORF26 WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      0    8
  C19ORF26 WILD-TYPE   10  390
                        clus
vv                       C19ORF26 MUTATED C19ORF26 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(474) Variable = PPP1R13B MUTATION ANALYSIS
D474V1, survival
                    sevent
clus2                  0   1
  PPP1R13B MUTATED    13   4
  PPP1R13B WILD-TYPE 325 212
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                17                537 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                 4                212 
$`PPP1R13B MUTATED`
TCGA-JY-A6FG TCGA-L5-A4OP TCGA-L5-A8NK TCGA-VR-AA4G TCGA-BR-6852 TCGA-BR-8059 
       41.52         7.17        13.55        18.05        44.94        14.43 
TCGA-BR-8081 TCGA-BR-8487 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5723 
       32.25         1.12         0.00        18.97         6.02       105.07 
TCGA-CG-5726 TCGA-D7-A74A TCGA-F1-A448 TCGA-FP-A9TM TCGA-HF-7132 
       28.96        19.96        21.27         6.21        77.29 

$`PPP1R13B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       37.25        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        19.07        12.03         9.01         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7133 
        5.03        13.58         0.56        11.08         5.52        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
               0.0                0.1 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
            105.07             122.30 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
             18.97              13.48 
[1] "0.0 - 105.1 (19.0)" "0.1 - 122.3 (13.5)"
[1] "hr=" "2.2"
D474V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R13B MUTATED         0        2        1        2         3         1
  PPP1R13B WILD-TYPE      10       18       45       29        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R13B MUTATED           2          2          1          0        2
  PPP1R13B WILD-TYPE        27         82         61         39       41
                    vv
clus                 STAGE IVA
  PPP1R13B MUTATED           0
  PPP1R13B WILD-TYPE         4
D474V3, multiclass
            clus
vv           PPP1R13B MUTATED PPP1R13B WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  2                 18
  STAGE IB                  1                 45
  STAGE II                  2                 29
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 2                 27
  STAGE IIIA                2                 82
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PPP1R13B MUTATED       3   4   7   3
  PPP1R13B WILD-TYPE    51 131 254  99
D474V4, multiclass
       clus
vv      PPP1R13B MUTATED PPP1R13B WILD-TYPE
  T0+T1                3                 51
  T2                   4                131
  T3                   7                254
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PPP1R13B MUTATED     7   6   2   2
  PPP1R13B WILD-TYPE 188 167  87  83
D474V5, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  N0                7                188
  N1                6                167
  N2                2                 87
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V6, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED    16   1
  PPP1R13B WILD-TYPE 466  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED     16    1
  PPP1R13B WILD-TYPE  466   37
   clus
vv  PPP1R13B MUTATED PPP1R13B WILD-TYPE
  0               16                466
  1                1                 37
[1] 2 2
[1] FALSE
D474V7, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED    10   8
  PPP1R13B WILD-TYPE 162 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED     10    8
  PPP1R13B WILD-TYPE  162  398
        clus
vv       PPP1R13B MUTATED PPP1R13B WILD-TYPE
  FEMALE               10                162
  MALE                  8                398
[1] 2 2
[1] FALSE
D474V8, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED    10   3
  PPP1R13B WILD-TYPE 406  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED     10    3
  PPP1R13B WILD-TYPE  406   99
     clus
vv    PPP1R13B MUTATED PPP1R13B WILD-TYPE
  NO                10                406
  YES                3                 99
[1] 2 2
[1] FALSE
D474V9, continuous
[1] "Remove cluster labels:" "PPP1R13B MUTATED"      
clus
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA7B 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" "PPP1R13B WILD-TYPE" 
        TCGA-Z6-A8JE 
"PPP1R13B WILD-TYPE" 
D474V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R13B MUTATED       0                         0
  PPP1R13B WILD-TYPE   133                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R13B MUTATED                                           0    12
  PPP1R13B WILD-TYPE                                         1   345
D474V11, multiclass
                                           clus
vv                                          PPP1R13B MUTATED PPP1R13B WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V12, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     1   7
  PPP1R13B WILD-TYPE   9 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      1    7
  PPP1R13B WILD-TYPE    9  391
                        clus
vv                       PPP1R13B MUTATED PPP1R13B WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(475) Variable = CDC25C MUTATION ANALYSIS
D475V1, survival
                  sevent
clus2                0   1
  CDC25C MUTATED     6   4
  CDC25C WILD-TYPE 332 212
  CDC25C MUTATED CDC25C WILD-TYPE 
              10              544 
  CDC25C MUTATED CDC25C WILD-TYPE 
               4              212 
$`CDC25C MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-8687 TCGA-D7-A4YU 
        6.97        34.68        32.25        31.96         8.22        16.44 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H8 
       26.47        29.98         0.10        14.07 

$`CDC25C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CDC25C MUTATED CDC25C WILD-TYPE 
             0.1              0.0 
  CDC25C MUTATED CDC25C WILD-TYPE 
           34.68           122.30 
  CDC25C MUTATED CDC25C WILD-TYPE 
          21.455           13.510 
[1] "0.1 - 34.7 (21.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D475V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC25C MUTATED         0        0        2        0         2         2
  CDC25C WILD-TYPE      10       20       44       31        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC25C MUTATED           0          1          1          2        1
  CDC25C WILD-TYPE        29         83         61         37       42
                  vv
clus               STAGE IVA
  CDC25C MUTATED           0
  CDC25C WILD-TYPE         4
D475V3, multiclass
            clus
vv           CDC25C MUTATED CDC25C WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CDC25C MUTATED       1   2   3   5
  CDC25C WILD-TYPE    53 133 258  97
D475V4, multiclass
       clus
vv      CDC25C MUTATED CDC25C WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 3              258
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CDC25C MUTATED     4   3   3   1
  CDC25C WILD-TYPE 191 170  86  84
D475V5, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  N0              4              191
  N1              3              170
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V6, binary
                  cls
clus                 0   1
  CDC25C MUTATED     8   1
  CDC25C WILD-TYPE 474  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      8    1
  CDC25C WILD-TYPE  474   37
   clus
vv  CDC25C MUTATED CDC25C WILD-TYPE
  0              8              474
  1              1               37
[1] 2 2
[1] FALSE
D475V7, binary
                  cls
clus                 0   1
  CDC25C MUTATED     4   7
  CDC25C WILD-TYPE 168 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      4    7
  CDC25C WILD-TYPE  168  399
        clus
vv       CDC25C MUTATED CDC25C WILD-TYPE
  FEMALE              4              168
  MALE                7              399
[1] 2 2
[1] FALSE
D475V8, binary
                  cls
clus                 0   1
  CDC25C MUTATED    11   0
  CDC25C WILD-TYPE 405 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED     11    0
  CDC25C WILD-TYPE  405  102
     clus
vv    CDC25C MUTATED CDC25C WILD-TYPE
  NO              11              405
  YES              0              102
[1] 2 2
[1] FALSE
D475V9, continuous
D475V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDC25C MUTATED       4                         0
  CDC25C WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC25C MUTATED                                           0     7
  CDC25C WILD-TYPE                                         1   350
D475V11, multiclass
                                           clus
vv                                          CDC25C MUTATED CDC25C WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V12, binary
                  cls
clus                 0   1
  CDC25C MUTATED     0  11
  CDC25C WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      0   11
  CDC25C WILD-TYPE   10  387
                        clus
vv                       CDC25C MUTATED CDC25C WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(476) Variable = IFRD1 MUTATION ANALYSIS
D476V1, survival
                 sevent
clus2               0   1
  IFRD1 MUTATED     2   6
  IFRD1 WILD-TYPE 336 210
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              8             546 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              6             210 
$`IFRD1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6455 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 
        6.97        30.90        13.87        44.94        29.59         0.26 
TCGA-CD-A4MG TCGA-IN-A6RL 
        6.58        13.35 

$`IFRD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  IFRD1 MUTATED IFRD1 WILD-TYPE 
           0.26            0.00 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
          44.94          122.30 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
         13.610          13.565 
[1] "0.3 - 44.9 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D476V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFRD1 MUTATED         1        0        1        0         2         2
  IFRD1 WILD-TYPE       9       20       45       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFRD1 MUTATED           0          2          0          0        0         0
  IFRD1 WILD-TYPE        29         82         62         39       43         4
D476V3, multiclass
            clus
vv           IFRD1 MUTATED IFRD1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IFRD1 MUTATED       1   3   4   1
  IFRD1 WILD-TYPE    53 132 257 101
D476V4, multiclass
       clus
vv      IFRD1 MUTATED IFRD1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IFRD1 MUTATED     4   5   0   0
  IFRD1 WILD-TYPE 191 168  89  85
D476V5, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  N0             4             191
  N1             5             168
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V6, binary
                 cls
clus                0   1
  IFRD1 MUTATED     8   0
  IFRD1 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      8    0
  IFRD1 WILD-TYPE  474   38
   clus
vv  IFRD1 MUTATED IFRD1 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D476V7, binary
                 cls
clus                0   1
  IFRD1 MUTATED     5   5
  IFRD1 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      5    5
  IFRD1 WILD-TYPE  167  401
        clus
vv       IFRD1 MUTATED IFRD1 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D476V8, binary
                 cls
clus                0   1
  IFRD1 MUTATED     9   0
  IFRD1 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      9    0
  IFRD1 WILD-TYPE  407  102
     clus
vv    IFRD1 MUTATED IFRD1 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D476V9, continuous
D476V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IFRD1 MUTATED       1                         1
  IFRD1 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFRD1 MUTATED                                           0     8
  IFRD1 WILD-TYPE                                         1   349
D476V11, multiclass
                                           clus
vv                                          IFRD1 MUTATED IFRD1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V12, binary
                 cls
clus                0   1
  IFRD1 MUTATED     0  10
  IFRD1 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      0   10
  IFRD1 WILD-TYPE   10  388
                        clus
vv                       IFRD1 MUTATED IFRD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(477) Variable = TM6SF1 MUTATION ANALYSIS
D477V1, survival
                  sevent
clus2                0   1
  TM6SF1 MUTATED     6   2
  TM6SF1 WILD-TYPE 332 214
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               8              546 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               2              214 
$`TM6SF1 MUTATED`
TCGA-L5-A4OI TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-CG-4465 
       19.99        26.70        34.68        28.14        12.62         9.01 
TCGA-CG-5728 TCGA-D7-A6EY 
       65.10        11.44 

$`TM6SF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
            9.01             0.00 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
            65.1            122.3 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
          23.345           13.530 
[1] "9.0 - 65.1 (23.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D477V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM6SF1 MUTATED         0        0        2        0         1         1
  TM6SF1 WILD-TYPE      10       20       44       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM6SF1 MUTATED           0          0          1          2        1
  TM6SF1 WILD-TYPE        29         84         61         37       42
                  vv
clus               STAGE IVA
  TM6SF1 MUTATED           0
  TM6SF1 WILD-TYPE         4
D477V3, multiclass
            clus
vv           TM6SF1 MUTATED TM6SF1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TM6SF1 MUTATED       1   2   3   3
  TM6SF1 WILD-TYPE    53 133 258  99
D477V4, multiclass
       clus
vv      TM6SF1 MUTATED TM6SF1 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 3              258
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TM6SF1 MUTATED     4   0   0   4
  TM6SF1 WILD-TYPE 191 173  89  81
D477V5, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  N0              4              191
  N1              0              173
  N2              0               89
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V6, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     7   1
  TM6SF1 WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      7    1
  TM6SF1 WILD-TYPE  475   37
   clus
vv  TM6SF1 MUTATED TM6SF1 WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D477V7, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     6   3
  TM6SF1 WILD-TYPE 166 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      6    3
  TM6SF1 WILD-TYPE  166  403
        clus
vv       TM6SF1 MUTATED TM6SF1 WILD-TYPE
  FEMALE              6              166
  MALE                3              403
[1] 2 2
[1] FALSE
D477V8, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     6   0
  TM6SF1 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      6    0
  TM6SF1 WILD-TYPE  410  102
     clus
vv    TM6SF1 MUTATED TM6SF1 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D477V9, continuous
D477V10, continuous
[1] "Remove cluster labels:" "TM6SF1 MUTATED"        
clus
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" "TM6SF1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"TM6SF1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM6SF1 MUTATED       1                         0
  TM6SF1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM6SF1 MUTATED                                           0     6
  TM6SF1 WILD-TYPE                                         1   351
D477V11, multiclass
                                           clus
vv                                          TM6SF1 MUTATED TM6SF1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V12, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     0   6
  TM6SF1 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      0    6
  TM6SF1 WILD-TYPE   10  392
                        clus
vv                       TM6SF1 MUTATED TM6SF1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(478) Variable = CUBN MUTATION ANALYSIS
D478V1, survival
                sevent
clus2              0   1
  CUBN MUTATED    38  28
  CUBN WILD-TYPE 300 188
  CUBN MUTATED CUBN WILD-TYPE 
            66            488 
  CUBN MUTATED CUBN WILD-TYPE 
            28            188 
$`CUBN MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GK TCGA-2H-A9GO TCGA-IC-A6RE TCGA-JY-A93E 
       19.99        21.99         7.63        16.24         7.69        25.22 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A8NM TCGA-LN-A49L TCGA-LN-A4A4 TCGA-LN-A9FP 
       58.59         4.90         7.76        10.45        12.59        12.03 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 
        7.59         7.04         7.00         6.97        30.90         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7197 TCGA-BR-7707 
        9.67        34.68        32.78        30.90         9.21        35.84 
TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8360 
       33.63         3.45         9.60        32.25         2.66         6.18 
TCGA-BR-8368 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J4 
        4.31         9.21         1.12        27.12        31.96         0.53 
TCGA-BR-A4J5 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG 
       28.34        21.44        16.14         6.31        11.61         6.58 
TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5723 
       11.77         3.02         1.02        12.03         6.02       105.07 
TCGA-CG-5728 TCGA-D7-6527 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-F1-6874 TCGA-FP-7829 
       65.10        10.26        16.44        11.31        14.47        19.53 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 
       11.08        30.51        22.68         6.58        20.25        12.95 
TCGA-IN-8663 TCGA-IN-A6RR TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-VQ-A8P3 TCGA-VQ-A91U 
        3.39         6.74        19.73        16.67        37.22         1.71 

$`CUBN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
        7.43        18.35         4.08         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.69        29.59         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.15         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
       11.31        12.43        12.20        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.99        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        8.98         0.10         6.51         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CUBN MUTATED CUBN WILD-TYPE 
          0.53           0.00 
  CUBN MUTATED CUBN WILD-TYPE 
        105.07         122.30 
  CUBN MUTATED CUBN WILD-TYPE 
        11.690         13.905 
[1] "0.5 - 105.1 (11.7)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D478V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUBN MUTATED         0        0        5        4        11        11
  CUBN WILD-TYPE      10       20       41       27        73        72
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUBN MUTATED           2         10          5          5        8         1
  CUBN WILD-TYPE        27         74         57         34       35         3
D478V3, multiclass
            clus
vv           CUBN MUTATED CUBN WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              5             41
  STAGE II              4             27
  STAGE IIA            11             73
  STAGE IIB            11             72
  STAGE III             2             27
  STAGE IIIA           10             74
  STAGE IIIB            5             57
  STAGE IIIC            5             34
  STAGE IV              8             35
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CUBN MUTATED       3  15  33  15
  CUBN WILD-TYPE    51 120 228  87
D478V4, multiclass
       clus
vv      CUBN MUTATED CUBN WILD-TYPE
  T0+T1            3             51
  T2              15            120
  T3              33            228
  T4              15             87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUBN MUTATED    18  29   9   8
  CUBN WILD-TYPE 177 144  80  77
D478V5, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  N0           18            177
  N1           29            144
  N2            9             80
  N3            8             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V6, binary
                cls
clus               0   1
  CUBN MUTATED    60   7
  CUBN WILD-TYPE 422  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     60    7
  CUBN WILD-TYPE  422   31
   clus
vv  CUBN MUTATED CUBN WILD-TYPE
  0           60            422
  1            7             31
[1] 2 2
[1] FALSE
D478V7, binary
                cls
clus               0   1
  CUBN MUTATED    32  40
  CUBN WILD-TYPE 140 366
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     32   40
  CUBN WILD-TYPE  140  366
        clus
vv       CUBN MUTATED CUBN WILD-TYPE
  FEMALE           32            140
  MALE             40            366
[1] 2 2
[1] FALSE
D478V8, binary
                cls
clus               0   1
  CUBN MUTATED    53   8
  CUBN WILD-TYPE 363  94
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     53    8
  CUBN WILD-TYPE  363   94
     clus
vv    CUBN MUTATED CUBN WILD-TYPE
  NO            53            363
  YES            8             94
[1] 2 2
[1] FALSE
D478V9, continuous
[1] "Remove cluster labels:" "CUBN MUTATED"          
clus
  CUBN MUTATED CUBN WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49M 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A5     TCGA-LN-A4A6     TCGA-LN-A4A8 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" "CUBN WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CUBN WILD-TYPE" "CUBN WILD-TYPE" 
D478V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUBN MUTATED      15                         1
  CUBN WILD-TYPE   118                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUBN MUTATED                                           0    46
  CUBN WILD-TYPE                                         1   311
D478V11, multiclass
                                           clus
vv                                          CUBN MUTATED CUBN WILD-TYPE
  ASIAN                                               15            118
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               46            311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V12, binary
                cls
clus               0   1
  CUBN MUTATED     0  55
  CUBN WILD-TYPE  10 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED      0   55
  CUBN WILD-TYPE   10  343
                        clus
vv                       CUBN MUTATED CUBN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           55            343
[1] 2 2
[1] FALSE

Clustering(479) Variable = EIF5A2 MUTATION ANALYSIS
D479V1, survival
                  sevent
clus2                0   1
  EIF5A2 MUTATED     3   1
  EIF5A2 WILD-TYPE 335 215
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               4              550 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               1              215 
$`EIF5A2 MUTATED`
TCGA-L5-A4OU TCGA-CG-5726 TCGA-HU-8602 TCGA-MX-A5UJ 
       29.00        28.96        22.32        19.73 

$`EIF5A2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
           19.73             0.00 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
            29.0            122.3 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
           25.64            13.51 
[1] "19.7 - 29.0 (25.6)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D479V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF5A2 MUTATED         1        1        0        0         1         2
  EIF5A2 WILD-TYPE       9       19       46       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF5A2 MUTATED           0          1          0          0        0
  EIF5A2 WILD-TYPE        29         83         62         39       43
                  vv
clus               STAGE IVA
  EIF5A2 MUTATED           0
  EIF5A2 WILD-TYPE         4
D479V3, multiclass
            clus
vv           EIF5A2 MUTATED EIF5A2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  EIF5A2 MUTATED       2   0   2   2
  EIF5A2 WILD-TYPE    52 135 259 100
D479V4, multiclass
       clus
vv      EIF5A2 MUTATED EIF5A2 WILD-TYPE
  T0+T1              2               52
  T2                 0              135
  T3                 2              259
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  EIF5A2 MUTATED     4   1   1   0
  EIF5A2 WILD-TYPE 191 172  88  85
D479V5, multiclass
    clus
vv   EIF5A2 MUTATED EIF5A2 WILD-TYPE
  N0              4              191
  N1              1              172
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V6, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     5   0
  EIF5A2 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      5    0
  EIF5A2 WILD-TYPE  477   38
   clus
vv  EIF5A2 MUTATED EIF5A2 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D479V7, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     2   4
  EIF5A2 WILD-TYPE 170 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      2    4
  EIF5A2 WILD-TYPE  170  402
        clus
vv       EIF5A2 MUTATED EIF5A2 WILD-TYPE
  FEMALE              2              170
  MALE                4              402
[1] 2 2
[1] FALSE
D479V8, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     5   0
  EIF5A2 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      5    0
  EIF5A2 WILD-TYPE  411  102
     clus
vv    EIF5A2 MUTATED EIF5A2 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D479V9, continuous
D479V10, continuous
[1] "Remove cluster labels:" "EIF5A2 MUTATED"        
clus
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OW       TCGA-L5-A4OX 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" "EIF5A2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"EIF5A2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EIF5A2 MUTATED       1                         1
  EIF5A2 WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF5A2 MUTATED                                           0     3
  EIF5A2 WILD-TYPE                                         1   354
D479V11, multiclass
                                           clus
vv                                          EIF5A2 MUTATED EIF5A2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V12, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     0   4
  EIF5A2 WILD-TYPE  10 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      0    4
  EIF5A2 WILD-TYPE   10  394
                        clus
vv                       EIF5A2 MUTATED EIF5A2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(480) Variable = HSPA14 MUTATION ANALYSIS
D480V1, survival
                  sevent
clus2                0   1
  HSPA14 MUTATED     4   2
  HSPA14 WILD-TYPE 334 214
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               6              548 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               2              214 
$`HSPA14 MUTATED`
TCGA-L5-A4OG TCGA-B7-5816 TCGA-CG-5733 TCGA-FP-A4BE TCGA-KB-A93J TCGA-VQ-A8DU 
        4.70        26.70        21.07        11.08        36.95         5.46 

$`HSPA14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  HSPA14 MUTATED HSPA14 WILD-TYPE 
             4.7              0.0 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
           36.95           122.30 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
          16.075           13.565 
[1] "4.7 - 37.0 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D480V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSPA14 MUTATED         1        0        0        1         1         1
  HSPA14 WILD-TYPE       9       20       46       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPA14 MUTATED           0          2          0          0        0
  HSPA14 WILD-TYPE        29         82         62         39       43
                  vv
clus               STAGE IVA
  HSPA14 MUTATED           0
  HSPA14 WILD-TYPE         4
D480V3, multiclass
            clus
vv           HSPA14 MUTATED HSPA14 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HSPA14 MUTATED       1   2   2   1
  HSPA14 WILD-TYPE    53 133 259 101
D480V4, multiclass
       clus
vv      HSPA14 MUTATED HSPA14 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 2              259
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HSPA14 MUTATED     3   1   2   0
  HSPA14 WILD-TYPE 192 172  87  85
D480V5, multiclass
    clus
vv   HSPA14 MUTATED HSPA14 WILD-TYPE
  N0              3              192
  N1              1              172
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V6, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     7   0
  HSPA14 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      7    0
  HSPA14 WILD-TYPE  475   38
   clus
vv  HSPA14 MUTATED HSPA14 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D480V7, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     4   3
  HSPA14 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      4    3
  HSPA14 WILD-TYPE  168  403
        clus
vv       HSPA14 MUTATED HSPA14 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D480V8, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     4   2
  HSPA14 WILD-TYPE 412 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      4    2
  HSPA14 WILD-TYPE  412  100
     clus
vv    HSPA14 MUTATED HSPA14 WILD-TYPE
  NO               4              412
  YES              2              100
[1] 2 2
[1] FALSE
D480V9, continuous
D480V10, continuous
[1] "Remove cluster labels:" "HSPA14 MUTATED"        
clus
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" "HSPA14 WILD-TYPE" 
      TCGA-Z6-AAPN 
"HSPA14 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HSPA14 MUTATED       0                         1
  HSPA14 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPA14 MUTATED                                           0     5
  HSPA14 WILD-TYPE                                         1   352
D480V11, multiclass
                                           clus
vv                                          HSPA14 MUTATED HSPA14 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V12, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     0   3
  HSPA14 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      0    3
  HSPA14 WILD-TYPE   10  395
                        clus
vv                       HSPA14 MUTATED HSPA14 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(481) Variable = CHPF2 MUTATION ANALYSIS
D481V1, survival
                 sevent
clus2               0   1
  CHPF2 MUTATED    13   7
  CHPF2 WILD-TYPE 325 209
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             20             534 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
              7             209 
$`CHPF2 MUTATED`
TCGA-L5-A4OI TCGA-IG-A97I TCGA-L5-A8NH TCGA-S8-A6BW TCGA-XP-A8T6 TCGA-BR-4201 
       19.99        12.16        12.92        20.38        25.08        30.90 
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8297 TCGA-BR-8381 TCGA-CD-A4MG 
       34.68        44.94        35.84         7.40         7.36         6.58 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT 
        1.02         8.05        28.96        22.32         0.10         6.51 
TCGA-HU-A4H4 TCGA-VQ-A8P2 
       23.84        38.14 

$`CHPF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       31.20        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27        14.79        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CHPF2 MUTATED CHPF2 WILD-TYPE 
            0.1             0.0 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
          44.94          122.30 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
         20.185          13.530 
[1] "0.1 - 44.9 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D481V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHPF2 MUTATED         0        1        2        1         5         4
  CHPF2 WILD-TYPE      10       19       44       30        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHPF2 MUTATED           0          1          0          3        3         0
  CHPF2 WILD-TYPE        29         83         62         36       40         4
D481V3, multiclass
            clus
vv           CHPF2 MUTATED CHPF2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CHPF2 MUTATED       2   7   7   5
  CHPF2 WILD-TYPE    52 128 254  97
D481V4, multiclass
       clus
vv      CHPF2 MUTATED CHPF2 WILD-TYPE
  T0+T1             2              52
  T2                7             128
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CHPF2 MUTATED    10   4   4   2
  CHPF2 WILD-TYPE 185 169  85  83
D481V5, multiclass
    clus
vv   CHPF2 MUTATED CHPF2 WILD-TYPE
  N0            10             185
  N1             4             169
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V6, binary
                 cls
clus                0   1
  CHPF2 MUTATED    17   2
  CHPF2 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED     17    2
  CHPF2 WILD-TYPE  465   36
   clus
vv  CHPF2 MUTATED CHPF2 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D481V7, binary
                 cls
clus                0   1
  CHPF2 MUTATED     8  13
  CHPF2 WILD-TYPE 164 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED      8   13
  CHPF2 WILD-TYPE  164  393
        clus
vv       CHPF2 MUTATED CHPF2 WILD-TYPE
  FEMALE             8             164
  MALE              13             393
[1] 2 2
[1] FALSE
D481V8, binary
                 cls
clus                0   1
  CHPF2 MUTATED    15   2
  CHPF2 WILD-TYPE 401 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED     15    2
  CHPF2 WILD-TYPE  401  100
     clus
vv    CHPF2 MUTATED CHPF2 WILD-TYPE
  NO             15             401
  YES             2             100
[1] 2 2
[1] FALSE
D481V9, continuous
[1] "Remove cluster labels:" "CHPF2 MUTATED"         
clus
  CHPF2 MUTATED CHPF2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T7 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
D481V10, continuous
[1] "Remove cluster labels:" "CHPF2 MUTATED"         
clus
  CHPF2 MUTATED CHPF2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" "CHPF2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHPF2 MUTATED       5                         1
  CHPF2 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHPF2 MUTATED                                           0    12
  CHPF2 WILD-TYPE                                         1   345
D481V11, multiclass
                                           clus
vv                                          CHPF2 MUTATED CHPF2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V12, binary
                 cls
clus                0   1
  CHPF2 MUTATED     1  14
  CHPF2 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED      1   14
  CHPF2 WILD-TYPE    9  384
                        clus
vv                       CHPF2 MUTATED CHPF2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(482) Variable = FCN2 MUTATION ANALYSIS
D482V1, survival
                sevent
clus2              0   1
  FCN2 MUTATED     8   4
  FCN2 WILD-TYPE 330 212
  FCN2 MUTATED FCN2 WILD-TYPE 
            12            542 
  FCN2 MUTATED FCN2 WILD-TYPE 
             4            212 
$`FCN2 MUTATED`
TCGA-2H-A9GQ TCGA-L5-A4OH TCGA-L5-A8NQ TCGA-LN-A5U6 TCGA-BR-8060 TCGA-BR-8360 
        4.21        32.61        21.37        12.33        11.44         6.18 
TCGA-BR-8487 TCGA-D7-A4YT TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-VQ-A8P2 
        1.12        14.27        21.27        30.51         0.10        38.14 

$`FCN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FCN2 MUTATED FCN2 WILD-TYPE 
           0.1            0.0 
  FCN2 MUTATED FCN2 WILD-TYPE 
         38.14         122.30 
  FCN2 MUTATED FCN2 WILD-TYPE 
        13.300         13.565 
[1] "0.1 - 38.1 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D482V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FCN2 MUTATED         1        0        0        0         3         3
  FCN2 WILD-TYPE       9       20       46       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FCN2 MUTATED           1          2          1          2        0         0
  FCN2 WILD-TYPE        28         82         61         37       43         4
D482V3, multiclass
            clus
vv           FCN2 MUTATED FCN2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FCN2 MUTATED       1   4   4   4
  FCN2 WILD-TYPE    53 131 257  98
D482V4, multiclass
       clus
vv      FCN2 MUTATED FCN2 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FCN2 MUTATED     5   4   2   3
  FCN2 WILD-TYPE 190 169  87  82
D482V5, multiclass
    clus
vv   FCN2 MUTATED FCN2 WILD-TYPE
  N0            5            190
  N1            4            169
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V6, binary
                cls
clus               0   1
  FCN2 MUTATED    14   0
  FCN2 WILD-TYPE 468  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED     14    0
  FCN2 WILD-TYPE  468   38
   clus
vv  FCN2 MUTATED FCN2 WILD-TYPE
  0           14            468
  1            0             38
[1] 2 2
[1] FALSE
D482V7, binary
                cls
clus               0   1
  FCN2 MUTATED     4  10
  FCN2 WILD-TYPE 168 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      4   10
  FCN2 WILD-TYPE  168  396
        clus
vv       FCN2 MUTATED FCN2 WILD-TYPE
  FEMALE            4            168
  MALE             10            396
[1] 2 2
[1] FALSE
D482V8, binary
                cls
clus               0   1
  FCN2 MUTATED     9   4
  FCN2 WILD-TYPE 407  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      9    4
  FCN2 WILD-TYPE  407   98
     clus
vv    FCN2 MUTATED FCN2 WILD-TYPE
  NO             9            407
  YES            4             98
[1] 2 2
[1] FALSE
D482V9, continuous
[1] "Remove cluster labels:" "FCN2 MUTATED"          
clus
  FCN2 MUTATED FCN2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U7     TCGA-LN-A7HV 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"FCN2 WILD-TYPE" "FCN2 WILD-TYPE" "FCN2 WILD-TYPE" 
D482V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FCN2 MUTATED       2                         0
  FCN2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FCN2 MUTATED                                           0    10
  FCN2 WILD-TYPE                                         1   347
D482V11, multiclass
                                           clus
vv                                          FCN2 MUTATED FCN2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V12, binary
                cls
clus               0   1
  FCN2 MUTATED     1   8
  FCN2 WILD-TYPE   9 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      1    8
  FCN2 WILD-TYPE    9  390
                        clus
vv                       FCN2 MUTATED FCN2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(483) Variable = FGF7 MUTATION ANALYSIS
D483V1, survival
                sevent
clus2              0   1
  FGF7 MUTATED     5   2
  FGF7 WILD-TYPE 333 214
  FGF7 MUTATED FGF7 WILD-TYPE 
             7            547 
  FGF7 MUTATED FGF7 WILD-TYPE 
             2            214 
$`FGF7 MUTATED`
TCGA-CG-4460 TCGA-L5-A88V TCGA-VR-A8EU TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8368 
       21.99         2.60        18.31        30.90        29.59         4.31 
TCGA-BR-8680 
       31.96 

$`FGF7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FGF7 MUTATED FGF7 WILD-TYPE 
           2.6            0.0 
  FGF7 MUTATED FGF7 WILD-TYPE 
         31.96         122.30 
  FGF7 MUTATED FGF7 WILD-TYPE 
         21.99          13.51 
[1] "2.6 - 32.0 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D483V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF7 MUTATED         0        0        1        0         0         1
  FGF7 WILD-TYPE      10       20       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGF7 MUTATED           1          1          0          0        3         0
  FGF7 WILD-TYPE        28         83         62         39       40         4
D483V3, multiclass
            clus
vv           FGF7 MUTATED FGF7 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FGF7 MUTATED       1   1   2   3
  FGF7 WILD-TYPE    53 134 259  99
D483V4, multiclass
       clus
vv      FGF7 MUTATED FGF7 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               2            259
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FGF7 MUTATED     2   3   2   0
  FGF7 WILD-TYPE 193 170  87  85
D483V5, multiclass
    clus
vv   FGF7 MUTATED FGF7 WILD-TYPE
  N0            2            193
  N1            3            170
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V6, binary
                cls
clus               0   1
  FGF7 MUTATED     3   3
  FGF7 WILD-TYPE 479  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      3    3
  FGF7 WILD-TYPE  479   35
   clus
vv  FGF7 MUTATED FGF7 WILD-TYPE
  0            3            479
  1            3             35
[1] 2 2
[1] FALSE
D483V7, binary
                cls
clus               0   1
  FGF7 MUTATED     3   4
  FGF7 WILD-TYPE 169 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      3    4
  FGF7 WILD-TYPE  169  402
        clus
vv       FGF7 MUTATED FGF7 WILD-TYPE
  FEMALE            3            169
  MALE              4            402
[1] 2 2
[1] FALSE
D483V8, binary
                cls
clus               0   1
  FGF7 MUTATED     6   1
  FGF7 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      6    1
  FGF7 WILD-TYPE  410  101
     clus
vv    FGF7 MUTATED FGF7 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D483V9, continuous
[1] "Remove cluster labels:" "FGF7 MUTATED"          
clus
  FGF7 MUTATED FGF7 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
D483V10, continuous
[1] "Remove cluster labels:" "FGF7 MUTATED"          
clus
  FGF7 MUTATED FGF7 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A893     TCGA-L5-A8NE 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" "FGF7 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FGF7 MUTATED       1                         0
  FGF7 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF7 MUTATED                                           0     5
  FGF7 WILD-TYPE                                         1   352
D483V11, multiclass
                                           clus
vv                                          FGF7 MUTATED FGF7 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V12, binary
                cls
clus               0   1
  FGF7 MUTATED     0   4
  FGF7 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      0    4
  FGF7 WILD-TYPE   10  394
                        clus
vv                       FGF7 MUTATED FGF7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(484) Variable = KIAA0240 MUTATION ANALYSIS
D484V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     8   3
  KIAA0240 WILD-TYPE 330 213
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                11                543 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 3                213 
$`KIAA0240 MUTATED`
TCGA-L5-A88Z TCGA-LN-A4A1 TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-5721 
        7.40        12.59        25.05         1.12        12.30         6.02 
TCGA-CG-5723 TCGA-HU-8243 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GQ 
      105.07         5.92        24.20        11.77         0.10 

$`KIAA0240 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
               0.1                0.0 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
            105.07             122.30 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             11.77              13.78 
[1] "0.1 - 105.1 (11.8)" "0.0 - 122.3 (13.8)"
[1] "hr=" "1.3"
D484V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0240 MUTATED         0        2        0        1         3         1
  KIAA0240 WILD-TYPE      10       18       46       30        81        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           0          1          0          3        2
  KIAA0240 WILD-TYPE        29         83         62         36       41
                    vv
clus                 STAGE IVA
  KIAA0240 MUTATED           0
  KIAA0240 WILD-TYPE         4
D484V3, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  2                 18
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0240 MUTATED       4   1   2   7
  KIAA0240 WILD-TYPE    50 134 259  95
D484V4, multiclass
       clus
vv      KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T0+T1                4                 50
  T2                   1                134
  T3                   2                259
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0240 MUTATED     7   4   1   2
  KIAA0240 WILD-TYPE 188 169  88  83
D484V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                7                188
  N1                4                169
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V6, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED    14   1
  KIAA0240 WILD-TYPE 468  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED     14    1
  KIAA0240 WILD-TYPE  468   37
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0               14                468
  1                1                 37
[1] 2 2
[1] FALSE
D484V7, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     7   8
  KIAA0240 WILD-TYPE 165 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      7    8
  KIAA0240 WILD-TYPE  165  398
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  FEMALE                7                165
  MALE                  8                398
[1] 2 2
[1] FALSE
D484V8, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED    11   1
  KIAA0240 WILD-TYPE 405 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED     11    1
  KIAA0240 WILD-TYPE  405  101
     clus
vv    KIAA0240 MUTATED KIAA0240 WILD-TYPE
  NO                11                405
  YES                1                101
[1] 2 2
[1] FALSE
D484V9, continuous
[1] "Remove cluster labels:" "KIAA0240 MUTATED"      
clus
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A2 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" "KIAA0240 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA0240 WILD-TYPE" 
D484V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0240 MUTATED       6                         0
  KIAA0240 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0240 MUTATED                                           0     7
  KIAA0240 WILD-TYPE                                         1   350
D484V11, multiclass
                                           clus
vv                                          KIAA0240 MUTATED KIAA0240 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V12, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     0  12
  KIAA0240 WILD-TYPE  10 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      0   12
  KIAA0240 WILD-TYPE   10  386
                        clus
vv                       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               12                386
[1] 2 2
[1] FALSE

Clustering(485) Variable = LRP12 MUTATION ANALYSIS
D485V1, survival
                 sevent
clus2               0   1
  LRP12 MUTATED    22  13
  LRP12 WILD-TYPE 316 203
  LRP12 MUTATED LRP12 WILD-TYPE 
             35             519 
  LRP12 MUTATED LRP12 WILD-TYPE 
             13             203 
$`LRP12 MUTATED`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-IG-A3QL TCGA-JY-A93F TCGA-L5-A43E TCGA-L5-A4OT 
       79.07         0.23        35.21        24.03        30.25         4.90 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-V5-A7RB TCGA-B7-A5TI 
        2.60         3.02         7.76        21.37         5.29        19.56 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 
        6.97        34.68        15.95        32.25         6.18        25.05 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 
       31.96        16.14         6.58        12.62         1.02         6.02 
TCGA-D7-A4YV TCGA-D7-A747 TCGA-HF-7134 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4H2 
        5.92         8.38        52.21         5.92        22.82        12.95 
TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       14.07        18.38        19.73        38.14        18.41 

$`LRP12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       16.24         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        25.22         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48        25.12         7.40         3.75        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        6.61        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       11.77        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29        15.65         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 
       20.81         1.71        42.64        66.81        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  LRP12 MUTATED LRP12 WILD-TYPE 
           0.23            0.00 
  LRP12 MUTATED LRP12 WILD-TYPE 
          79.07          122.30 
  LRP12 MUTATED LRP12 WILD-TYPE 
          15.95           13.51 
[1] "0.2 - 79.1 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D485V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP12 MUTATED         4        2        3        1         7         4
  LRP12 WILD-TYPE       6       18       43       30        77        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP12 MUTATED           1          4          3          4        5         0
  LRP12 WILD-TYPE        28         80         59         35       38         4
D485V3, multiclass
            clus
vv           LRP12 MUTATED LRP12 WILD-TYPE
  STAGE I                4               6
  STAGE IA               2              18
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              7              77
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             3              59
  STAGE IIIC             4              35
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LRP12 MUTATED       8   6  15  10
  LRP12 WILD-TYPE    46 129 246  92
D485V4, multiclass
       clus
vv      LRP12 MUTATED LRP12 WILD-TYPE
  T0+T1             8              46
  T2                6             129
  T3               15             246
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LRP12 MUTATED    16  12   5   6
  LRP12 WILD-TYPE 179 161  84  79
D485V5, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  N0            16             179
  N1            12             161
  N2             5              84
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V6, binary
                 cls
clus                0   1
  LRP12 MUTATED    31   3
  LRP12 WILD-TYPE 451  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     31    3
  LRP12 WILD-TYPE  451   35
   clus
vv  LRP12 MUTATED LRP12 WILD-TYPE
  0            31             451
  1             3              35
[1] 2 2
[1] FALSE
D485V7, binary
                 cls
clus                0   1
  LRP12 MUTATED    13  26
  LRP12 WILD-TYPE 159 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     13   26
  LRP12 WILD-TYPE  159  380
        clus
vv       LRP12 MUTATED LRP12 WILD-TYPE
  FEMALE            13             159
  MALE              26             380
[1] 2 2
[1] FALSE
D485V8, binary
                 cls
clus                0   1
  LRP12 MUTATED    32   3
  LRP12 WILD-TYPE 384  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     32    3
  LRP12 WILD-TYPE  384   99
     clus
vv    LRP12 MUTATED LRP12 WILD-TYPE
  NO             32             384
  YES             3              99
[1] 2 2
[1] FALSE
D485V9, continuous
[1] "Remove cluster labels:" "LRP12 MUTATED"         
clus
  LRP12 MUTATED LRP12 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"LRP12 WILD-TYPE" "LRP12 WILD-TYPE" 
D485V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRP12 MUTATED       8                         1
  LRP12 WILD-TYPE   125                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRP12 MUTATED                                           0    25
  LRP12 WILD-TYPE                                         1   332
D485V11, multiclass
                                           clus
vv                                          LRP12 MUTATED LRP12 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                25             332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V12, binary
                 cls
clus                0   1
  LRP12 MUTATED     1  25
  LRP12 WILD-TYPE   9 373
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED      1   25
  LRP12 WILD-TYPE    9  373
                        clus
vv                       LRP12 MUTATED LRP12 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            25             373
[1] 2 2
[1] FALSE

Clustering(486) Variable = EFHA1 MUTATION ANALYSIS
D486V1, survival
                 sevent
clus2               0   1
  EFHA1 MUTATED    11   4
  EFHA1 WILD-TYPE 327 212
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             15             539 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              4             212 
$`EFHA1 MUTATED`
TCGA-2H-A9GR TCGA-LN-A49K TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-8360 TCGA-CG-5721 
       32.45         5.92         9.67        35.84         6.18         6.02 
TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-8604 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H4 
       21.27        30.51        22.82        29.98         0.10        23.84 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       19.73        74.53        38.14 

$`EFHA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  EFHA1 MUTATED EFHA1 WILD-TYPE 
            0.1             0.0 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
          74.53          122.30 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
          22.82           13.51 
[1] "0.1 - 74.5 (22.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D486V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHA1 MUTATED         0        0        2        0         5         1
  EFHA1 WILD-TYPE      10       20       44       31        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHA1 MUTATED           0          2          1          2        2         0
  EFHA1 WILD-TYPE        29         82         61         37       41         4
D486V3, multiclass
            clus
vv           EFHA1 MUTATED EFHA1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFHA1 MUTATED       0   4   6   5
  EFHA1 WILD-TYPE    54 131 255  97
D486V4, multiclass
       clus
vv      EFHA1 MUTATED EFHA1 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFHA1 MUTATED     6   4   3   2
  EFHA1 WILD-TYPE 189 169  86  83
D486V5, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V6, binary
                 cls
clus                0   1
  EFHA1 MUTATED    15   1
  EFHA1 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED     15    1
  EFHA1 WILD-TYPE  467   37
   clus
vv  EFHA1 MUTATED EFHA1 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D486V7, binary
                 cls
clus                0   1
  EFHA1 MUTATED     7   9
  EFHA1 WILD-TYPE 165 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      7    9
  EFHA1 WILD-TYPE  165  397
        clus
vv       EFHA1 MUTATED EFHA1 WILD-TYPE
  FEMALE             7             165
  MALE               9             397
[1] 2 2
[1] FALSE
D486V8, binary
                 cls
clus                0   1
  EFHA1 MUTATED    12   3
  EFHA1 WILD-TYPE 404  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED     12    3
  EFHA1 WILD-TYPE  404   99
     clus
vv    EFHA1 MUTATED EFHA1 WILD-TYPE
  NO             12             404
  YES             3              99
[1] 2 2
[1] FALSE
D486V9, continuous
[1] "Remove cluster labels:" "EFHA1 MUTATED"         
clus
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49M 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" "EFHA1 WILD-TYPE" 
D486V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHA1 MUTATED       5                         0
  EFHA1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHA1 MUTATED                                           0     7
  EFHA1 WILD-TYPE                                         1   350
D486V11, multiclass
                                           clus
vv                                          EFHA1 MUTATED EFHA1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V12, binary
                 cls
clus                0   1
  EFHA1 MUTATED     2   9
  EFHA1 WILD-TYPE   8 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      2    9
  EFHA1 WILD-TYPE    8  389
                        clus
vv                       EFHA1 MUTATED EFHA1 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(487) Variable = GTF3C1 MUTATION ANALYSIS
D487V1, survival
                  sevent
clus2                0   1
  GTF3C1 MUTATED    19  16
  GTF3C1 WILD-TYPE 319 200
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              35              519 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              16              200 
$`GTF3C1 MUTATED`
TCGA-L5-A43J TCGA-IG-A5B8 TCGA-L5-A8NM TCGA-RE-A7BO TCGA-B7-5816 TCGA-BR-4184 
        4.31         0.79         7.76         7.00        26.70         6.97 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8081 
       30.90        34.68        36.16        35.24        35.84        32.25 
TCGA-BR-8363 TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
        0.26        14.04        31.27        25.05         1.12        28.14 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 
       20.65        16.14        13.18        12.43         6.58         1.02 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-F1-6874 TCGA-HJ-7597 
        6.02       105.07         5.92        11.44        14.47        26.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-IN-A6RL TCGA-VQ-A8P2 
       22.32        22.68        29.98        13.35        38.14 

$`GTF3C1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       44.94        21.90         9.21        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
            0.26             0.00 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
          105.07           122.30 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
           16.14            13.51 
[1] "0.3 - 105.1 (16.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D487V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C1 MUTATED         0        1        5        3         4         9
  GTF3C1 WILD-TYPE      10       19       41       28        80        74
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C1 MUTATED           0          5          3          3        3
  GTF3C1 WILD-TYPE        29         79         59         36       40
                  vv
clus               STAGE IVA
  GTF3C1 MUTATED           0
  GTF3C1 WILD-TYPE         4
D487V3, multiclass
            clus
vv           GTF3C1 MUTATED GTF3C1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                5               41
  STAGE II                3               28
  STAGE IIA               4               80
  STAGE IIB               9               74
  STAGE III               0               29
  STAGE IIIA              5               79
  STAGE IIIB              3               59
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GTF3C1 MUTATED       3   9  15  11
  GTF3C1 WILD-TYPE    51 126 246  91
D487V4, multiclass
       clus
vv      GTF3C1 MUTATED GTF3C1 WILD-TYPE
  T0+T1              3               51
  T2                 9              126
  T3                15              246
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GTF3C1 MUTATED    17  12   2   6
  GTF3C1 WILD-TYPE 178 161  87  79
D487V5, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  N0             17              178
  N1             12              161
  N2              2               87
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V6, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    35   1
  GTF3C1 WILD-TYPE 447  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     35    1
  GTF3C1 WILD-TYPE  447   37
   clus
vv  GTF3C1 MUTATED GTF3C1 WILD-TYPE
  0             35              447
  1              1               37
[1] 2 2
[1] FALSE
D487V7, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    23  16
  GTF3C1 WILD-TYPE 149 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     23   16
  GTF3C1 WILD-TYPE  149  390
        clus
vv       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  FEMALE             23              149
  MALE               16              390
[1] 2 2
[1] FALSE
D487V8, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    32   1
  GTF3C1 WILD-TYPE 384 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     32    1
  GTF3C1 WILD-TYPE  384  101
     clus
vv    GTF3C1 MUTATED GTF3C1 WILD-TYPE
  NO              32              384
  YES              1              101
[1] 2 2
[1] FALSE
D487V9, continuous
D487V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GTF3C1 MUTATED       6                         0
  GTF3C1 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF3C1 MUTATED                                           0    30
  GTF3C1 WILD-TYPE                                         1   327
D487V11, multiclass
                                           clus
vv                                          GTF3C1 MUTATED GTF3C1 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 30              327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V12, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED     0  33
  GTF3C1 WILD-TYPE  10 365
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED      0   33
  GTF3C1 WILD-TYPE   10  365
                        clus
vv                       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             33              365
[1] 2 2
[1] FALSE

Clustering(488) Variable = KIAA0100 MUTATION ANALYSIS
D488V1, survival
                    sevent
clus2                  0   1
  KIAA0100 MUTATED    13   9
  KIAA0100 WILD-TYPE 325 207
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                22                532 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                 9                207 
$`KIAA0100 MUTATED`
TCGA-IG-A4P3 TCGA-R6-A6KZ TCGA-V5-AASW TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 
       18.64         5.06         9.27        34.68        36.16        31.10 
TCGA-BR-8382 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5723 
       25.05         6.58         1.02         9.01        30.97       105.07 
TCGA-CG-5726 TCGA-D7-A4YT TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
       28.96        14.27        11.44        22.68        24.20        11.77 
TCGA-HU-A4GQ TCGA-IN-A6RS TCGA-MX-A5UJ TCGA-RD-A8N9 
        0.10        12.59        19.73        35.61 

$`KIAA0100 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
        0.76        24.30         5.59        24.26         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44         6.74         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
               0.1                0.0 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
            105.07             122.30 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
            19.185             13.510 
[1] "0.1 - 105.1 (19.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D488V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0100 MUTATED         0        5        2        2         2         3
  KIAA0100 WILD-TYPE      10       15       44       29        82        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0100 MUTATED           0          3          1          3        3
  KIAA0100 WILD-TYPE        29         81         61         36       40
                    vv
clus                 STAGE IVA
  KIAA0100 MUTATED           0
  KIAA0100 WILD-TYPE         4
D488V3, multiclass
            clus
vv           KIAA0100 MUTATED KIAA0100 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  5                 15
  STAGE IB                  2                 44
  STAGE II                  2                 29
  STAGE IIA                 2                 82
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                1                 61
  STAGE IIIC                3                 36
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0100 MUTATED       6   6   6   7
  KIAA0100 WILD-TYPE    48 129 255  95
D488V4, multiclass
       clus
vv      KIAA0100 MUTATED KIAA0100 WILD-TYPE
  T0+T1                6                 48
  T2                   6                129
  T3                   6                255
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0100 MUTATED    11   5   5   4
  KIAA0100 WILD-TYPE 184 168  84  81
D488V5, multiclass
    clus
vv   KIAA0100 MUTATED KIAA0100 WILD-TYPE
  N0               11                184
  N1                5                168
  N2                5                 84
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V6, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    25   2
  KIAA0100 WILD-TYPE 457  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     25    2
  KIAA0100 WILD-TYPE  457   36
   clus
vv  KIAA0100 MUTATED KIAA0100 WILD-TYPE
  0               25                457
  1                2                 36
[1] 2 2
[1] FALSE
D488V7, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    15  14
  KIAA0100 WILD-TYPE 157 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     15   14
  KIAA0100 WILD-TYPE  157  392
        clus
vv       KIAA0100 MUTATED KIAA0100 WILD-TYPE
  FEMALE               15                157
  MALE                 14                392
[1] 2 2
[1] FALSE
D488V8, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    16   4
  KIAA0100 WILD-TYPE 400  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     16    4
  KIAA0100 WILD-TYPE  400   98
     clus
vv    KIAA0100 MUTATED KIAA0100 WILD-TYPE
  NO                16                400
  YES                4                 98
[1] 2 2
[1] FALSE
D488V9, continuous
[1] "Remove cluster labels:" "KIAA0100 MUTATED"      
clus
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA0100 WILD-TYPE" 
D488V10, continuous
[1] "Remove cluster labels:" "KIAA0100 MUTATED"      
clus
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4QT         TCGA-IG-A50L 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" "KIAA0100 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KIAA0100 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0100 MUTATED       6                         0
  KIAA0100 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0100 MUTATED                                           0    17
  KIAA0100 WILD-TYPE                                         1   340
D488V11, multiclass
                                           clus
vv                                          KIAA0100 MUTATED KIAA0100 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   17                340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V12, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED     0  23
  KIAA0100 WILD-TYPE  10 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED      0   23
  KIAA0100 WILD-TYPE   10  375
                        clus
vv                       KIAA0100 MUTATED KIAA0100 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               23                375
[1] 2 2
[1] FALSE

Clustering(489) Variable = RPS20 MUTATION ANALYSIS
D489V1, survival
                 sevent
clus2               0   1
  RPS20 MUTATED     2   1
  RPS20 WILD-TYPE 336 215
  RPS20 MUTATED RPS20 WILD-TYPE 
              3             551 
  RPS20 MUTATED RPS20 WILD-TYPE 
              1             215 
$`RPS20 MUTATED`
TCGA-BR-8284 TCGA-D7-8573 TCGA-D7-8574 
        8.05        19.50        17.19 

$`RPS20 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RPS20 MUTATED RPS20 WILD-TYPE 
           8.05            0.00 
  RPS20 MUTATED RPS20 WILD-TYPE 
           19.5           122.3 
  RPS20 MUTATED RPS20 WILD-TYPE 
          17.19           13.55 
[1] "8.1 - 19.5 (17.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D489V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RPS20 MUTATED         0        0        0        0         1         0
  RPS20 WILD-TYPE      10       20       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPS20 MUTATED           0          1          0          1        0         0
  RPS20 WILD-TYPE        29         83         62         38       43         4
D489V3, multiclass
            clus
vv           RPS20 MUTATED RPS20 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RPS20 MUTATED       0   1   2   1
  RPS20 WILD-TYPE    54 134 259 101
D489V4, multiclass
       clus
vv      RPS20 MUTATED RPS20 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RPS20 MUTATED     1   0   0   2
  RPS20 WILD-TYPE 194 173  89  83
D489V5, multiclass
    clus
vv   RPS20 MUTATED RPS20 WILD-TYPE
  N0             1             194
  N1             0             173
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V6, binary
                 cls
clus                0   1
  RPS20 MUTATED     3   0
  RPS20 WILD-TYPE 479  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      3    0
  RPS20 WILD-TYPE  479   38
   clus
vv  RPS20 MUTATED RPS20 WILD-TYPE
  0             3             479
  1             0              38
[1] 2 2
[1] FALSE
D489V7, binary
                 cls
clus                0   1
  RPS20 MUTATED     2   2
  RPS20 WILD-TYPE 170 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      2    2
  RPS20 WILD-TYPE  170  404
        clus
vv       RPS20 MUTATED RPS20 WILD-TYPE
  FEMALE             2             170
  MALE               2             404
[1] 2 2
[1] FALSE
D489V8, binary
                 cls
clus                0   1
  RPS20 MUTATED     3   0
  RPS20 WILD-TYPE 413 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      3    0
  RPS20 WILD-TYPE  413  102
     clus
vv    RPS20 MUTATED RPS20 WILD-TYPE
  NO              3             413
  YES             0             102
[1] 2 2
[1] FALSE
D489V9, continuous
D489V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RPS20 MUTATED       0                         0
  RPS20 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPS20 MUTATED                                           0     4
  RPS20 WILD-TYPE                                         1   353
D489V11, multiclass
                                           clus
vv                                          RPS20 MUTATED RPS20 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V12, binary
                 cls
clus                0   1
  RPS20 MUTATED     0   4
  RPS20 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      0    4
  RPS20 WILD-TYPE   10  394
                        clus
vv                       RPS20 MUTATED RPS20 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(490) Variable = FASTKD1 MUTATION ANALYSIS
D490V1, survival
                   sevent
clus2                 0   1
  FASTKD1 MUTATED     9   5
  FASTKD1 WILD-TYPE 329 211
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               14               540 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
                5               211 
$`FASTKD1 MUTATED`
TCGA-L5-A891 TCGA-VR-A8EQ TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-A4QL 
        3.75        22.82        32.25         4.31        27.12        16.14 
TCGA-CD-8527 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4GX 
        7.17         6.02        28.96         5.92         6.51        20.25 
TCGA-HU-A4H3 TCGA-VQ-A8P2 
       29.00        38.14 

$`FASTKD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.76        12.59        12.53        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        0.10         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
             3.75              0.00 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
            38.14            122.30 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
           18.195            13.530 
[1] "3.8 - 38.1 (18.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D490V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FASTKD1 MUTATED         0        1        1        1         1         2
  FASTKD1 WILD-TYPE      10       19       45       30        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FASTKD1 MUTATED           1          1          2          2        1
  FASTKD1 WILD-TYPE        28         83         60         37       42
                   vv
clus                STAGE IVA
  FASTKD1 MUTATED           0
  FASTKD1 WILD-TYPE         4
D490V3, multiclass
            clus
vv           FASTKD1 MUTATED FASTKD1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FASTKD1 MUTATED       1   2   5   6
  FASTKD1 WILD-TYPE    53 133 256  96
D490V4, multiclass
       clus
vv      FASTKD1 MUTATED FASTKD1 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  5               256
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FASTKD1 MUTATED     4   7   1   2
  FASTKD1 WILD-TYPE 191 166  88  83
D490V5, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  N0               4               191
  N1               7               166
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V6, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED    14   0
  FASTKD1 WILD-TYPE 468  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED     14    0
  FASTKD1 WILD-TYPE  468   38
   clus
vv  FASTKD1 MUTATED FASTKD1 WILD-TYPE
  0              14               468
  1               0                38
[1] 2 2
[1] FALSE
D490V7, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     8   6
  FASTKD1 WILD-TYPE 164 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      8    6
  FASTKD1 WILD-TYPE  164  400
        clus
vv       FASTKD1 MUTATED FASTKD1 WILD-TYPE
  FEMALE               8               164
  MALE                 6               400
[1] 2 2
[1] FALSE
D490V8, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     9   2
  FASTKD1 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      9    2
  FASTKD1 WILD-TYPE  407  100
     clus
vv    FASTKD1 MUTATED FASTKD1 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D490V9, continuous
[1] "Remove cluster labels:" "FASTKD1 MUTATED"       
clus
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" "FASTKD1 WILD-TYPE" 
D490V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FASTKD1 MUTATED       4                         0
  FASTKD1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FASTKD1 MUTATED                                           0     8
  FASTKD1 WILD-TYPE                                         1   349
D490V11, multiclass
                                           clus
vv                                          FASTKD1 MUTATED FASTKD1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V12, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     0   9
  FASTKD1 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      0    9
  FASTKD1 WILD-TYPE   10  389
                        clus
vv                       FASTKD1 MUTATED FASTKD1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(491) Variable = EOMES MUTATION ANALYSIS
D491V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     6   5
  EOMES WILD-TYPE 332 211
  EOMES MUTATED EOMES WILD-TYPE 
             11             543 
  EOMES MUTATED EOMES WILD-TYPE 
              5             211 
$`EOMES MUTATED`
TCGA-L5-A891 TCGA-L5-A8NU TCGA-BR-4256 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-A4QL 
        3.75        83.24         9.34        35.24        29.59        16.14 
TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4306 TCGA-D7-A6EV TCGA-VQ-A92D 
       12.43        11.77         1.02        11.24        66.81 

$`EOMES WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        42.64        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  EOMES MUTATED EOMES WILD-TYPE 
           1.02            0.00 
  EOMES MUTATED EOMES WILD-TYPE 
          83.24          122.30 
  EOMES MUTATED EOMES WILD-TYPE 
          12.43           13.58 
[1] "1.0 - 83.2 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D491V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EOMES MUTATED         0        0        1        2         1         2
  EOMES WILD-TYPE      10       20       45       29        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EOMES MUTATED           0          1          1          0        1         0
  EOMES WILD-TYPE        29         83         61         39       42         4
D491V3, multiclass
            clus
vv           EOMES MUTATED EOMES WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EOMES MUTATED       0   3   6   1
  EOMES WILD-TYPE    54 132 255 101
D491V4, multiclass
       clus
vv      EOMES MUTATED EOMES WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EOMES MUTATED     5   3   2   1
  EOMES WILD-TYPE 190 170  87  84
D491V5, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V6, binary
                 cls
clus                0   1
  EOMES MUTATED    10   1
  EOMES WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED     10    1
  EOMES WILD-TYPE  472   37
   clus
vv  EOMES MUTATED EOMES WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D491V7, binary
                 cls
clus                0   1
  EOMES MUTATED     4   7
  EOMES WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      4    7
  EOMES WILD-TYPE  168  399
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D491V8, binary
                 cls
clus                0   1
  EOMES MUTATED     8   0
  EOMES WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      8    0
  EOMES WILD-TYPE  408  102
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D491V9, continuous
D491V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EOMES MUTATED       2                         0
  EOMES WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EOMES MUTATED                                           0     8
  EOMES WILD-TYPE                                         1   349
D491V11, multiclass
                                           clus
vv                                          EOMES MUTATED EOMES WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V12, binary
                 cls
clus                0   1
  EOMES MUTATED     0   7
  EOMES WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    7
  EOMES WILD-TYPE   10  391
                        clus
vv                       EOMES MUTATED EOMES WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(492) Variable = ULK2 MUTATION ANALYSIS
D492V1, survival
                sevent
clus2              0   1
  ULK2 MUTATED     9   4
  ULK2 WILD-TYPE 329 212
  ULK2 MUTATED ULK2 WILD-TYPE 
            13            541 
  ULK2 MUTATED ULK2 WILD-TYPE 
             4            212 
$`ULK2 MUTATED`
TCGA-2H-A9GO TCGA-R6-A6DN TCGA-BR-6452 TCGA-BR-8591 TCGA-CD-8528 TCGA-CG-4306 
       16.24         8.02        34.68        28.14        12.33         1.02 
TCGA-CG-5728 TCGA-D7-5579 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX 
       65.10        20.91        11.77        29.98         0.10        20.25 
TCGA-HU-A4H4 
       23.84 

$`ULK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        21.37         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ULK2 MUTATED ULK2 WILD-TYPE 
           0.1            0.0 
  ULK2 MUTATED ULK2 WILD-TYPE 
          65.1          122.3 
  ULK2 MUTATED ULK2 WILD-TYPE 
         20.25          13.51 
[1] "0.1 - 65.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D492V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ULK2 MUTATED         0        1        1        0         2         1
  ULK2 WILD-TYPE      10       19       45       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ULK2 MUTATED           0          2          0          3        1         1
  ULK2 WILD-TYPE        29         82         62         36       42         3
D492V3, multiclass
            clus
vv           ULK2 MUTATED ULK2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ULK2 MUTATED       1   3   4   4
  ULK2 WILD-TYPE    53 132 257  98
D492V4, multiclass
       clus
vv      ULK2 MUTATED ULK2 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ULK2 MUTATED     4   2   5   1
  ULK2 WILD-TYPE 191 171  84  84
D492V5, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  N0            4            191
  N1            2            171
  N2            5             84
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V6, binary
                cls
clus               0   1
  ULK2 MUTATED    10   2
  ULK2 WILD-TYPE 472  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED     10    2
  ULK2 WILD-TYPE  472   36
   clus
vv  ULK2 MUTATED ULK2 WILD-TYPE
  0           10            472
  1            2             36
[1] 2 2
[1] FALSE
D492V7, binary
                cls
clus               0   1
  ULK2 MUTATED     5   8
  ULK2 WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      5    8
  ULK2 WILD-TYPE  167  398
        clus
vv       ULK2 MUTATED ULK2 WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D492V8, binary
                cls
clus               0   1
  ULK2 MUTATED     9   1
  ULK2 WILD-TYPE 407 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      9    1
  ULK2 WILD-TYPE  407  101
     clus
vv    ULK2 MUTATED ULK2 WILD-TYPE
  NO             9            407
  YES            1            101
[1] 2 2
[1] FALSE
D492V9, continuous
D492V10, continuous
[1] "Remove cluster labels:" "ULK2 MUTATED"          
clus
  ULK2 MUTATED ULK2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" "ULK2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"ULK2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ULK2 MUTATED       6                         0
  ULK2 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ULK2 MUTATED                                           0     4
  ULK2 WILD-TYPE                                         1   353
D492V11, multiclass
                                           clus
vv                                          ULK2 MUTATED ULK2 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V12, binary
                cls
clus               0   1
  ULK2 MUTATED     0  10
  ULK2 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      0   10
  ULK2 WILD-TYPE   10  388
                        clus
vv                       ULK2 MUTATED ULK2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(493) Variable = INSIG2 MUTATION ANALYSIS
D493V1, survival
                  sevent
clus2                0   1
  INSIG2 MUTATED     6   1
  INSIG2 WILD-TYPE 332 215
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               7              547 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               1              215 
$`INSIG2 MUTATED`
TCGA-IG-A97H TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-CD-A4MI TCGA-HF-7132 
       14.50        34.68        29.59         6.18        11.77        77.29 
TCGA-HF-A5NB 
       30.51 

$`INSIG2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  INSIG2 MUTATED INSIG2 WILD-TYPE 
            6.18             0.00 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
           77.29           122.30 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
           29.59            13.51 
[1] "6.2 - 77.3 (29.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.2"
D493V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INSIG2 MUTATED         0        0        0        1         3         1
  INSIG2 WILD-TYPE      10       20       46       30        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INSIG2 MUTATED           0          1          0          1        0
  INSIG2 WILD-TYPE        29         83         62         38       43
                  vv
clus               STAGE IVA
  INSIG2 MUTATED           0
  INSIG2 WILD-TYPE         4
D493V3, multiclass
            clus
vv           INSIG2 MUTATED INSIG2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  INSIG2 MUTATED       1   1   4   2
  INSIG2 WILD-TYPE    53 134 257 100
D493V4, multiclass
       clus
vv      INSIG2 MUTATED INSIG2 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  INSIG2 MUTATED     3   2   0   1
  INSIG2 WILD-TYPE 192 171  89  84
D493V5, multiclass
    clus
vv   INSIG2 MUTATED INSIG2 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V6, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     8   0
  INSIG2 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      8    0
  INSIG2 WILD-TYPE  474   38
   clus
vv  INSIG2 MUTATED INSIG2 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D493V7, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     4   4
  INSIG2 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      4    4
  INSIG2 WILD-TYPE  168  402
        clus
vv       INSIG2 MUTATED INSIG2 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D493V8, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     4   2
  INSIG2 WILD-TYPE 412 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      4    2
  INSIG2 WILD-TYPE  412  100
     clus
vv    INSIG2 MUTATED INSIG2 WILD-TYPE
  NO               4              412
  YES              2              100
[1] 2 2
[1] FALSE
D493V9, continuous
D493V10, continuous
[1] "Remove cluster labels:" "INSIG2 MUTATED"        
clus
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-JY-A6FA       TCGA-JY-A6FE 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" "INSIG2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"INSIG2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INSIG2 MUTATED       2                         0
  INSIG2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INSIG2 MUTATED                                           0     4
  INSIG2 WILD-TYPE                                         1   353
D493V11, multiclass
                                           clus
vv                                          INSIG2 MUTATED INSIG2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V12, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     0   6
  INSIG2 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      0    6
  INSIG2 WILD-TYPE   10  392
                        clus
vv                       INSIG2 MUTATED INSIG2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(494) Variable = DPAGT1 MUTATION ANALYSIS
D494V1, survival
                  sevent
clus2                0   1
  DPAGT1 MUTATED     2   2
  DPAGT1 WILD-TYPE 336 214
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               4              550 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               2              214 
$`DPAGT1 MUTATED`
TCGA-BR-8059 TCGA-CD-A4MG TCGA-R5-A7ZI TCGA-VQ-A91V 
       14.43         6.58        74.53        42.64 

$`DPAGT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
            6.58             0.00 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
           74.53           122.30 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
          28.535           13.530 
[1] "6.6 - 74.5 (28.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D494V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DPAGT1 MUTATED         0        0        0        0         1         1
  DPAGT1 WILD-TYPE      10       20       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DPAGT1 MUTATED           1          1          0          0        1
  DPAGT1 WILD-TYPE        28         83         62         39       42
                  vv
clus               STAGE IVA
  DPAGT1 MUTATED           0
  DPAGT1 WILD-TYPE         4
D494V3, multiclass
            clus
vv           DPAGT1 MUTATED DPAGT1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DPAGT1 MUTATED       1   0   2   3
  DPAGT1 WILD-TYPE    53 135 259  99
D494V4, multiclass
       clus
vv      DPAGT1 MUTATED DPAGT1 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 2              259
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DPAGT1 MUTATED     2   2   1   0
  DPAGT1 WILD-TYPE 193 171  88  85
D494V5, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V6, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     5   1
  DPAGT1 WILD-TYPE 477  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      5    1
  DPAGT1 WILD-TYPE  477   37
   clus
vv  DPAGT1 MUTATED DPAGT1 WILD-TYPE
  0              5              477
  1              1               37
[1] 2 2
[1] FALSE
D494V7, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     2   4
  DPAGT1 WILD-TYPE 170 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      2    4
  DPAGT1 WILD-TYPE  170  402
        clus
vv       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  FEMALE              2              170
  MALE                4              402
[1] 2 2
[1] FALSE
D494V8, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     4   1
  DPAGT1 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      4    1
  DPAGT1 WILD-TYPE  412  101
     clus
vv    DPAGT1 MUTATED DPAGT1 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D494V9, continuous
D494V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DPAGT1 MUTATED       1                         0
  DPAGT1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DPAGT1 MUTATED                                           0     4
  DPAGT1 WILD-TYPE                                         1   353
D494V11, multiclass
                                           clus
vv                                          DPAGT1 MUTATED DPAGT1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V12, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     1   4
  DPAGT1 WILD-TYPE   9 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      1    4
  DPAGT1 WILD-TYPE    9  394
                        clus
vv                       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(495) Variable = C6ORF165 MUTATION ANALYSIS
D495V1, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED    12   6
  C6ORF165 WILD-TYPE 326 210
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                18                536 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 6                210 
$`C6ORF165 MUTATED`
TCGA-L5-A43I TCGA-KB-A93G TCGA-R6-A8WG TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8368 
       18.28        20.15        12.69         6.97        32.25         4.31 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-6818 
       31.27        25.05        31.96         1.02       105.07        12.36 
TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H4 
       21.27        22.32        24.26        22.68        20.25        23.84 

$`C6ORF165 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              1.02               0.00 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            105.07             122.30 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            21.795             13.445 
[1] "1.0 - 105.1 (21.8)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D495V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C6ORF165 MUTATED         0        1        2        1         0         4
  C6ORF165 WILD-TYPE      10       19       44       30        84        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF165 MUTATED           0          3          1          3        2
  C6ORF165 WILD-TYPE        29         81         61         36       41
                    vv
clus                 STAGE IVA
  C6ORF165 MUTATED           0
  C6ORF165 WILD-TYPE         4
D495V3, multiclass
            clus
vv           C6ORF165 MUTATED C6ORF165 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 0                 84
  STAGE IIB                 4                 79
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                1                 61
  STAGE IIIC                3                 36
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C6ORF165 MUTATED       1   5   5   6
  C6ORF165 WILD-TYPE    53 130 256  96
D495V4, multiclass
       clus
vv      C6ORF165 MUTATED C6ORF165 WILD-TYPE
  T0+T1                1                 53
  T2                   5                130
  T3                   5                256
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C6ORF165 MUTATED     5   4   4   4
  C6ORF165 WILD-TYPE 190 169  85  81
D495V5, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  N0                5                190
  N1                4                169
  N2                4                 85
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V6, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED    13   2
  C6ORF165 WILD-TYPE 469  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED     13    2
  C6ORF165 WILD-TYPE  469   36
   clus
vv  C6ORF165 MUTATED C6ORF165 WILD-TYPE
  0               13                469
  1                2                 36
[1] 2 2
[1] FALSE
D495V7, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     7  11
  C6ORF165 WILD-TYPE 165 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      7   11
  C6ORF165 WILD-TYPE  165  395
        clus
vv       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  FEMALE                7                165
  MALE                 11                395
[1] 2 2
[1] FALSE
D495V8, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED    14   3
  C6ORF165 WILD-TYPE 402  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED     14    3
  C6ORF165 WILD-TYPE  402   99
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                14                402
  YES                3                 99
[1] 2 2
[1] FALSE
D495V9, continuous
D495V10, continuous
[1] "Remove cluster labels:" "C6ORF165 MUTATED"      
clus
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43J         TCGA-L5-A4OE 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" "C6ORF165 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C6ORF165 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C6ORF165 MUTATED       6                         0
  C6ORF165 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6ORF165 MUTATED                                           0    10
  C6ORF165 WILD-TYPE                                         1   347
D495V11, multiclass
                                           clus
vv                                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V12, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     2  12
  C6ORF165 WILD-TYPE   8 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      2   12
  C6ORF165 WILD-TYPE    8  386
                        clus
vv                       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               12                386
[1] 2 2
[1] FALSE

Clustering(496) Variable = YBX2 MUTATION ANALYSIS
D496V1, survival
                sevent
clus2              0   1
  YBX2 MUTATED     6   2
  YBX2 WILD-TYPE 332 214
  YBX2 MUTATED YBX2 WILD-TYPE 
             8            546 
  YBX2 MUTATED YBX2 WILD-TYPE 
             2            214 
$`YBX2 MUTATED`
TCGA-LN-A49M TCGA-LN-A4A4 TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-A4QL 
       12.66        12.59        19.56        34.68         4.31        16.14 
TCGA-CG-4465 TCGA-HU-A4H4 
        9.01        23.84 

$`YBX2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  YBX2 MUTATED YBX2 WILD-TYPE 
          4.31           0.00 
  YBX2 MUTATED YBX2 WILD-TYPE 
         34.68         122.30 
  YBX2 MUTATED YBX2 WILD-TYPE 
        14.400         13.565 
[1] "4.3 - 34.7 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D496V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YBX2 MUTATED         0        0        1        0         2         1
  YBX2 WILD-TYPE      10       20       45       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YBX2 MUTATED           1          0          1          1        1         0
  YBX2 WILD-TYPE        28         84         61         38       42         4
D496V3, multiclass
            clus
vv           YBX2 MUTATED YBX2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  YBX2 MUTATED       0   3   3   2
  YBX2 WILD-TYPE    54 132 258 100
D496V4, multiclass
       clus
vv      YBX2 MUTATED YBX2 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  YBX2 MUTATED     3   1   1   3
  YBX2 WILD-TYPE 192 172  88  82
D496V5, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  N0            3            192
  N1            1            172
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V6, binary
                cls
clus               0   1
  YBX2 MUTATED     7   1
  YBX2 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      7    1
  YBX2 WILD-TYPE  475   37
   clus
vv  YBX2 MUTATED YBX2 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D496V7, binary
                cls
clus               0   1
  YBX2 MUTATED     5   3
  YBX2 WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      5    3
  YBX2 WILD-TYPE  167  403
        clus
vv       YBX2 MUTATED YBX2 WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D496V8, binary
                cls
clus               0   1
  YBX2 MUTATED     5   2
  YBX2 WILD-TYPE 411 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      5    2
  YBX2 WILD-TYPE  411  100
     clus
vv    YBX2 MUTATED YBX2 WILD-TYPE
  NO             5            411
  YES            2            100
[1] 2 2
[1] FALSE
D496V9, continuous
[1] "Remove cluster labels:" "YBX2 MUTATED"          
clus
  YBX2 MUTATED YBX2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A5     TCGA-LN-A4A6     TCGA-LN-A4A8 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"YBX2 WILD-TYPE" "YBX2 WILD-TYPE" 
D496V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  YBX2 MUTATED       3                         0
  YBX2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YBX2 MUTATED                                           0     4
  YBX2 WILD-TYPE                                         1   353
D496V11, multiclass
                                           clus
vv                                          YBX2 MUTATED YBX2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V12, binary
                cls
clus               0   1
  YBX2 MUTATED     0   7
  YBX2 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      0    7
  YBX2 WILD-TYPE   10  391
                        clus
vv                       YBX2 MUTATED YBX2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(497) Variable = CCDC138 MUTATION ANALYSIS
D497V1, survival
                   sevent
clus2                 0   1
  CCDC138 MUTATED     9   1
  CCDC138 WILD-TYPE 329 215
  CCDC138 MUTATED CCDC138 WILD-TYPE 
               10               544 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
                1               215 
$`CCDC138 MUTATED`
TCGA-FP-A8CX TCGA-KH-A6WC TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-8680 
        0.23         6.28        34.68        44.94        28.14        31.96 
TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-5721 TCGA-HU-A4H5 
        6.58         7.99         6.02        23.80 

$`CCDC138 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CCDC138 MUTATED CCDC138 WILD-TYPE 
             0.23              0.00 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
            44.94            122.30 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
           15.895            13.565 
[1] "0.2 - 44.9 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "4.1"
D497V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC138 MUTATED         0        1        2        0         3         0
  CCDC138 WILD-TYPE      10       19       44       31        81        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC138 MUTATED           0          0          0          2        2
  CCDC138 WILD-TYPE        29         84         62         37       41
                   vv
clus                STAGE IVA
  CCDC138 MUTATED           0
  CCDC138 WILD-TYPE         4
D497V3, multiclass
            clus
vv           CCDC138 MUTATED CCDC138 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC138 MUTATED       1   2   3   4
  CCDC138 WILD-TYPE    53 133 258  98
D497V4, multiclass
       clus
vv      CCDC138 MUTATED CCDC138 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  3               258
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC138 MUTATED     6   1   1   2
  CCDC138 WILD-TYPE 189 172  88  83
D497V5, multiclass
    clus
vv   CCDC138 MUTATED CCDC138 WILD-TYPE
  N0               6               189
  N1               1               172
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V6, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     9   1
  CCDC138 WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      9    1
  CCDC138 WILD-TYPE  473   37
   clus
vv  CCDC138 MUTATED CCDC138 WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D497V7, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     3   8
  CCDC138 WILD-TYPE 169 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      3    8
  CCDC138 WILD-TYPE  169  398
        clus
vv       CCDC138 MUTATED CCDC138 WILD-TYPE
  FEMALE               3               169
  MALE                 8               398
[1] 2 2
[1] FALSE
D497V8, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     8   1
  CCDC138 WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      8    1
  CCDC138 WILD-TYPE  408  101
     clus
vv    CCDC138 MUTATED CCDC138 WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D497V9, continuous
[1] "Remove cluster labels:" "CCDC138 MUTATED"       
clus
  CCDC138 MUTATED CCDC138 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
D497V10, continuous
[1] "Remove cluster labels:" "CCDC138 MUTATED"       
clus
  CCDC138 MUTATED CCDC138 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-L5-A43C 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" "CCDC138 WILD-TYPE" 
       TCGA-Z6-AAPN 
"CCDC138 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC138 MUTATED       3                         0
  CCDC138 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC138 MUTATED                                           0     6
  CCDC138 WILD-TYPE                                         1   351
D497V11, multiclass
                                           clus
vv                                          CCDC138 MUTATED CCDC138 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V12, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     0   9
  CCDC138 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      0    9
  CCDC138 WILD-TYPE   10  389
                        clus
vv                       CCDC138 MUTATED CCDC138 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(498) Variable = METTL6 MUTATION ANALYSIS
D498V1, survival
                  sevent
clus2                0   1
  METTL6 MUTATED     2   2
  METTL6 WILD-TYPE 336 214
  METTL6 MUTATED METTL6 WILD-TYPE 
               4              550 
  METTL6 MUTATED METTL6 WILD-TYPE 
               2              214 
$`METTL6 MUTATED`
TCGA-BR-4201 TCGA-BR-8680 TCGA-CG-4306 TCGA-VQ-A8P2 
       30.90        31.96         1.02        38.14 

$`METTL6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  METTL6 MUTATED METTL6 WILD-TYPE 
            1.02             0.00 
  METTL6 MUTATED METTL6 WILD-TYPE 
           38.14           122.30 
  METTL6 MUTATED METTL6 WILD-TYPE 
           31.43            13.53 
[1] "1.0 - 38.1 (31.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D498V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  METTL6 MUTATED         1        0        0        0         0         0
  METTL6 WILD-TYPE       9       20       46       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL6 MUTATED           0          1          0          0        2
  METTL6 WILD-TYPE        29         83         62         39       41
                  vv
clus               STAGE IVA
  METTL6 MUTATED           0
  METTL6 WILD-TYPE         4
D498V3, multiclass
            clus
vv           METTL6 MUTATED METTL6 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  METTL6 MUTATED       1   1   1   2
  METTL6 WILD-TYPE    53 134 260 100
D498V4, multiclass
       clus
vv      METTL6 MUTATED METTL6 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 1              260
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  METTL6 MUTATED     0   2   2   0
  METTL6 WILD-TYPE 195 171  87  85
D498V5, multiclass
    clus
vv   METTL6 MUTATED METTL6 WILD-TYPE
  N0              0              195
  N1              2              171
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V6, binary
                  cls
clus                 0   1
  METTL6 MUTATED     2   2
  METTL6 WILD-TYPE 480  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      2    2
  METTL6 WILD-TYPE  480   36
   clus
vv  METTL6 MUTATED METTL6 WILD-TYPE
  0              2              480
  1              2               36
[1] 2 2
[1] FALSE
D498V7, binary
                  cls
clus                 0   1
  METTL6 MUTATED     1   4
  METTL6 WILD-TYPE 171 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      1    4
  METTL6 WILD-TYPE  171  402
        clus
vv       METTL6 MUTATED METTL6 WILD-TYPE
  FEMALE              1              171
  MALE                4              402
[1] 2 2
[1] FALSE
D498V8, binary
                  cls
clus                 0   1
  METTL6 MUTATED     3   1
  METTL6 WILD-TYPE 413 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      3    1
  METTL6 WILD-TYPE  413  101
     clus
vv    METTL6 MUTATED METTL6 WILD-TYPE
  NO               3              413
  YES              1              101
[1] 2 2
[1] FALSE
D498V9, continuous
D498V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  METTL6 MUTATED       1                         1
  METTL6 WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  METTL6 MUTATED                                           0     2
  METTL6 WILD-TYPE                                         1   355
D498V11, multiclass
                                           clus
vv                                          METTL6 MUTATED METTL6 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V12, binary
                  cls
clus                 0   1
  METTL6 MUTATED     0   3
  METTL6 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      0    3
  METTL6 WILD-TYPE   10  395
                        clus
vv                       METTL6 MUTATED METTL6 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(499) Variable = TRIP10 MUTATION ANALYSIS
D499V1, survival
                  sevent
clus2                0   1
  TRIP10 MUTATED    13   2
  TRIP10 WILD-TYPE 325 214
  TRIP10 MUTATED TRIP10 WILD-TYPE 
              15              539 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               2              214 
$`TRIP10 MUTATED`
TCGA-L5-A4OI TCGA-L5-A891 TCGA-LN-A4A2 TCGA-R6-A8WG TCGA-VR-AA4D TCGA-XP-A8T8 
       19.99         3.75        12.49        12.69        46.19        14.37 
TCGA-BR-6452 TCGA-CG-5721 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GT 
       34.68         6.02       105.07        11.08        30.51         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-MX-A5UJ 
        6.58        29.00        19.73 

$`TRIP10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TRIP10 MUTATED TRIP10 WILD-TYPE 
            3.75             0.00 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
          105.07           122.30 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
           14.37            13.55 
[1] "3.8 - 105.1 (14.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "3.6"
D499V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP10 MUTATED         0        0        0        1         4         3
  TRIP10 WILD-TYPE      10       20       46       30        80        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP10 MUTATED           0          1          0          3        1
  TRIP10 WILD-TYPE        29         83         62         36       42
                  vv
clus               STAGE IVA
  TRIP10 MUTATED           0
  TRIP10 WILD-TYPE         4
D499V3, multiclass
            clus
vv           TRIP10 MUTATED TRIP10 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TRIP10 MUTATED       2   1   8   3
  TRIP10 WILD-TYPE    52 134 253  99
D499V4, multiclass
       clus
vv      TRIP10 MUTATED TRIP10 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 8              253
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TRIP10 MUTATED     4   6   1   3
  TRIP10 WILD-TYPE 191 167  88  82
D499V5, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  N0              4              191
  N1              6              167
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V6, binary
                  cls
clus                 0   1
  TRIP10 MUTATED    13   0
  TRIP10 WILD-TYPE 469  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED     13    0
  TRIP10 WILD-TYPE  469   38
   clus
vv  TRIP10 MUTATED TRIP10 WILD-TYPE
  0             13              469
  1              0               38
[1] 2 2
[1] FALSE
D499V7, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     5  10
  TRIP10 WILD-TYPE 167 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      5   10
  TRIP10 WILD-TYPE  167  396
        clus
vv       TRIP10 MUTATED TRIP10 WILD-TYPE
  FEMALE              5              167
  MALE               10              396
[1] 2 2
[1] FALSE
D499V8, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     8   5
  TRIP10 WILD-TYPE 408  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      8    5
  TRIP10 WILD-TYPE  408   97
     clus
vv    TRIP10 MUTATED TRIP10 WILD-TYPE
  NO               8              408
  YES              5               97
[1] 2 2
[1] FALSE
D499V9, continuous
D499V10, continuous
[1] "Remove cluster labels:" "TRIP10 MUTATED"        
clus
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-Z6-AAPN 
"TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" "TRIP10 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIP10 MUTATED       4                         2
  TRIP10 WILD-TYPE   129                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP10 MUTATED                                           0     6
  TRIP10 WILD-TYPE                                         1   351
D499V11, multiclass
                                           clus
vv                                          TRIP10 MUTATED TRIP10 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V12, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     2   7
  TRIP10 WILD-TYPE   8 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      2    7
  TRIP10 WILD-TYPE    8  391
                        clus
vv                       TRIP10 MUTATED TRIP10 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(500) Variable = C19ORF70 MUTATION ANALYSIS
D500V1, survival
                    sevent
clus2                  0   1
  C19ORF70 MUTATED     3   3
  C19ORF70 WILD-TYPE 335 213
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 6                548 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 3                213 
$`C19ORF70 MUTATED`
TCGA-L5-A8NM TCGA-BR-4257 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MG TCGA-HU-A4G8 
        7.76         9.67         6.18        31.10         6.58        22.68 

$`C19ORF70 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 
       29.42         2.66        19.96         2.20         7.40         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              6.18               0.00 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              31.1              122.3 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
             8.715             13.630 
[1] "6.2 - 31.1 (8.7)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D500V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF70 MUTATED         0        0        0        0         2         3
  C19ORF70 WILD-TYPE      10       20       46       31        82        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF70 MUTATED           0          0          0          1        0
  C19ORF70 WILD-TYPE        29         84         62         38       43
                    vv
clus                 STAGE IVA
  C19ORF70 MUTATED           0
  C19ORF70 WILD-TYPE         4
D500V3, multiclass
            clus
vv           C19ORF70 MUTATED C19ORF70 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C19ORF70 MUTATED       0   1   3   2
  C19ORF70 WILD-TYPE    54 134 258 100
D500V4, multiclass
       clus
vv      C19ORF70 MUTATED C19ORF70 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   3                258
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C19ORF70 MUTATED     3   2   1   0
  C19ORF70 WILD-TYPE 192 171  88  85
D500V5, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V6, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     7   0
  C19ORF70 WILD-TYPE 475  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      7    0
  C19ORF70 WILD-TYPE  475   38
   clus
vv  C19ORF70 MUTATED C19ORF70 WILD-TYPE
  0                7                475
  1                0                 38
[1] 2 2
[1] FALSE
D500V7, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     4   3
  C19ORF70 WILD-TYPE 168 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      4    3
  C19ORF70 WILD-TYPE  168  403
        clus
vv       C19ORF70 MUTATED C19ORF70 WILD-TYPE
  FEMALE                4                168
  MALE                  3                403
[1] 2 2
[1] FALSE
D500V8, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     7   0
  C19ORF70 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      7    0
  C19ORF70 WILD-TYPE  409  102
     clus
vv    C19ORF70 MUTATED C19ORF70 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D500V9, continuous
D500V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF70 MUTATED       2                         0
  C19ORF70 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF70 MUTATED                                           0     5
  C19ORF70 WILD-TYPE                                         1   352
D500V11, multiclass
                                           clus
vv                                          C19ORF70 MUTATED C19ORF70 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V12, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     0   6
  C19ORF70 WILD-TYPE  10 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      0    6
  C19ORF70 WILD-TYPE   10  392
                        clus
vv                       C19ORF70 MUTATED C19ORF70 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                6                392
[1] 2 2
[1] FALSE

Clustering(501) Variable = C16ORF70 MUTATION ANALYSIS
D501V1, survival
                    sevent
clus2                  0   1
  C16ORF70 MUTATED     5   1
  C16ORF70 WILD-TYPE 333 215
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 6                548 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 1                215 
$`C16ORF70 MUTATED`
TCGA-LN-A8I1 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8591 TCGA-F1-A448 TCGA-HU-A4H8 
       13.18         6.97        34.68        28.14        21.27        14.07 

$`C16ORF70 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
              6.97               0.00 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             34.68             122.30 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             17.67              13.53 
[1] "7.0 - 34.7 (17.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D501V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF70 MUTATED         0        0        1        0         2         0
  C16ORF70 WILD-TYPE      10       20       45       31        82        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF70 MUTATED           0          1          1          1        0
  C16ORF70 WILD-TYPE        29         83         61         38       43
                    vv
clus                 STAGE IVA
  C16ORF70 MUTATED           0
  C16ORF70 WILD-TYPE         4
D501V3, multiclass
            clus
vv           C16ORF70 MUTATED C16ORF70 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C16ORF70 MUTATED       1   1   3   1
  C16ORF70 WILD-TYPE    53 134 258 101
D501V4, multiclass
       clus
vv      C16ORF70 MUTATED C16ORF70 WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   3                258
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C16ORF70 MUTATED     2   2   0   2
  C16ORF70 WILD-TYPE 193 171  89  83
D501V5, multiclass
    clus
vv   C16ORF70 MUTATED C16ORF70 WILD-TYPE
  N0                2                193
  N1                2                171
  N2                0                 89
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V6, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     6   0
  C16ORF70 WILD-TYPE 476  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      6    0
  C16ORF70 WILD-TYPE  476   38
   clus
vv  C16ORF70 MUTATED C16ORF70 WILD-TYPE
  0                6                476
  1                0                 38
[1] 2 2
[1] FALSE
D501V7, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     3   4
  C16ORF70 WILD-TYPE 169 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      3    4
  C16ORF70 WILD-TYPE  169  402
        clus
vv       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  FEMALE                3                169
  MALE                  4                402
[1] 2 2
[1] FALSE
D501V8, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     4   2
  C16ORF70 WILD-TYPE 412 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      4    2
  C16ORF70 WILD-TYPE  412  100
     clus
vv    C16ORF70 MUTATED C16ORF70 WILD-TYPE
  NO                 4                412
  YES                2                100
[1] 2 2
[1] FALSE
D501V9, continuous
D501V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF70 MUTATED       2                         0
  C16ORF70 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF70 MUTATED                                           0     5
  C16ORF70 WILD-TYPE                                         1   352
D501V11, multiclass
                                           clus
vv                                          C16ORF70 MUTATED C16ORF70 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V12, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     1   6
  C16ORF70 WILD-TYPE   9 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    6
  C16ORF70 WILD-TYPE    9  392
                        clus
vv                       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO                6                392
[1] 2 2
[1] FALSE

Clustering(502) Variable = MARCH7 MUTATION ANALYSIS
D502V1, survival
                  sevent
clus2                0   1
  MARCH7 MUTATED     5   4
  MARCH7 WILD-TYPE 333 212
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               9              545 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               4              212 
$`MARCH7 MUTATED`
TCGA-CG-4460 TCGA-IG-A4QT TCGA-L5-A8NM TCGA-LN-A49X TCGA-BR-4184 TCGA-BR-6852 
       21.99         9.30         7.76        12.62         6.97        44.94 
TCGA-BR-8368 TCGA-CG-5728 TCGA-HU-A4G8 
        4.31        65.10        22.68 

$`MARCH7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MARCH7 MUTATED MARCH7 WILD-TYPE 
            4.31             0.00 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
            65.1            122.3 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
           12.62            13.58 
[1] "4.3 - 65.1 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D502V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MARCH7 MUTATED         0        0        2        0         3         2
  MARCH7 WILD-TYPE      10       20       44       31        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARCH7 MUTATED           0          1          0          0        1
  MARCH7 WILD-TYPE        29         83         62         39       42
                  vv
clus               STAGE IVA
  MARCH7 MUTATED           0
  MARCH7 WILD-TYPE         4
D502V3, multiclass
            clus
vv           MARCH7 MUTATED MARCH7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MARCH7 MUTATED       0   3   5   1
  MARCH7 WILD-TYPE    54 132 256 101
D502V4, multiclass
       clus
vv      MARCH7 MUTATED MARCH7 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MARCH7 MUTATED     5   4   0   0
  MARCH7 WILD-TYPE 190 169  89  85
D502V5, multiclass
    clus
vv   MARCH7 MUTATED MARCH7 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V6, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     7   1
  MARCH7 WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      7    1
  MARCH7 WILD-TYPE  475   37
   clus
vv  MARCH7 MUTATED MARCH7 WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D502V7, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     6   3
  MARCH7 WILD-TYPE 166 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      6    3
  MARCH7 WILD-TYPE  166  403
        clus
vv       MARCH7 MUTATED MARCH7 WILD-TYPE
  FEMALE              6              166
  MALE                3              403
[1] 2 2
[1] FALSE
D502V8, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     6   2
  MARCH7 WILD-TYPE 410 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      6    2
  MARCH7 WILD-TYPE  410  100
     clus
vv    MARCH7 MUTATED MARCH7 WILD-TYPE
  NO               6              410
  YES              2              100
[1] 2 2
[1] FALSE
D502V9, continuous
[1] "Remove cluster labels:" "MARCH7 MUTATED"        
clus
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
D502V10, continuous
[1] "Remove cluster labels:" "MARCH7 MUTATED"        
clus
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-Z6-AAPN 
"MARCH7 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MARCH7 MUTATED       2                         0
  MARCH7 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MARCH7 MUTATED                                           0     5
  MARCH7 WILD-TYPE                                         1   352
D502V11, multiclass
                                           clus
vv                                          MARCH7 MUTATED MARCH7 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V12, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     0   6
  MARCH7 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      0    6
  MARCH7 WILD-TYPE   10  392
                        clus
vv                       MARCH7 MUTATED MARCH7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(503) Variable = PPP1R15A MUTATION ANALYSIS
D503V1, survival
                    sevent
clus2                  0   1
  PPP1R15A MUTATED     4   2
  PPP1R15A WILD-TYPE 334 214
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 6                548 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 2                214 
$`PPP1R15A MUTATED`
TCGA-L5-A4OM TCGA-L5-A8NL TCGA-B7-5816 TCGA-BR-A4QL TCGA-F1-6874 TCGA-MX-A5UJ 
       47.93        13.22        26.70        16.14        14.47        19.73 

$`PPP1R15A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
             13.22               0.00 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
             47.93             122.30 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
            17.935             13.510 
[1] "13.2 - 47.9 (17.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D503V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R15A MUTATED         0        1        1        0         0         1
  PPP1R15A WILD-TYPE      10       19       45       31        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R15A MUTATED           1          1          1          0        1
  PPP1R15A WILD-TYPE        28         83         61         39       42
                    vv
clus                 STAGE IVA
  PPP1R15A MUTATED           0
  PPP1R15A WILD-TYPE         4
D503V3, multiclass
            clus
vv           PPP1R15A MUTATED PPP1R15A WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 1                 28
  STAGE IIIA                1                 83
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PPP1R15A MUTATED       1   1   3   2
  PPP1R15A WILD-TYPE    53 134 258 100
D503V4, multiclass
       clus
vv      PPP1R15A MUTATED PPP1R15A WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   3                258
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PPP1R15A MUTATED     3   1   2   1
  PPP1R15A WILD-TYPE 192 172  87  84
D503V5, multiclass
    clus
vv   PPP1R15A MUTATED PPP1R15A WILD-TYPE
  N0                3                192
  N1                1                172
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V6, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     6   0
  PPP1R15A WILD-TYPE 476  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      6    0
  PPP1R15A WILD-TYPE  476   38
   clus
vv  PPP1R15A MUTATED PPP1R15A WILD-TYPE
  0                6                476
  1                0                 38
[1] 2 2
[1] FALSE
D503V7, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     5   2
  PPP1R15A WILD-TYPE 167 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      5    2
  PPP1R15A WILD-TYPE  167  404
        clus
vv       PPP1R15A MUTATED PPP1R15A WILD-TYPE
  FEMALE                5                167
  MALE                  2                404
[1] 2 2
[1] FALSE
D503V8, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     5   0
  PPP1R15A WILD-TYPE 411 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      5    0
  PPP1R15A WILD-TYPE  411  102
     clus
vv    PPP1R15A MUTATED PPP1R15A WILD-TYPE
  NO                 5                411
  YES                0                102
[1] 2 2
[1] FALSE
D503V9, continuous
D503V10, continuous
[1] "Remove cluster labels:" "PPP1R15A MUTATED"      
clus
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4ON 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" "PPP1R15A WILD-TYPE" 
        TCGA-Z6-AAPN 
"PPP1R15A WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R15A MUTATED       0                         0
  PPP1R15A WILD-TYPE   133                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R15A MUTATED                                           0     7
  PPP1R15A WILD-TYPE                                         1   350
D503V11, multiclass
                                           clus
vv                                          PPP1R15A MUTATED PPP1R15A WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V12, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     0   5
  PPP1R15A WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      0    5
  PPP1R15A WILD-TYPE   10  393
                        clus
vv                       PPP1R15A MUTATED PPP1R15A WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(504) Variable = USP13 MUTATION ANALYSIS
D504V1, survival
                 sevent
clus2               0   1
  USP13 MUTATED     6   6
  USP13 WILD-TYPE 332 210
  USP13 MUTATED USP13 WILD-TYPE 
             12             542 
  USP13 MUTATED USP13 WILD-TYPE 
              6             210 
$`USP13 MUTATED`
TCGA-IG-A8O2 TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-5801 
        4.67         6.97        29.59        25.05        28.14        13.18 
TCGA-CD-8527 TCGA-CG-4305 TCGA-CG-4469 TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA68 
        7.17        15.95         7.07        74.53        38.14        43.66 

$`USP13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.76        12.59        12.53        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  USP13 MUTATED USP13 WILD-TYPE 
           4.67            0.00 
  USP13 MUTATED USP13 WILD-TYPE 
          74.53          122.30 
  USP13 MUTATED USP13 WILD-TYPE 
          20.50           13.53 
[1] "4.7 - 74.5 (20.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D504V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP13 MUTATED         0        0        1        2         0         1
  USP13 WILD-TYPE      10       20       45       29        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP13 MUTATED           0          3          1          3        2         0
  USP13 WILD-TYPE        29         81         61         36       41         4
D504V3, multiclass
            clus
vv           USP13 MUTATED USP13 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP13 MUTATED       0   3   4   6
  USP13 WILD-TYPE    54 132 257  96
D504V4, multiclass
       clus
vv      USP13 MUTATED USP13 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP13 MUTATED     2   6   1   4
  USP13 WILD-TYPE 193 167  88  81
D504V5, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  N0             2             193
  N1             6             167
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V6, binary
                 cls
clus                0   1
  USP13 MUTATED    11   1
  USP13 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED     11    1
  USP13 WILD-TYPE  471   37
   clus
vv  USP13 MUTATED USP13 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D504V7, binary
                 cls
clus                0   1
  USP13 MUTATED     5   8
  USP13 WILD-TYPE 167 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      5    8
  USP13 WILD-TYPE  167  398
        clus
vv       USP13 MUTATED USP13 WILD-TYPE
  FEMALE             5             167
  MALE               8             398
[1] 2 2
[1] FALSE
D504V8, binary
                 cls
clus                0   1
  USP13 MUTATED     8   2
  USP13 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      8    2
  USP13 WILD-TYPE  408  100
     clus
vv    USP13 MUTATED USP13 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D504V9, continuous
D504V10, continuous
[1] "Remove cluster labels:" "USP13 MUTATED"         
clus
  USP13 MUTATED USP13 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" "USP13 WILD-TYPE" 
     TCGA-Z6-AAPN 
"USP13 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP13 MUTATED       3                         0
  USP13 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP13 MUTATED                                           0     7
  USP13 WILD-TYPE                                         1   350
D504V11, multiclass
                                           clus
vv                                          USP13 MUTATED USP13 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V12, binary
                 cls
clus                0   1
  USP13 MUTATED     1   7
  USP13 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      1    7
  USP13 WILD-TYPE    9  391
                        clus
vv                       USP13 MUTATED USP13 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(505) Variable = DOK1 MUTATION ANALYSIS
D505V1, survival
                sevent
clus2              0   1
  DOK1 MUTATED     3   3
  DOK1 WILD-TYPE 335 213
  DOK1 MUTATED DOK1 WILD-TYPE 
             6            548 
  DOK1 MUTATED DOK1 WILD-TYPE 
             3            213 
$`DOK1 MUTATED`
TCGA-L5-A43J TCGA-L7-A56G TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-VQ-A8DT 
        4.31        10.85        34.68        16.14        12.62        48.79 

$`DOK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DOK1 MUTATED DOK1 WILD-TYPE 
          4.31           0.00 
  DOK1 MUTATED DOK1 WILD-TYPE 
         48.79         122.30 
  DOK1 MUTATED DOK1 WILD-TYPE 
        14.380         13.565 
[1] "4.3 - 48.8 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D505V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOK1 MUTATED         0        0        1        0         1         1
  DOK1 WILD-TYPE      10       20       45       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOK1 MUTATED           0          0          2          0        0         0
  DOK1 WILD-TYPE        29         84         60         39       43         4
D505V3, multiclass
            clus
vv           DOK1 MUTATED DOK1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DOK1 MUTATED       0   1   4   0
  DOK1 WILD-TYPE    54 134 257 102
D505V4, multiclass
       clus
vv      DOK1 MUTATED DOK1 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               4            257
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DOK1 MUTATED     3   1   0   2
  DOK1 WILD-TYPE 192 172  89  83
D505V5, multiclass
    clus
vv   DOK1 MUTATED DOK1 WILD-TYPE
  N0            3            192
  N1            1            172
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V6, binary
                cls
clus               0   1
  DOK1 MUTATED     5   0
  DOK1 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      5    0
  DOK1 WILD-TYPE  477   38
   clus
vv  DOK1 MUTATED DOK1 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D505V7, binary
                cls
clus               0   1
  DOK1 MUTATED     3   4
  DOK1 WILD-TYPE 169 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      3    4
  DOK1 WILD-TYPE  169  402
        clus
vv       DOK1 MUTATED DOK1 WILD-TYPE
  FEMALE            3            169
  MALE              4            402
[1] 2 2
[1] FALSE
D505V8, binary
                cls
clus               0   1
  DOK1 MUTATED     3   2
  DOK1 WILD-TYPE 413 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      3    2
  DOK1 WILD-TYPE  413  100
     clus
vv    DOK1 MUTATED DOK1 WILD-TYPE
  NO             3            413
  YES            2            100
[1] 2 2
[1] FALSE
D505V9, continuous
D505V10, continuous
[1] "Remove cluster labels:" "DOK1 MUTATED"          
clus
  DOK1 MUTATED DOK1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" "DOK1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"DOK1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DOK1 MUTATED       1                         1
  DOK1 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOK1 MUTATED                                           0     4
  DOK1 WILD-TYPE                                         1   353
D505V11, multiclass
                                           clus
vv                                          DOK1 MUTATED DOK1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V12, binary
                cls
clus               0   1
  DOK1 MUTATED     0   5
  DOK1 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      0    5
  DOK1 WILD-TYPE   10  393
                        clus
vv                       DOK1 MUTATED DOK1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(506) Variable = CD33 MUTATION ANALYSIS
D506V1, survival
                sevent
clus2              0   1
  CD33 MUTATED     5   5
  CD33 WILD-TYPE 333 211
  CD33 MUTATED CD33 WILD-TYPE 
            10            544 
  CD33 MUTATED CD33 WILD-TYPE 
             5            211 
$`CD33 MUTATED`
TCGA-JY-A6FG TCGA-L5-A8NJ TCGA-BR-6452 TCGA-BR-7723 TCGA-BR-8373 TCGA-BR-8589 
       41.52        16.47        34.68        28.73        14.79        27.12 
TCGA-HU-A4GQ TCGA-IN-A6RL TCGA-RD-A7BT TCGA-VQ-AA6A 
        0.10        13.35         8.61        38.93 

$`CD33 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CD33 MUTATED CD33 WILD-TYPE 
           0.1            0.0 
  CD33 MUTATED CD33 WILD-TYPE 
         41.52         122.30 
  CD33 MUTATED CD33 WILD-TYPE 
        21.795         13.510 
[1] "0.1 - 41.5 (21.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D506V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD33 MUTATED         0        0        1        0         1         0
  CD33 WILD-TYPE      10       20       45       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD33 MUTATED           2          2          2          2        1         0
  CD33 WILD-TYPE        27         82         60         37       42         4
D506V3, multiclass
            clus
vv           CD33 MUTATED CD33 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CD33 MUTATED       0   2   5   4
  CD33 WILD-TYPE    54 133 256  98
D506V4, multiclass
       clus
vv      CD33 MUTATED CD33 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CD33 MUTATED     2   5   1   3
  CD33 WILD-TYPE 193 168  88  82
D506V5, multiclass
    clus
vv   CD33 MUTATED CD33 WILD-TYPE
  N0            2            193
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V6, binary
                cls
clus               0   1
  CD33 MUTATED    11   0
  CD33 WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED     11    0
  CD33 WILD-TYPE  471   38
   clus
vv  CD33 MUTATED CD33 WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D506V7, binary
                cls
clus               0   1
  CD33 MUTATED     2   9
  CD33 WILD-TYPE 170 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      2    9
  CD33 WILD-TYPE  170  397
        clus
vv       CD33 MUTATED CD33 WILD-TYPE
  FEMALE            2            170
  MALE              9            397
[1] 2 2
[1] FALSE
D506V8, binary
                cls
clus               0   1
  CD33 MUTATED     9   1
  CD33 WILD-TYPE 407 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      9    1
  CD33 WILD-TYPE  407  101
     clus
vv    CD33 MUTATED CD33 WILD-TYPE
  NO             9            407
  YES            1            101
[1] 2 2
[1] FALSE
D506V9, continuous
D506V10, continuous
[1] "Remove cluster labels:" "CD33 MUTATED"          
clus
  CD33 MUTATED CD33 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" "CD33 WILD-TYPE" 
    TCGA-Z6-AAPN 
"CD33 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD33 MUTATED       1                         0
  CD33 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD33 MUTATED                                           1     8
  CD33 WILD-TYPE                                         0   349
D506V11, multiclass
                                           clus
vv                                          CD33 MUTATED CD33 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V12, binary
                cls
clus               0   1
  CD33 MUTATED     0   7
  CD33 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      0    7
  CD33 WILD-TYPE   10  391
                        clus
vv                       CD33 MUTATED CD33 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(507) Variable = MYLK3 MUTATION ANALYSIS
D507V1, survival
                 sevent
clus2               0   1
  MYLK3 MUTATED     7   5
  MYLK3 WILD-TYPE 331 211
  MYLK3 MUTATED MYLK3 WILD-TYPE 
             12             542 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
              5             211 
$`MYLK3 MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-L5-A8NF TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8371 
       19.99         5.16         2.66         8.05         2.20        11.80 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-8534 TCGA-VQ-A8P2 
       12.79        27.12        31.96        12.30        12.07        38.14 

$`MYLK3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22         1.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MYLK3 MUTATED MYLK3 WILD-TYPE 
            2.2             0.0 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
          38.14          122.30 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
         12.185          13.730 
[1] "2.2 - 38.1 (12.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D507V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYLK3 MUTATED         0        0        0        1         0         2
  MYLK3 WILD-TYPE      10       20       46       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYLK3 MUTATED           0          1          3          2        2         1
  MYLK3 WILD-TYPE        29         83         59         37       41         3
D507V3, multiclass
            clus
vv           MYLK3 MUTATED MYLK3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYLK3 MUTATED       1   0   4   7
  MYLK3 WILD-TYPE    53 135 257  95
D507V4, multiclass
       clus
vv      MYLK3 MUTATED MYLK3 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                4             257
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYLK3 MUTATED     5   2   2   3
  MYLK3 WILD-TYPE 190 171  87  82
D507V5, multiclass
    clus
vv   MYLK3 MUTATED MYLK3 WILD-TYPE
  N0             5             190
  N1             2             171
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V6, binary
                 cls
clus                0   1
  MYLK3 MUTATED     8   3
  MYLK3 WILD-TYPE 474  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      8    3
  MYLK3 WILD-TYPE  474   35
   clus
vv  MYLK3 MUTATED MYLK3 WILD-TYPE
  0             8             474
  1             3              35
[1] 2 2
[1] FALSE
D507V7, binary
                 cls
clus                0   1
  MYLK3 MUTATED     4   8
  MYLK3 WILD-TYPE 168 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      4    8
  MYLK3 WILD-TYPE  168  398
        clus
vv       MYLK3 MUTATED MYLK3 WILD-TYPE
  FEMALE             4             168
  MALE               8             398
[1] 2 2
[1] FALSE
D507V8, binary
                 cls
clus                0   1
  MYLK3 MUTATED    10   2
  MYLK3 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED     10    2
  MYLK3 WILD-TYPE  406  100
     clus
vv    MYLK3 MUTATED MYLK3 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D507V9, continuous
D507V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYLK3 MUTATED       3                         0
  MYLK3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYLK3 MUTATED                                           0     9
  MYLK3 WILD-TYPE                                         1   348
D507V11, multiclass
                                           clus
vv                                          MYLK3 MUTATED MYLK3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V12, binary
                 cls
clus                0   1
  MYLK3 MUTATED     0   9
  MYLK3 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      0    9
  MYLK3 WILD-TYPE   10  389
                        clus
vv                       MYLK3 MUTATED MYLK3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(508) Variable = GPATCH4 MUTATION ANALYSIS
D508V1, survival
                   sevent
clus2                 0   1
  GPATCH4 MUTATED     6   6
  GPATCH4 WILD-TYPE 332 210
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
               12               542 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                6               210 
$`GPATCH4 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GK TCGA-L5-A8NM TCGA-BR-4201 TCGA-CD-8536 
        4.31        19.99         7.63         7.76        30.90        12.43 
TCGA-CD-A4MG TCGA-D7-6526 TCGA-F1-6875 TCGA-HU-A4GN TCGA-VQ-A8DT TCGA-VQ-A8P2 
        6.58        17.19        72.23        29.98        48.79        38.14 

$`GPATCH4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
             4.31              0.00 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            72.23            122.30 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            18.59             13.53 
[1] "4.3 - 72.2 (18.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D508V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH4 MUTATED         0        1        0        1         2         2
  GPATCH4 WILD-TYPE      10       19       46       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH4 MUTATED           1          2          1          1        0
  GPATCH4 WILD-TYPE        28         82         61         38       43
                   vv
clus                STAGE IVA
  GPATCH4 MUTATED           0
  GPATCH4 WILD-TYPE         4
D508V3, multiclass
            clus
vv           GPATCH4 MUTATED GPATCH4 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GPATCH4 MUTATED       0   4   8   1
  GPATCH4 WILD-TYPE    54 131 253 101
D508V4, multiclass
       clus
vv      GPATCH4 MUTATED GPATCH4 WILD-TYPE
  T0+T1               0                54
  T2                  4               131
  T3                  8               253
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GPATCH4 MUTATED     4   4   1   2
  GPATCH4 WILD-TYPE 191 169  88  83
D508V5, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  N0               4               191
  N1               4               169
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V6, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED    10   0
  GPATCH4 WILD-TYPE 472  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED     10    0
  GPATCH4 WILD-TYPE  472   38
   clus
vv  GPATCH4 MUTATED GPATCH4 WILD-TYPE
  0              10               472
  1               0                38
[1] 2 2
[1] FALSE
D508V7, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     3  10
  GPATCH4 WILD-TYPE 169 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      3   10
  GPATCH4 WILD-TYPE  169  396
        clus
vv       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FEMALE               3               169
  MALE                10               396
[1] 2 2
[1] FALSE
D508V8, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     9   2
  GPATCH4 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      9    2
  GPATCH4 WILD-TYPE  407  100
     clus
vv    GPATCH4 MUTATED GPATCH4 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D508V9, continuous
D508V10, continuous
[1] "Remove cluster labels:" "GPATCH4 MUTATED"       
clus
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG        TCGA-L5-A8NT 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL        TCGA-IG-A3Y9 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QT 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS        TCGA-IG-A8O2 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE        TCGA-JY-A6FG 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C        TCGA-L5-A43E 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM        TCGA-L5-A4ON 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OT 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" "GPATCH4 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPATCH4 MUTATED       3                         1
  GPATCH4 WILD-TYPE   130                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPATCH4 MUTATED                                           0     7
  GPATCH4 WILD-TYPE                                         1   350
D508V11, multiclass
                                           clus
vv                                          GPATCH4 MUTATED GPATCH4 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V12, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0   7
  GPATCH4 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0    7
  GPATCH4 WILD-TYPE   10  391
                        clus
vv                       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(509) Variable = CADPS2 MUTATION ANALYSIS
D509V1, survival
                  sevent
clus2                0   1
  CADPS2 MUTATED     9   3
  CADPS2 WILD-TYPE 329 213
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              12              542 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
               3              213 
$`CADPS2 MUTATED`
TCGA-L5-A4OO TCGA-R6-A6L6 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-7707 TCGA-BR-8078 
        3.32         7.04        34.68        15.95        35.84        29.59 
TCGA-BR-8361 TCGA-CD-A4MG TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4H2 
       31.10         6.58        14.47        11.08         0.10        12.95 

$`CADPS2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CADPS2 MUTATED CADPS2 WILD-TYPE 
             0.1              0.0 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
           35.84           122.30 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
          13.710           13.565 
[1] "0.1 - 35.8 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D509V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CADPS2 MUTATED         0        0        2        0         4         1
  CADPS2 WILD-TYPE      10       20       44       31        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CADPS2 MUTATED           0          0          1          3        0
  CADPS2 WILD-TYPE        29         84         61         36       43
                  vv
clus               STAGE IVA
  CADPS2 MUTATED           0
  CADPS2 WILD-TYPE         4
D509V3, multiclass
            clus
vv           CADPS2 MUTATED CADPS2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CADPS2 MUTATED       0   3   5   3
  CADPS2 WILD-TYPE    54 132 256  99
D509V4, multiclass
       clus
vv      CADPS2 MUTATED CADPS2 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CADPS2 MUTATED     6   1   2   2
  CADPS2 WILD-TYPE 189 172  87  83
D509V5, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  N0              6              189
  N1              1              172
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V6, binary
                  cls
clus                 0   1
  CADPS2 MUTATED    11   0
  CADPS2 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED     11    0
  CADPS2 WILD-TYPE  471   38
   clus
vv  CADPS2 MUTATED CADPS2 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D509V7, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     5   7
  CADPS2 WILD-TYPE 167 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      5    7
  CADPS2 WILD-TYPE  167  399
        clus
vv       CADPS2 MUTATED CADPS2 WILD-TYPE
  FEMALE              5              167
  MALE                7              399
[1] 2 2
[1] FALSE
D509V8, binary
                  cls
clus                 0   1
  CADPS2 MUTATED    10   1
  CADPS2 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED     10    1
  CADPS2 WILD-TYPE  406  101
     clus
vv    CADPS2 MUTATED CADPS2 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D509V9, continuous
D509V10, continuous
[1] "Remove cluster labels:" "CADPS2 MUTATED"        
clus
  CADPS2 MUTATED CADPS2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" "CADPS2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CADPS2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CADPS2 MUTATED       3                         1
  CADPS2 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CADPS2 MUTATED                                           0     8
  CADPS2 WILD-TYPE                                         1   349
D509V11, multiclass
                                           clus
vv                                          CADPS2 MUTATED CADPS2 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V12, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     0  11
  CADPS2 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      0   11
  CADPS2 WILD-TYPE   10  387
                        clus
vv                       CADPS2 MUTATED CADPS2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(510) Variable = LTBP3 MUTATION ANALYSIS
D510V1, survival
                 sevent
clus2               0   1
  LTBP3 MUTATED    11   9
  LTBP3 WILD-TYPE 327 207
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             20             534 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              9             207 
$`LTBP3 MUTATED`
TCGA-L5-A4OI TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A88W TCGA-R6-A6XQ TCGA-BR-8078 
       19.99        31.56        25.22        25.12         6.35        29.59 
TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4465 TCGA-CG-5723 
        0.26         1.12        11.77        12.62         9.01       105.07 
TCGA-CG-5726 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GX 
       28.96         5.92        11.44        77.29        30.51        20.25 
TCGA-HU-A4H3 TCGA-R5-A7ZI 
       29.00        74.53 

$`LTBP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04        38.40        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LTBP3 MUTATED LTBP3 WILD-TYPE 
           0.26            0.00 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
         105.07          122.30 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
         22.685          13.510 
[1] "0.3 - 105.1 (22.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D510V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LTBP3 MUTATED         0        1        2        2         2         2
  LTBP3 WILD-TYPE      10       19       44       29        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LTBP3 MUTATED           0          3          1          5        2         0
  LTBP3 WILD-TYPE        29         81         61         34       41         4
D510V3, multiclass
            clus
vv           LTBP3 MUTATED LTBP3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             5              34
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LTBP3 MUTATED       1   5   7   7
  LTBP3 WILD-TYPE    53 130 254  95
D510V4, multiclass
       clus
vv      LTBP3 MUTATED LTBP3 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                7             254
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LTBP3 MUTATED     7   6   1   6
  LTBP3 WILD-TYPE 188 167  88  79
D510V5, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             1              88
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V6, binary
                 cls
clus                0   1
  LTBP3 MUTATED    17   2
  LTBP3 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     17    2
  LTBP3 WILD-TYPE  465   36
   clus
vv  LTBP3 MUTATED LTBP3 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D510V7, binary
                 cls
clus                0   1
  LTBP3 MUTATED    12  10
  LTBP3 WILD-TYPE 160 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     12   10
  LTBP3 WILD-TYPE  160  396
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  FEMALE            12             160
  MALE              10             396
[1] 2 2
[1] FALSE
D510V8, binary
                 cls
clus                0   1
  LTBP3 MUTATED    13   4
  LTBP3 WILD-TYPE 403  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     13    4
  LTBP3 WILD-TYPE  403   98
     clus
vv    LTBP3 MUTATED LTBP3 WILD-TYPE
  NO             13             403
  YES             4              98
[1] 2 2
[1] FALSE
D510V9, continuous
D510V10, continuous
[1] "Remove cluster labels:" "LTBP3 MUTATED"         
clus
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" "LTBP3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LTBP3 MUTATED       4                         0
  LTBP3 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LTBP3 MUTATED                                           0    13
  LTBP3 WILD-TYPE                                         1   344
D510V11, multiclass
                                           clus
vv                                          LTBP3 MUTATED LTBP3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V12, binary
                 cls
clus                0   1
  LTBP3 MUTATED     1  12
  LTBP3 WILD-TYPE   9 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      1   12
  LTBP3 WILD-TYPE    9  386
                        clus
vv                       LTBP3 MUTATED LTBP3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(511) Variable = GALNTL1 MUTATION ANALYSIS
D511V1, survival
                   sevent
clus2                 0   1
  GALNTL1 MUTATED     4   9
  GALNTL1 WILD-TYPE 334 207
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               13               541 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
                9               207 
$`GALNTL1 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OH TCGA-L5-A8NI TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7957 
       34.85        32.61        13.48         6.97        34.68         9.07 
TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-5728 TCGA-F1-6875 TCGA-HJ-7597 
       14.43         0.26        16.14        65.10        72.23        26.47 
TCGA-HU-A4GQ 
        0.10 

$`GALNTL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         3.45        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
              0.1               0.0 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
            72.23            122.30 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
            16.14             13.51 
[1] "0.1 - 72.2 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D511V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GALNTL1 MUTATED         1        1        3        0         1         1
  GALNTL1 WILD-TYPE       9       19       43       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GALNTL1 MUTATED           2          1          1          1        1
  GALNTL1 WILD-TYPE        27         83         61         38       42
                   vv
clus                STAGE IVA
  GALNTL1 MUTATED           0
  GALNTL1 WILD-TYPE         4
D511V3, multiclass
            clus
vv           GALNTL1 MUTATED GALNTL1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                2                27
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GALNTL1 MUTATED       1   4   6   2
  GALNTL1 WILD-TYPE    53 131 255 100
D511V4, multiclass
       clus
vv      GALNTL1 MUTATED GALNTL1 WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  6               255
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GALNTL1 MUTATED     7   3   1   2
  GALNTL1 WILD-TYPE 188 170  88  83
D511V5, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  N0               7               188
  N1               3               170
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V6, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED    10   1
  GALNTL1 WILD-TYPE 472  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED     10    1
  GALNTL1 WILD-TYPE  472   37
   clus
vv  GALNTL1 MUTATED GALNTL1 WILD-TYPE
  0              10               472
  1               1                37
[1] 2 2
[1] FALSE
D511V7, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     6   7
  GALNTL1 WILD-TYPE 166 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      6    7
  GALNTL1 WILD-TYPE  166  399
        clus
vv       GALNTL1 MUTATED GALNTL1 WILD-TYPE
  FEMALE               6               166
  MALE                 7               399
[1] 2 2
[1] FALSE
D511V8, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED    12   0
  GALNTL1 WILD-TYPE 404 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED     12    0
  GALNTL1 WILD-TYPE  404  102
     clus
vv    GALNTL1 MUTATED GALNTL1 WILD-TYPE
  NO               12               404
  YES               0               102
[1] 2 2
[1] FALSE
D511V9, continuous
D511V10, continuous
[1] "Remove cluster labels:" "GALNTL1 MUTATED"       
clus
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OM 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" "GALNTL1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"GALNTL1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GALNTL1 MUTATED       1                         1
  GALNTL1 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GALNTL1 MUTATED                                           0    10
  GALNTL1 WILD-TYPE                                         1   347
D511V11, multiclass
                                           clus
vv                                          GALNTL1 MUTATED GALNTL1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V12, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     0   9
  GALNTL1 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      0    9
  GALNTL1 WILD-TYPE   10  389
                        clus
vv                       GALNTL1 MUTATED GALNTL1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(512) Variable = RGS12 MUTATION ANALYSIS
D512V1, survival
                 sevent
clus2               0   1
  RGS12 MUTATED    24  11
  RGS12 WILD-TYPE 314 205
  RGS12 MUTATED RGS12 WILD-TYPE 
             35             519 
  RGS12 MUTATED RGS12 WILD-TYPE 
             11             205 
$`RGS12 MUTATED`
TCGA-S8-A6BV TCGA-CG-4460 TCGA-2H-A9GI TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A8NV 
       20.02        21.99        14.30        30.25        21.01        52.57 
TCGA-LN-A49W TCGA-LN-A8I1 TCGA-Q9-A6FW TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 
       13.25        13.18         7.82         6.97         9.67        34.68 
TCGA-BR-7197 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8680 
        9.21        31.10        31.27        14.79         1.12        31.96 
TCGA-BR-8686 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4441 
       20.88        12.43         6.58        11.77        12.62        14.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GX 
        6.02       105.07        28.96        22.32         0.10        20.25 
TCGA-HU-A4H8 TCGA-IP-7968 TCGA-MX-A5UJ TCGA-SW-A7EB TCGA-VQ-A8P2 
       14.07         2.53        19.73         5.79        38.14 

$`RGS12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       27.12         5.16        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04         3.32        11.80         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        32.58         9.86         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RGS12 MUTATED RGS12 WILD-TYPE 
            0.1             0.0 
  RGS12 MUTATED RGS12 WILD-TYPE 
         105.07          122.30 
  RGS12 MUTATED RGS12 WILD-TYPE 
          14.30           13.51 
[1] "0.1 - 105.1 (14.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D512V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS12 MUTATED         2        1        3        3         5         1
  RGS12 WILD-TYPE       8       19       43       28        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS12 MUTATED           2          9          3          4        3         0
  RGS12 WILD-TYPE        27         75         59         35       40         4
D512V3, multiclass
            clus
vv           RGS12 MUTATED RGS12 WILD-TYPE
  STAGE I                2               8
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               3              28
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             9              75
  STAGE IIIB             3              59
  STAGE IIIC             4              35
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RGS12 MUTATED       4   5  15  12
  RGS12 WILD-TYPE    50 130 246  90
D512V4, multiclass
       clus
vv      RGS12 MUTATED RGS12 WILD-TYPE
  T0+T1             4              50
  T2                5             130
  T3               15             246
  T4               12              90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RGS12 MUTATED    14  12   9   1
  RGS12 WILD-TYPE 181 161  80  84
D512V5, multiclass
    clus
vv   RGS12 MUTATED RGS12 WILD-TYPE
  N0            14             181
  N1            12             161
  N2             9              80
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V6, binary
                 cls
clus                0   1
  RGS12 MUTATED    33   2
  RGS12 WILD-TYPE 449  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     33    2
  RGS12 WILD-TYPE  449   36
   clus
vv  RGS12 MUTATED RGS12 WILD-TYPE
  0            33             449
  1             2              36
[1] 2 2
[1] FALSE
D512V7, binary
                 cls
clus                0   1
  RGS12 MUTATED    13  25
  RGS12 WILD-TYPE 159 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     13   25
  RGS12 WILD-TYPE  159  381
        clus
vv       RGS12 MUTATED RGS12 WILD-TYPE
  FEMALE            13             159
  MALE              25             381
[1] 2 2
[1] FALSE
D512V8, binary
                 cls
clus                0   1
  RGS12 MUTATED    29   3
  RGS12 WILD-TYPE 387  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     29    3
  RGS12 WILD-TYPE  387   99
     clus
vv    RGS12 MUTATED RGS12 WILD-TYPE
  NO             29             387
  YES             3              99
[1] 2 2
[1] FALSE
D512V9, continuous
[1] "Remove cluster labels:" "RGS12 MUTATED"         
clus
  RGS12 MUTATED RGS12 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RGS12 WILD-TYPE" "RGS12 WILD-TYPE" "RGS12 WILD-TYPE" 
D512V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RGS12 MUTATED      12                         0
  RGS12 WILD-TYPE   121                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS12 MUTATED                                           0    19
  RGS12 WILD-TYPE                                         1   338
D512V11, multiclass
                                           clus
vv                                          RGS12 MUTATED RGS12 WILD-TYPE
  ASIAN                                                12             121
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V12, binary
                 cls
clus                0   1
  RGS12 MUTATED     0  26
  RGS12 WILD-TYPE  10 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED      0   26
  RGS12 WILD-TYPE   10  372
                        clus
vv                       RGS12 MUTATED RGS12 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            26             372
[1] 2 2
[1] FALSE

Clustering(513) Variable = PLA2G15 MUTATION ANALYSIS
D513V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     6   6
  PLA2G15 WILD-TYPE 332 210
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
               12               542 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                6               210 
$`PLA2G15 MUTATED`
TCGA-KH-A6WC TCGA-L7-A56G TCGA-R6-A8WG TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6802 
        6.28        10.85        12.69         6.97         6.61        30.90 
TCGA-BR-8360 TCGA-CD-A4MJ TCGA-CG-5726 TCGA-HF-7132 TCGA-HU-A4GH TCGA-HU-A4GQ 
        6.18        12.62        28.96        77.29        11.77         0.10 

$`PLA2G15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
              0.1               0.0 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            77.29            122.30 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           11.310            13.825 
[1] "0.1 - 77.3 (11.3)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.4"
D513V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G15 MUTATED         0        3        2        1         1         0
  PLA2G15 WILD-TYPE      10       17       44       30        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          2          0          1        0
  PLA2G15 WILD-TYPE        28         82         62         38       43
                   vv
clus                STAGE IVA
  PLA2G15 MUTATED           0
  PLA2G15 WILD-TYPE         4
D513V3, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 3                17
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PLA2G15 MUTATED       3   4   3   1
  PLA2G15 WILD-TYPE    51 131 258 101
D513V4, multiclass
       clus
vv      PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T0+T1               3                51
  T2                  4               131
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PLA2G15 MUTATED     6   3   2   0
  PLA2G15 WILD-TYPE 189 170  87  85
D513V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               6               189
  N1               3               170
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V6, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED    10   0
  PLA2G15 WILD-TYPE 472  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED     10    0
  PLA2G15 WILD-TYPE  472   38
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0              10               472
  1               0                38
[1] 2 2
[1] FALSE
D513V7, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     1  12
  PLA2G15 WILD-TYPE 171 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      1   12
  PLA2G15 WILD-TYPE  171  394
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  FEMALE               1               171
  MALE                12               394
[1] 2 2
[1] FALSE
D513V8, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     8   3
  PLA2G15 WILD-TYPE 408  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      8    3
  PLA2G15 WILD-TYPE  408   99
     clus
vv    PLA2G15 MUTATED PLA2G15 WILD-TYPE
  NO                8               408
  YES               3                99
[1] 2 2
[1] FALSE
D513V9, continuous
[1] "Remove cluster labels:" "PLA2G15 MUTATED"       
clus
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
D513V10, continuous
[1] "Remove cluster labels:" "PLA2G15 MUTATED"       
clus
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-L5-A43C 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" "PLA2G15 WILD-TYPE" 
       TCGA-Z6-AAPN 
"PLA2G15 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLA2G15 MUTATED       3                         1
  PLA2G15 WILD-TYPE   130                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLA2G15 MUTATED                                           0     6
  PLA2G15 WILD-TYPE                                         1   351
D513V11, multiclass
                                           clus
vv                                          PLA2G15 MUTATED PLA2G15 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V12, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     1   9
  PLA2G15 WILD-TYPE   9 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      1    9
  PLA2G15 WILD-TYPE    9  389
                        clus
vv                       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(514) Variable = SPTA1 MUTATION ANALYSIS
D514V1, survival
                 sevent
clus2               0   1
  SPTA1 MUTATED    60  29
  SPTA1 WILD-TYPE 278 187
  SPTA1 MUTATED SPTA1 WILD-TYPE 
             89             465 
  SPTA1 MUTATED SPTA1 WILD-TYPE 
             29             187 
$`SPTA1 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A8NG TCGA-CG-4460 TCGA-KB-A93G TCGA-MX-A663 
       34.85        19.99        35.97        21.99        20.15         9.86 
TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-JY-A6F8 
        5.92        16.24         7.69         2.63        18.64       122.10 
TCGA-L5-A43E TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NV 
       30.25        18.35         3.32         7.76         5.49        52.57 
TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG 
       25.25        12.03         0.13         7.82         5.06        38.40 
TCGA-R6-A6Y2 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-Z6-A9VB TCGA-BR-4256 TCGA-BR-4257 
        9.30        46.19        18.05         1.32         9.34         9.67 
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-7703 TCGA-BR-7716 
       34.68        19.33        32.78        25.61        36.16        39.78 
TCGA-BR-7901 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8368 
        3.45         9.60        32.25         7.40         0.26         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4IU 
       14.04         3.32         9.21        31.96        34.98        27.55 
TCGA-BR-A4IV TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A487 
       28.57        13.18         7.17        12.30        12.43        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5725 
       12.43         6.58         0.00        18.97         7.07        15.02 
TCGA-CG-5726 TCGA-D7-5578 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-A4YU 
       28.96        12.66        17.85        10.26        24.72        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-HF-7134 TCGA-HU-A4G8 
       36.43        13.78        14.76        11.31        52.21        22.68 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
        3.25        25.81        11.77        29.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-RD-A8N9 
       20.25        29.00        23.84        19.73        74.53        35.61 
TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-AA68 
       48.79        13.02        37.41        38.14        43.66 

$`SPTA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-2H-A9GF 
       47.05        22.98        79.07        16.24         0.23        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
       13.18        12.03        12.85        12.26        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59        16.31         7.04         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        18.18        52.27        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         4.08         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        26.10         9.17        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69        29.59         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
        2.66        19.96         2.20         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       17.52         0.95        26.33        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        1.48        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.59        12.53        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
       15.39        12.07        12.82         6.31        11.31        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4477 
       14.01        29.98        19.07        12.03         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
        5.92        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GP 
        5.59        24.26        24.20        22.75        21.37         8.98 
TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.51         0.26         2.10        12.95        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        19.04         5.79         0.92         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SPTA1 MUTATED SPTA1 WILD-TYPE 
           0.00            0.23 
  SPTA1 MUTATED SPTA1 WILD-TYPE 
          122.1           122.3 
  SPTA1 MUTATED SPTA1 WILD-TYPE 
          16.44           13.41 
[1] "0.0 - 122.1 (16.4)" "0.2 - 122.3 (13.4)"
[1] "hr=" "1.4"
D514V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTA1 MUTATED         2        4        7        5        10        16
  SPTA1 WILD-TYPE       8       16       39       26        74        67
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPTA1 MUTATED           4         10         10          9        8         1
  SPTA1 WILD-TYPE        25         74         52         30       35         3
D514V3, multiclass
            clus
vv           SPTA1 MUTATED SPTA1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               4              16
  STAGE IB               7              39
  STAGE II               5              26
  STAGE IIA             10              74
  STAGE IIB             16              67
  STAGE III              4              25
  STAGE IIIA            10              74
  STAGE IIIB            10              52
  STAGE IIIC             9              30
  STAGE IV               8              35
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SPTA1 MUTATED       9  19  41  18
  SPTA1 WILD-TYPE    45 116 220  84
D514V4, multiclass
       clus
vv      SPTA1 MUTATED SPTA1 WILD-TYPE
  T0+T1             9              45
  T2               19             116
  T3               41             220
  T4               18              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SPTA1 MUTATED    26  32  12  17
  SPTA1 WILD-TYPE 169 141  77  68
D514V5, multiclass
    clus
vv   SPTA1 MUTATED SPTA1 WILD-TYPE
  N0            26             169
  N1            32             141
  N2            12              77
  N3            17              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V6, binary
                 cls
clus                0   1
  SPTA1 MUTATED    79   8
  SPTA1 WILD-TYPE 403  30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPTA1 MUTATED     79    8
  SPTA1 WILD-TYPE  403   30
   clus
vv  SPTA1 MUTATED SPTA1 WILD-TYPE
  0            79             403
  1             8              30
[1] 2 2
[1] FALSE
D514V7, binary
                 cls
clus                0   1
  SPTA1 MUTATED    30  64
  SPTA1 WILD-TYPE 142 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPTA1 MUTATED     30   64
  SPTA1 WILD-TYPE  142  342
        clus
vv       SPTA1 MUTATED SPTA1 WILD-TYPE
  FEMALE            30             142
  MALE              64             342
[1] 2 2
[1] FALSE
D514V8, binary
                 cls
clus                0   1
  SPTA1 MUTATED    71  13
  SPTA1 WILD-TYPE 345  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPTA1 MUTATED     71   13
  SPTA1 WILD-TYPE  345   89
     clus
vv    SPTA1 MUTATED SPTA1 WILD-TYPE
  NO             71             345
  YES            13              89
[1] 2 2
[1] FALSE
D514V9, continuous
D514V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SPTA1 MUTATED      24                         1
  SPTA1 WILD-TYPE   109                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPTA1 MUTATED                                           0    57
  SPTA1 WILD-TYPE                                         1   300
D514V11, multiclass
                                           clus
vv                                          SPTA1 MUTATED SPTA1 WILD-TYPE
  ASIAN                                                24             109
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                57             300
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V12, binary
                 cls
clus                0   1
  SPTA1 MUTATED     2  63
  SPTA1 WILD-TYPE   8 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPTA1 MUTATED      2   63
  SPTA1 WILD-TYPE    8  335
                        clus
vv                       SPTA1 MUTATED SPTA1 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            63             335
[1] 2 2
[1] FALSE

Clustering(515) Variable = ZNF292 MUTATION ANALYSIS
D515V1, survival
                  sevent
clus2                0   1
  ZNF292 MUTATED    22  16
  ZNF292 WILD-TYPE 316 200
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              38              516 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              16              200 
$`ZNF292 MUTATED`
TCGA-L5-A43I TCGA-CG-4460 TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A93D TCGA-L5-A8NI 
       18.28        21.99        18.64         0.79        31.56        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49U TCGA-LN-A8I1 TCGA-VR-AA7B 
        7.76        21.37        12.66        15.35        13.18        11.24 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7703 
        6.97         9.34        34.68        32.78        30.90        36.16 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       32.25        29.42        31.27         1.12        28.14        31.96 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-5577 
       12.59        12.43         6.58        11.77         6.02        25.71 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GX 
       11.44        11.08        30.51        26.47        22.68        20.25 
TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       38.14        22.19 

$`ZNF292 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        18.05         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PK 
       13.25        13.02        43.36        37.41        37.22        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF292 MUTATED ZNF292 WILD-TYPE 
            0.79             0.00 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
           38.14           122.30 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
          19.445           13.460 
[1] "0.8 - 38.1 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D515V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF292 MUTATED         0        1        3        2         9         4
  ZNF292 WILD-TYPE      10       19       43       29        75        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF292 MUTATED           1          7          2          5        4
  ZNF292 WILD-TYPE        28         77         60         34       39
                  vv
clus               STAGE IVA
  ZNF292 MUTATED           0
  ZNF292 WILD-TYPE         4
D515V3, multiclass
            clus
vv           ZNF292 MUTATED ZNF292 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               9               75
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              7               77
  STAGE IIIB              2               60
  STAGE IIIC              5               34
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF292 MUTATED       1   9  19   9
  ZNF292 WILD-TYPE    53 126 242  93
D515V4, multiclass
       clus
vv      ZNF292 MUTATED ZNF292 WILD-TYPE
  T0+T1              1               53
  T2                 9              126
  T3                19              242
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF292 MUTATED    16  13   3   8
  ZNF292 WILD-TYPE 179 160  86  77
D515V5, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  N0             16              179
  N1             13              160
  N2              3               86
  N3              8               77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V6, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    34   3
  ZNF292 WILD-TYPE 448  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     34    3
  ZNF292 WILD-TYPE  448   35
   clus
vv  ZNF292 MUTATED ZNF292 WILD-TYPE
  0             34              448
  1              3               35
[1] 2 2
[1] FALSE
D515V7, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    16  24
  ZNF292 WILD-TYPE 156 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     16   24
  ZNF292 WILD-TYPE  156  382
        clus
vv       ZNF292 MUTATED ZNF292 WILD-TYPE
  FEMALE             16              156
  MALE               24              382
[1] 2 2
[1] FALSE
D515V8, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    28  10
  ZNF292 WILD-TYPE 388  92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     28   10
  ZNF292 WILD-TYPE  388   92
     clus
vv    ZNF292 MUTATED ZNF292 WILD-TYPE
  NO              28              388
  YES             10               92
[1] 2 2
[1] FALSE
D515V9, continuous
D515V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF292 MUTATED      10                         1
  ZNF292 WILD-TYPE   123                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF292 MUTATED                                           0    25
  ZNF292 WILD-TYPE                                         1   332
D515V11, multiclass
                                           clus
vv                                          ZNF292 MUTATED ZNF292 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 25              332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V12, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     0  28
  ZNF292 WILD-TYPE  10 370
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      0   28
  ZNF292 WILD-TYPE   10  370
                        clus
vv                       ZNF292 MUTATED ZNF292 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             28              370
[1] 2 2
[1] FALSE

Clustering(516) Variable = ART5 MUTATION ANALYSIS
D516V1, survival
                sevent
clus2              0   1
  ART5 MUTATED     3   3
  ART5 WILD-TYPE 335 213
  ART5 MUTATED ART5 WILD-TYPE 
             6            548 
  ART5 MUTATED ART5 WILD-TYPE 
             3            213 
$`ART5 MUTATED`
TCGA-L5-A8NH TCGA-BR-4201 TCGA-BR-8591 TCGA-D7-6822 TCGA-D7-A4YV TCGA-HF-7132 
       12.92        30.90        28.14        12.33         5.92        77.29 

$`ART5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ART5 MUTATED ART5 WILD-TYPE 
          5.92           0.00 
  ART5 MUTATED ART5 WILD-TYPE 
         77.29         122.30 
  ART5 MUTATED ART5 WILD-TYPE 
        20.530         13.565 
[1] "5.9 - 77.3 (20.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D516V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ART5 MUTATED         0        0        1        1         0         1
  ART5 WILD-TYPE      10       20       45       30        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ART5 MUTATED           0          0          0          1        1         0
  ART5 WILD-TYPE        29         84         62         38       42         4
D516V3, multiclass
            clus
vv           ART5 MUTATED ART5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ART5 MUTATED       1   3   1   1
  ART5 WILD-TYPE    53 132 260 101
D516V4, multiclass
       clus
vv      ART5 MUTATED ART5 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               1            260
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ART5 MUTATED     2   2   0   1
  ART5 WILD-TYPE 193 171  89  84
D516V5, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V6, binary
                cls
clus               0   1
  ART5 MUTATED     5   1
  ART5 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      5    1
  ART5 WILD-TYPE  477   37
   clus
vv  ART5 MUTATED ART5 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D516V7, binary
                cls
clus               0   1
  ART5 MUTATED     2   4
  ART5 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      2    4
  ART5 WILD-TYPE  170  402
        clus
vv       ART5 MUTATED ART5 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D516V8, binary
                cls
clus               0   1
  ART5 MUTATED     4   1
  ART5 WILD-TYPE 412 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      4    1
  ART5 WILD-TYPE  412  101
     clus
vv    ART5 MUTATED ART5 WILD-TYPE
  NO             4            412
  YES            1            101
[1] 2 2
[1] FALSE
D516V9, continuous
D516V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ART5 MUTATED       0                         0
  ART5 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ART5 MUTATED                                           0     5
  ART5 WILD-TYPE                                         1   352
D516V11, multiclass
                                           clus
vv                                          ART5 MUTATED ART5 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V12, binary
                cls
clus               0   1
  ART5 MUTATED     0   4
  ART5 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      0    4
  ART5 WILD-TYPE   10  394
                        clus
vv                       ART5 MUTATED ART5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(517) Variable = CCDC80 MUTATION ANALYSIS
D517V1, survival
                  sevent
clus2                0   1
  CCDC80 MUTATED    14   8
  CCDC80 WILD-TYPE 324 208
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              22              532 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
               8              208 
$`CCDC80 MUTATED`
TCGA-L5-A4OE TCGA-JY-A6F8 TCGA-LN-A49W TCGA-R6-A6KZ TCGA-BR-4184 TCGA-BR-4255 
       24.00       122.10        13.25         5.06         6.97         4.08 
TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 
       30.90        29.59         1.12        31.96         6.58        15.95 
TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4G9 
        8.05         6.02         5.92        11.08        26.47        24.20 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       29.98         0.10         6.51         6.58 

$`CCDC80 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        21.37         8.98        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CCDC80 MUTATED CCDC80 WILD-TYPE 
             0.1              0.0 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
           122.1            122.3 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
           9.565           13.730 
[1] "0.1 - 122.1 (9.6)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D517V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC80 MUTATED         2        1        1        2         5         3
  CCDC80 WILD-TYPE       8       19       45       29        79        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC80 MUTATED           1          3          1          1        2
  CCDC80 WILD-TYPE        28         81         61         38       41
                  vv
clus               STAGE IVA
  CCDC80 MUTATED           0
  CCDC80 WILD-TYPE         4
D517V3, multiclass
            clus
vv           CCDC80 MUTATED CCDC80 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               5               79
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CCDC80 MUTATED       3   4  11   4
  CCDC80 WILD-TYPE    51 131 250  98
D517V4, multiclass
       clus
vv      CCDC80 MUTATED CCDC80 WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                11              250
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CCDC80 MUTATED     8  10   4   0
  CCDC80 WILD-TYPE 187 163  85  85
D517V5, multiclass
    clus
vv   CCDC80 MUTATED CCDC80 WILD-TYPE
  N0              8              187
  N1             10              163
  N2              4               85
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V6, binary
                  cls
clus                 0   1
  CCDC80 MUTATED    17   1
  CCDC80 WILD-TYPE 465  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED     17    1
  CCDC80 WILD-TYPE  465   37
   clus
vv  CCDC80 MUTATED CCDC80 WILD-TYPE
  0             17              465
  1              1               37
[1] 2 2
[1] FALSE
D517V7, binary
                  cls
clus                 0   1
  CCDC80 MUTATED     7  16
  CCDC80 WILD-TYPE 165 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED      7   16
  CCDC80 WILD-TYPE  165  390
        clus
vv       CCDC80 MUTATED CCDC80 WILD-TYPE
  FEMALE              7              165
  MALE               16              390
[1] 2 2
[1] FALSE
D517V8, binary
                  cls
clus                 0   1
  CCDC80 MUTATED    21   2
  CCDC80 WILD-TYPE 395 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED     21    2
  CCDC80 WILD-TYPE  395  100
     clus
vv    CCDC80 MUTATED CCDC80 WILD-TYPE
  NO              21              395
  YES              2              100
[1] 2 2
[1] FALSE
D517V9, continuous
[1] "Remove cluster labels:" "CCDC80 MUTATED"        
clus
  CCDC80 MUTATED CCDC80 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
D517V10, continuous
[1] "Remove cluster labels:" "CCDC80 MUTATED"        
clus
  CCDC80 MUTATED CCDC80 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OG 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" "CCDC80 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC80 MUTATED       8                         2
  CCDC80 WILD-TYPE   125                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC80 MUTATED                                           0    10
  CCDC80 WILD-TYPE                                         1   347
D517V11, multiclass
                                           clus
vv                                          CCDC80 MUTATED CCDC80 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V12, binary
                  cls
clus                 0   1
  CCDC80 MUTATED     0  17
  CCDC80 WILD-TYPE  10 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED      0   17
  CCDC80 WILD-TYPE   10  381
                        clus
vv                       CCDC80 MUTATED CCDC80 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             17              381
[1] 2 2
[1] FALSE

Clustering(518) Variable = ACAT1 MUTATION ANALYSIS
D518V1, survival
                 sevent
clus2               0   1
  ACAT1 MUTATED     4   5
  ACAT1 WILD-TYPE 334 211
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              9             545 
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              5             211 
$`ACAT1 MUTATED`
TCGA-L5-A43J TCGA-2H-A9GH TCGA-VR-A8EX TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8369 
        4.31        31.27        28.11        26.70         6.97        14.04 
TCGA-BR-8382 TCGA-CG-5721 TCGA-HU-A4GN 
       25.05         6.02        29.98 

$`ACAT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ACAT1 MUTATED ACAT1 WILD-TYPE 
           4.31            0.00 
  ACAT1 MUTATED ACAT1 WILD-TYPE 
          31.27          122.30 
  ACAT1 MUTATED ACAT1 WILD-TYPE 
          25.05           13.51 
[1] "4.3 - 31.3 (25.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D518V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACAT1 MUTATED         0        0        0        0         1         3
  ACAT1 WILD-TYPE      10       20       46       31        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAT1 MUTATED           0          1          1          1        1         1
  ACAT1 WILD-TYPE        29         83         61         38       42         3
D518V3, multiclass
            clus
vv           ACAT1 MUTATED ACAT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ACAT1 MUTATED       2   1   3   3
  ACAT1 WILD-TYPE    52 134 258  99
D518V4, multiclass
       clus
vv      ACAT1 MUTATED ACAT1 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACAT1 MUTATED     2   5   0   2
  ACAT1 WILD-TYPE 193 168  89  83
D518V5, multiclass
    clus
vv   ACAT1 MUTATED ACAT1 WILD-TYPE
  N0             2             193
  N1             5             168
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V6, binary
                 cls
clus                0   1
  ACAT1 MUTATED     6   1
  ACAT1 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT1 MUTATED      6    1
  ACAT1 WILD-TYPE  476   37
   clus
vv  ACAT1 MUTATED ACAT1 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D518V7, binary
                 cls
clus                0   1
  ACAT1 MUTATED     3   6
  ACAT1 WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT1 MUTATED      3    6
  ACAT1 WILD-TYPE  169  400
        clus
vv       ACAT1 MUTATED ACAT1 WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D518V8, binary
                 cls
clus                0   1
  ACAT1 MUTATED     8   0
  ACAT1 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT1 MUTATED      8    0
  ACAT1 WILD-TYPE  408  102
     clus
vv    ACAT1 MUTATED ACAT1 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D518V9, continuous
[1] "Remove cluster labels:" "ACAT1 MUTATED"         
clus
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
D518V10, continuous
[1] "Remove cluster labels:" "ACAT1 MUTATED"         
clus
  ACAT1 MUTATED ACAT1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" "ACAT1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACAT1 MUTATED       1                         0
  ACAT1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACAT1 MUTATED                                           0     5
  ACAT1 WILD-TYPE                                         1   352
D518V11, multiclass
                                           clus
vv                                          ACAT1 MUTATED ACAT1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V12, binary
                 cls
clus                0   1
  ACAT1 MUTATED     0   5
  ACAT1 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT1 MUTATED      0    5
  ACAT1 WILD-TYPE   10  393
                        clus
vv                       ACAT1 MUTATED ACAT1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(519) Variable = ZCRB1 MUTATION ANALYSIS
D519V1, survival
                 sevent
clus2               0   1
  ZCRB1 MUTATED     6   0
  ZCRB1 WILD-TYPE 332 216
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              6             548 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              0             216 
$`ZCRB1 MUTATED`
TCGA-JY-A93E TCGA-BR-8591 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-VQ-A8P2 
       25.22        28.14        30.51        24.20        29.98        38.14 

$`ZCRB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
           24.2             0.0 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
          38.14          122.30 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
         29.060          13.495 
[1] "24.2 - 38.1 (29.1)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9200000"
D519V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCRB1 MUTATED         0        1        0        0         1         0
  ZCRB1 WILD-TYPE      10       19       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZCRB1 MUTATED           0          3          0          2        0         0
  ZCRB1 WILD-TYPE        29         81         62         37       43         4
D519V3, multiclass
            clus
vv           ZCRB1 MUTATED ZCRB1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZCRB1 MUTATED       1   1   1   4
  ZCRB1 WILD-TYPE    53 134 260  98
D519V4, multiclass
       clus
vv      ZCRB1 MUTATED ZCRB1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                1             260
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZCRB1 MUTATED     2   3   0   2
  ZCRB1 WILD-TYPE 193 170  89  83
D519V5, multiclass
    clus
vv   ZCRB1 MUTATED ZCRB1 WILD-TYPE
  N0             2             193
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V6, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     7   0
  ZCRB1 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      7    0
  ZCRB1 WILD-TYPE  475   38
   clus
vv  ZCRB1 MUTATED ZCRB1 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D519V7, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     3   4
  ZCRB1 WILD-TYPE 169 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      3    4
  ZCRB1 WILD-TYPE  169  402
        clus
vv       ZCRB1 MUTATED ZCRB1 WILD-TYPE
  FEMALE             3             169
  MALE               4             402
[1] 2 2
[1] FALSE
D519V8, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     4   2
  ZCRB1 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      4    2
  ZCRB1 WILD-TYPE  412  100
     clus
vv    ZCRB1 MUTATED ZCRB1 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D519V9, continuous
D519V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZCRB1 MUTATED       2                         0
  ZCRB1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCRB1 MUTATED                                           0     4
  ZCRB1 WILD-TYPE                                         1   353
D519V11, multiclass
                                           clus
vv                                          ZCRB1 MUTATED ZCRB1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V12, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     0   4
  ZCRB1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      0    4
  ZCRB1 WILD-TYPE   10  394
                        clus
vv                       ZCRB1 MUTATED ZCRB1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(520) Variable = PLA2G7 MUTATION ANALYSIS
D520V1, survival
                  sevent
clus2                0   1
  PLA2G7 MUTATED     1   5
  PLA2G7 WILD-TYPE 337 211
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
               6              548 
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
               5              211 
$`PLA2G7 MUTATED`
TCGA-L5-A4OM TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-RD-A7BT 
       47.93         0.26        31.96        16.14        11.77         8.61 

$`PLA2G7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
            0.26             0.00 
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
           47.93           122.30 
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
          13.955           13.565 
[1] "0.3 - 47.9 (14.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D520V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G7 MUTATED         0        1        1        0         0         0
  PLA2G7 WILD-TYPE      10       19       45       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G7 MUTATED           0          1          1          0        2
  PLA2G7 WILD-TYPE        29         83         61         39       41
                  vv
clus               STAGE IVA
  PLA2G7 MUTATED           0
  PLA2G7 WILD-TYPE         4
D520V3, multiclass
            clus
vv           PLA2G7 MUTATED PLA2G7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PLA2G7 MUTATED       2   1   3   1
  PLA2G7 WILD-TYPE    52 134 258 101
D520V4, multiclass
       clus
vv      PLA2G7 MUTATED PLA2G7 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PLA2G7 MUTATED     2   2   1   2
  PLA2G7 WILD-TYPE 193 171  88  83
D520V5, multiclass
    clus
vv   PLA2G7 MUTATED PLA2G7 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V6, binary
                  cls
clus                 0   1
  PLA2G7 MUTATED     6   1
  PLA2G7 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G7 MUTATED      6    1
  PLA2G7 WILD-TYPE  476   37
   clus
vv  PLA2G7 MUTATED PLA2G7 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D520V7, binary
                  cls
clus                 0   1
  PLA2G7 MUTATED     5   3
  PLA2G7 WILD-TYPE 167 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G7 MUTATED      5    3
  PLA2G7 WILD-TYPE  167  403
        clus
vv       PLA2G7 MUTATED PLA2G7 WILD-TYPE
  FEMALE              5              167
  MALE                3              403
[1] 2 2
[1] FALSE
D520V8, binary
                  cls
clus                 0   1
  PLA2G7 MUTATED     6   0
  PLA2G7 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G7 MUTATED      6    0
  PLA2G7 WILD-TYPE  410  102
     clus
vv    PLA2G7 MUTATED PLA2G7 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D520V9, continuous
D520V10, continuous
[1] "Remove cluster labels:" "PLA2G7 MUTATED"        
clus
  PLA2G7 MUTATED PLA2G7 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" "PLA2G7 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PLA2G7 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PLA2G7 MUTATED       2                         0
  PLA2G7 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLA2G7 MUTATED                                           1     5
  PLA2G7 WILD-TYPE                                         0   352
D520V11, multiclass
                                           clus
vv                                          PLA2G7 MUTATED PLA2G7 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V12, binary
                  cls
clus                 0   1
  PLA2G7 MUTATED     0   7
  PLA2G7 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G7 MUTATED      0    7
  PLA2G7 WILD-TYPE   10  391
                        clus
vv                       PLA2G7 MUTATED PLA2G7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(521) Variable = FBN3 MUTATION ANALYSIS
D521V1, survival
                sevent
clus2              0   1
  FBN3 MUTATED    25  14
  FBN3 WILD-TYPE 313 202
  FBN3 MUTATED FBN3 WILD-TYPE 
            39            515 
  FBN3 MUTATED FBN3 WILD-TYPE 
            14            202 
$`FBN3 MUTATED`
TCGA-L5-A4OI TCGA-IG-A97I TCGA-L5-A4OJ TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NR 
       19.99        12.16        21.01         7.13         2.60         8.71 
TCGA-LN-A49Y TCGA-LN-A9FP TCGA-R6-A6XG TCGA-VR-A8EX TCGA-BR-4280 TCGA-BR-6453 
       12.46        12.03        38.40        28.11         6.61        15.95 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8368 
        9.17        32.78        35.84        29.59        32.25         4.31 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CD-5801 
       31.27        25.05         1.12        31.96         1.48        13.18 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 
        6.58        15.95         7.07         6.02        28.96        21.07 
TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H5 
        5.92        11.44        24.20         6.51         6.58        23.80 
TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       48.79        38.14        17.85 

$`FBN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.43        15.48        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        34.68        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       13.68        19.33        39.12        26.10        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        19.04         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM 
       13.02        43.36        37.41        37.22        22.19         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FBN3 MUTATED FBN3 WILD-TYPE 
          1.12           0.00 
  FBN3 MUTATED FBN3 WILD-TYPE 
         48.79         122.30 
  FBN3 MUTATED FBN3 WILD-TYPE 
         15.95          13.55 
[1] "1.1 - 48.8 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D521V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBN3 MUTATED         1        2        4        1         8         7
  FBN3 WILD-TYPE       9       18       42       30        76        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBN3 MUTATED           3          4          3          4        3         1
  FBN3 WILD-TYPE        26         80         59         35       40         3
D521V3, multiclass
            clus
vv           FBN3 MUTATED FBN3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             8             76
  STAGE IIB             7             76
  STAGE III             3             26
  STAGE IIIA            4             80
  STAGE IIIB            3             59
  STAGE IIIC            4             35
  STAGE IV              3             40
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FBN3 MUTATED       4  11  15  11
  FBN3 WILD-TYPE    50 124 246  91
D521V4, multiclass
       clus
vv      FBN3 MUTATED FBN3 WILD-TYPE
  T0+T1            4             50
  T2              11            124
  T3              15            246
  T4              11             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FBN3 MUTATED    19  13   2   8
  FBN3 WILD-TYPE 176 160  87  77
D521V5, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  N0           19            176
  N1           13            160
  N2            2             87
  N3            8             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V6, binary
                cls
clus               0   1
  FBN3 MUTATED    38   2
  FBN3 WILD-TYPE 444  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     38    2
  FBN3 WILD-TYPE  444   36
   clus
vv  FBN3 MUTATED FBN3 WILD-TYPE
  0           38            444
  1            2             36
[1] 2 2
[1] FALSE
D521V7, binary
                cls
clus               0   1
  FBN3 MUTATED    19  24
  FBN3 WILD-TYPE 153 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     19   24
  FBN3 WILD-TYPE  153  382
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  FEMALE           19            153
  MALE             24            382
[1] 2 2
[1] FALSE
D521V8, binary
                cls
clus               0   1
  FBN3 MUTATED    34   4
  FBN3 WILD-TYPE 382  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     34    4
  FBN3 WILD-TYPE  382   98
     clus
vv    FBN3 MUTATED FBN3 WILD-TYPE
  NO            34            382
  YES            4             98
[1] 2 2
[1] FALSE
D521V9, continuous
[1] "Remove cluster labels:" "FBN3 MUTATED"          
clus
  FBN3 MUTATED FBN3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A4A1     TCGA-LN-A4A2 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"FBN3 WILD-TYPE" "FBN3 WILD-TYPE" 
D521V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FBN3 MUTATED       9                         0
  FBN3 WILD-TYPE   124                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBN3 MUTATED                                           0    24
  FBN3 WILD-TYPE                                         1   333
D521V11, multiclass
                                           clus
vv                                          FBN3 MUTATED FBN3 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               24            333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V12, binary
                cls
clus               0   1
  FBN3 MUTATED     0  28
  FBN3 WILD-TYPE  10 370
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      0   28
  FBN3 WILD-TYPE   10  370
                        clus
vv                       FBN3 MUTATED FBN3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           28            370
[1] 2 2
[1] FALSE

Clustering(522) Variable = CA2 MUTATION ANALYSIS
D522V1, survival
               sevent
clus2             0   1
  CA2 MUTATED     5   1
  CA2 WILD-TYPE 333 215
  CA2 MUTATED CA2 WILD-TYPE 
            6           548 
  CA2 MUTATED CA2 WILD-TYPE 
            1           215 
$`CA2 MUTATED`
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8372 TCGA-CD-A4MG TCGA-HU-8602 TCGA-HU-A4GX 
        4.31        14.04        31.27         6.58        22.32        20.25 

$`CA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        0.95        26.33         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CA2 MUTATED CA2 WILD-TYPE 
         4.31          0.00 
  CA2 MUTATED CA2 WILD-TYPE 
        31.27        122.30 
  CA2 MUTATED CA2 WILD-TYPE 
       17.145        13.530 
[1] "4.3 - 31.3 (17.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D522V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CA2 MUTATED         1        0        1        0         1         1
  CA2 WILD-TYPE       9       20       45       31        83        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CA2 MUTATED           0          0          1          2        0         0
  CA2 WILD-TYPE        29         84         61         37       43         4
D522V3, multiclass
            clus
vv           CA2 MUTATED CA2 WILD-TYPE
  STAGE I              1             9
  STAGE IA             0            20
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            1            83
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           0            84
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CA2 MUTATED       1   1   2   3
  CA2 WILD-TYPE    53 134 259  99
D522V4, multiclass
       clus
vv      CA2 MUTATED CA2 WILD-TYPE
  T0+T1           1            53
  T2              1           134
  T3              2           259
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CA2 MUTATED     3   1   1   2
  CA2 WILD-TYPE 192 172  88  83
D522V5, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  N0           3           192
  N1           1           172
  N2           1            88
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V6, binary
               cls
clus              0   1
  CA2 MUTATED     6   0
  CA2 WILD-TYPE 476  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      6    0
  CA2 WILD-TYPE  476   38
   clus
vv  CA2 MUTATED CA2 WILD-TYPE
  0           6           476
  1           0            38
[1] 2 2
[1] FALSE
D522V7, binary
               cls
clus              0   1
  CA2 MUTATED     4   3
  CA2 WILD-TYPE 168 403
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      4    3
  CA2 WILD-TYPE  168  403
        clus
vv       CA2 MUTATED CA2 WILD-TYPE
  FEMALE           4           168
  MALE             3           403
[1] 2 2
[1] FALSE
D522V8, binary
               cls
clus              0   1
  CA2 MUTATED     7   0
  CA2 WILD-TYPE 409 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      7    0
  CA2 WILD-TYPE  409  102
     clus
vv    CA2 MUTATED CA2 WILD-TYPE
  NO            7           409
  YES           0           102
[1] 2 2
[1] FALSE
D522V9, continuous
D522V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CA2 MUTATED       3                         1
  CA2 WILD-TYPE   130                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CA2 MUTATED                                           0     3
  CA2 WILD-TYPE                                         1   354
D522V11, multiclass
                                           clus
vv                                          CA2 MUTATED CA2 WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V12, binary
               cls
clus              0   1
  CA2 MUTATED     0   7
  CA2 WILD-TYPE  10 391
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      0    7
  CA2 WILD-TYPE   10  391
                        clus
vv                       CA2 MUTATED CA2 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           7           391
[1] 2 2
[1] FALSE

Clustering(523) Variable = GTF3C4 MUTATION ANALYSIS
D523V1, survival
                  sevent
clus2                0   1
  GTF3C4 MUTATED    11   2
  GTF3C4 WILD-TYPE 327 214
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              13              541 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
               2              214 
$`GTF3C4 MUTATED`
TCGA-JY-A938 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 
       34.85         9.34        34.68        32.25         4.31         1.12 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-F1-6874 
       28.14        16.14       105.07        65.10        13.78        14.47 
TCGA-VQ-A91V 
       42.64 

$`GTF3C4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
            1.12             0.00 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
          105.07           122.30 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
           28.14            13.48 
[1] "1.1 - 105.1 (28.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.9"
D523V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C4 MUTATED         0        0        3        1         2         2
  GTF3C4 WILD-TYPE      10       20       43       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C4 MUTATED           0          1          2          1        0
  GTF3C4 WILD-TYPE        29         83         60         38       43
                  vv
clus               STAGE IVA
  GTF3C4 MUTATED           0
  GTF3C4 WILD-TYPE         4
D523V3, multiclass
            clus
vv           GTF3C4 MUTATED GTF3C4 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GTF3C4 MUTATED       0   4   6   2
  GTF3C4 WILD-TYPE    54 131 255 100
D523V4, multiclass
       clus
vv      GTF3C4 MUTATED GTF3C4 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 6              255
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GTF3C4 MUTATED     7   2   1   3
  GTF3C4 WILD-TYPE 188 171  88  82
D523V5, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  N0              7              188
  N1              2              171
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V6, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED    14   0
  GTF3C4 WILD-TYPE 468  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED     14    0
  GTF3C4 WILD-TYPE  468   38
   clus
vv  GTF3C4 MUTATED GTF3C4 WILD-TYPE
  0             14              468
  1              0               38
[1] 2 2
[1] FALSE
D523V7, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     7   7
  GTF3C4 WILD-TYPE 165 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      7    7
  GTF3C4 WILD-TYPE  165  399
        clus
vv       GTF3C4 MUTATED GTF3C4 WILD-TYPE
  FEMALE              7              165
  MALE                7              399
[1] 2 2
[1] FALSE
D523V8, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED    10   2
  GTF3C4 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED     10    2
  GTF3C4 WILD-TYPE  406  100
     clus
vv    GTF3C4 MUTATED GTF3C4 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D523V9, continuous
D523V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GTF3C4 MUTATED       0                         0
  GTF3C4 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF3C4 MUTATED                                           0    11
  GTF3C4 WILD-TYPE                                         1   346
D523V11, multiclass
                                           clus
vv                                          GTF3C4 MUTATED GTF3C4 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V12, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     0  10
  GTF3C4 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      0   10
  GTF3C4 WILD-TYPE   10  388
                        clus
vv                       GTF3C4 MUTATED GTF3C4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(524) Variable = TERF1 MUTATION ANALYSIS
D524V1, survival
                 sevent
clus2               0   1
  TERF1 MUTATED     5   5
  TERF1 WILD-TYPE 333 211
  TERF1 MUTATED TERF1 WILD-TYPE 
             10             544 
  TERF1 MUTATED TERF1 WILD-TYPE 
              5             211 
$`TERF1 MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8360 TCGA-CD-8526 
       25.78        58.55         6.97        35.84         6.18        12.53 
TCGA-CG-4469 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HU-A4H3 
        7.07        11.44        21.27        29.00 

$`TERF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.39        12.76        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TERF1 MUTATED TERF1 WILD-TYPE 
           6.18            0.00 
  TERF1 MUTATED TERF1 WILD-TYPE 
          58.55          122.30 
  TERF1 MUTATED TERF1 WILD-TYPE 
         16.900          13.565 
[1] "6.2 - 58.5 (16.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D524V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TERF1 MUTATED         1        0        1        0         1         0
  TERF1 WILD-TYPE       9       20       45       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TERF1 MUTATED           1          2          2          1        1         0
  TERF1 WILD-TYPE        28         82         60         38       42         4
D524V3, multiclass
            clus
vv           TERF1 MUTATED TERF1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TERF1 MUTATED       1   1   7   1
  TERF1 WILD-TYPE    53 134 254 101
D524V4, multiclass
       clus
vv      TERF1 MUTATED TERF1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                7             254
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TERF1 MUTATED     3   3   0   4
  TERF1 WILD-TYPE 192 170  89  81
D524V5, multiclass
    clus
vv   TERF1 MUTATED TERF1 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             0              89
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V6, binary
                 cls
clus                0   1
  TERF1 MUTATED     9   0
  TERF1 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      9    0
  TERF1 WILD-TYPE  473   38
   clus
vv  TERF1 MUTATED TERF1 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D524V7, binary
                 cls
clus                0   1
  TERF1 MUTATED     4   6
  TERF1 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      4    6
  TERF1 WILD-TYPE  168  400
        clus
vv       TERF1 MUTATED TERF1 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D524V8, binary
                 cls
clus                0   1
  TERF1 MUTATED     7   1
  TERF1 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      7    1
  TERF1 WILD-TYPE  409  101
     clus
vv    TERF1 MUTATED TERF1 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D524V9, continuous
D524V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TERF1 MUTATED       2                         0
  TERF1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TERF1 MUTATED                                           0     5
  TERF1 WILD-TYPE                                         1   352
D524V11, multiclass
                                           clus
vv                                          TERF1 MUTATED TERF1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V12, binary
                 cls
clus                0   1
  TERF1 MUTATED     1   6
  TERF1 WILD-TYPE   9 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      1    6
  TERF1 WILD-TYPE    9  392
                        clus
vv                       TERF1 MUTATED TERF1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(525) Variable = PLEKHO1 MUTATION ANALYSIS
D525V1, survival
                   sevent
clus2                 0   1
  PLEKHO1 MUTATED     3   2
  PLEKHO1 WILD-TYPE 335 214
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                5               549 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                2               214 
$`PLEKHO1 MUTATED`
TCGA-L5-A8NV TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8680 TCGA-CG-5723 
       52.57        34.68         0.26        31.96       105.07 

$`PLEKHO1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
             0.26              0.00 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
           105.07            122.30 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
            34.68             13.51 
[1] "0.3 - 105.1 (34.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D525V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHO1 MUTATED         1        0        1        1         2         0
  PLEKHO1 WILD-TYPE       9       20       45       30        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHO1 MUTATED           0          0          0          0        1
  PLEKHO1 WILD-TYPE        29         84         62         39       42
                   vv
clus                STAGE IVA
  PLEKHO1 MUTATED           0
  PLEKHO1 WILD-TYPE         4
D525V3, multiclass
            clus
vv           PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PLEKHO1 MUTATED       2   2   2   1
  PLEKHO1 WILD-TYPE    52 133 259 101
D525V4, multiclass
       clus
vv      PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PLEKHO1 MUTATED     3   2   1   0
  PLEKHO1 WILD-TYPE 192 171  88  85
D525V5, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  N0               3               192
  N1               2               171
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V6, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     6   1
  PLEKHO1 WILD-TYPE 476  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      6    1
  PLEKHO1 WILD-TYPE  476   37
   clus
vv  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  0               6               476
  1               1                37
[1] 2 2
[1] FALSE
D525V7, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     4   4
  PLEKHO1 WILD-TYPE 168 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      4    4
  PLEKHO1 WILD-TYPE  168  402
        clus
vv       PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  FEMALE               4               168
  MALE                 4               402
[1] 2 2
[1] FALSE
D525V8, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     6   0
  PLEKHO1 WILD-TYPE 410 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      6    0
  PLEKHO1 WILD-TYPE  410  102
     clus
vv    PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  NO                6               410
  YES               0               102
[1] 2 2
[1] FALSE
D525V9, continuous
D525V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHO1 MUTATED       1                         1
  PLEKHO1 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHO1 MUTATED                                           0     5
  PLEKHO1 WILD-TYPE                                         1   352
D525V11, multiclass
                                           clus
vv                                          PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V12, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     0   6
  PLEKHO1 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      0    6
  PLEKHO1 WILD-TYPE   10  392
                        clus
vv                       PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(526) Variable = FAM109B MUTATION ANALYSIS
D526V1, survival
                   sevent
clus2                 0   1
  FAM109B MUTATED     5   2
  FAM109B WILD-TYPE 333 214
  FAM109B MUTATED FAM109B WILD-TYPE 
                7               547 
  FAM109B MUTATED FAM109B WILD-TYPE 
                2               214 
$`FAM109B MUTATED`
TCGA-L5-A8NM TCGA-BR-8363 TCGA-BR-8487 TCGA-CG-4437 TCGA-HU-A4GH TCGA-HU-A4H8 
        7.76         0.26         1.12         8.05        11.77        14.07 
TCGA-VQ-A8P2 
       38.14 

$`FAM109B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FAM109B MUTATED FAM109B WILD-TYPE 
             0.26              0.00 
  FAM109B MUTATED FAM109B WILD-TYPE 
            38.14            122.30 
  FAM109B MUTATED FAM109B WILD-TYPE 
             8.05             13.68 
[1] "0.3 - 38.1 (8.1)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D526V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM109B MUTATED         0        1        2        1         1         1
  FAM109B WILD-TYPE      10       19       44       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM109B MUTATED           0          1          0          0        1
  FAM109B WILD-TYPE        29         83         62         39       42
                   vv
clus                STAGE IVA
  FAM109B MUTATED           0
  FAM109B WILD-TYPE         4
D526V3, multiclass
            clus
vv           FAM109B MUTATED FAM109B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM109B MUTATED       2   3   1   2
  FAM109B WILD-TYPE    52 132 260 100
D526V4, multiclass
       clus
vv      FAM109B MUTATED FAM109B WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  1               260
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM109B MUTATED     3   4   1   0
  FAM109B WILD-TYPE 192 169  88  85
D526V5, multiclass
    clus
vv   FAM109B MUTATED FAM109B WILD-TYPE
  N0               3               192
  N1               4               169
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V6, binary
                   cls
clus                  0   1
  FAM109B MUTATED     8   0
  FAM109B WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      8    0
  FAM109B WILD-TYPE  474   38
   clus
vv  FAM109B MUTATED FAM109B WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D526V7, binary
                   cls
clus                  0   1
  FAM109B MUTATED     4   4
  FAM109B WILD-TYPE 168 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      4    4
  FAM109B WILD-TYPE  168  402
        clus
vv       FAM109B MUTATED FAM109B WILD-TYPE
  FEMALE               4               168
  MALE                 4               402
[1] 2 2
[1] FALSE
D526V8, binary
                   cls
clus                  0   1
  FAM109B MUTATED     6   1
  FAM109B WILD-TYPE 410 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      6    1
  FAM109B WILD-TYPE  410  101
     clus
vv    FAM109B MUTATED FAM109B WILD-TYPE
  NO                6               410
  YES               1               101
[1] 2 2
[1] FALSE
D526V9, continuous
D526V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM109B MUTATED       2                         0
  FAM109B WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM109B MUTATED                                           0     5
  FAM109B WILD-TYPE                                         1   352
D526V11, multiclass
                                           clus
vv                                          FAM109B MUTATED FAM109B WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V12, binary
                   cls
clus                  0   1
  FAM109B MUTATED     0   5
  FAM109B WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      0    5
  FAM109B WILD-TYPE   10  393
                        clus
vv                       FAM109B MUTATED FAM109B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(527) Variable = DNAH7 MUTATION ANALYSIS
D527V1, survival
                 sevent
clus2               0   1
  DNAH7 MUTATED    42  22
  DNAH7 WILD-TYPE 296 194
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             64             490 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             22             194 
$`DNAH7 MUTATED`
TCGA-L5-A4OE TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-2H-A9GO 
       24.00        21.99        79.07        16.24         9.86        16.24 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93D TCGA-L5-A43E 
        7.69         0.85         3.88       122.10        31.56        30.25 
TCGA-L5-A4OP TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L7-A6VZ TCGA-LN-A49P TCGA-LN-A4A3 
        7.17         7.40        55.50        10.36        12.33        12.76 
TCGA-R6-A8WG TCGA-VR-A8EU TCGA-XP-A8T6 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 
       12.69        18.31        25.08         6.97        18.35        30.90 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
        9.34        34.68        44.94        36.16        35.84        33.63 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8592 
        0.69        29.59        31.10         4.31         1.12         6.28 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4QL 
       31.96         8.22        34.98        12.89        14.17        16.14 
TCGA-CD-5801 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
       13.18        11.61         6.58        12.62        27.02        15.95 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-A4Z0 
        6.02       105.07        10.26        15.22        11.31        14.76 
TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GF TCGA-HU-A4GH 
       11.24        15.65        77.29        26.47        25.81        11.77 
TCGA-HU-A4GT TCGA-IN-8462 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        6.51        18.81        74.53        38.14 

$`DNAH7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
        5.16        20.02        47.05        22.98         0.23        20.15 
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
        5.92        13.94         8.94         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       35.21        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60        25.12         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        7.43         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        35.24        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        7.53         6.08         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.43         6.31        12.30        11.31        12.43        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       11.77        20.02         3.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX 
       16.44         5.92        36.43        13.78        26.43        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DNAH7 MUTATED DNAH7 WILD-TYPE 
           0.69            0.00 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          122.1           122.3 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
         15.800          13.445 
[1] "0.7 - 122.1 (15.8)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D527V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH7 MUTATED         2        4        8        5        10        12
  DNAH7 WILD-TYPE       8       16       38       26        74        71
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH7 MUTATED           1          5          6          4        6         1
  DNAH7 WILD-TYPE        28         79         56         35       37         3
D527V3, multiclass
            clus
vv           DNAH7 MUTATED DNAH7 WILD-TYPE
  STAGE I                2               8
  STAGE IA               4              16
  STAGE IB               8              38
  STAGE II               5              26
  STAGE IIA             10              74
  STAGE IIB             12              71
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             6              56
  STAGE IIIC             4              35
  STAGE IV               6              37
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DNAH7 MUTATED       9  20  19  17
  DNAH7 WILD-TYPE    45 115 242  85
D527V4, multiclass
       clus
vv      DNAH7 MUTATED DNAH7 WILD-TYPE
  T0+T1             9              45
  T2               20             115
  T3               19             242
  T4               17              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DNAH7 MUTATED    29  26   8   3
  DNAH7 WILD-TYPE 166 147  81  82
D527V5, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  N0            29             166
  N1            26             147
  N2             8              81
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V6, binary
                 cls
clus                0   1
  DNAH7 MUTATED    57   5
  DNAH7 WILD-TYPE 425  33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     57    5
  DNAH7 WILD-TYPE  425   33
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0            57             425
  1             5              33
[1] 2 2
[1] FALSE
D527V7, binary
                 cls
clus                0   1
  DNAH7 MUTATED    24  45
  DNAH7 WILD-TYPE 148 361
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     24   45
  DNAH7 WILD-TYPE  148  361
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE            24             148
  MALE              45             361
[1] 2 2
[1] FALSE
D527V8, binary
                 cls
clus                0   1
  DNAH7 MUTATED    52  11
  DNAH7 WILD-TYPE 364  91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     52   11
  DNAH7 WILD-TYPE  364   91
     clus
vv    DNAH7 MUTATED DNAH7 WILD-TYPE
  NO             52             364
  YES            11              91
[1] 2 2
[1] FALSE
D527V9, continuous
D527V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DNAH7 MUTATED      13                         1
  DNAH7 WILD-TYPE   120                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAH7 MUTATED                                           0    46
  DNAH7 WILD-TYPE                                         1   311
D527V11, multiclass
                                           clus
vv                                          DNAH7 MUTATED DNAH7 WILD-TYPE
  ASIAN                                                13             120
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                46             311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V12, binary
                 cls
clus                0   1
  DNAH7 MUTATED     3  48
  DNAH7 WILD-TYPE   7 350
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      3   48
  DNAH7 WILD-TYPE    7  350
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 3               7
  NOT HISPANIC OR LATINO            48             350
[1] 2 2
[1] FALSE

Clustering(528) Variable = MAP7D3 MUTATION ANALYSIS
D528V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    11   3
  MAP7D3 WILD-TYPE 327 213
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              14              540 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               3              213 
$`MAP7D3 MUTATED`
TCGA-BR-6566 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8588 
       32.78         0.69        29.59        32.25         0.26        12.79 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-D7-6522 TCGA-HU-8602 
       28.14        31.96        16.14        12.62        18.61        22.32 
TCGA-HU-A4GX TCGA-VQ-A8DU 
       20.25         5.46 

$`MAP7D3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        5.39        25.18         9.21        20.22         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.54        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
            0.26             0.00 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           32.78           122.30 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           19.43            13.51 
[1] "0.3 - 32.8 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D528V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP7D3 MUTATED         0        0        4        0         1         4
  MAP7D3 WILD-TYPE      10       20       42       31        83        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          2          2          2        2
  MAP7D3 WILD-TYPE        29         82         60         37       41
                  vv
clus               STAGE IVA
  MAP7D3 MUTATED           0
  MAP7D3 WILD-TYPE         4
D528V3, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAP7D3 MUTATED       0   4   3  10
  MAP7D3 WILD-TYPE    54 131 258  92
D528V4, multiclass
       clus
vv      MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 3              258
  T4                10               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP7D3 MUTATED    10   1   4   2
  MAP7D3 WILD-TYPE 185 172  85  83
D528V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0             10              185
  N1              1              172
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V6, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    17   1
  MAP7D3 WILD-TYPE 465  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     17    1
  MAP7D3 WILD-TYPE  465   37
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             17              465
  1              1               37
[1] 2 2
[1] FALSE
D528V7, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    12   6
  MAP7D3 WILD-TYPE 160 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     12    6
  MAP7D3 WILD-TYPE  160  400
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE             12              160
  MALE                6              400
[1] 2 2
[1] FALSE
D528V8, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    13   0
  MAP7D3 WILD-TYPE 403 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     13    0
  MAP7D3 WILD-TYPE  403  102
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO              13              403
  YES              0              102
[1] 2 2
[1] FALSE
D528V9, continuous
D528V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP7D3 MUTATED       4                         0
  MAP7D3 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP7D3 MUTATED                                           0    13
  MAP7D3 WILD-TYPE                                         1   344
D528V11, multiclass
                                           clus
vv                                          MAP7D3 MUTATED MAP7D3 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V12, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED     0  16
  MAP7D3 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      0   16
  MAP7D3 WILD-TYPE   10  382
                        clus
vv                       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(529) Variable = SFRS18 MUTATION ANALYSIS
D529V1, survival
                  sevent
clus2                0   1
  SFRS18 MUTATED    15   3
  SFRS18 WILD-TYPE 323 213
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              18              536 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
               3              213 
$`SFRS18 MUTATED`
TCGA-L5-A4OI TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NM TCGA-L5-A8NR TCGA-B7-5818 
       19.99         2.60         3.75         7.76         8.71        11.70 
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8372 
        6.97         6.61        34.68        32.25         4.31        31.27 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8533 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GT 
        1.12        31.96        15.39        30.51        24.20         6.51 

$`SFRS18 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SFRS18 MUTATED SFRS18 WILD-TYPE 
            1.12             0.00 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           34.68           122.30 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
          10.205           13.630 
[1] "1.1 - 34.7 (10.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D529V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SFRS18 MUTATED         0        1        3        1         3         2
  SFRS18 WILD-TYPE      10       19       43       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS18 MUTATED           3          1          0          3        1
  SFRS18 WILD-TYPE        26         83         62         36       42
                  vv
clus               STAGE IVA
  SFRS18 MUTATED           0
  SFRS18 WILD-TYPE         4
D529V3, multiclass
            clus
vv           SFRS18 MUTATED SFRS18 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               3               26
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SFRS18 MUTATED       1   5   9   4
  SFRS18 WILD-TYPE    53 130 252  98
D529V4, multiclass
       clus
vv      SFRS18 MUTATED SFRS18 WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 9              252
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SFRS18 MUTATED     9   6   1   3
  SFRS18 WILD-TYPE 186 167  88  82
D529V5, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  N0              9              186
  N1              6              167
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V6, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    16   1
  SFRS18 WILD-TYPE 466  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     16    1
  SFRS18 WILD-TYPE  466   37
   clus
vv  SFRS18 MUTATED SFRS18 WILD-TYPE
  0             16              466
  1              1               37
[1] 2 2
[1] FALSE
D529V7, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    11   9
  SFRS18 WILD-TYPE 161 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     11    9
  SFRS18 WILD-TYPE  161  397
        clus
vv       SFRS18 MUTATED SFRS18 WILD-TYPE
  FEMALE             11              161
  MALE                9              397
[1] 2 2
[1] FALSE
D529V8, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    16   1
  SFRS18 WILD-TYPE 400 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     16    1
  SFRS18 WILD-TYPE  400  101
     clus
vv    SFRS18 MUTATED SFRS18 WILD-TYPE
  NO              16              400
  YES              1              101
[1] 2 2
[1] FALSE
D529V9, continuous
D529V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SFRS18 MUTATED       4                         0
  SFRS18 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SFRS18 MUTATED                                           0    13
  SFRS18 WILD-TYPE                                         1   344
D529V11, multiclass
                                           clus
vv                                          SFRS18 MUTATED SFRS18 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V12, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     0  13
  SFRS18 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      0   13
  SFRS18 WILD-TYPE   10  385
                        clus
vv                       SFRS18 MUTATED SFRS18 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(530) Variable = PRPF4B MUTATION ANALYSIS
D530V1, survival
                  sevent
clus2                0   1
  PRPF4B MUTATED     6   3
  PRPF4B WILD-TYPE 332 213
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               9              545 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               3              213 
$`PRPF4B MUTATED`
TCGA-2H-A9GF TCGA-L5-A8NM TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8368 
       25.78         7.76        34.68        44.94        36.16         4.31 
TCGA-BR-8678 TCGA-BR-A4QL TCGA-CG-5728 
       24.79        16.14        65.10 

$`PRPF4B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PRPF4B MUTATED PRPF4B WILD-TYPE 
            4.31             0.00 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
            65.1            122.3 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
           25.78            13.51 
[1] "4.3 - 65.1 (25.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D530V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRPF4B MUTATED         0        1        3        0         2         1
  PRPF4B WILD-TYPE      10       19       43       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF4B MUTATED           1          1          1          0        1
  PRPF4B WILD-TYPE        28         83         61         39       42
                  vv
clus               STAGE IVA
  PRPF4B MUTATED           0
  PRPF4B WILD-TYPE         4
D530V3, multiclass
            clus
vv           PRPF4B MUTATED PRPF4B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PRPF4B MUTATED       1   4   4   2
  PRPF4B WILD-TYPE    53 131 257 100
D530V4, multiclass
       clus
vv      PRPF4B MUTATED PRPF4B WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PRPF4B MUTATED     7   3   1   1
  PRPF4B WILD-TYPE 188 170  88  84
D530V5, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  N0              7              188
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V6, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    12   0
  PRPF4B WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     12    0
  PRPF4B WILD-TYPE  470   38
   clus
vv  PRPF4B MUTATED PRPF4B WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D530V7, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     9   3
  PRPF4B WILD-TYPE 163 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      9    3
  PRPF4B WILD-TYPE  163  403
        clus
vv       PRPF4B MUTATED PRPF4B WILD-TYPE
  FEMALE              9              163
  MALE                3              403
[1] 2 2
[1] FALSE
D530V8, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     8   0
  PRPF4B WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      8    0
  PRPF4B WILD-TYPE  408  102
     clus
vv    PRPF4B MUTATED PRPF4B WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D530V9, continuous
D530V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRPF4B MUTATED       0                         0
  PRPF4B WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRPF4B MUTATED                                           0    10
  PRPF4B WILD-TYPE                                         1   347
D530V11, multiclass
                                           clus
vv                                          PRPF4B MUTATED PRPF4B WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V12, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     0   9
  PRPF4B WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      0    9
  PRPF4B WILD-TYPE   10  389
                        clus
vv                       PRPF4B MUTATED PRPF4B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(531) Variable = SP100 MUTATION ANALYSIS
D531V1, survival
                 sevent
clus2               0   1
  SP100 MUTATED    14  11
  SP100 WILD-TYPE 324 205
  SP100 MUTATED SP100 WILD-TYPE 
             25             529 
  SP100 MUTATED SP100 WILD-TYPE 
             11             205 
$`SP100 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3Y9 TCGA-JY-A6FE TCGA-L5-A893 TCGA-LN-A8HZ TCGA-R6-A8WG 
       19.99         0.85         3.68         3.02        12.33        12.69 
TCGA-V5-A7RB TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-6456 TCGA-BR-8361 
        5.29        26.70        11.70        19.56        17.29        31.10 
TCGA-BR-8382 TCGA-CD-5813 TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5728 
       25.05        12.39         6.58        18.97         6.02        65.10 
TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-VQ-A8DL 
       24.20         6.58        20.25        14.07        13.35         0.92 
TCGA-VQ-A8DU 
        5.46 

$`SP100 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV 
        8.94        35.61        19.04         5.79        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SP100 MUTATED SP100 WILD-TYPE 
           0.85            0.00 
  SP100 MUTATED SP100 WILD-TYPE 
           65.1           122.3 
  SP100 MUTATED SP100 WILD-TYPE 
          12.69           13.68 
[1] "0.8 - 65.1 (12.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.4"
D531V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP100 MUTATED         1        1        4        1         3         3
  SP100 WILD-TYPE       9       19       42       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP100 MUTATED           1          3          0          5        1         0
  SP100 WILD-TYPE        28         81         62         34       42         4
D531V3, multiclass
            clus
vv           SP100 MUTATED SP100 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             5              34
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SP100 MUTATED       4   5   8   7
  SP100 WILD-TYPE    50 130 253  95
D531V4, multiclass
       clus
vv      SP100 MUTATED SP100 WILD-TYPE
  T0+T1             4              50
  T2                5             130
  T3                8             253
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SP100 MUTATED    11   7   3   3
  SP100 WILD-TYPE 184 166  86  82
D531V5, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  N0            11             184
  N1             7             166
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V6, binary
                 cls
clus                0   1
  SP100 MUTATED    22   0
  SP100 WILD-TYPE 460  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     22    0
  SP100 WILD-TYPE  460   38
   clus
vv  SP100 MUTATED SP100 WILD-TYPE
  0            22             460
  1             0              38
[1] 2 2
[1] FALSE
D531V7, binary
                 cls
clus                0   1
  SP100 MUTATED    10  15
  SP100 WILD-TYPE 162 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     10   15
  SP100 WILD-TYPE  162  391
        clus
vv       SP100 MUTATED SP100 WILD-TYPE
  FEMALE            10             162
  MALE              15             391
[1] 2 2
[1] FALSE
D531V8, binary
                 cls
clus                0   1
  SP100 MUTATED    23   1
  SP100 WILD-TYPE 393 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     23    1
  SP100 WILD-TYPE  393  101
     clus
vv    SP100 MUTATED SP100 WILD-TYPE
  NO             23             393
  YES             1             101
[1] 2 2
[1] FALSE
D531V9, continuous
[1] "Remove cluster labels:" "SP100 MUTATED"         
clus
  SP100 MUTATED SP100 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" "SP100 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SP100 WILD-TYPE" "SP100 WILD-TYPE" 
D531V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SP100 MUTATED       7                         0
  SP100 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SP100 MUTATED                                           0    14
  SP100 WILD-TYPE                                         1   343
D531V11, multiclass
                                           clus
vv                                          SP100 MUTATED SP100 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V12, binary
                 cls
clus                0   1
  SP100 MUTATED     2  15
  SP100 WILD-TYPE   8 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      2   15
  SP100 WILD-TYPE    8  383
                        clus
vv                       SP100 MUTATED SP100 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(532) Variable = UHRF1BP1 MUTATION ANALYSIS
D532V1, survival
                    sevent
clus2                  0   1
  UHRF1BP1 MUTATED    13   7
  UHRF1BP1 WILD-TYPE 325 209
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                20                534 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 7                209 
$`UHRF1BP1 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-VR-A8EO TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 
       21.99         5.92        25.81        30.90        34.68        32.78 
TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5717 TCGA-CG-5722 TCGA-CG-5723 
        0.26        31.96        11.77         6.97         0.99       105.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-A4G3 TCGA-HU-A4H3 TCGA-HU-A4H4 
       65.10        21.07        21.27         5.59        29.00        23.84 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`UHRF1BP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97        36.00         1.02         0.99         6.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        28.96         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.95        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
              0.26               0.00 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
            105.07             122.30 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
            22.915             13.445 
[1] "0.3 - 105.1 (22.9)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D532V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UHRF1BP1 MUTATED         0        0        3        2         3         2
  UHRF1BP1 WILD-TYPE      10       20       43       29        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UHRF1BP1 MUTATED           1          2          1          1        4
  UHRF1BP1 WILD-TYPE        28         82         61         38       39
                    vv
clus                 STAGE IVA
  UHRF1BP1 MUTATED           0
  UHRF1BP1 WILD-TYPE         4
D532V3, multiclass
            clus
vv           UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  3                 43
  STAGE II                  2                 29
  STAGE IIA                 3                 81
  STAGE IIB                 2                 81
  STAGE III                 1                 28
  STAGE IIIA                2                 82
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  4                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  UHRF1BP1 MUTATED       2   8   7   4
  UHRF1BP1 WILD-TYPE    52 127 254  98
D532V4, multiclass
       clus
vv      UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  T0+T1                2                 52
  T2                   8                127
  T3                   7                254
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  UHRF1BP1 MUTATED     5   7   5   2
  UHRF1BP1 WILD-TYPE 190 166  84  83
D532V5, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  N0                5                190
  N1                7                166
  N2                5                 84
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V6, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    17   4
  UHRF1BP1 WILD-TYPE 465  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     17    4
  UHRF1BP1 WILD-TYPE  465   34
   clus
vv  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  0               17                465
  1                4                 34
[1] 2 2
[1] FALSE
D532V7, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    12   9
  UHRF1BP1 WILD-TYPE 160 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     12    9
  UHRF1BP1 WILD-TYPE  160  397
        clus
vv       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  FEMALE               12                160
  MALE                  9                397
[1] 2 2
[1] FALSE
D532V8, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    15   2
  UHRF1BP1 WILD-TYPE 401 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     15    2
  UHRF1BP1 WILD-TYPE  401  100
     clus
vv    UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  NO                15                401
  YES                2                100
[1] 2 2
[1] FALSE
D532V9, continuous
[1] "Remove cluster labels:" "UHRF1BP1 MUTATED"      
clus
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EP 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"UHRF1BP1 WILD-TYPE" 
D532V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  UHRF1BP1 MUTATED       6                         0
  UHRF1BP1 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UHRF1BP1 MUTATED                                           0     8
  UHRF1BP1 WILD-TYPE                                         1   349
D532V11, multiclass
                                           clus
vv                                          UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V12, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED     2  11
  UHRF1BP1 WILD-TYPE   8 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      2   11
  UHRF1BP1 WILD-TYPE    8  387
                        clus
vv                       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               11                387
[1] 2 2
[1] FALSE

Clustering(533) Variable = MRGPRF MUTATION ANALYSIS
D533V1, survival
                  sevent
clus2                0   1
  MRGPRF MUTATED     3   4
  MRGPRF WILD-TYPE 335 212
  MRGPRF MUTATED MRGPRF WILD-TYPE 
               7              547 
  MRGPRF MUTATED MRGPRF WILD-TYPE 
               4              212 
$`MRGPRF MUTATED`
TCGA-L5-A4OI TCGA-JY-A93C TCGA-L5-A4ON TCGA-LN-A4A6 TCGA-VR-AA7D TCGA-CD-A4MG 
       19.99        23.18        18.35        12.85         9.17         6.58 
TCGA-HU-8243 
        5.92 

$`MRGPRF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MRGPRF MUTATED MRGPRF WILD-TYPE 
            5.92             0.00 
  MRGPRF MUTATED MRGPRF WILD-TYPE 
           23.18           122.30 
  MRGPRF MUTATED MRGPRF WILD-TYPE 
           12.85            13.58 
[1] "5.9 - 23.2 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D533V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRGPRF MUTATED         0        0        0        1         1         1
  MRGPRF WILD-TYPE      10       20       46       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRGPRF MUTATED           0          0          1          3        0
  MRGPRF WILD-TYPE        29         84         61         36       43
                  vv
clus               STAGE IVA
  MRGPRF MUTATED           0
  MRGPRF WILD-TYPE         4
D533V3, multiclass
            clus
vv           MRGPRF MUTATED MRGPRF WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MRGPRF MUTATED       1   1   4   1
  MRGPRF WILD-TYPE    53 134 257 101
D533V4, multiclass
       clus
vv      MRGPRF MUTATED MRGPRF WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 4              257
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MRGPRF MUTATED     2   1   1   3
  MRGPRF WILD-TYPE 193 172  88  82
D533V5, multiclass
    clus
vv   MRGPRF MUTATED MRGPRF WILD-TYPE
  N0              2              193
  N1              1              172
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V6, binary
                  cls
clus                 0   1
  MRGPRF MUTATED     5   0
  MRGPRF WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRGPRF MUTATED      5    0
  MRGPRF WILD-TYPE  477   38
   clus
vv  MRGPRF MUTATED MRGPRF WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D533V7, binary
                  cls
clus                 0   1
  MRGPRF MUTATED     0   7
  MRGPRF WILD-TYPE 172 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRGPRF MUTATED      0    7
  MRGPRF WILD-TYPE  172  399
        clus
vv       MRGPRF MUTATED MRGPRF WILD-TYPE
  FEMALE              0              172
  MALE                7              399
[1] 2 2
[1] FALSE
D533V8, binary
                  cls
clus                 0   1
  MRGPRF MUTATED     5   1
  MRGPRF WILD-TYPE 411 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRGPRF MUTATED      5    1
  MRGPRF WILD-TYPE  411  101
     clus
vv    MRGPRF MUTATED MRGPRF WILD-TYPE
  NO               5              411
  YES              1              101
[1] 2 2
[1] FALSE
D533V9, continuous
[1] "Remove cluster labels:" "MRGPRF MUTATED"        
clus
  MRGPRF MUTATED MRGPRF WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"MRGPRF WILD-TYPE" "MRGPRF WILD-TYPE" 
D533V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MRGPRF MUTATED       4                         0
  MRGPRF WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRGPRF MUTATED                                           0     2
  MRGPRF WILD-TYPE                                         1   355
D533V11, multiclass
                                           clus
vv                                          MRGPRF MUTATED MRGPRF WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V12, binary
                  cls
clus                 0   1
  MRGPRF MUTATED     0   3
  MRGPRF WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRGPRF MUTATED      0    3
  MRGPRF WILD-TYPE   10  395
                        clus
vv                       MRGPRF MUTATED MRGPRF WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(534) Variable = ELL2 MUTATION ANALYSIS
D534V1, survival
                sevent
clus2              0   1
  ELL2 MUTATED    10   6
  ELL2 WILD-TYPE 328 210
  ELL2 MUTATED ELL2 WILD-TYPE 
            16            538 
  ELL2 MUTATED ELL2 WILD-TYPE 
             6            210 
$`ELL2 MUTATED`
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-A4QL 
       58.59        29.00         4.08         6.18        34.68        16.14 
TCGA-CD-A4MI TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HF-7132 
       11.77         8.05         6.02       105.07        11.44        77.29 
TCGA-HU-8602 TCGA-HU-A4H2 TCGA-RD-A7BW TCGA-VQ-A8P2 
       22.32        12.95         5.13        38.14 

$`ELL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ELL2 MUTATED ELL2 WILD-TYPE 
          4.08           0.00 
  ELL2 MUTATED ELL2 WILD-TYPE 
        105.07         122.30 
  ELL2 MUTATED ELL2 WILD-TYPE 
        14.545         13.565 
[1] "4.1 - 105.1 (14.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D534V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELL2 MUTATED         0        0        2        3         2         2
  ELL2 WILD-TYPE      10       20       44       28        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELL2 MUTATED           0          4          3          0        1         0
  ELL2 WILD-TYPE        29         80         59         39       42         4
D534V3, multiclass
            clus
vv           ELL2 MUTATED ELL2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              3             28
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            3             59
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ELL2 MUTATED       0   6   7   4
  ELL2 WILD-TYPE    54 129 254  98
D534V4, multiclass
       clus
vv      ELL2 MUTATED ELL2 WILD-TYPE
  T0+T1            0             54
  T2               6            129
  T3               7            254
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ELL2 MUTATED     6   8   0   3
  ELL2 WILD-TYPE 189 165  89  82
D534V5, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  N0            6            189
  N1            8            165
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V6, binary
                cls
clus               0   1
  ELL2 MUTATED    17   0
  ELL2 WILD-TYPE 465  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED     17    0
  ELL2 WILD-TYPE  465   38
   clus
vv  ELL2 MUTATED ELL2 WILD-TYPE
  0           17            465
  1            0             38
[1] 2 2
[1] FALSE
D534V7, binary
                cls
clus               0   1
  ELL2 MUTATED     9   8
  ELL2 WILD-TYPE 163 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      9    8
  ELL2 WILD-TYPE  163  398
        clus
vv       ELL2 MUTATED ELL2 WILD-TYPE
  FEMALE            9            163
  MALE              8            398
[1] 2 2
[1] FALSE
D534V8, binary
                cls
clus               0   1
  ELL2 MUTATED    13   3
  ELL2 WILD-TYPE 403  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED     13    3
  ELL2 WILD-TYPE  403   99
     clus
vv    ELL2 MUTATED ELL2 WILD-TYPE
  NO            13            403
  YES            3             99
[1] 2 2
[1] FALSE
D534V9, continuous
D534V10, continuous
[1] "Remove cluster labels:" "ELL2 MUTATED"          
clus
  ELL2 MUTATED ELL2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OW     TCGA-L5-A4OX 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" "ELL2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"ELL2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ELL2 MUTATED       3                         0
  ELL2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELL2 MUTATED                                           0    10
  ELL2 WILD-TYPE                                         1   347
D534V11, multiclass
                                           clus
vv                                          ELL2 MUTATED ELL2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V12, binary
                cls
clus               0   1
  ELL2 MUTATED     0  10
  ELL2 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      0   10
  ELL2 WILD-TYPE   10  388
                        clus
vv                       ELL2 MUTATED ELL2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(535) Variable = PCGF3 MUTATION ANALYSIS
D535V1, survival
                 sevent
clus2               0   1
  PCGF3 MUTATED     3   3
  PCGF3 WILD-TYPE 335 213
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              6             548 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              3             213 
$`PCGF3 MUTATED`
TCGA-BR-7703 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-A4YY TCGA-HU-A4H8 
       36.16        25.05        16.14         6.58        13.78        14.07 

$`PCGF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PCGF3 MUTATED PCGF3 WILD-TYPE 
           6.58            0.00 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
          36.16          122.30 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
         15.105          13.510 
[1] "6.6 - 36.2 (15.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D535V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCGF3 MUTATED         1        1        1        0         1         0
  PCGF3 WILD-TYPE       9       19       45       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCGF3 MUTATED           0          0          2          1        0         0
  PCGF3 WILD-TYPE        29         84         60         38       43         4
D535V3, multiclass
            clus
vv           PCGF3 MUTATED PCGF3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PCGF3 MUTATED       3   0   3   1
  PCGF3 WILD-TYPE    51 135 258 101
D535V4, multiclass
       clus
vv      PCGF3 MUTATED PCGF3 WILD-TYPE
  T0+T1             3              51
  T2                0             135
  T3                3             258
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PCGF3 MUTATED     2   2   0   3
  PCGF3 WILD-TYPE 193 171  89  82
D535V5, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V6, binary
                 cls
clus                0   1
  PCGF3 MUTATED     6   0
  PCGF3 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      6    0
  PCGF3 WILD-TYPE  476   38
   clus
vv  PCGF3 MUTATED PCGF3 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D535V7, binary
                 cls
clus                0   1
  PCGF3 MUTATED     2   5
  PCGF3 WILD-TYPE 170 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      2    5
  PCGF3 WILD-TYPE  170  401
        clus
vv       PCGF3 MUTATED PCGF3 WILD-TYPE
  FEMALE             2             170
  MALE               5             401
[1] 2 2
[1] FALSE
D535V8, binary
                 cls
clus                0   1
  PCGF3 MUTATED     6   1
  PCGF3 WILD-TYPE 410 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      6    1
  PCGF3 WILD-TYPE  410  101
     clus
vv    PCGF3 MUTATED PCGF3 WILD-TYPE
  NO              6             410
  YES             1             101
[1] 2 2
[1] FALSE
D535V9, continuous
D535V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PCGF3 MUTATED       2                         1
  PCGF3 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCGF3 MUTATED                                           0     4
  PCGF3 WILD-TYPE                                         1   353
D535V11, multiclass
                                           clus
vv                                          PCGF3 MUTATED PCGF3 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V12, binary
                 cls
clus                0   1
  PCGF3 MUTATED     0   7
  PCGF3 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      0    7
  PCGF3 WILD-TYPE   10  391
                        clus
vv                       PCGF3 MUTATED PCGF3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(536) Variable = RSF1 MUTATION ANALYSIS
D536V1, survival
                sevent
clus2              0   1
  RSF1 MUTATED    11   3
  RSF1 WILD-TYPE 327 213
  RSF1 MUTATED RSF1 WILD-TYPE 
            14            540 
  RSF1 MUTATED RSF1 WILD-TYPE 
             3            213 
$`RSF1 MUTATED`
TCGA-JY-A6FB TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 
       60.39         7.43        30.90        34.68        44.94        32.25 
TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4437 TCGA-FP-7916 TCGA-HU-A4G3 TCGA-HU-A4GX 
       31.96        15.95         8.05        14.07         5.59        20.25 
TCGA-HU-A4HD TCGA-IP-7968 
       33.40         2.53 

$`RSF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         6.97         4.64        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RSF1 MUTATED RSF1 WILD-TYPE 
          2.53           0.00 
  RSF1 MUTATED RSF1 WILD-TYPE 
         60.39         122.30 
  RSF1 MUTATED RSF1 WILD-TYPE 
        25.575         13.495 
[1] "2.5 - 60.4 (25.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D536V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RSF1 MUTATED         1        0        1        2         2         2
  RSF1 WILD-TYPE       9       20       45       29        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSF1 MUTATED           0          1          1          2        1         0
  RSF1 WILD-TYPE        29         83         61         37       42         4
D536V3, multiclass
            clus
vv           RSF1 MUTATED RSF1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RSF1 MUTATED       1   5   4   4
  RSF1 WILD-TYPE    53 130 257  98
D536V4, multiclass
       clus
vv      RSF1 MUTATED RSF1 WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RSF1 MUTATED     5   4   5   1
  RSF1 WILD-TYPE 190 169  84  84
D536V5, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  N0            5            190
  N1            4            169
  N2            5             84
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V6, binary
                cls
clus               0   1
  RSF1 MUTATED    13   1
  RSF1 WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED     13    1
  RSF1 WILD-TYPE  469   37
   clus
vv  RSF1 MUTATED RSF1 WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D536V7, binary
                cls
clus               0   1
  RSF1 MUTATED     7   9
  RSF1 WILD-TYPE 165 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      7    9
  RSF1 WILD-TYPE  165  397
        clus
vv       RSF1 MUTATED RSF1 WILD-TYPE
  FEMALE            7            165
  MALE              9            397
[1] 2 2
[1] FALSE
D536V8, binary
                cls
clus               0   1
  RSF1 MUTATED    13   0
  RSF1 WILD-TYPE 403 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED     13    0
  RSF1 WILD-TYPE  403  102
     clus
vv    RSF1 MUTATED RSF1 WILD-TYPE
  NO            13            403
  YES            0            102
[1] 2 2
[1] FALSE
D536V9, continuous
D536V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RSF1 MUTATED       5                         0
  RSF1 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RSF1 MUTATED                                           0     8
  RSF1 WILD-TYPE                                         1   349
D536V11, multiclass
                                           clus
vv                                          RSF1 MUTATED RSF1 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V12, binary
                cls
clus               0   1
  RSF1 MUTATED     0  12
  RSF1 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      0   12
  RSF1 WILD-TYPE   10  386
                        clus
vv                       RSF1 MUTATED RSF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(537) Variable = ARID1B MUTATION ANALYSIS
D537V1, survival
                  sevent
clus2                0   1
  ARID1B MUTATED    20  12
  ARID1B WILD-TYPE 318 204
  ARID1B MUTATED ARID1B WILD-TYPE 
              32              522 
  ARID1B MUTATED ARID1B WILD-TYPE 
              12              204 
$`ARID1B MUTATED`
TCGA-JY-A6FB TCGA-IG-A50L TCGA-IG-A97H TCGA-L5-A4OH TCGA-L5-A8NF TCGA-L5-A8NI 
       60.39         0.53        14.50        32.61         2.66        13.48 
TCGA-L5-A8NM TCGA-LN-A49S TCGA-R6-A6KZ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-BR-4184 
        7.76        13.15         5.06         8.12        33.70         6.97 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8361 
       30.90         9.34        34.68        32.25         8.05        31.10 
TCGA-BR-8591 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 
       28.14         0.53        16.14         9.01         6.02       105.07 
TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H3 
       65.10        11.08        22.32        22.68        20.25        29.00 
TCGA-VQ-A8DL TCGA-VQ-AA68 
        0.92        43.66 

$`ARID1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.75         3.02        55.50        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         1.55        18.31        28.11        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       29.59         9.60         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        19.04         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ARID1B MUTATED ARID1B WILD-TYPE 
            0.53             0.00 
  ARID1B MUTATED ARID1B WILD-TYPE 
          105.07           122.30 
  ARID1B MUTATED ARID1B WILD-TYPE 
           15.32            13.53 
[1] "0.5 - 105.1 (15.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D537V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1B MUTATED         2        0        1        1         6         4
  ARID1B WILD-TYPE       8       20       45       30        78        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1B MUTATED           1          2          3          6        3
  ARID1B WILD-TYPE        28         82         59         33       40
                  vv
clus               STAGE IVA
  ARID1B MUTATED           1
  ARID1B WILD-TYPE         3
D537V3, multiclass
            clus
vv           ARID1B MUTATED ARID1B WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              3               59
  STAGE IIIC              6               33
  STAGE IV                3               40
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ARID1B MUTATED       3   4  13  12
  ARID1B WILD-TYPE    51 131 248  90
D537V4, multiclass
       clus
vv      ARID1B MUTATED ARID1B WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                13              248
  T4                12               90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID1B MUTATED    11   9   5   6
  ARID1B WILD-TYPE 184 164  84  79
D537V5, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  N0             11              184
  N1              9              164
  N2              5               84
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V6, binary
                  cls
clus                 0   1
  ARID1B MUTATED    32   2
  ARID1B WILD-TYPE 450  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     32    2
  ARID1B WILD-TYPE  450   36
   clus
vv  ARID1B MUTATED ARID1B WILD-TYPE
  0             32              450
  1              2               36
[1] 2 2
[1] FALSE
D537V7, binary
                  cls
clus                 0   1
  ARID1B MUTATED    20  17
  ARID1B WILD-TYPE 152 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     20   17
  ARID1B WILD-TYPE  152  389
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE             20              152
  MALE               17              389
[1] 2 2
[1] FALSE
D537V8, binary
                  cls
clus                 0   1
  ARID1B MUTATED    23   3
  ARID1B WILD-TYPE 393  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     23    3
  ARID1B WILD-TYPE  393   99
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO              23              393
  YES              3               99
[1] 2 2
[1] FALSE
D537V9, continuous
D537V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID1B MUTATED       9                         1
  ARID1B WILD-TYPE   124                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1B MUTATED                                           0    23
  ARID1B WILD-TYPE                                         1   334
D537V11, multiclass
                                           clus
vv                                          ARID1B MUTATED ARID1B WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 23              334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V12, binary
                  cls
clus                 0   1
  ARID1B MUTATED     0  24
  ARID1B WILD-TYPE  10 374
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      0   24
  ARID1B WILD-TYPE   10  374
                        clus
vv                       ARID1B MUTATED ARID1B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             24              374
[1] 2 2
[1] FALSE

Clustering(538) Variable = TNK2 MUTATION ANALYSIS
D538V1, survival
                sevent
clus2              0   1
  TNK2 MUTATED    16   5
  TNK2 WILD-TYPE 322 211
  TNK2 MUTATED TNK2 WILD-TYPE 
            21            533 
  TNK2 MUTATED TNK2 WILD-TYPE 
             5            211 
$`TNK2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IC-A6RE TCGA-IG-A4P3 TCGA-L5-A8NS TCGA-BR-8078 
       19.99        21.99         7.69        18.64        13.41        29.59 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CG-5728 TCGA-D7-A4YT 
       31.27        25.05        31.96        20.42        65.10        14.27 
TCGA-D7-A4YV TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H3 
        5.92        26.47        22.32        22.68        20.25        29.00 
TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.73        19.04        38.14 

$`TNK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TNK2 MUTATED TNK2 WILD-TYPE 
          5.92           0.00 
  TNK2 MUTATED TNK2 WILD-TYPE 
          65.1          122.3 
  TNK2 MUTATED TNK2 WILD-TYPE 
         21.99          13.38 
[1] "5.9 - 65.1 (22.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.3"
D538V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNK2 MUTATED         0        0        4        0         0         7
  TNK2 WILD-TYPE      10       20       42       31        84        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNK2 MUTATED           0          3          0          5        2         0
  TNK2 WILD-TYPE        29         81         62         34       41         4
D538V3, multiclass
            clus
vv           TNK2 MUTATED TNK2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             7             76
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            5             34
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TNK2 MUTATED       2   6   5   9
  TNK2 WILD-TYPE    52 129 256  93
D538V4, multiclass
       clus
vv      TNK2 MUTATED TNK2 WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3               5            256
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TNK2 MUTATED     7   6   3   5
  TNK2 WILD-TYPE 188 167  86  80
D538V5, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  N0            7            188
  N1            6            167
  N2            3             86
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V6, binary
                cls
clus               0   1
  TNK2 MUTATED    18   2
  TNK2 WILD-TYPE 464  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     18    2
  TNK2 WILD-TYPE  464   36
   clus
vv  TNK2 MUTATED TNK2 WILD-TYPE
  0           18            464
  1            2             36
[1] 2 2
[1] FALSE
D538V7, binary
                cls
clus               0   1
  TNK2 MUTATED    14   8
  TNK2 WILD-TYPE 158 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     14    8
  TNK2 WILD-TYPE  158  398
        clus
vv       TNK2 MUTATED TNK2 WILD-TYPE
  FEMALE           14            158
  MALE              8            398
[1] 2 2
[1] FALSE
D538V8, binary
                cls
clus               0   1
  TNK2 MUTATED    16   3
  TNK2 WILD-TYPE 400  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     16    3
  TNK2 WILD-TYPE  400   99
     clus
vv    TNK2 MUTATED TNK2 WILD-TYPE
  NO            16            400
  YES            3             99
[1] 2 2
[1] FALSE
D538V9, continuous
D538V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TNK2 MUTATED       5                         0
  TNK2 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNK2 MUTATED                                           0    15
  TNK2 WILD-TYPE                                         1   342
D538V11, multiclass
                                           clus
vv                                          TNK2 MUTATED TNK2 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V12, binary
                cls
clus               0   1
  TNK2 MUTATED     0  17
  TNK2 WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED      0   17
  TNK2 WILD-TYPE   10  381
                        clus
vv                       TNK2 MUTATED TNK2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(539) Variable = ABCE1 MUTATION ANALYSIS
D539V1, survival
                 sevent
clus2               0   1
  ABCE1 MUTATED     6   4
  ABCE1 WILD-TYPE 332 212
  ABCE1 MUTATED ABCE1 WILD-TYPE 
             10             544 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
              4             212 
$`ABCE1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-8081 
       19.99         7.76        30.90         9.34        32.78        32.25 
TCGA-D7-A6EZ TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-IN-A6RI 
       20.32        22.68        20.25        18.38 

$`ABCE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ABCE1 MUTATED ABCE1 WILD-TYPE 
           7.76            0.00 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
          32.78          122.30 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
         20.285          13.495 
[1] "7.8 - 32.8 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D539V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCE1 MUTATED         1        0        1        0         1         4
  ABCE1 WILD-TYPE       9       20       45       31        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCE1 MUTATED           0          1          0          2        0         0
  ABCE1 WILD-TYPE        29         83         62         37       43         4
D539V3, multiclass
            clus
vv           ABCE1 MUTATED ABCE1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCE1 MUTATED       1   3   4   3
  ABCE1 WILD-TYPE    53 132 257  99
D539V4, multiclass
       clus
vv      ABCE1 MUTATED ABCE1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCE1 MUTATED     5   3   2   1
  ABCE1 WILD-TYPE 190 170  87  84
D539V5, multiclass
    clus
vv   ABCE1 MUTATED ABCE1 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V6, binary
                 cls
clus                0   1
  ABCE1 MUTATED    11   0
  ABCE1 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED     11    0
  ABCE1 WILD-TYPE  471   38
   clus
vv  ABCE1 MUTATED ABCE1 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D539V7, binary
                 cls
clus                0   1
  ABCE1 MUTATED     6   6
  ABCE1 WILD-TYPE 166 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED      6    6
  ABCE1 WILD-TYPE  166  400
        clus
vv       ABCE1 MUTATED ABCE1 WILD-TYPE
  FEMALE             6             166
  MALE               6             400
[1] 2 2
[1] FALSE
D539V8, binary
                 cls
clus                0   1
  ABCE1 MUTATED    11   0
  ABCE1 WILD-TYPE 405 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED     11    0
  ABCE1 WILD-TYPE  405  102
     clus
vv    ABCE1 MUTATED ABCE1 WILD-TYPE
  NO             11             405
  YES             0             102
[1] 2 2
[1] FALSE
D539V9, continuous
D539V10, continuous
[1] "Remove cluster labels:" "ABCE1 MUTATED"         
clus
  ABCE1 MUTATED ABCE1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" "ABCE1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ABCE1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCE1 MUTATED       2                         0
  ABCE1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCE1 MUTATED                                           0     9
  ABCE1 WILD-TYPE                                         1   348
D539V11, multiclass
                                           clus
vv                                          ABCE1 MUTATED ABCE1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V12, binary
                 cls
clus                0   1
  ABCE1 MUTATED     0   9
  ABCE1 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED      0    9
  ABCE1 WILD-TYPE   10  389
                        clus
vv                       ABCE1 MUTATED ABCE1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(540) Variable = PNMT MUTATION ANALYSIS
D540V1, survival
                sevent
clus2              0   1
  PNMT MUTATED     8   1
  PNMT WILD-TYPE 330 215
  PNMT MUTATED PNMT WILD-TYPE 
             9            545 
  PNMT MUTATED PNMT WILD-TYPE 
             1            215 
$`PNMT MUTATED`
TCGA-BR-7715 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-A4J7 TCGA-CG-4306 TCGA-CG-5721 
       33.63        32.25         6.18        32.52         1.02         6.02 
TCGA-HF-7132 TCGA-HU-A4GU TCGA-KB-A93J 
       77.29         6.58        36.95 

$`PNMT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        63.62         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PNMT MUTATED PNMT WILD-TYPE 
          1.02           0.00 
  PNMT MUTATED PNMT WILD-TYPE 
         77.29         122.30 
  PNMT MUTATED PNMT WILD-TYPE 
         32.25          13.55 
[1] "1.0 - 77.3 (32.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "4.7"
D540V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNMT MUTATED         1        0        0        2         2         3
  PNMT WILD-TYPE       9       20       46       29        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PNMT MUTATED           0          0          0          0        2         0
  PNMT WILD-TYPE        29         84         62         39       41         4
D540V3, multiclass
            clus
vv           PNMT MUTATED PNMT WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PNMT MUTATED       1   2   4   3
  PNMT WILD-TYPE    53 133 257  99
D540V4, multiclass
       clus
vv      PNMT MUTATED PNMT WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PNMT MUTATED     3   6   1   0
  PNMT WILD-TYPE 192 167  88  85
D540V5, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  N0            3            192
  N1            6            167
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V6, binary
                cls
clus               0   1
  PNMT MUTATED     9   1
  PNMT WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      9    1
  PNMT WILD-TYPE  473   37
   clus
vv  PNMT MUTATED PNMT WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D540V7, binary
                cls
clus               0   1
  PNMT MUTATED     2   9
  PNMT WILD-TYPE 170 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      2    9
  PNMT WILD-TYPE  170  397
        clus
vv       PNMT MUTATED PNMT WILD-TYPE
  FEMALE            2            170
  MALE              9            397
[1] 2 2
[1] FALSE
D540V8, binary
                cls
clus               0   1
  PNMT MUTATED     7   2
  PNMT WILD-TYPE 409 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      7    2
  PNMT WILD-TYPE  409  100
     clus
vv    PNMT MUTATED PNMT WILD-TYPE
  NO             7            409
  YES            2            100
[1] 2 2
[1] FALSE
D540V9, continuous
D540V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PNMT MUTATED       2                         1
  PNMT WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PNMT MUTATED                                           0     5
  PNMT WILD-TYPE                                         1   352
D540V11, multiclass
                                           clus
vv                                          PNMT MUTATED PNMT WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V12, binary
                cls
clus               0   1
  PNMT MUTATED     0   7
  PNMT WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      0    7
  PNMT WILD-TYPE   10  391
                        clus
vv                       PNMT MUTATED PNMT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(541) Variable = C8ORF46 MUTATION ANALYSIS
D541V1, survival
                   sevent
clus2                 0   1
  C8ORF46 MUTATED     4   4
  C8ORF46 WILD-TYPE 334 212
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
                8               546 
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
                4               212 
$`C8ORF46 MUTATED`
TCGA-L5-A8NQ TCGA-R6-A6L6 TCGA-B7-5818 TCGA-CD-8536 TCGA-CD-A4MI TCGA-D7-A6EY 
       21.37         7.04        11.70        12.43        11.77        11.44 
TCGA-HU-A4GT TCGA-HU-A4GX 
        6.51        20.25 

$`C8ORF46 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
             6.51              0.00 
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
            21.37            122.30 
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
           11.735            13.730 
[1] "6.5 - 21.4 (11.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.8"
D541V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C8ORF46 MUTATED         0        0        2        1         2         0
  C8ORF46 WILD-TYPE      10       20       44       30        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C8ORF46 MUTATED           0          1          1          1        0
  C8ORF46 WILD-TYPE        29         83         61         38       43
                   vv
clus                STAGE IVA
  C8ORF46 MUTATED           0
  C8ORF46 WILD-TYPE         4
D541V3, multiclass
            clus
vv           C8ORF46 MUTATED C8ORF46 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C8ORF46 MUTATED       0   3   4   1
  C8ORF46 WILD-TYPE    54 132 257 101
D541V4, multiclass
       clus
vv      C8ORF46 MUTATED C8ORF46 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  4               257
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C8ORF46 MUTATED     5   1   1   1
  C8ORF46 WILD-TYPE 190 172  88  84
D541V5, multiclass
    clus
vv   C8ORF46 MUTATED C8ORF46 WILD-TYPE
  N0               5               190
  N1               1               172
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V6, binary
                   cls
clus                  0   1
  C8ORF46 MUTATED     8   0
  C8ORF46 WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF46 MUTATED      8    0
  C8ORF46 WILD-TYPE  474   38
   clus
vv  C8ORF46 MUTATED C8ORF46 WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D541V7, binary
                   cls
clus                  0   1
  C8ORF46 MUTATED     3   6
  C8ORF46 WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF46 MUTATED      3    6
  C8ORF46 WILD-TYPE  169  400
        clus
vv       C8ORF46 MUTATED C8ORF46 WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D541V8, binary
                   cls
clus                  0   1
  C8ORF46 MUTATED     8   0
  C8ORF46 WILD-TYPE 408 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF46 MUTATED      8    0
  C8ORF46 WILD-TYPE  408  102
     clus
vv    C8ORF46 MUTATED C8ORF46 WILD-TYPE
  NO                8               408
  YES               0               102
[1] 2 2
[1] FALSE
D541V9, continuous
D541V10, continuous
[1] "Remove cluster labels:" "C8ORF46 MUTATED"       
clus
  C8ORF46 MUTATED C8ORF46 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" "C8ORF46 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C8ORF46 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C8ORF46 MUTATED       4                         0
  C8ORF46 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C8ORF46 MUTATED                                           0     4
  C8ORF46 WILD-TYPE                                         1   353
D541V11, multiclass
                                           clus
vv                                          C8ORF46 MUTATED C8ORF46 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V12, binary
                   cls
clus                  0   1
  C8ORF46 MUTATED     0   7
  C8ORF46 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF46 MUTATED      0    7
  C8ORF46 WILD-TYPE   10  391
                        clus
vv                       C8ORF46 MUTATED C8ORF46 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(542) Variable = NOX5 MUTATION ANALYSIS
D542V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED    10   6
  NOX5 WILD-TYPE 328 210
  NOX5 MUTATED NOX5 WILD-TYPE 
            16            538 
  NOX5 MUTATED NOX5 WILD-TYPE 
             6            210 
$`NOX5 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8361 
        6.97         9.67        19.33        11.44        32.25        31.10 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-A4YV TCGA-F1-6874 
       31.96        16.14        15.95         6.02         5.92        14.47 
TCGA-HU-8602 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-MX-A5UJ 
       22.32        20.25        14.07        19.73 

$`NOX5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NOX5 MUTATED NOX5 WILD-TYPE 
          5.92           0.00 
  NOX5 MUTATED NOX5 WILD-TYPE 
         32.25         122.30 
  NOX5 MUTATED NOX5 WILD-TYPE 
        16.045         13.495 
[1] "5.9 - 32.2 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D542V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOX5 MUTATED         0        0        2        1         0         5
  NOX5 WILD-TYPE      10       20       44       30        84        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOX5 MUTATED           0          2          1          3        2         0
  NOX5 WILD-TYPE        29         82         61         36       41         4
D542V3, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NOX5 MUTATED       1   3   5   7
  NOX5 WILD-TYPE    53 132 256  95
D542V4, multiclass
       clus
vv      NOX5 MUTATED NOX5 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               5            256
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NOX5 MUTATED     3   6   5   2
  NOX5 WILD-TYPE 192 167  84  83
D542V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            3            192
  N1            6            167
  N2            5             84
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V6, binary
                cls
clus               0   1
  NOX5 MUTATED    15   1
  NOX5 WILD-TYPE 467  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     15    1
  NOX5 WILD-TYPE  467   37
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0           15            467
  1            1             37
[1] 2 2
[1] FALSE
D542V7, binary
                cls
clus               0   1
  NOX5 MUTATED    10   7
  NOX5 WILD-TYPE 162 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     10    7
  NOX5 WILD-TYPE  162  399
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE           10            162
  MALE              7            399
[1] 2 2
[1] FALSE
D542V8, binary
                cls
clus               0   1
  NOX5 MUTATED    17   0
  NOX5 WILD-TYPE 399 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     17    0
  NOX5 WILD-TYPE  399  102
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO            17            399
  YES            0            102
[1] 2 2
[1] FALSE
D542V9, continuous
D542V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOX5 MUTATED       4                         0
  NOX5 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOX5 MUTATED                                           0    11
  NOX5 WILD-TYPE                                         1   346
D542V11, multiclass
                                           clus
vv                                          NOX5 MUTATED NOX5 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V12, binary
                cls
clus               0   1
  NOX5 MUTATED     0  15
  NOX5 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      0   15
  NOX5 WILD-TYPE   10  383
                        clus
vv                       NOX5 MUTATED NOX5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(543) Variable = SGK3 MUTATION ANALYSIS
D543V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     4   2
  SGK3 WILD-TYPE 334 214
  SGK3 MUTATED SGK3 WILD-TYPE 
             6            548 
  SGK3 MUTATED SGK3 WILD-TYPE 
             2            214 
$`SGK3 MUTATED`
TCGA-L5-A4OR TCGA-L5-A88S TCGA-BR-4184 TCGA-BR-8372 TCGA-BR-8591 TCGA-HU-A4GU 
        3.16        15.48         6.97        31.27        28.14         6.58 

$`SGK3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SGK3 MUTATED SGK3 WILD-TYPE 
          3.16           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         31.27         122.30 
  SGK3 MUTATED SGK3 WILD-TYPE 
        11.225         13.565 
[1] "3.2 - 31.3 (11.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D543V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGK3 MUTATED         0        1        1        0         0         2
  SGK3 WILD-TYPE      10       19       45       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGK3 MUTATED           0          2          0          2        0         0
  SGK3 WILD-TYPE        29         82         62         37       43         4
D543V3, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SGK3 MUTATED       1   0   3   4
  SGK3 WILD-TYPE    53 135 258  98
D543V4, multiclass
       clus
vv      SGK3 MUTATED SGK3 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               3            258
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SGK3 MUTATED     4   2   0   2
  SGK3 WILD-TYPE 191 171  89  83
D543V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            4            191
  N1            2            171
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V6, binary
                cls
clus               0   1
  SGK3 MUTATED     6   0
  SGK3 WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      6    0
  SGK3 WILD-TYPE  476   38
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D543V7, binary
                cls
clus               0   1
  SGK3 MUTATED     2   7
  SGK3 WILD-TYPE 170 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      2    7
  SGK3 WILD-TYPE  170  399
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  FEMALE            2            170
  MALE              7            399
[1] 2 2
[1] FALSE
D543V8, binary
                cls
clus               0   1
  SGK3 MUTATED     7   0
  SGK3 WILD-TYPE 409 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      7    0
  SGK3 WILD-TYPE  409  102
     clus
vv    SGK3 MUTATED SGK3 WILD-TYPE
  NO             7            409
  YES            0            102
[1] 2 2
[1] FALSE
D543V9, continuous
D543V10, continuous
[1] "Remove cluster labels:" "SGK3 MUTATED"          
clus
  SGK3 MUTATED SGK3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" "SGK3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"SGK3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SGK3 MUTATED       1                         0
  SGK3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGK3 MUTATED                                           0     8
  SGK3 WILD-TYPE                                         1   349
D543V11, multiclass
                                           clus
vv                                          SGK3 MUTATED SGK3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V12, binary
                cls
clus               0   1
  SGK3 MUTATED     0   7
  SGK3 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      0    7
  SGK3 WILD-TYPE   10  391
                        clus
vv                       SGK3 MUTATED SGK3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(544) Variable = ZFC3H1 MUTATION ANALYSIS
D544V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    13   7
  ZFC3H1 WILD-TYPE 325 209
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              20              534 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               7              209 
$`ZFC3H1 MUTATED`
TCGA-CG-4475 TCGA-IG-A50L TCGA-L5-A88W TCGA-L5-A8NF TCGA-LN-A49L TCGA-LN-A7HW 
       22.98         0.53        25.12         2.66        10.45        12.00 
TCGA-VR-AA7I TCGA-BR-4187 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 
       15.91         4.64        34.68        31.10         1.12        31.96 
TCGA-BR-A4CQ TCGA-CD-8530 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-HU-A4GN 
       34.98        12.39         6.58         1.02         6.02        29.98 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`ZFC3H1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        21.99        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
            0.53             0.00 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           38.14           122.30 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
          14.150           13.565 
[1] "0.5 - 38.1 (14.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D544V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFC3H1 MUTATED         0        0        1        1         7         1
  ZFC3H1 WILD-TYPE      10       20       45       30        77        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           1          4          0          2        3
  ZFC3H1 WILD-TYPE        28         80         62         37       40
                  vv
clus               STAGE IVA
  ZFC3H1 MUTATED           1
  ZFC3H1 WILD-TYPE         3
D544V3, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               7               77
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZFC3H1 MUTATED       1   4   8   8
  ZFC3H1 WILD-TYPE    53 131 253  94
D544V4, multiclass
       clus
vv      ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 8              253
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZFC3H1 MUTATED    11   6   4   0
  ZFC3H1 WILD-TYPE 184 167  85  85
D544V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0             11              184
  N1              6              167
  N2              4               85
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V6, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    18   3
  ZFC3H1 WILD-TYPE 464  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     18    3
  ZFC3H1 WILD-TYPE  464   35
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             18              464
  1              3               35
[1] 2 2
[1] FALSE
D544V7, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     6  16
  ZFC3H1 WILD-TYPE 166 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      6   16
  ZFC3H1 WILD-TYPE  166  390
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  FEMALE              6              166
  MALE               16              390
[1] 2 2
[1] FALSE
D544V8, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    15   4
  ZFC3H1 WILD-TYPE 401  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     15    4
  ZFC3H1 WILD-TYPE  401   98
     clus
vv    ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  NO              15              401
  YES              4               98
[1] 2 2
[1] FALSE
D544V9, continuous
D544V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZFC3H1 MUTATED       8                         0
  ZFC3H1 WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFC3H1 MUTATED                                           0    11
  ZFC3H1 WILD-TYPE                                         1   346
D544V11, multiclass
                                           clus
vv                                          ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V12, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     0  15
  ZFC3H1 WILD-TYPE  10 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      0   15
  ZFC3H1 WILD-TYPE   10  383
                        clus
vv                       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(545) Variable = TAS2R42 MUTATION ANALYSIS
D545V1, survival
                   sevent
clus2                 0   1
  TAS2R42 MUTATED     4   2
  TAS2R42 WILD-TYPE 334 214
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               548 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                2               214 
$`TAS2R42 MUTATED`
TCGA-BR-8081 TCGA-BR-8363 TCGA-D7-A6EY TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H2 
       32.25         0.26        11.44        22.75        11.77        12.95 

$`TAS2R42 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
             0.26              0.00 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
            32.25            122.30 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
            12.36             13.63 
[1] "0.3 - 32.2 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D545V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAS2R42 MUTATED         0        1        1        0         0         2
  TAS2R42 WILD-TYPE      10       19       45       31        84        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R42 MUTATED           0          0          2          0        0
  TAS2R42 WILD-TYPE        29         84         60         39       43
                   vv
clus                STAGE IVA
  TAS2R42 MUTATED           0
  TAS2R42 WILD-TYPE         4
D545V3, multiclass
            clus
vv           TAS2R42 MUTATED TAS2R42 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TAS2R42 MUTATED       1   1   3   1
  TAS2R42 WILD-TYPE    53 134 258 101
D545V4, multiclass
       clus
vv      TAS2R42 MUTATED TAS2R42 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TAS2R42 MUTATED     3   1   0   2
  TAS2R42 WILD-TYPE 192 172  89  83
D545V5, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  N0               3               192
  N1               1               172
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V6, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     6   0
  TAS2R42 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      6    0
  TAS2R42 WILD-TYPE  476   38
   clus
vv  TAS2R42 MUTATED TAS2R42 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D545V7, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     4   2
  TAS2R42 WILD-TYPE 168 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      4    2
  TAS2R42 WILD-TYPE  168  404
        clus
vv       TAS2R42 MUTATED TAS2R42 WILD-TYPE
  FEMALE               4               168
  MALE                 2               404
[1] 2 2
[1] FALSE
D545V8, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     6   0
  TAS2R42 WILD-TYPE 410 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      6    0
  TAS2R42 WILD-TYPE  410  102
     clus
vv    TAS2R42 MUTATED TAS2R42 WILD-TYPE
  NO                6               410
  YES               0               102
[1] 2 2
[1] FALSE
D545V9, continuous
D545V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TAS2R42 MUTATED       3                         0
  TAS2R42 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAS2R42 MUTATED                                           0     3
  TAS2R42 WILD-TYPE                                         1   354
D545V11, multiclass
                                           clus
vv                                          TAS2R42 MUTATED TAS2R42 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V12, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     0   6
  TAS2R42 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      0    6
  TAS2R42 WILD-TYPE   10  392
                        clus
vv                       TAS2R42 MUTATED TAS2R42 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(546) Variable = CDKL3 MUTATION ANALYSIS
D546V1, survival
                 sevent
clus2               0   1
  CDKL3 MUTATED     6   2
  CDKL3 WILD-TYPE 332 214
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              8             546 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              2             214 
$`CDKL3 MUTATED`
TCGA-LN-A49R TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8589 TCGA-CG-5721 TCGA-CG-5723 
       13.38         6.97        32.78        27.12         6.02       105.07 
TCGA-D7-A6EY TCGA-VQ-A8P2 
       11.44        38.14 

$`CDKL3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CDKL3 MUTATED CDKL3 WILD-TYPE 
           6.02            0.00 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
         105.07          122.30 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
         20.250          13.565 
[1] "6.0 - 105.1 (20.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D546V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKL3 MUTATED         0        0        0        1         1         0
  CDKL3 WILD-TYPE      10       20       46       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDKL3 MUTATED           1          2          2          0        1         0
  CDKL3 WILD-TYPE        28         82         60         39       42         4
D546V3, multiclass
            clus
vv           CDKL3 MUTATED CDKL3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CDKL3 MUTATED       0   1   4   3
  CDKL3 WILD-TYPE    54 134 257  99
D546V4, multiclass
       clus
vv      CDKL3 MUTATED CDKL3 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CDKL3 MUTATED     1   6   0   1
  CDKL3 WILD-TYPE 194 167  89  84
D546V5, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  N0             1             194
  N1             6             167
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V6, binary
                 cls
clus                0   1
  CDKL3 MUTATED     7   0
  CDKL3 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      7    0
  CDKL3 WILD-TYPE  475   38
   clus
vv  CDKL3 MUTATED CDKL3 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D546V7, binary
                 cls
clus                0   1
  CDKL3 MUTATED     2   6
  CDKL3 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      2    6
  CDKL3 WILD-TYPE  170  400
        clus
vv       CDKL3 MUTATED CDKL3 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D546V8, binary
                 cls
clus                0   1
  CDKL3 MUTATED     6   2
  CDKL3 WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      6    2
  CDKL3 WILD-TYPE  410  100
     clus
vv    CDKL3 MUTATED CDKL3 WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D546V9, continuous
[1] "Remove cluster labels:" "CDKL3 MUTATED"         
clus
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
D546V10, continuous
[1] "Remove cluster labels:" "CDKL3 MUTATED"         
clus
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49S      TCGA-LN-A49U 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" "CDKL3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CDKL3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDKL3 MUTATED       1                         0
  CDKL3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKL3 MUTATED                                           0     5
  CDKL3 WILD-TYPE                                         1   352
D546V11, multiclass
                                           clus
vv                                          CDKL3 MUTATED CDKL3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V12, binary
                 cls
clus                0   1
  CDKL3 MUTATED     0   5
  CDKL3 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      0    5
  CDKL3 WILD-TYPE   10  393
                        clus
vv                       CDKL3 MUTATED CDKL3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(547) Variable = USP21 MUTATION ANALYSIS
D547V1, survival
                 sevent
clus2               0   1
  USP21 MUTATED     9   6
  USP21 WILD-TYPE 329 210
  USP21 MUTATED USP21 WILD-TYPE 
             15             539 
  USP21 MUTATED USP21 WILD-TYPE 
              6             210 
$`USP21 MUTATED`
TCGA-L5-A4OU TCGA-LN-A4A9 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 
       29.00        11.54        26.70         6.97         9.34         9.67 
TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4466 TCGA-CG-5718 
       44.94        31.27         1.12        16.14        18.97        36.00 
TCGA-D7-A74A TCGA-F1-6874 TCGA-FP-A4BE 
       19.96        14.47        11.08 

$`USP21 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         4.08         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  USP21 MUTATED USP21 WILD-TYPE 
           1.12            0.00 
  USP21 MUTATED USP21 WILD-TYPE 
          44.94          122.30 
  USP21 MUTATED USP21 WILD-TYPE 
          16.14           13.51 
[1] "1.1 - 44.9 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D547V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP21 MUTATED         0        0        2        1         5         1
  USP21 WILD-TYPE      10       20       44       30        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP21 MUTATED           0          2          1          1        0         0
  USP21 WILD-TYPE        29         82         61         38       43         4
D547V3, multiclass
            clus
vv           USP21 MUTATED USP21 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP21 MUTATED       0   4   7   2
  USP21 WILD-TYPE    54 131 254 100
D547V4, multiclass
       clus
vv      USP21 MUTATED USP21 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                7             254
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP21 MUTATED     8   3   1   2
  USP21 WILD-TYPE 187 170  88  83
D547V5, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  N0             8             187
  N1             3             170
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V6, binary
                 cls
clus                0   1
  USP21 MUTATED    14   0
  USP21 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED     14    0
  USP21 WILD-TYPE  468   38
   clus
vv  USP21 MUTATED USP21 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D547V7, binary
                 cls
clus                0   1
  USP21 MUTATED     8   7
  USP21 WILD-TYPE 164 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      8    7
  USP21 WILD-TYPE  164  399
        clus
vv       USP21 MUTATED USP21 WILD-TYPE
  FEMALE             8             164
  MALE               7             399
[1] 2 2
[1] FALSE
D547V8, binary
                 cls
clus                0   1
  USP21 MUTATED    14   1
  USP21 WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED     14    1
  USP21 WILD-TYPE  402  101
     clus
vv    USP21 MUTATED USP21 WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D547V9, continuous
[1] "Remove cluster labels:" "USP21 MUTATED"         
clus
  USP21 MUTATED USP21 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
D547V10, continuous
[1] "Remove cluster labels:" "USP21 MUTATED"         
clus
  USP21 MUTATED USP21 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OW      TCGA-L5-A4OX 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" "USP21 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP21 MUTATED       1                         1
  USP21 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP21 MUTATED                                           0    11
  USP21 WILD-TYPE                                         1   346
D547V11, multiclass
                                           clus
vv                                          USP21 MUTATED USP21 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V12, binary
                 cls
clus                0   1
  USP21 MUTATED     0  12
  USP21 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      0   12
  USP21 WILD-TYPE   10  386
                        clus
vv                       USP21 MUTATED USP21 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(548) Variable = SERPINB12 MUTATION ANALYSIS
D548V1, survival
                     sevent
clus2                   0   1
  SERPINB12 MUTATED     5   2
  SERPINB12 WILD-TYPE 333 214
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  7                 547 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  2                 214 
$`SERPINB12 MUTATED`
TCGA-2H-A9GJ TCGA-LN-A7HX TCGA-VR-A8EZ TCGA-BR-8286 TCGA-BR-8487 TCGA-HU-A4GH 
       58.55        12.23        18.18        29.42         1.12        11.77 
TCGA-HU-A4GN 
       29.98 

$`SERPINB12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       29.59         9.60        32.25         8.05         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
               1.12                0.00 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
              58.55              122.30 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
              18.18               13.55 
[1] "1.1 - 58.5 (18.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D548V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB12 MUTATED         1        1        0        1         3         0
  SERPINB12 WILD-TYPE       9       19       46       30        81        83
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB12 MUTATED           0          1          0          1        0
  SERPINB12 WILD-TYPE        29         83         62         38       43
                     vv
clus                  STAGE IVA
  SERPINB12 MUTATED           0
  SERPINB12 WILD-TYPE         4
D548V3, multiclass
            clus
vv           SERPINB12 MUTATED SERPINB12 WILD-TYPE
  STAGE I                    1                   9
  STAGE IA                   1                  19
  STAGE IB                   0                  46
  STAGE II                   1                  30
  STAGE IIA                  3                  81
  STAGE IIB                  0                  83
  STAGE III                  0                  29
  STAGE IIIA                 1                  83
  STAGE IIIB                 0                  62
  STAGE IIIC                 1                  38
  STAGE IV                   0                  43
  STAGE IVA                  0                   4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  SERPINB12 MUTATED       2   3   3   1
  SERPINB12 WILD-TYPE    52 132 258 101
D548V4, multiclass
       clus
vv      SERPINB12 MUTATED SERPINB12 WILD-TYPE
  T0+T1                 2                  52
  T2                    3                 132
  T3                    3                 258
  T4                    1                 101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  SERPINB12 MUTATED     6   1   0   1
  SERPINB12 WILD-TYPE 189 172  89  84
D548V5, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  N0                 6                 189
  N1                 1                 172
  N2                 0                  89
  N3                 1                  84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V6, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     9   0
  SERPINB12 WILD-TYPE 473  38
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      9    0
  SERPINB12 WILD-TYPE  473   38
   clus
vv  SERPINB12 MUTATED SERPINB12 WILD-TYPE
  0                 9                 473
  1                 0                  38
[1] 2 2
[1] FALSE
D548V7, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     3   6
  SERPINB12 WILD-TYPE 169 400
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      3    6
  SERPINB12 WILD-TYPE  169  400
        clus
vv       SERPINB12 MUTATED SERPINB12 WILD-TYPE
  FEMALE                 3                 169
  MALE                   6                 400
[1] 2 2
[1] FALSE
D548V8, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     6   1
  SERPINB12 WILD-TYPE 410 101
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      6    1
  SERPINB12 WILD-TYPE  410  101
     clus
vv    SERPINB12 MUTATED SERPINB12 WILD-TYPE
  NO                  6                 410
  YES                 1                 101
[1] 2 2
[1] FALSE
D548V9, continuous
[1] "Remove cluster labels:" "SERPINB12 MUTATED"     
clus
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  2                  66 
         TCGA-IG-A3I8          TCGA-IG-A3QL          TCGA-IG-A3Y9 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A3YA          TCGA-IG-A3YB          TCGA-IG-A3YC 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A51D          TCGA-IG-A5S3          TCGA-IG-A7DP 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-KH-A6WC          TCGA-LN-A49K          TCGA-LN-A49L 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49M          TCGA-LN-A49N          TCGA-LN-A49O 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49P          TCGA-LN-A49R          TCGA-LN-A49S 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49U          TCGA-LN-A49V          TCGA-LN-A49W 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49X          TCGA-LN-A49Y          TCGA-LN-A4A1 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A4A2          TCGA-LN-A4A3          TCGA-LN-A4A4 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A4A5          TCGA-LN-A4A6          TCGA-LN-A4A8 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A4A9          TCGA-LN-A4MQ          TCGA-LN-A4MR 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A5U5          TCGA-LN-A5U6          TCGA-LN-A5U7 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A7HV          TCGA-LN-A7HW          TCGA-LN-A7HY 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A7HZ          TCGA-V5-A7RB          TCGA-V5-A7RC 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-V5-A7RE          TCGA-V5-AASV          TCGA-V5-AASW 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-V5-AASX          TCGA-VR-A8EO          TCGA-VR-A8EP 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-A8EQ          TCGA-VR-A8ER          TCGA-VR-A8ET 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-A8EU          TCGA-VR-A8EW          TCGA-VR-A8EX 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-A8EY          TCGA-VR-A8Q7          TCGA-VR-AA4D 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-AA4G          TCGA-VR-AA7B          TCGA-VR-AA7D 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-AA7I          TCGA-XP-A8T6          TCGA-XP-A8T7 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-XP-A8T8          TCGA-Z6-A8JD          TCGA-Z6-A8JE 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
D548V10, continuous
[1] "Remove cluster labels:" "SERPINB12 MUTATED"     
clus
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  2                  96 
         TCGA-IC-A6RF          TCGA-L5-A43I          TCGA-L5-A43J 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A4OE          TCGA-L5-A4OG          TCGA-L5-A4OI 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A88T          TCGA-L5-A88Y          TCGA-L5-A8NG 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A8NT          TCGA-Q9-A6FU          TCGA-IC-A6RE 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A3QL          TCGA-IG-A3Y9          TCGA-IG-A3YA 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A3YC          TCGA-IG-A4P3          TCGA-IG-A4QT 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A50L          TCGA-IG-A5B8          TCGA-IG-A6QS 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-IG-A8O2          TCGA-IG-A97H          TCGA-JY-A6FA 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-JY-A6FE          TCGA-JY-A6FG          TCGA-JY-A6FH 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-KH-A6WC          TCGA-L5-A43C          TCGA-L5-A43E 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A43H          TCGA-L5-A4OH          TCGA-L5-A4OM 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A4ON          TCGA-L5-A4OO          TCGA-L5-A4OP 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A4OQ          TCGA-L5-A4OT          TCGA-L5-A4OU 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A4OW          TCGA-L5-A4OX          TCGA-L5-A88S 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A88V          TCGA-L5-A893          TCGA-L5-A8NE 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A8NF          TCGA-L5-A8NK          TCGA-L5-A8NN 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A8NQ          TCGA-L5-A8NR          TCGA-L5-A8NS 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-L5-A8NW          TCGA-LN-A49O          TCGA-LN-A49P 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49R          TCGA-LN-A49S          TCGA-LN-A49U 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A49V          TCGA-LN-A49W          TCGA-LN-A4A3 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A4A6          TCGA-LN-A4A9          TCGA-LN-A5U6 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A5U7          TCGA-LN-A7HV          TCGA-LN-A7HW 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-LN-A7HZ          TCGA-LN-A8HZ          TCGA-LN-A8I0 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-M9-A5M8          TCGA-Q9-A6FW          TCGA-R6-A6DN 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-R6-A6L4          TCGA-R6-A6XQ          TCGA-R6-A6Y2 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-R6-A8W5          TCGA-R6-A8W8          TCGA-R6-A8WC 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-RE-A7BO          TCGA-V5-A7RB          TCGA-V5-A7RC 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-V5-AASV          TCGA-VR-A8EP          TCGA-VR-A8ER 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-A8EU          TCGA-VR-A8EW          TCGA-VR-A8EX 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-A8Q7          TCGA-VR-AA4G          TCGA-VR-AA7D 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-VR-AA7I          TCGA-X8-AAAR          TCGA-XP-A8T6 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
         TCGA-XP-A8T7          TCGA-XP-A8T8          TCGA-Z6-AAPN 
"SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" "SERPINB12 WILD-TYPE" 
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB12 MUTATED       3                         0
  SERPINB12 WILD-TYPE   130                        14
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB12 MUTATED                                           0     5
  SERPINB12 WILD-TYPE                                         1   352
D548V11, multiclass
                                           clus
vv                                          SERPINB12 MUTATED
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     5
                                           clus
vv                                          SERPINB12 WILD-TYPE
  ASIAN                                                     130
  BLACK OR AFRICAN AMERICAN                                  14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V12, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     0   7
  SERPINB12 WILD-TYPE  10 391
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      0    7
  SERPINB12 WILD-TYPE   10  391
                        clus
vv                       SERPINB12 MUTATED SERPINB12 WILD-TYPE
  HISPANIC OR LATINO                     0                  10
  NOT HISPANIC OR LATINO                 7                 391
[1] 2 2
[1] FALSE

Clustering(549) Variable = GCG MUTATION ANALYSIS
D549V1, survival
               sevent
clus2             0   1
  GCG MUTATED     9   1
  GCG WILD-TYPE 329 215
  GCG MUTATED GCG WILD-TYPE 
           10           544 
  GCG MUTATED GCG WILD-TYPE 
            1           215 
$`GCG MUTATED`
TCGA-S8-A6BV TCGA-L5-A88Z TCGA-Z6-A8JD TCGA-B7-5816 TCGA-BR-6706 TCGA-BR-8487 
       20.02         7.40         3.42        26.70        18.05         1.12 
TCGA-BR-8680 TCGA-CG-5721 TCGA-VQ-A8DT TCGA-VQ-A8P2 
       31.96         6.02        48.79        38.14 

$`GCG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GCG MUTATED GCG WILD-TYPE 
         1.12          0.00 
  GCG MUTATED GCG WILD-TYPE 
        48.79        122.30 
  GCG MUTATED GCG WILD-TYPE 
       19.035        13.530 
[1] "1.1 - 48.8 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.3"
D549V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCG MUTATED         0        0        0        0         2         2
  GCG WILD-TYPE      10       20       46       31        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCG MUTATED           0          3          1          0        2         0
  GCG WILD-TYPE        29         81         61         39       41         4
D549V3, multiclass
            clus
vv           GCG MUTATED GCG WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           3            81
  STAGE IIIB           1            61
  STAGE IIIC           0            39
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  GCG MUTATED       1   0   5   4
  GCG WILD-TYPE    53 135 256  98
D549V4, multiclass
       clus
vv      GCG MUTATED GCG WILD-TYPE
  T0+T1           1            53
  T2              0           135
  T3              5           256
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  GCG MUTATED     3   5   1   1
  GCG WILD-TYPE 192 168  88  84
D549V5, multiclass
    clus
vv   GCG MUTATED GCG WILD-TYPE
  N0           3           192
  N1           5           168
  N2           1            88
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V6, binary
               cls
clus              0   1
  GCG MUTATED     8   1
  GCG WILD-TYPE 474  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      8    1
  GCG WILD-TYPE  474   37
   clus
vv  GCG MUTATED GCG WILD-TYPE
  0           8           474
  1           1            37
[1] 2 2
[1] FALSE
D549V7, binary
               cls
clus              0   1
  GCG MUTATED     3   7
  GCG WILD-TYPE 169 399
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      3    7
  GCG WILD-TYPE  169  399
        clus
vv       GCG MUTATED GCG WILD-TYPE
  FEMALE           3           169
  MALE             7           399
[1] 2 2
[1] FALSE
D549V8, binary
               cls
clus              0   1
  GCG MUTATED     8   2
  GCG WILD-TYPE 408 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      8    2
  GCG WILD-TYPE  408  100
     clus
vv    GCG MUTATED GCG WILD-TYPE
  NO            8           408
  YES           2           100
[1] 2 2
[1] FALSE
D549V9, continuous
[1] "Remove cluster labels:" "GCG MUTATED"           
clus
  GCG MUTATED GCG WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-V5-AASW    TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-VR-A8ER    TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-VR-A8EY    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-VR-AA7B    TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7 
"GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" "GCG WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-A8JE 
"GCG WILD-TYPE" "GCG WILD-TYPE" 
D549V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  GCG MUTATED       1                         0
  GCG WILD-TYPE   132                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCG MUTATED                                           0     7
  GCG WILD-TYPE                                         1   350
D549V11, multiclass
                                           clus
vv                                          GCG MUTATED GCG WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V12, binary
               cls
clus              0   1
  GCG MUTATED     0   6
  GCG WILD-TYPE  10 392
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      0    6
  GCG WILD-TYPE   10  392
                        clus
vv                       GCG MUTATED GCG WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           6           392
[1] 2 2
[1] FALSE

Clustering(550) Variable = DYRK4 MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  DYRK4 MUTATED     6   4
  DYRK4 WILD-TYPE 332 212
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             10             544 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              4             212 
$`DYRK4 MUTATED`
TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-L5-A4OR TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8361 
       18.64        23.41         3.16         9.34        29.59        31.10 
TCGA-BR-8680 TCGA-D7-A4YV TCGA-HF-7132 TCGA-HU-A4H3 
       31.96         5.92        77.29        29.00 

$`DYRK4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DYRK4 MUTATED DYRK4 WILD-TYPE 
           3.16            0.00 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          77.29          122.30 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
         26.205          13.510 
[1] "3.2 - 77.3 (26.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYRK4 MUTATED         0        1        0        1         0         4
  DYRK4 WILD-TYPE      10       19       46       30        84        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DYRK4 MUTATED           0          0          0          2        1         0
  DYRK4 WILD-TYPE        29         84         62         37       42         4
D550V3, multiclass
            clus
vv           DYRK4 MUTATED DYRK4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DYRK4 MUTATED       2   2   2   4
  DYRK4 WILD-TYPE    52 133 259  98
D550V4, multiclass
       clus
vv      DYRK4 MUTATED DYRK4 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                2             259
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DYRK4 MUTATED     3   4   2   1
  DYRK4 WILD-TYPE 192 169  87  84
D550V5, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  N0             3             192
  N1             4             169
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V6, binary
                 cls
clus                0   1
  DYRK4 MUTATED     9   1
  DYRK4 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      9    1
  DYRK4 WILD-TYPE  473   37
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D550V7, binary
                 cls
clus                0   1
  DYRK4 MUTATED     6   5
  DYRK4 WILD-TYPE 166 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      6    5
  DYRK4 WILD-TYPE  166  401
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  FEMALE             6             166
  MALE               5             401
[1] 2 2
[1] FALSE
D550V8, binary
                 cls
clus                0   1
  DYRK4 MUTATED     7   2
  DYRK4 WILD-TYPE 409 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      7    2
  DYRK4 WILD-TYPE  409  100
     clus
vv    DYRK4 MUTATED DYRK4 WILD-TYPE
  NO              7             409
  YES             2             100
[1] 2 2
[1] FALSE
D550V9, continuous
[1] "Remove cluster labels:" "DYRK4 MUTATED"         
clus
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A7DP 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
D550V10, continuous
[1] "Remove cluster labels:" "DYRK4 MUTATED"         
clus
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"DYRK4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DYRK4 MUTATED       2                         0
  DYRK4 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYRK4 MUTATED                                           0     8
  DYRK4 WILD-TYPE                                         1   349
D550V11, multiclass
                                           clus
vv                                          DYRK4 MUTATED DYRK4 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V12, binary
                 cls
clus                0   1
  DYRK4 MUTATED     0   9
  DYRK4 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      0    9
  DYRK4 WILD-TYPE   10  389
                        clus
vv                       DYRK4 MUTATED DYRK4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(551) Variable = LINGO4 MUTATION ANALYSIS
D551V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     6   4
  LINGO4 WILD-TYPE 332 212
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              544 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               4              212 
$`LINGO4 MUTATED`
TCGA-L5-A8NS TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-CD-A489 
       13.41         6.97        34.68        35.84        32.25        11.31 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GT 
        5.92        11.08        26.47         6.51 

$`LINGO4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        12.30        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  LINGO4 MUTATED LINGO4 WILD-TYPE 
            5.92             0.00 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           35.84           122.30 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           12.36            13.63 
[1] "5.9 - 35.8 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D551V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LINGO4 MUTATED         0        0        2        0         5         3
  LINGO4 WILD-TYPE      10       20       44       31        79        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           0          1          0          0        1
  LINGO4 WILD-TYPE        29         83         62         39       42
                  vv
clus               STAGE IVA
  LINGO4 MUTATED           0
  LINGO4 WILD-TYPE         4
D551V3, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  LINGO4 MUTATED       0   2   8   2
  LINGO4 WILD-TYPE    54 133 253 100
D551V4, multiclass
       clus
vv      LINGO4 MUTATED LINGO4 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 8              253
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LINGO4 MUTATED     9   2   1   0
  LINGO4 WILD-TYPE 186 171  88  85
D551V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              9              186
  N1              2              171
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V6, binary
                  cls
clus                 0   1
  LINGO4 MUTATED    10   0
  LINGO4 WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED     10    0
  LINGO4 WILD-TYPE  472   38
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D551V7, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   5
  LINGO4 WILD-TYPE 165 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    5
  LINGO4 WILD-TYPE  165  401
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  FEMALE              7              165
  MALE                5              401
[1] 2 2
[1] FALSE
D551V8, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     8   2
  LINGO4 WILD-TYPE 408 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      8    2
  LINGO4 WILD-TYPE  408  100
     clus
vv    LINGO4 MUTATED LINGO4 WILD-TYPE
  NO               8              408
  YES              2              100
[1] 2 2
[1] FALSE
D551V9, continuous
D551V10, continuous
[1] "Remove cluster labels:" "LINGO4 MUTATED"        
clus
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" "LINGO4 WILD-TYPE" 
      TCGA-Z6-AAPN 
"LINGO4 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LINGO4 MUTATED       2                         1
  LINGO4 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LINGO4 MUTATED                                           0     9
  LINGO4 WILD-TYPE                                         1   348
D551V11, multiclass
                                           clus
vv                                          LINGO4 MUTATED LINGO4 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V12, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     0  11
  LINGO4 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      0   11
  LINGO4 WILD-TYPE   10  387
                        clus
vv                       LINGO4 MUTATED LINGO4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(552) Variable = ZDHHC7 MUTATION ANALYSIS
D552V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     6   2
  ZDHHC7 WILD-TYPE 332 214
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               8              546 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               2              214 
$`ZDHHC7 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4P3 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MI 
       19.99        18.64        34.68         1.12        28.14        11.77 
TCGA-HF-7132 TCGA-HU-A4G8 
       77.29        22.68 

$`ZDHHC7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            1.12             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           77.29           122.30 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
          21.335           13.510 
[1] "1.1 - 77.3 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D552V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZDHHC7 MUTATED         0        0        1        1         2         2
  ZDHHC7 WILD-TYPE      10       20       45       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           0          1          0          2        0
  ZDHHC7 WILD-TYPE        29         83         62         37       43
                  vv
clus               STAGE IVA
  ZDHHC7 MUTATED           0
  ZDHHC7 WILD-TYPE         4
D552V3, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZDHHC7 MUTATED       0   3   5   1
  ZDHHC7 WILD-TYPE    54 132 256 101
D552V4, multiclass
       clus
vv      ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZDHHC7 MUTATED     3   4   0   2
  ZDHHC7 WILD-TYPE 192 169  89  83
D552V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V6, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     8   0
  ZDHHC7 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      8    0
  ZDHHC7 WILD-TYPE  474   38
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D552V7, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     3   6
  ZDHHC7 WILD-TYPE 169 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      3    6
  ZDHHC7 WILD-TYPE  169  400
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  FEMALE              3              169
  MALE                6              400
[1] 2 2
[1] FALSE
D552V8, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     6   2
  ZDHHC7 WILD-TYPE 410 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      6    2
  ZDHHC7 WILD-TYPE  410  100
     clus
vv    ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  NO               6              410
  YES              2              100
[1] 2 2
[1] FALSE
D552V9, continuous
D552V10, continuous
[1] "Remove cluster labels:" "ZDHHC7 MUTATED"        
clus
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4QT 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS       TCGA-IG-A8O2 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" "ZDHHC7 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZDHHC7 MUTATED       2                         0
  ZDHHC7 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZDHHC7 MUTATED                                           0     5
  ZDHHC7 WILD-TYPE                                         1   352
D552V11, multiclass
                                           clus
vv                                          ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V12, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     0   6
  ZDHHC7 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      0    6
  ZDHHC7 WILD-TYPE   10  392
                        clus
vv                       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(553) Variable = CNNM2 MUTATION ANALYSIS
D553V1, survival
                 sevent
clus2               0   1
  CNNM2 MUTATED    12   4
  CNNM2 WILD-TYPE 326 212
  CNNM2 MUTATED CNNM2 WILD-TYPE 
             16             538 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              4             212 
$`CNNM2 MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
       19.99         7.69         7.40        55.50         2.66        16.47 
TCGA-LN-A7HX TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 TCGA-CG-4443 
       12.23        34.68        44.94        29.59        31.10        29.98 
TCGA-CG-5718 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       36.00         0.10        38.14        17.85 

$`CNNM2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       25.12         3.75         3.02        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CNNM2 MUTATED CNNM2 WILD-TYPE 
            0.1             0.0 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
           55.5           122.3 
  CNNM2 MUTATED CNNM2 WILD-TYPE 
         24.790          13.495 
[1] "0.1 - 55.5 (24.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D553V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNNM2 MUTATED         0        1        0        1         4         3
  CNNM2 WILD-TYPE      10       19       46       30        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNNM2 MUTATED           1          2          1          3        0         1
  CNNM2 WILD-TYPE        28         82         61         36       43         3
D553V3, multiclass
            clus
vv           CNNM2 MUTATED CNNM2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CNNM2 MUTATED       5   3   5   5
  CNNM2 WILD-TYPE    49 132 256  97
D553V4, multiclass
       clus
vv      CNNM2 MUTATED CNNM2 WILD-TYPE
  T0+T1             5              49
  T2                3             132
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNNM2 MUTATED     7   6   2   2
  CNNM2 WILD-TYPE 188 167  87  83
D553V5, multiclass
    clus
vv   CNNM2 MUTATED CNNM2 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V6, binary
                 cls
clus                0   1
  CNNM2 MUTATED    16   1
  CNNM2 WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED     16    1
  CNNM2 WILD-TYPE  466   37
   clus
vv  CNNM2 MUTATED CNNM2 WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D553V7, binary
                 cls
clus                0   1
  CNNM2 MUTATED     8  10
  CNNM2 WILD-TYPE 164 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      8   10
  CNNM2 WILD-TYPE  164  396
        clus
vv       CNNM2 MUTATED CNNM2 WILD-TYPE
  FEMALE             8             164
  MALE              10             396
[1] 2 2
[1] FALSE
D553V8, binary
                 cls
clus                0   1
  CNNM2 MUTATED    13   2
  CNNM2 WILD-TYPE 403 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED     13    2
  CNNM2 WILD-TYPE  403  100
     clus
vv    CNNM2 MUTATED CNNM2 WILD-TYPE
  NO             13             403
  YES             2             100
[1] 2 2
[1] FALSE
D553V9, continuous
[1] "Remove cluster labels:" "CNNM2 MUTATED"         
clus
  CNNM2 MUTATED CNNM2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" "CNNM2 WILD-TYPE" 
D553V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNNM2 MUTATED       2                         0
  CNNM2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNNM2 MUTATED                                           0    14
  CNNM2 WILD-TYPE                                         1   343
D553V11, multiclass
                                           clus
vv                                          CNNM2 MUTATED CNNM2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V12, binary
                 cls
clus                0   1
  CNNM2 MUTATED     0   9
  CNNM2 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM2 MUTATED      0    9
  CNNM2 WILD-TYPE   10  389
                        clus
vv                       CNNM2 MUTATED CNNM2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(554) Variable = CNNM1 MUTATION ANALYSIS
D554V1, survival
                 sevent
clus2               0   1
  CNNM1 MUTATED     7   5
  CNNM1 WILD-TYPE 331 211
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             12             542 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
              5             211 
$`CNNM1 MUTATED`
TCGA-L5-A8NM TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 
        7.76        34.68        44.94        32.25        31.10         1.12 
TCGA-BR-A4QL TCGA-CD-5813 TCGA-CG-4465 TCGA-D7-A6EZ TCGA-HF-A5NB TCGA-R5-A7ZI 
       16.14        12.39         9.01        20.32        30.51        74.53 

$`CNNM1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CNNM1 MUTATED CNNM1 WILD-TYPE 
           1.12            0.00 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
          74.53          122.30 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
         25.415          13.510 
[1] "1.1 - 74.5 (25.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D554V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNNM1 MUTATED         0        0        0        1         3         2
  CNNM1 WILD-TYPE      10       20       46       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNNM1 MUTATED           0          1          1          2        2         0
  CNNM1 WILD-TYPE        29         83         61         37       41         4
D554V3, multiclass
            clus
vv           CNNM1 MUTATED CNNM1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CNNM1 MUTATED       1   1   6   5
  CNNM1 WILD-TYPE    53 134 255  97
D554V4, multiclass
       clus
vv      CNNM1 MUTATED CNNM1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNNM1 MUTATED     5   2   2   3
  CNNM1 WILD-TYPE 190 171  87  82
D554V5, multiclass
    clus
vv   CNNM1 MUTATED CNNM1 WILD-TYPE
  N0             5             190
  N1             2             171
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V6, binary
                 cls
clus                0   1
  CNNM1 MUTATED    11   2
  CNNM1 WILD-TYPE 471  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED     11    2
  CNNM1 WILD-TYPE  471   36
   clus
vv  CNNM1 MUTATED CNNM1 WILD-TYPE
  0            11             471
  1             2              36
[1] 2 2
[1] FALSE
D554V7, binary
                 cls
clus                0   1
  CNNM1 MUTATED    11   2
  CNNM1 WILD-TYPE 161 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED     11    2
  CNNM1 WILD-TYPE  161  404
        clus
vv       CNNM1 MUTATED CNNM1 WILD-TYPE
  FEMALE            11             161
  MALE               2             404
[1] 2 2
[1] FALSE
D554V8, binary
                 cls
clus                0   1
  CNNM1 MUTATED    10   1
  CNNM1 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED     10    1
  CNNM1 WILD-TYPE  406  101
     clus
vv    CNNM1 MUTATED CNNM1 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D554V9, continuous
D554V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNNM1 MUTATED       1                         0
  CNNM1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNNM1 MUTATED                                           0    10
  CNNM1 WILD-TYPE                                         1   347
D554V11, multiclass
                                           clus
vv                                          CNNM1 MUTATED CNNM1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V12, binary
                 cls
clus                0   1
  CNNM1 MUTATED     1   9
  CNNM1 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED      1    9
  CNNM1 WILD-TYPE    9  389
                        clus
vv                       CNNM1 MUTATED CNNM1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(555) Variable = AFF3 MUTATION ANALYSIS
D555V1, survival
                sevent
clus2              0   1
  AFF3 MUTATED    18  13
  AFF3 WILD-TYPE 320 203
  AFF3 MUTATED AFF3 WILD-TYPE 
            31            523 
  AFF3 MUTATED AFF3 WILD-TYPE 
            13            203 
$`AFF3 MUTATED`
TCGA-Q9-A6FU TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A8NM TCGA-LN-A49U TCGA-LN-A4A8 
        5.16         0.30        26.33         7.76        15.35        15.52 
TCGA-LN-A8HZ TCGA-R6-A6Y2 TCGA-BR-6566 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8078 
       12.33         9.30        32.78        39.78         3.45        29.59 
TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4QL 
       32.25         1.12        27.12        24.79        31.96        16.14 
TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A6EZ 
       12.30        12.82         6.58         6.02        28.96        20.32 
TCGA-F1-6874 TCGA-FP-7735 TCGA-HU-A4GT TCGA-HU-A4HD TCGA-IN-A6RL TCGA-R5-A7ZI 
       14.47         3.48         6.51        33.40        13.35        74.53 
TCGA-RD-A7BT 
        8.61 

$`AFF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44         0.69         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  AFF3 MUTATED AFF3 WILD-TYPE 
           0.3            0.0 
  AFF3 MUTATED AFF3 WILD-TYPE 
         74.53         122.30 
  AFF3 MUTATED AFF3 WILD-TYPE 
         14.47          13.55 
[1] "0.3 - 74.5 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D555V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AFF3 MUTATED         1        1        3        0         7         7
  AFF3 WILD-TYPE       9       19       43       31        77        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFF3 MUTATED           1          4          3          1        5         0
  AFF3 WILD-TYPE        28         80         59         38       38         4
D555V3, multiclass
            clus
vv           AFF3 MUTATED AFF3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             7             77
  STAGE IIB             7             76
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            3             59
  STAGE IIIC            1             38
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  AFF3 MUTATED       3   7  14   9
  AFF3 WILD-TYPE    51 128 247  93
D555V4, multiclass
       clus
vv      AFF3 MUTATED AFF3 WILD-TYPE
  T0+T1            3             51
  T2               7            128
  T3              14            247
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  AFF3 MUTATED    15  11   4   3
  AFF3 WILD-TYPE 180 162  85  82
D555V5, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  N0           15            180
  N1           11            162
  N2            4             85
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V6, binary
                cls
clus               0   1
  AFF3 MUTATED    27   3
  AFF3 WILD-TYPE 455  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     27    3
  AFF3 WILD-TYPE  455   35
   clus
vv  AFF3 MUTATED AFF3 WILD-TYPE
  0           27            455
  1            3             35
[1] 2 2
[1] FALSE
D555V7, binary
                cls
clus               0   1
  AFF3 MUTATED    11  23
  AFF3 WILD-TYPE 161 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     11   23
  AFF3 WILD-TYPE  161  383
        clus
vv       AFF3 MUTATED AFF3 WILD-TYPE
  FEMALE           11            161
  MALE             23            383
[1] 2 2
[1] FALSE
D555V8, binary
                cls
clus               0   1
  AFF3 MUTATED    30   3
  AFF3 WILD-TYPE 386  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     30    3
  AFF3 WILD-TYPE  386   99
     clus
vv    AFF3 MUTATED AFF3 WILD-TYPE
  NO            30            386
  YES            3             99
[1] 2 2
[1] FALSE
D555V9, continuous
[1] "Remove cluster labels:" "AFF3 MUTATED"          
clus
  AFF3 MUTATED AFF3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49V     TCGA-LN-A49W 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"AFF3 WILD-TYPE" "AFF3 WILD-TYPE" 
D555V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AFF3 MUTATED       9                         2
  AFF3 WILD-TYPE   124                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AFF3 MUTATED                                           1    20
  AFF3 WILD-TYPE                                         0   337
D555V11, multiclass
                                           clus
vv                                          AFF3 MUTATED AFF3 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               20            337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V12, binary
                cls
clus               0   1
  AFF3 MUTATED     2  27
  AFF3 WILD-TYPE   8 371
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED      2   27
  AFF3 WILD-TYPE    8  371
                        clus
vv                       AFF3 MUTATED AFF3 WILD-TYPE
  HISPANIC OR LATINO                2              8
  NOT HISPANIC OR LATINO           27            371
[1] 2 2
[1] FALSE

Clustering(556) Variable = PPIAL4A MUTATION ANALYSIS
D556V1, survival
                   sevent
clus2                 0   1
  PPIAL4A MUTATED     2   1
  PPIAL4A WILD-TYPE 336 215
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               551 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                1               215 
$`PPIAL4A MUTATED`
TCGA-BR-7958 TCGA-BR-8370 TCGA-CD-A4MG 
       29.56         3.32         6.58 

$`PPIAL4A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
             3.32              0.00 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
            29.56            122.30 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
             6.58             13.58 
[1] "3.3 - 29.6 (6.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D556V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPIAL4A MUTATED         0        0        0        0         1         0
  PPIAL4A WILD-TYPE      10       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPIAL4A MUTATED           0          0          2          0        0
  PPIAL4A WILD-TYPE        29         84         60         39       43
                   vv
clus                STAGE IVA
  PPIAL4A MUTATED           0
  PPIAL4A WILD-TYPE         4
D556V3, multiclass
            clus
vv           PPIAL4A MUTATED PPIAL4A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PPIAL4A MUTATED       0   0   2   1
  PPIAL4A WILD-TYPE    54 135 259 101
D556V4, multiclass
       clus
vv      PPIAL4A MUTATED PPIAL4A WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PPIAL4A MUTATED     2   0   0   1
  PPIAL4A WILD-TYPE 193 173  89  84
D556V5, multiclass
    clus
vv   PPIAL4A MUTATED PPIAL4A WILD-TYPE
  N0               2               193
  N1               0               173
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V6, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     3   0
  PPIAL4A WILD-TYPE 479  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      3    0
  PPIAL4A WILD-TYPE  479   38
   clus
vv  PPIAL4A MUTATED PPIAL4A WILD-TYPE
  0               3               479
  1               0                38
[1] 2 2
[1] FALSE
D556V7, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     0   3
  PPIAL4A WILD-TYPE 172 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      0    3
  PPIAL4A WILD-TYPE  172  403
        clus
vv       PPIAL4A MUTATED PPIAL4A WILD-TYPE
  FEMALE               0               172
  MALE                 3               403
[1] 2 2
[1] FALSE
D556V8, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     3   0
  PPIAL4A WILD-TYPE 413 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      3    0
  PPIAL4A WILD-TYPE  413  102
     clus
vv    PPIAL4A MUTATED PPIAL4A WILD-TYPE
  NO                3               413
  YES               0               102
[1] 2 2
[1] FALSE
D556V9, continuous
D556V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PPIAL4A MUTATED       1                         0
  PPIAL4A WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIAL4A MUTATED                                           0     2
  PPIAL4A WILD-TYPE                                         1   355
D556V11, multiclass
                                           clus
vv                                          PPIAL4A MUTATED PPIAL4A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V12, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     0   3
  PPIAL4A WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      0    3
  PPIAL4A WILD-TYPE   10  395
                        clus
vv                       PPIAL4A MUTATED PPIAL4A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(557) Variable = MKL2 MUTATION ANALYSIS
D557V1, survival
                sevent
clus2              0   1
  MKL2 MUTATED     9   8
  MKL2 WILD-TYPE 329 208
  MKL2 MUTATED MKL2 WILD-TYPE 
            17            537 
  MKL2 MUTATED MKL2 WILD-TYPE 
             8            208 
$`MKL2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NG TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-R6-A6L6 
        4.31        19.99        35.97       122.10         7.76         7.04 
TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5718 
        9.34        35.84        25.05        31.96         1.02        36.00 
TCGA-CG-5723 TCGA-HU-8238 TCGA-HU-A4GU TCGA-IN-A6RR TCGA-VQ-A8P2 
      105.07         1.51         6.58         6.74        38.14 

$`MKL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
        6.97         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MKL2 MUTATED MKL2 WILD-TYPE 
          1.02           0.00 
  MKL2 MUTATED MKL2 WILD-TYPE 
         122.1          122.3 
  MKL2 MUTATED MKL2 WILD-TYPE 
         19.99          13.55 
[1] "1.0 - 122.1 (20.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D557V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MKL2 MUTATED         1        0        1        2         0         3
  MKL2 WILD-TYPE       9       20       45       29        84        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKL2 MUTATED           1          2          0          2        2         0
  MKL2 WILD-TYPE        28         82         62         37       41         4
D557V3, multiclass
            clus
vv           MKL2 MUTATED MKL2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             0             84
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MKL2 MUTATED       1   4   7   3
  MKL2 WILD-TYPE    53 131 254  99
D557V4, multiclass
       clus
vv      MKL2 MUTATED MKL2 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               7            254
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MKL2 MUTATED     3   9   3   2
  MKL2 WILD-TYPE 192 164  86  83
D557V5, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  N0            3            192
  N1            9            164
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V6, binary
                cls
clus               0   1
  MKL2 MUTATED    13   2
  MKL2 WILD-TYPE 469  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED     13    2
  MKL2 WILD-TYPE  469   36
   clus
vv  MKL2 MUTATED MKL2 WILD-TYPE
  0           13            469
  1            2             36
[1] 2 2
[1] FALSE
D557V7, binary
                cls
clus               0   1
  MKL2 MUTATED     5  13
  MKL2 WILD-TYPE 167 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      5   13
  MKL2 WILD-TYPE  167  393
        clus
vv       MKL2 MUTATED MKL2 WILD-TYPE
  FEMALE            5            167
  MALE             13            393
[1] 2 2
[1] FALSE
D557V8, binary
                cls
clus               0   1
  MKL2 MUTATED    14   1
  MKL2 WILD-TYPE 402 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED     14    1
  MKL2 WILD-TYPE  402  101
     clus
vv    MKL2 MUTATED MKL2 WILD-TYPE
  NO            14            402
  YES            1            101
[1] 2 2
[1] FALSE
D557V9, continuous
D557V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MKL2 MUTATED       3                         0
  MKL2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKL2 MUTATED                                           0    12
  MKL2 WILD-TYPE                                         1   345
D557V11, multiclass
                                           clus
vv                                          MKL2 MUTATED MKL2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V12, binary
                cls
clus               0   1
  MKL2 MUTATED     0   9
  MKL2 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      0    9
  MKL2 WILD-TYPE   10  389
                        clus
vv                       MKL2 MUTATED MKL2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(558) Variable = PLAG1 MUTATION ANALYSIS
D558V1, survival
                 sevent
clus2               0   1
  PLAG1 MUTATED     6   6
  PLAG1 WILD-TYPE 332 210
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             12             542 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
              6             210 
$`PLAG1 MUTATED`
TCGA-IG-A6QS TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8592 
        9.96        20.38         6.97        34.68         1.12         6.28 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A6EZ TCGA-HU-A4H8 TCGA-KB-A6F7 
        9.01         6.02        28.96        20.32        14.07        63.62 

$`PLAG1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLAG1 MUTATED PLAG1 WILD-TYPE 
           1.12            0.00 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
          63.62          122.30 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
         12.015          13.565 
[1] "1.1 - 63.6 (12.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D558V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAG1 MUTATED         0        1        3        0         2         1
  PLAG1 WILD-TYPE      10       19       43       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLAG1 MUTATED           0          3          1          0        3         0
  PLAG1 WILD-TYPE        29         81         61         39       40         4
D558V3, multiclass
            clus
vv           PLAG1 MUTATED PLAG1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PLAG1 MUTATED       3   2   4   5
  PLAG1 WILD-TYPE    51 133 257  97
D558V4, multiclass
       clus
vv      PLAG1 MUTATED PLAG1 WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3                4             257
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PLAG1 MUTATED     5   6   2   1
  PLAG1 WILD-TYPE 190 167  87  84
D558V5, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  N0             5             190
  N1             6             167
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V6, binary
                 cls
clus                0   1
  PLAG1 MUTATED    11   1
  PLAG1 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED     11    1
  PLAG1 WILD-TYPE  471   37
   clus
vv  PLAG1 MUTATED PLAG1 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D558V7, binary
                 cls
clus                0   1
  PLAG1 MUTATED     7   7
  PLAG1 WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      7    7
  PLAG1 WILD-TYPE  165  399
        clus
vv       PLAG1 MUTATED PLAG1 WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D558V8, binary
                 cls
clus                0   1
  PLAG1 MUTATED     9   1
  PLAG1 WILD-TYPE 407 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      9    1
  PLAG1 WILD-TYPE  407  101
     clus
vv    PLAG1 MUTATED PLAG1 WILD-TYPE
  NO              9             407
  YES             1             101
[1] 2 2
[1] FALSE
D558V9, continuous
D558V10, continuous
[1] "Remove cluster labels:" "PLAG1 MUTATED"         
clus
  PLAG1 MUTATED PLAG1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" "PLAG1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"PLAG1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PLAG1 MUTATED       1                         0
  PLAG1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLAG1 MUTATED                                           0     9
  PLAG1 WILD-TYPE                                         1   348
D558V11, multiclass
                                           clus
vv                                          PLAG1 MUTATED PLAG1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V12, binary
                 cls
clus                0   1
  PLAG1 MUTATED     0  10
  PLAG1 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      0   10
  PLAG1 WILD-TYPE   10  388
                        clus
vv                       PLAG1 MUTATED PLAG1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(559) Variable = EXPH5 MUTATION ANALYSIS
D559V1, survival
                 sevent
clus2               0   1
  EXPH5 MUTATED    11   4
  EXPH5 WILD-TYPE 327 212
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             15             539 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              4             212 
$`EXPH5 MUTATED`
TCGA-L5-A8NT TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7723 
       27.12         7.76         6.97        34.68        32.78        28.73 
TCGA-BR-8368 TCGA-BR-8589 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6528 
        4.31        27.12        12.43         6.58         6.02        15.22 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-VQ-A8P2 
       30.51        22.68        38.14 

$`EXPH5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  EXPH5 MUTATED EXPH5 WILD-TYPE 
           4.31            0.00 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
          38.14          122.30 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
          22.68           13.51 
[1] "4.3 - 38.1 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D559V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXPH5 MUTATED         0        0        2        1         3         3
  EXPH5 WILD-TYPE      10       20       44       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXPH5 MUTATED           0          2          2          1        1         0
  EXPH5 WILD-TYPE        29         82         60         38       42         4
D559V3, multiclass
            clus
vv           EXPH5 MUTATED EXPH5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EXPH5 MUTATED       1   3   8   4
  EXPH5 WILD-TYPE    53 132 253  98
D559V4, multiclass
       clus
vv      EXPH5 MUTATED EXPH5 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EXPH5 MUTATED     7   6   0   2
  EXPH5 WILD-TYPE 188 167  89  83
D559V5, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V6, binary
                 cls
clus                0   1
  EXPH5 MUTATED    16   0
  EXPH5 WILD-TYPE 466  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     16    0
  EXPH5 WILD-TYPE  466   38
   clus
vv  EXPH5 MUTATED EXPH5 WILD-TYPE
  0            16             466
  1             0              38
[1] 2 2
[1] FALSE
D559V7, binary
                 cls
clus                0   1
  EXPH5 MUTATED     9   8
  EXPH5 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      9    8
  EXPH5 WILD-TYPE  163  398
        clus
vv       EXPH5 MUTATED EXPH5 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D559V8, binary
                 cls
clus                0   1
  EXPH5 MUTATED    12   3
  EXPH5 WILD-TYPE 404  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     12    3
  EXPH5 WILD-TYPE  404   99
     clus
vv    EXPH5 MUTATED EXPH5 WILD-TYPE
  NO             12             404
  YES             3              99
[1] 2 2
[1] FALSE
D559V9, continuous
D559V10, continuous
[1] "Remove cluster labels:" "EXPH5 MUTATED"         
clus
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" "EXPH5 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EXPH5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EXPH5 MUTATED       3                         0
  EXPH5 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXPH5 MUTATED                                           0    12
  EXPH5 WILD-TYPE                                         1   345
D559V11, multiclass
                                           clus
vv                                          EXPH5 MUTATED EXPH5 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V12, binary
                 cls
clus                0   1
  EXPH5 MUTATED     0  12
  EXPH5 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      0   12
  EXPH5 WILD-TYPE   10  386
                        clus
vv                       EXPH5 MUTATED EXPH5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(560) Variable = ARMC4 MUTATION ANALYSIS
D560V1, survival
                 sevent
clus2               0   1
  ARMC4 MUTATED    17   9
  ARMC4 WILD-TYPE 321 207
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             26             528 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
              9             207 
$`ARMC4 MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OI TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-L5-A4OJ TCGA-LN-A49K 
       60.39        19.99        35.97         5.16        21.01         5.92 
TCGA-LN-A49V TCGA-R6-A6Y2 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-8078 TCGA-BR-8289 
       12.59         9.30         6.61        15.95        29.59         2.66 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-D7-A4Z0 
       14.04         5.39        31.96         6.58         5.92        14.76 
TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-KB-A6F7 TCGA-MX-A5UJ 
       22.32        29.98         0.10        29.00        63.62        19.73 
TCGA-R5-A7ZE TCGA-VQ-A8P2 
       18.21        38.14 

$`ARMC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 
        4.70        22.82         0.36        27.12        20.02        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36        25.05         3.72        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        2.53         5.56        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ARMC4 MUTATED ARMC4 WILD-TYPE 
            0.1             0.0 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
          63.62          122.30 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
         17.080          13.495 
[1] "0.1 - 63.6 (17.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D560V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARMC4 MUTATED         2        0        1        0         5         4
  ARMC4 WILD-TYPE       8       20       45       31        79        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARMC4 MUTATED           2          4          2          3        2         0
  ARMC4 WILD-TYPE        27         80         60         36       41         4
D560V3, multiclass
            clus
vv           ARMC4 MUTATED ARMC4 WILD-TYPE
  STAGE I                2               8
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              4              79
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ARMC4 MUTATED       3   4  11   7
  ARMC4 WILD-TYPE    51 131 250  95
D560V4, multiclass
       clus
vv      ARMC4 MUTATED ARMC4 WILD-TYPE
  T0+T1             3              51
  T2                4             131
  T3               11             250
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ARMC4 MUTATED     7   7   7   4
  ARMC4 WILD-TYPE 188 166  82  81
D560V5, multiclass
    clus
vv   ARMC4 MUTATED ARMC4 WILD-TYPE
  N0             7             188
  N1             7             166
  N2             7              82
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V6, binary
                 cls
clus                0   1
  ARMC4 MUTATED    22   2
  ARMC4 WILD-TYPE 460  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     22    2
  ARMC4 WILD-TYPE  460   36
   clus
vv  ARMC4 MUTATED ARMC4 WILD-TYPE
  0            22             460
  1             2              36
[1] 2 2
[1] FALSE
D560V7, binary
                 cls
clus                0   1
  ARMC4 MUTATED    12  14
  ARMC4 WILD-TYPE 160 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     12   14
  ARMC4 WILD-TYPE  160  392
        clus
vv       ARMC4 MUTATED ARMC4 WILD-TYPE
  FEMALE            12             160
  MALE              14             392
[1] 2 2
[1] FALSE
D560V8, binary
                 cls
clus                0   1
  ARMC4 MUTATED    21   4
  ARMC4 WILD-TYPE 395  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     21    4
  ARMC4 WILD-TYPE  395   98
     clus
vv    ARMC4 MUTATED ARMC4 WILD-TYPE
  NO             21             395
  YES             4              98
[1] 2 2
[1] FALSE
D560V9, continuous
[1] "Remove cluster labels:" "ARMC4 MUTATED"         
clus
  ARMC4 MUTATED ARMC4 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49M 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49W      TCGA-LN-A49X 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2      TCGA-LN-A4A3 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
D560V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ARMC4 MUTATED       8                         0
  ARMC4 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARMC4 MUTATED                                           0    17
  ARMC4 WILD-TYPE                                         1   340
D560V11, multiclass
                                           clus
vv                                          ARMC4 MUTATED ARMC4 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V12, binary
                 cls
clus                0   1
  ARMC4 MUTATED     1  19
  ARMC4 WILD-TYPE   9 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED      1   19
  ARMC4 WILD-TYPE    9  379
                        clus
vv                       ARMC4 MUTATED ARMC4 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(561) Variable = MAGEE2 MUTATION ANALYSIS
D561V1, survival
                  sevent
clus2                0   1
  MAGEE2 MUTATED    11   6
  MAGEE2 WILD-TYPE 327 210
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              17              537 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
               6              210 
$`MAGEE2 MUTATED`
TCGA-L5-A8NG TCGA-2H-A9GK TCGA-JY-A93E TCGA-L5-A4OP TCGA-L5-A4OT TCGA-R6-A8W8 
       35.97         7.63        25.22         7.17         4.90         2.89 
TCGA-B7-5816 TCGA-BR-8081 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MI 
       26.70        32.25         7.40         6.18        31.10        11.77 
TCGA-CG-5726 TCGA-D7-6521 TCGA-IN-8663 TCGA-SW-A7EA TCGA-VQ-A8P2 
       28.96        18.54         3.39        19.04        38.14 

$`MAGEE2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8364 
       29.42         2.66        19.96         2.20         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
            2.89             0.00 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
           38.14           122.30 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
           18.54            13.55 
[1] "2.9 - 38.1 (18.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D561V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAGEE2 MUTATED         0        2        1        0         1         3
  MAGEE2 WILD-TYPE      10       18       45       31        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEE2 MUTATED           2          3          0          2        1
  MAGEE2 WILD-TYPE        27         81         62         37       42
                  vv
clus               STAGE IVA
  MAGEE2 MUTATED           0
  MAGEE2 WILD-TYPE         4
D561V3, multiclass
            clus
vv           MAGEE2 MUTATED MAGEE2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAGEE2 MUTATED       2   3   6   5
  MAGEE2 WILD-TYPE    52 132 255  97
D561V4, multiclass
       clus
vv      MAGEE2 MUTATED MAGEE2 WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 6              255
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAGEE2 MUTATED     6   6   3   1
  MAGEE2 WILD-TYPE 189 167  86  84
D561V5, multiclass
    clus
vv   MAGEE2 MUTATED MAGEE2 WILD-TYPE
  N0              6              189
  N1              6              167
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V6, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED    14   1
  MAGEE2 WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED     14    1
  MAGEE2 WILD-TYPE  468   37
   clus
vv  MAGEE2 MUTATED MAGEE2 WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D561V7, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED     5  12
  MAGEE2 WILD-TYPE 167 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED      5   12
  MAGEE2 WILD-TYPE  167  394
        clus
vv       MAGEE2 MUTATED MAGEE2 WILD-TYPE
  FEMALE              5              167
  MALE               12              394
[1] 2 2
[1] FALSE
D561V8, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED    14   1
  MAGEE2 WILD-TYPE 402 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED     14    1
  MAGEE2 WILD-TYPE  402  101
     clus
vv    MAGEE2 MUTATED MAGEE2 WILD-TYPE
  NO              14              402
  YES              1              101
[1] 2 2
[1] FALSE
D561V9, continuous
D561V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAGEE2 MUTATED       1                         0
  MAGEE2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAGEE2 MUTATED                                           0    14
  MAGEE2 WILD-TYPE                                         1   343
D561V11, multiclass
                                           clus
vv                                          MAGEE2 MUTATED MAGEE2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V12, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED     0  10
  MAGEE2 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED      0   10
  MAGEE2 WILD-TYPE   10  388
                        clus
vv                       MAGEE2 MUTATED MAGEE2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(562) Variable = FGF1 MUTATION ANALYSIS
D562V1, survival
                sevent
clus2              0   1
  FGF1 MUTATED     4   1
  FGF1 WILD-TYPE 334 215
  FGF1 MUTATED FGF1 WILD-TYPE 
             5            549 
  FGF1 MUTATED FGF1 WILD-TYPE 
             1            215 
$`FGF1 MUTATED`
TCGA-CG-5727 TCGA-2H-A9GO TCGA-L5-A88V TCGA-CD-8536 TCGA-CG-4437 
       79.07        16.24         2.60        12.43         8.05 

$`FGF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
        4.90        29.00         7.13         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FGF1 MUTATED FGF1 WILD-TYPE 
           2.6            0.0 
  FGF1 MUTATED FGF1 WILD-TYPE 
         79.07         122.30 
  FGF1 MUTATED FGF1 WILD-TYPE 
         12.43          13.58 
[1] "2.6 - 79.1 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D562V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF1 MUTATED         0        0        0        3         0         0
  FGF1 WILD-TYPE      10       20       46       28        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGF1 MUTATED           1          0          0          0        0         1
  FGF1 WILD-TYPE        28         84         62         39       43         3
D562V3, multiclass
            clus
vv           FGF1 MUTATED FGF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              3             28
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FGF1 MUTATED       0   1   4   0
  FGF1 WILD-TYPE    54 134 257 102
D562V4, multiclass
       clus
vv      FGF1 MUTATED FGF1 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               4            257
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FGF1 MUTATED     2   3   0   0
  FGF1 WILD-TYPE 193 170  89  85
D562V5, multiclass
    clus
vv   FGF1 MUTATED FGF1 WILD-TYPE
  N0            2            193
  N1            3            170
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V6, binary
                cls
clus               0   1
  FGF1 MUTATED     3   1
  FGF1 WILD-TYPE 479  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF1 MUTATED      3    1
  FGF1 WILD-TYPE  479   37
   clus
vv  FGF1 MUTATED FGF1 WILD-TYPE
  0            3            479
  1            1             37
[1] 2 2
[1] FALSE
D562V7, binary
                cls
clus               0   1
  FGF1 MUTATED     0   5
  FGF1 WILD-TYPE 172 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF1 MUTATED      0    5
  FGF1 WILD-TYPE  172  401
        clus
vv       FGF1 MUTATED FGF1 WILD-TYPE
  FEMALE            0            172
  MALE              5            401
[1] 2 2
[1] FALSE
D562V8, binary
                cls
clus               0   1
  FGF1 MUTATED     5   0
  FGF1 WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF1 MUTATED      5    0
  FGF1 WILD-TYPE  411  102
     clus
vv    FGF1 MUTATED FGF1 WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D562V9, continuous
D562V10, continuous
[1] "Remove cluster labels:" "FGF1 MUTATED"          
clus
  FGF1 MUTATED FGF1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A893     TCGA-L5-A8NE 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"FGF1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FGF1 MUTATED       1                         0
  FGF1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF1 MUTATED                                           0     1
  FGF1 WILD-TYPE                                         1   356
D562V11, multiclass
[1] "Remove cluster labels:" "FGF1 MUTATED"          
clus
  FGF1 MUTATED FGF1 WILD-TYPE 
             2            503 
    TCGA-IC-A6RF     TCGA-JY-A6FB     TCGA-JY-A938     TCGA-L5-A43I 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A43J     TCGA-L5-A4OE     TCGA-L5-A4OG     TCGA-L5-A4OI 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG     TCGA-L5-A8NT 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-Q9-A6FU     TCGA-S8-A6BV     TCGA-EQ-A4SO     TCGA-F1-6177 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-KB-A93G     TCGA-MX-A663     TCGA-IC-A6RE 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A4P3     TCGA-IG-A4QS 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A51D     TCGA-IG-A5B8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A5S3     TCGA-IG-A625     TCGA-IG-A6QS     TCGA-IG-A7DP 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-IG-A97I     TCGA-JY-A6F8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-JY-A6FA     TCGA-JY-A6FD     TCGA-JY-A6FE     TCGA-JY-A6FG 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-JY-A939     TCGA-JY-A93C     TCGA-JY-A93D 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-JY-A93E     TCGA-JY-A93F     TCGA-KH-A6WC     TCGA-L5-A43C 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OF     TCGA-L5-A4OH 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OJ     TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OR     TCGA-L5-A4OS 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OX     TCGA-L5-A88S 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A88W     TCGA-L5-A88Z     TCGA-L5-A891     TCGA-L5-A893 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NH     TCGA-L5-A8NI 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NJ     TCGA-L5-A8NK     TCGA-L5-A8NL     TCGA-L5-A8NM 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NS     TCGA-L5-A8NU 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-L5-A8NV     TCGA-L5-A8NW     TCGA-L7-A56G     TCGA-L7-A6VZ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M     TCGA-LN-A49N 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A49X 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2     TCGA-LN-A4A3 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6     TCGA-LN-A4A8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-LN-A8I1     TCGA-LN-A9FO     TCGA-LN-A9FP 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-LN-A9FQ     TCGA-LN-A9FR     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R6-A6DQ     TCGA-R6-A6KZ     TCGA-R6-A6L4     TCGA-R6-A6L6 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R6-A6XG     TCGA-R6-A6XQ     TCGA-R6-A6Y0     TCGA-R6-A6Y2 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-R6-A8WG 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-RE-A7BO     TCGA-S8-A6BW     TCGA-V5-A7RC     TCGA-V5-A7RE 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ET     TCGA-VR-A8EU 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7I 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE     TCGA-Z6-A9VB     TCGA-Z6-AAPN 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-ZR-A9CJ     TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-B7-A5TJ     TCGA-B7-A5TK     TCGA-B7-A5TN     TCGA-BR-4183 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4184     TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4201     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4257     TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4292     TCGA-BR-4294     TCGA-BR-4357     TCGA-BR-4361 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4362     TCGA-BR-4363     TCGA-BR-4366     TCGA-BR-4368 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-4369     TCGA-BR-4370     TCGA-BR-4371     TCGA-BR-6452 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7707 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8     TCGA-BR-A4PD 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-BR-A4QM     TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5804 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8533     TCGA-CD-8534 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-8535     TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG     TCGA-CD-A4MH 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-D7-5577     TCGA-D7-5578 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-A6EX     TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-A6F2     TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-D7-A74B     TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-FP-A9TM     TCGA-HJ-7597 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-8238     TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-HU-A4HB     TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-KB-A93J     TCGA-MX-A5UG     TCGA-MX-A5UJ     TCGA-MX-A666 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R5-A7O7     TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-R5-A7ZR     TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-RD-A7BT     TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-RD-A8MW     TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-RD-A8N4     TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-SW-A7EA     TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DU 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91U     TCGA-VQ-A92D 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-AA64     TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-AA6B     TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
    TCGA-VQ-AA6J     TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"FGF1 WILD-TYPE" "FGF1 WILD-TYPE" "FGF1 WILD-TYPE" 
D562V12, binary
                cls
clus               0   1
  FGF1 MUTATED     0   1
  FGF1 WILD-TYPE  10 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF1 MUTATED      0    1
  FGF1 WILD-TYPE   10  397
                        clus
vv                       FGF1 MUTATED FGF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            1            397
[1] 2 2
[1] FALSE

Clustering(563) Variable = KIF13A MUTATION ANALYSIS
D563V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    14  10
  KIF13A WILD-TYPE 324 206
  KIF13A MUTATED KIF13A WILD-TYPE 
              24              530 
  KIF13A MUTATED KIF13A WILD-TYPE 
              10              206 
$`KIF13A MUTATED`
TCGA-JY-A6FB TCGA-JY-A939 TCGA-L5-A8NM TCGA-L5-A8NV TCGA-LN-A4A1 TCGA-XP-A8T6 
       60.39        21.70         7.76        52.57        12.59        25.08 
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8372 
       26.70        30.90         9.34        34.68         0.26        31.27 
TCGA-BR-8589 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5721 
       27.12         6.58        12.62        15.95         9.01         6.02 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.44        11.08        30.51        22.32         0.10         6.51 

$`KIF13A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        11.77        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIF13A MUTATED KIF13A WILD-TYPE 
             0.1              0.0 
  KIF13A MUTATED KIF13A WILD-TYPE 
           60.39           122.30 
  KIF13A MUTATED KIF13A WILD-TYPE 
          14.285           13.565 
[1] "0.1 - 60.4 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D563V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF13A MUTATED         1        0        3        1         6         5
  KIF13A WILD-TYPE       9       20       43       30        78        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          0          2          3        2
  KIF13A WILD-TYPE        29         84         60         36       41
                  vv
clus               STAGE IVA
  KIF13A MUTATED           0
  KIF13A WILD-TYPE         4
D563V3, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              2               60
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KIF13A MUTATED       2   7   7   8
  KIF13A WILD-TYPE    52 128 254  94
D563V4, multiclass
       clus
vv      KIF13A MUTATED KIF13A WILD-TYPE
  T0+T1              2               52
  T2                 7              128
  T3                 7              254
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KIF13A MUTATED    12   7   1   4
  KIF13A WILD-TYPE 183 166  88  81
D563V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0             12              183
  N1              7              166
  N2              1               88
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V6, binary
                  cls
clus                 0   1
  KIF13A MUTATED    24   1
  KIF13A WILD-TYPE 458  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     24    1
  KIF13A WILD-TYPE  458   37
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             24              458
  1              1               37
[1] 2 2
[1] FALSE
D563V7, binary
                  cls
clus                 0   1
  KIF13A MUTATED    10  15
  KIF13A WILD-TYPE 162 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     10   15
  KIF13A WILD-TYPE  162  391
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  FEMALE             10              162
  MALE               15              391
[1] 2 2
[1] FALSE
D563V8, binary
                  cls
clus                 0   1
  KIF13A MUTATED    21   2
  KIF13A WILD-TYPE 395 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     21    2
  KIF13A WILD-TYPE  395  100
     clus
vv    KIF13A MUTATED KIF13A WILD-TYPE
  NO              21              395
  YES              2              100
[1] 2 2
[1] FALSE
D563V9, continuous
[1] "Remove cluster labels:" "KIF13A MUTATED"        
clus
  KIF13A MUTATED KIF13A WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A2 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
D563V10, continuous
[1] "Remove cluster labels:" "KIF13A MUTATED"        
clus
  KIF13A MUTATED KIF13A WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-X8-AAAR       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" "KIF13A WILD-TYPE" 
      TCGA-Z6-AAPN 
"KIF13A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF13A MUTATED       6                         2
  KIF13A WILD-TYPE   127                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF13A MUTATED                                           0    12
  KIF13A WILD-TYPE                                         1   345
D563V11, multiclass
                                           clus
vv                                          KIF13A MUTATED KIF13A WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V12, binary
                  cls
clus                 0   1
  KIF13A MUTATED     1  15
  KIF13A WILD-TYPE   9 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      1   15
  KIF13A WILD-TYPE    9  383
                        clus
vv                       KIF13A MUTATED KIF13A WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(564) Variable = GLT8D1 MUTATION ANALYSIS
D564V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     4   2
  GLT8D1 WILD-TYPE 334 214
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               6              548 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               2              214 
$`GLT8D1 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-7703 TCGA-CG-5726 TCGA-HU-A4GN TCGA-VQ-A8P2 
       26.70        30.90        36.16        28.96        29.98        38.14 

$`GLT8D1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
            26.7              0.0 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           38.14           122.30 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
          30.440           13.495 
[1] "26.7 - 38.1 (30.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D564V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLT8D1 MUTATED         0        2        0        0         1         1
  GLT8D1 WILD-TYPE      10       18       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           0          1          0          0        0
  GLT8D1 WILD-TYPE        29         83         62         39       43
                  vv
clus               STAGE IVA
  GLT8D1 MUTATED           0
  GLT8D1 WILD-TYPE         4
D564V3, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GLT8D1 MUTATED       3   2   0   2
  GLT8D1 WILD-TYPE    51 133 261 100
D564V4, multiclass
       clus
vv      GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                 0              261
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GLT8D1 MUTATED     3   2   0   0
  GLT8D1 WILD-TYPE 192 171  89  85
D564V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V6, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     7   0
  GLT8D1 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      7    0
  GLT8D1 WILD-TYPE  475   38
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D564V7, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     3   4
  GLT8D1 WILD-TYPE 169 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      3    4
  GLT8D1 WILD-TYPE  169  402
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  FEMALE              3              169
  MALE                4              402
[1] 2 2
[1] FALSE
D564V8, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   1
  GLT8D1 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    1
  GLT8D1 WILD-TYPE  412  101
     clus
vv    GLT8D1 MUTATED GLT8D1 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D564V9, continuous
D564V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLT8D1 MUTATED       1                         0
  GLT8D1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLT8D1 MUTATED                                           0     5
  GLT8D1 WILD-TYPE                                         1   352
D564V11, multiclass
                                           clus
vv                                          GLT8D1 MUTATED GLT8D1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V12, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     0   5
  GLT8D1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      0    5
  GLT8D1 WILD-TYPE   10  393
                        clus
vv                       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(565) Variable = SMARCB1 MUTATION ANALYSIS
D565V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     9   5
  SMARCB1 WILD-TYPE 329 211
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               14               540 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5               211 
$`SMARCB1 MUTATED`
TCGA-L5-A8NT TCGA-2H-A9GL TCGA-Q9-A6FW TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
       27.12         5.92         7.82         6.97        30.90        34.68 
TCGA-BR-8368 TCGA-CD-A4MI TCGA-CG-4305 TCGA-F1-6874 TCGA-HU-A4GQ TCGA-HU-A4H3 
        4.31        11.77        15.95        14.47         0.10        29.00 
TCGA-HU-A4H8 TCGA-VQ-A8DT 
       14.07        48.79 

$`SMARCB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              0.1               0.0 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            48.79            122.30 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            14.27             13.53 
[1] "0.1 - 48.8 (14.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D565V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCB1 MUTATED         0        1        3        1         1         2
  SMARCB1 WILD-TYPE      10       19       43       30        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           1          2          2          2        0
  SMARCB1 WILD-TYPE        28         82         60         37       43
                   vv
clus                STAGE IVA
  SMARCB1 MUTATED           0
  SMARCB1 WILD-TYPE         4
D565V3, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SMARCB1 MUTATED       2   4   7   3
  SMARCB1 WILD-TYPE    52 131 254  99
D565V4, multiclass
       clus
vv      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T0+T1               2                52
  T2                  4               131
  T3                  7               254
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SMARCB1 MUTATED     6   5   2   2
  SMARCB1 WILD-TYPE 189 168  87  83
D565V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0               6               189
  N1               5               168
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    15   0
  SMARCB1 WILD-TYPE 467  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     15    0
  SMARCB1 WILD-TYPE  467   38
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              15               467
  1               0                38
[1] 2 2
[1] FALSE
D565V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     4  12
  SMARCB1 WILD-TYPE 168 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      4   12
  SMARCB1 WILD-TYPE  168  394
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               4               168
  MALE                12               394
[1] 2 2
[1] FALSE
D565V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    12   3
  SMARCB1 WILD-TYPE 404  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     12    3
  SMARCB1 WILD-TYPE  404   99
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO               12               404
  YES               3                99
[1] 2 2
[1] FALSE
D565V9, continuous
D565V10, continuous
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-R6-A6DN        TCGA-R6-A6L4 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SMARCB1 MUTATED       5                         0
  SMARCB1 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMARCB1 MUTATED                                           0     8
  SMARCB1 WILD-TYPE                                         1   349
D565V11, multiclass
                                           clus
vv                                          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V12, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0  12
  SMARCB1 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0   12
  SMARCB1 WILD-TYPE   10  386
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(566) Variable = PRRG3 MUTATION ANALYSIS
D566V1, survival
                 sevent
clus2               0   1
  PRRG3 MUTATED     6   3
  PRRG3 WILD-TYPE 332 213
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              9             545 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              3             213 
$`PRRG3 MUTATED`
TCGA-L5-A8NK TCGA-L5-A8NR TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 TCGA-CG-5721 
       13.55         8.71         6.61        29.59         6.18         6.02 
TCGA-CG-5723 TCGA-D7-5577 TCGA-HJ-7597 
      105.07        25.71        26.47 

$`PRRG3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PRRG3 MUTATED PRRG3 WILD-TYPE 
           6.02            0.00 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
         105.07          122.30 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
          13.55           13.58 
[1] "6.0 - 105.1 (13.6)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D566V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRRG3 MUTATED         0        0        1        1         2         1
  PRRG3 WILD-TYPE      10       20       45       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRG3 MUTATED           2          1          0          0        1         0
  PRRG3 WILD-TYPE        27         83         62         39       42         4
D566V3, multiclass
            clus
vv           PRRG3 MUTATED PRRG3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PRRG3 MUTATED       1   4   3   2
  PRRG3 WILD-TYPE    53 131 258 100
D566V4, multiclass
       clus
vv      PRRG3 MUTATED PRRG3 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PRRG3 MUTATED     4   4   0   1
  PRRG3 WILD-TYPE 191 169  89  84
D566V5, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V6, binary
                 cls
clus                0   1
  PRRG3 MUTATED     9   0
  PRRG3 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      9    0
  PRRG3 WILD-TYPE  473   38
   clus
vv  PRRG3 MUTATED PRRG3 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D566V7, binary
                 cls
clus                0   1
  PRRG3 MUTATED     7   3
  PRRG3 WILD-TYPE 165 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      7    3
  PRRG3 WILD-TYPE  165  403
        clus
vv       PRRG3 MUTATED PRRG3 WILD-TYPE
  FEMALE             7             165
  MALE               3             403
[1] 2 2
[1] FALSE
D566V8, binary
                 cls
clus                0   1
  PRRG3 MUTATED     8   0
  PRRG3 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      8    0
  PRRG3 WILD-TYPE  408  102
     clus
vv    PRRG3 MUTATED PRRG3 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D566V9, continuous
D566V10, continuous
[1] "Remove cluster labels:" "PRRG3 MUTATED"         
clus
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" "PRRG3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRRG3 MUTATED       0                         0
  PRRG3 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRRG3 MUTATED                                           0     7
  PRRG3 WILD-TYPE                                         1   350
D566V11, multiclass
                                           clus
vv                                          PRRG3 MUTATED PRRG3 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V12, binary
                 cls
clus                0   1
  PRRG3 MUTATED     0   6
  PRRG3 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      0    6
  PRRG3 WILD-TYPE   10  392
                        clus
vv                       PRRG3 MUTATED PRRG3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(567) Variable = CSGALNACT1 MUTATION ANALYSIS
D567V1, survival
                      sevent
clus2                    0   1
  CSGALNACT1 MUTATED    10   8
  CSGALNACT1 WILD-TYPE 328 208
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  18                  536 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  208 
$`CSGALNACT1 MUTATED`
TCGA-CG-4460 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7723 TCGA-BR-8059 
       21.99        19.56         6.97         9.67        28.73        14.43 
TCGA-BR-8060 TCGA-BR-8361 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8678 TCGA-CG-5723 
       11.44        31.10         3.32        31.27        24.79       105.07 
TCGA-CG-5728 TCGA-D7-A6EY TCGA-D7-A747 TCGA-HU-A4GT TCGA-KB-A6F7 TCGA-VQ-A8P2 
       65.10        11.44         8.38         6.51        63.62        38.14 

$`CSGALNACT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29        15.65         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                3.32                 0.00 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
              105.07               122.30 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
              20.775               13.510 
[1] "3.3 - 105.1 (20.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D567V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSGALNACT1 MUTATED         0        0        3        1         1         2
  CSGALNACT1 WILD-TYPE      10       20       43       30        83        81
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSGALNACT1 MUTATED           1          3          3          3        1
  CSGALNACT1 WILD-TYPE        28         81         59         36       42
                      vv
clus                   STAGE IVA
  CSGALNACT1 MUTATED           0
  CSGALNACT1 WILD-TYPE         4
D567V3, multiclass
            clus
vv           CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  STAGE I                     0                   10
  STAGE IA                    0                   20
  STAGE IB                    3                   43
  STAGE II                    1                   30
  STAGE IIA                   1                   83
  STAGE IIB                   2                   81
  STAGE III                   1                   28
  STAGE IIIA                  3                   81
  STAGE IIIB                  3                   59
  STAGE IIIC                  3                   36
  STAGE IV                    1                   42
  STAGE IVA                   0                    4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   T0+T1  T2  T3  T4
  CSGALNACT1 MUTATED       1   4   6   7
  CSGALNACT1 WILD-TYPE    53 131 255  95
D567V4, multiclass
       clus
vv      CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  T0+T1                  1                   53
  T2                     4                  131
  T3                     6                  255
  T4                     7                   95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2  N3
  CSGALNACT1 MUTATED     4   7   2   5
  CSGALNACT1 WILD-TYPE 191 166  87  80
D567V5, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  N0                  4                  191
  N1                  7                  166
  N2                  2                   87
  N3                  5                   80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V6, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED    17   1
  CSGALNACT1 WILD-TYPE 465  37
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED     17    1
  CSGALNACT1 WILD-TYPE  465   37
   clus
vv  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  0                 17                  465
  1                  1                   37
[1] 2 2
[1] FALSE
D567V7, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     9  10
  CSGALNACT1 WILD-TYPE 163 396
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      9   10
  CSGALNACT1 WILD-TYPE  163  396
        clus
vv       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  FEMALE                  9                  163
  MALE                   10                  396
[1] 2 2
[1] FALSE
D567V8, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED    15   2
  CSGALNACT1 WILD-TYPE 401 100
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED     15    2
  CSGALNACT1 WILD-TYPE  401  100
     clus
vv    CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  NO                  15                  401
  YES                  2                  100
[1] 2 2
[1] FALSE
D567V9, continuous
D567V10, continuous
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN
  CSGALNACT1 MUTATED       1                         0
  CSGALNACT1 WILD-TYPE   132                        14
                      vv
clus                   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSGALNACT1 MUTATED                                           0    14
  CSGALNACT1 WILD-TYPE                                         1   343
D567V11, multiclass
                                           clus
vv                                          CSGALNACT1 MUTATED
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                  0
  WHITE                                                     14
                                           clus
vv                                          CSGALNACT1 WILD-TYPE
  ASIAN                                                      132
  BLACK OR AFRICAN AMERICAN                                   14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                    1
  WHITE                                                      343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V12, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     0  14
  CSGALNACT1 WILD-TYPE  10 384
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      0   14
  CSGALNACT1 WILD-TYPE   10  384
                        clus
vv                       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  HISPANIC OR LATINO                      0                   10
  NOT HISPANIC OR LATINO                 14                  384
[1] 2 2
[1] FALSE

Clustering(568) Variable = BEND3 MUTATION ANALYSIS
D568V1, survival
                 sevent
clus2               0   1
  BEND3 MUTATED     7   5
  BEND3 WILD-TYPE 331 211
  BEND3 MUTATED BEND3 WILD-TYPE 
             12             542 
  BEND3 MUTATED BEND3 WILD-TYPE 
              5             211 
$`BEND3 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3Y9 TCGA-BR-4257 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8536 
       19.99         0.85         9.67         0.26         1.12        12.43 
TCGA-CD-A4MI TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6528 TCGA-HU-A4H8 TCGA-MX-A5UJ 
       11.77       105.07        21.07        15.22        14.07        19.73 

$`BEND3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BEND3 MUTATED BEND3 WILD-TYPE 
           0.26            0.00 
  BEND3 MUTATED BEND3 WILD-TYPE 
         105.07          122.30 
  BEND3 MUTATED BEND3 WILD-TYPE 
         13.250          13.565 
[1] "0.3 - 105.1 (13.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D568V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEND3 MUTATED         0        0        4        2         1         0
  BEND3 WILD-TYPE      10       20       42       29        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BEND3 MUTATED           0          4          0          1        0         0
  BEND3 WILD-TYPE        29         80         62         38       43         4
D568V3, multiclass
            clus
vv           BEND3 MUTATED BEND3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               4              42
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BEND3 MUTATED       1   5   5   1
  BEND3 WILD-TYPE    53 130 256 101
D568V4, multiclass
       clus
vv      BEND3 MUTATED BEND3 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                5             256
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BEND3 MUTATED     6   3   2   1
  BEND3 WILD-TYPE 189 170  87  84
D568V5, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V6, binary
                 cls
clus                0   1
  BEND3 MUTATED    13   0
  BEND3 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED     13    0
  BEND3 WILD-TYPE  469   38
   clus
vv  BEND3 MUTATED BEND3 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D568V7, binary
                 cls
clus                0   1
  BEND3 MUTATED     7   7
  BEND3 WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      7    7
  BEND3 WILD-TYPE  165  399
        clus
vv       BEND3 MUTATED BEND3 WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D568V8, binary
                 cls
clus                0   1
  BEND3 MUTATED    12   0
  BEND3 WILD-TYPE 404 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED     12    0
  BEND3 WILD-TYPE  404  102
     clus
vv    BEND3 MUTATED BEND3 WILD-TYPE
  NO             12             404
  YES             0             102
[1] 2 2
[1] FALSE
D568V9, continuous
[1] "Remove cluster labels:" "BEND3 MUTATED"         
clus
  BEND3 MUTATED BEND3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
D568V10, continuous
[1] "Remove cluster labels:" "BEND3 MUTATED"         
clus
  BEND3 MUTATED BEND3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" "BEND3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BEND3 MUTATED       3                         0
  BEND3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BEND3 MUTATED                                           0     8
  BEND3 WILD-TYPE                                         1   349
D568V11, multiclass
                                           clus
vv                                          BEND3 MUTATED BEND3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V12, binary
                 cls
clus                0   1
  BEND3 MUTATED     0  10
  BEND3 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      0   10
  BEND3 WILD-TYPE   10  388
                        clus
vv                       BEND3 MUTATED BEND3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(569) Variable = TPD52L1 MUTATION ANALYSIS
D569V1, survival
                   sevent
clus2                 0   1
  TPD52L1 MUTATED     8   4
  TPD52L1 WILD-TYPE 330 212
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
               12               542 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
                4               212 
$`TPD52L1 MUTATED`
TCGA-L5-A4OG TCGA-LN-A9FP TCGA-RE-A7BO TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8060 
        4.70        12.03         7.00         6.97        34.68        11.44 
TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J5 TCGA-CG-4306 TCGA-HF-7132 TCGA-HU-A4GX 
       31.96        10.68        28.34         1.02        77.29        20.25 

$`TPD52L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88         8.22        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
             1.02              0.00 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
            77.29            122.30 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
           11.735            13.630 
[1] "1.0 - 77.3 (11.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D569V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPD52L1 MUTATED         1        0        1        1         2         2
  TPD52L1 WILD-TYPE       9       20       45       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TPD52L1 MUTATED           0          2          1          1        2
  TPD52L1 WILD-TYPE        29         82         61         38       41
                   vv
clus                STAGE IVA
  TPD52L1 MUTATED           0
  TPD52L1 WILD-TYPE         4
D569V3, multiclass
            clus
vv           TPD52L1 MUTATED TPD52L1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TPD52L1 MUTATED       2   4   4   3
  TPD52L1 WILD-TYPE    52 131 257  99
D569V4, multiclass
       clus
vv      TPD52L1 MUTATED TPD52L1 WILD-TYPE
  T0+T1               2                52
  T2                  4               131
  T3                  4               257
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TPD52L1 MUTATED     4   4   4   1
  TPD52L1 WILD-TYPE 191 169  85  84
D569V5, multiclass
    clus
vv   TPD52L1 MUTATED TPD52L1 WILD-TYPE
  N0               4               191
  N1               4               169
  N2               4                85
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V6, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED    10   2
  TPD52L1 WILD-TYPE 472  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED     10    2
  TPD52L1 WILD-TYPE  472   36
   clus
vv  TPD52L1 MUTATED TPD52L1 WILD-TYPE
  0              10               472
  1               2                36
[1] 2 2
[1] FALSE
D569V7, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     7   6
  TPD52L1 WILD-TYPE 165 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      7    6
  TPD52L1 WILD-TYPE  165  400
        clus
vv       TPD52L1 MUTATED TPD52L1 WILD-TYPE
  FEMALE               7               165
  MALE                 6               400
[1] 2 2
[1] FALSE
D569V8, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     9   2
  TPD52L1 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      9    2
  TPD52L1 WILD-TYPE  407  100
     clus
vv    TPD52L1 MUTATED TPD52L1 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D569V9, continuous
D569V10, continuous
[1] "Remove cluster labels:" "TPD52L1 MUTATED"       
clus
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-V5-A7RB        TCGA-V5-A7RC 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" "TPD52L1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TPD52L1 MUTATED       4                         0
  TPD52L1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TPD52L1 MUTATED                                           0     6
  TPD52L1 WILD-TYPE                                         1   351
D569V11, multiclass
                                           clus
vv                                          TPD52L1 MUTATED TPD52L1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V12, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     0   9
  TPD52L1 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      0    9
  TPD52L1 WILD-TYPE   10  389
                        clus
vv                       TPD52L1 MUTATED TPD52L1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(570) Variable = R3HDM2 MUTATION ANALYSIS
D570V1, survival
                  sevent
clus2                0   1
  R3HDM2 MUTATED     7   5
  R3HDM2 WILD-TYPE 331 211
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
              12              542 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               5              211 
$`R3HDM2 MUTATED`
TCGA-L5-A4OI TCGA-LN-A49L TCGA-LN-A7HX TCGA-VR-A8ER TCGA-XP-A8T6 TCGA-Z6-A9VB 
       19.99        10.45        12.23        12.43        25.08         1.32 
TCGA-B7-5816 TCGA-BR-8360 TCGA-BR-8372 TCGA-CD-5813 TCGA-CG-4465 TCGA-R5-A7ZI 
       26.70         6.18        31.27        12.39         9.01        74.53 

$`R3HDM2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.21        41.23        14.37         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
            1.32             0.00 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
           74.53           122.30 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
           12.41            13.63 
[1] "1.3 - 74.5 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D570V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  R3HDM2 MUTATED         0        0        0        1         3         2
  R3HDM2 WILD-TYPE      10       20       46       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  R3HDM2 MUTATED           1          1          0          2        2
  R3HDM2 WILD-TYPE        28         83         62         37       41
                  vv
clus               STAGE IVA
  R3HDM2 MUTATED           0
  R3HDM2 WILD-TYPE         4
D570V3, multiclass
            clus
vv           R3HDM2 MUTATED R3HDM2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  R3HDM2 MUTATED       1   3   5   5
  R3HDM2 WILD-TYPE    53 132 256  97
D570V4, multiclass
       clus
vv      R3HDM2 MUTATED R3HDM2 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  R3HDM2 MUTATED     5   4   0   3
  R3HDM2 WILD-TYPE 190 169  89  82
D570V5, multiclass
    clus
vv   R3HDM2 MUTATED R3HDM2 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              0               89
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V6, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED    11   2
  R3HDM2 WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED     11    2
  R3HDM2 WILD-TYPE  471   36
   clus
vv  R3HDM2 MUTATED R3HDM2 WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D570V7, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     6   9
  R3HDM2 WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      6    9
  R3HDM2 WILD-TYPE  166  397
        clus
vv       R3HDM2 MUTATED R3HDM2 WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D570V8, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     8   3
  R3HDM2 WILD-TYPE 408  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      8    3
  R3HDM2 WILD-TYPE  408   99
     clus
vv    R3HDM2 MUTATED R3HDM2 WILD-TYPE
  NO               8              408
  YES              3               99
[1] 2 2
[1] FALSE
D570V9, continuous
D570V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  R3HDM2 MUTATED       3                         1
  R3HDM2 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  R3HDM2 MUTATED                                           0     9
  R3HDM2 WILD-TYPE                                         1   348
D570V11, multiclass
                                           clus
vv                                          R3HDM2 MUTATED R3HDM2 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V12, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     2  10
  R3HDM2 WILD-TYPE   8 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      2   10
  R3HDM2 WILD-TYPE    8  388
                        clus
vv                       R3HDM2 MUTATED R3HDM2 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(571) Variable = INPP5F MUTATION ANALYSIS
D571V1, survival
                  sevent
clus2                0   1
  INPP5F MUTATED    14   5
  INPP5F WILD-TYPE 324 211
  INPP5F MUTATED INPP5F WILD-TYPE 
              19              535 
  INPP5F MUTATED INPP5F WILD-TYPE 
               5              211 
$`INPP5F MUTATED`
TCGA-L5-A43J TCGA-IC-A6RE TCGA-L5-A4OJ TCGA-L5-A4OU TCGA-L5-A8NM TCGA-LN-A49Y 
        4.31         7.69        21.01        29.00         7.76        12.46 
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8487 
       26.70        30.90        34.68        32.78         0.26         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-A6F2 TCGA-HU-A4GT 
       28.14        31.96         1.02       105.07        15.65         6.51 
TCGA-VQ-A8P2 
       38.14 

$`INPP5F WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  INPP5F MUTATED INPP5F WILD-TYPE 
            0.26             0.00 
  INPP5F MUTATED INPP5F WILD-TYPE 
          105.07           122.30 
  INPP5F MUTATED INPP5F WILD-TYPE 
           21.01            13.51 
[1] "0.3 - 105.1 (21.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D571V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INPP5F MUTATED         1        0        2        1         6         4
  INPP5F WILD-TYPE       9       20       44       30        78        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPP5F MUTATED           0          2          0          1        2
  INPP5F WILD-TYPE        29         82         62         38       41
                  vv
clus               STAGE IVA
  INPP5F MUTATED           0
  INPP5F WILD-TYPE         4
D571V3, multiclass
            clus
vv           INPP5F MUTATED INPP5F WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  INPP5F MUTATED       3   5   8   5
  INPP5F WILD-TYPE    51 130 253  97
D571V4, multiclass
       clus
vv      INPP5F MUTATED INPP5F WILD-TYPE
  T0+T1              3               51
  T2                 5              130
  T3                 8              253
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  INPP5F MUTATED    12   4   2   1
  INPP5F WILD-TYPE 183 169  87  84
D571V5, multiclass
    clus
vv   INPP5F MUTATED INPP5F WILD-TYPE
  N0             12              183
  N1              4              169
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V6, binary
                  cls
clus                 0   1
  INPP5F MUTATED    18   2
  INPP5F WILD-TYPE 464  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED     18    2
  INPP5F WILD-TYPE  464   36
   clus
vv  INPP5F MUTATED INPP5F WILD-TYPE
  0             18              464
  1              2               36
[1] 2 2
[1] FALSE
D571V7, binary
                  cls
clus                 0   1
  INPP5F MUTATED    11  10
  INPP5F WILD-TYPE 161 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED     11   10
  INPP5F WILD-TYPE  161  396
        clus
vv       INPP5F MUTATED INPP5F WILD-TYPE
  FEMALE             11              161
  MALE               10              396
[1] 2 2
[1] FALSE
D571V8, binary
                  cls
clus                 0   1
  INPP5F MUTATED    16   1
  INPP5F WILD-TYPE 400 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED     16    1
  INPP5F WILD-TYPE  400  101
     clus
vv    INPP5F MUTATED INPP5F WILD-TYPE
  NO              16              400
  YES              1              101
[1] 2 2
[1] FALSE
D571V9, continuous
[1] "Remove cluster labels:" "INPP5F MUTATED"        
clus
  INPP5F MUTATED INPP5F WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A4A1       TCGA-LN-A4A2 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"INPP5F WILD-TYPE" "INPP5F WILD-TYPE" "INPP5F WILD-TYPE" 
D571V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INPP5F MUTATED       3                         0
  INPP5F WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INPP5F MUTATED                                           0    16
  INPP5F WILD-TYPE                                         1   341
D571V11, multiclass
                                           clus
vv                                          INPP5F MUTATED INPP5F WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V12, binary
                  cls
clus                 0   1
  INPP5F MUTATED     0  14
  INPP5F WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED      0   14
  INPP5F WILD-TYPE   10  384
                        clus
vv                       INPP5F MUTATED INPP5F WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(572) Variable = KIAA1632 MUTATION ANALYSIS
D572V1, survival
                    sevent
clus2                  0   1
  KIAA1632 MUTATED    18  11
  KIAA1632 WILD-TYPE 320 205
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                29                525 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                11                205 
$`KIAA1632 MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NV TCGA-LN-A9FQ TCGA-Z6-A8JD 
       60.39         4.31        19.99        52.57        12.85         3.42 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8680 
        9.67        34.68        32.78         8.05        31.27        31.96 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5718 TCGA-CG-5721 TCGA-D7-8576 TCGA-D7-A4YU 
       11.77         1.02        36.00         6.02        14.66        16.44 
TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GH 
        5.92        11.31        11.44        22.32        22.68        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        8.98         0.10        14.07        74.53        38.14 

$`KIAA1632 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.24        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        21.37        29.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
               0.1                0.0 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
             74.53             122.30 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
             14.07              13.55 
[1] "0.1 - 74.5 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D572V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1632 MUTATED         1        1        2        1         5         6
  KIAA1632 WILD-TYPE       9       19       44       30        79        77
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1632 MUTATED           0          3          3          4        4
  KIAA1632 WILD-TYPE        29         81         59         35       39
                    vv
clus                 STAGE IVA
  KIAA1632 MUTATED           0
  KIAA1632 WILD-TYPE         4
D572V3, multiclass
            clus
vv           KIAA1632 MUTATED KIAA1632 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 5                 79
  STAGE IIB                 6                 77
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                3                 59
  STAGE IIIC                4                 35
  STAGE IV                  4                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1632 MUTATED       4   3  15   9
  KIAA1632 WILD-TYPE    50 132 246  93
D572V4, multiclass
       clus
vv      KIAA1632 MUTATED KIAA1632 WILD-TYPE
  T0+T1                4                 50
  T2                   3                132
  T3                  15                246
  T4                   9                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1632 MUTATED    11  10   4   6
  KIAA1632 WILD-TYPE 184 163  85  79
D572V5, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  N0               11                184
  N1               10                163
  N2                4                 85
  N3                6                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V6, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    28   3
  KIAA1632 WILD-TYPE 454  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     28    3
  KIAA1632 WILD-TYPE  454   35
   clus
vv  KIAA1632 MUTATED KIAA1632 WILD-TYPE
  0               28                454
  1                3                 35
[1] 2 2
[1] FALSE
D572V7, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    15  18
  KIAA1632 WILD-TYPE 157 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     15   18
  KIAA1632 WILD-TYPE  157  388
        clus
vv       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  FEMALE               15                157
  MALE                 18                388
[1] 2 2
[1] FALSE
D572V8, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    27   1
  KIAA1632 WILD-TYPE 389 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     27    1
  KIAA1632 WILD-TYPE  389  101
     clus
vv    KIAA1632 MUTATED KIAA1632 WILD-TYPE
  NO                27                389
  YES                1                101
[1] 2 2
[1] FALSE
D572V9, continuous
[1] "Remove cluster labels:" "KIAA1632 MUTATED"      
clus
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-VR-AA7I 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1632 WILD-TYPE" 
D572V10, continuous
[1] "Remove cluster labels:" "KIAA1632 MUTATED"      
clus
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A4OE 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A88T         TCGA-L5-A88Y 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A8NG         TCGA-L5-A8NT         TCGA-Q9-A6FU 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IC-A6RE         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YC         TCGA-IG-A4P3 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IG-A4QT         TCGA-IG-A50L         TCGA-IG-A5B8 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-IG-A6QS         TCGA-IG-A8O2         TCGA-IG-A97H 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-JY-A6FA         TCGA-JY-A6FE         TCGA-JY-A6FG 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-JY-A6FH         TCGA-KH-A6WC         TCGA-L5-A43C 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A43E         TCGA-L5-A43H         TCGA-L5-A4OH 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OT 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" "KIAA1632 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1632 MUTATED       9                         0
  KIAA1632 WILD-TYPE   124                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1632 MUTATED                                           0    20
  KIAA1632 WILD-TYPE                                         1   337
D572V11, multiclass
                                           clus
vv                                          KIAA1632 MUTATED KIAA1632 WILD-TYPE
  ASIAN                                                    9                124
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   20                337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V12, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED     1  23
  KIAA1632 WILD-TYPE   9 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED      1   23
  KIAA1632 WILD-TYPE    9  375
                        clus
vv                       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               23                375
[1] 2 2
[1] FALSE

Clustering(573) Variable = PHACTR1 MUTATION ANALYSIS
D573V1, survival
                   sevent
clus2                 0   1
  PHACTR1 MUTATED     3   5
  PHACTR1 WILD-TYPE 335 211
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                8               546 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                5               211 
$`PHACTR1 MUTATED`
TCGA-LN-A9FP TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-A4QL TCGA-CG-4305 TCGA-D7-A6EY 
       12.03         6.61        14.43        16.14        15.95        11.44 
TCGA-HU-A4GQ TCGA-VQ-A8P2 
        0.10        38.14 

$`PHACTR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
              0.1               0.0 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            38.14            122.30 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
           13.230            13.565 
[1] "0.1 - 38.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D573V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR1 MUTATED         1        0        0        1         1         0
  PHACTR1 WILD-TYPE       9       20       46       30        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR1 MUTATED           2          2          2          1        0
  PHACTR1 WILD-TYPE        27         82         60         38       43
                   vv
clus                STAGE IVA
  PHACTR1 MUTATED           0
  PHACTR1 WILD-TYPE         4
D573V3, multiclass
            clus
vv           PHACTR1 MUTATED PHACTR1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                2                27
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PHACTR1 MUTATED       1   3   2   4
  PHACTR1 WILD-TYPE    53 132 259  98
D573V4, multiclass
       clus
vv      PHACTR1 MUTATED PHACTR1 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  2               259
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PHACTR1 MUTATED     2   5   1   2
  PHACTR1 WILD-TYPE 193 168  88  83
D573V5, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  N0               2               193
  N1               5               168
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V6, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED    10   0
  PHACTR1 WILD-TYPE 472  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED     10    0
  PHACTR1 WILD-TYPE  472   38
   clus
vv  PHACTR1 MUTATED PHACTR1 WILD-TYPE
  0              10               472
  1               0                38
[1] 2 2
[1] FALSE
D573V7, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     6   5
  PHACTR1 WILD-TYPE 166 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      6    5
  PHACTR1 WILD-TYPE  166  401
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  FEMALE               6               166
  MALE                 5               401
[1] 2 2
[1] FALSE
D573V8, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     7   2
  PHACTR1 WILD-TYPE 409 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      7    2
  PHACTR1 WILD-TYPE  409  100
     clus
vv    PHACTR1 MUTATED PHACTR1 WILD-TYPE
  NO                7               409
  YES               2               100
[1] 2 2
[1] FALSE
D573V9, continuous
D573V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR1 MUTATED       2                         1
  PHACTR1 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR1 MUTATED                                           0     7
  PHACTR1 WILD-TYPE                                         1   350
D573V11, multiclass
                                           clus
vv                                          PHACTR1 MUTATED PHACTR1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V12, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     0   9
  PHACTR1 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      0    9
  PHACTR1 WILD-TYPE   10  389
                        clus
vv                       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(574) Variable = PHACTR4 MUTATION ANALYSIS
D574V1, survival
                   sevent
clus2                 0   1
  PHACTR4 MUTATED     8   3
  PHACTR4 WILD-TYPE 330 213
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
               11               543 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                3               213 
$`PHACTR4 MUTATED`
TCGA-IC-A6RE TCGA-L5-A4OJ TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-5733 
        7.69        21.01        34.68         6.18         1.12        21.07 
TCGA-D7-6525 TCGA-FP-7829 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-VQ-A8P2 
       13.35        19.53        29.98         0.10        38.14 

$`PHACTR4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
              0.1               0.0 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
            38.14            122.30 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
            19.53             13.55 
[1] "0.1 - 38.1 (19.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D574V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR4 MUTATED         1        0        0        0         4         2
  PHACTR4 WILD-TYPE       9       20       46       31        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR4 MUTATED           0          3          0          1        0
  PHACTR4 WILD-TYPE        29         81         62         38       43
                   vv
clus                STAGE IVA
  PHACTR4 MUTATED           0
  PHACTR4 WILD-TYPE         4
D574V3, multiclass
            clus
vv           PHACTR4 MUTATED PHACTR4 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                4                80
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PHACTR4 MUTATED       2   3   4   2
  PHACTR4 WILD-TYPE    52 132 257 100
D574V4, multiclass
       clus
vv      PHACTR4 MUTATED PHACTR4 WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PHACTR4 MUTATED     4   5   3   0
  PHACTR4 WILD-TYPE 191 168  86  85
D574V5, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  N0               4               191
  N1               5               168
  N2               3                86
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V6, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED    12   0
  PHACTR4 WILD-TYPE 470  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED     12    0
  PHACTR4 WILD-TYPE  470   38
   clus
vv  PHACTR4 MUTATED PHACTR4 WILD-TYPE
  0              12               470
  1               0                38
[1] 2 2
[1] FALSE
D574V7, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     5   7
  PHACTR4 WILD-TYPE 167 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      5    7
  PHACTR4 WILD-TYPE  167  399
        clus
vv       PHACTR4 MUTATED PHACTR4 WILD-TYPE
  FEMALE               5               167
  MALE                 7               399
[1] 2 2
[1] FALSE
D574V8, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     9   2
  PHACTR4 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      9    2
  PHACTR4 WILD-TYPE  407  100
     clus
vv    PHACTR4 MUTATED PHACTR4 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D574V9, continuous
D574V10, continuous
[1] "Remove cluster labels:" "PHACTR4 MUTATED"       
clus
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IG-A3QL 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" "PHACTR4 WILD-TYPE" 
       TCGA-Z6-AAPN 
"PHACTR4 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR4 MUTATED       2                         0
  PHACTR4 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR4 MUTATED                                           0     9
  PHACTR4 WILD-TYPE                                         1   348
D574V11, multiclass
                                           clus
vv                                          PHACTR4 MUTATED PHACTR4 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V12, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     0   9
  PHACTR4 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      0    9
  PHACTR4 WILD-TYPE   10  389
                        clus
vv                       PHACTR4 MUTATED PHACTR4 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(575) Variable = MRPS5 MUTATION ANALYSIS
D575V1, survival
                 sevent
clus2               0   1
  MRPS5 MUTATED     7   2
  MRPS5 WILD-TYPE 331 214
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              9             545 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              2             214 
$`MRPS5 MUTATED`
TCGA-LN-A9FR TCGA-R6-A8WC TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5723 
       12.26         2.30        34.68        31.96         6.58       105.07 
TCGA-D7-A6EY TCGA-F1-A448 TCGA-FP-A4BE 
       11.44        21.27        11.08 

$`MRPS5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
            2.3             0.0 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
         105.07          122.30 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          12.26           13.58 
[1] "2.3 - 105.1 (12.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D575V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRPS5 MUTATED         0        0        0        1         3         1
  MRPS5 WILD-TYPE      10       20       46       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MRPS5 MUTATED           0          0          2          0        1         0
  MRPS5 WILD-TYPE        29         84         60         39       42         4
D575V3, multiclass
            clus
vv           MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MRPS5 MUTATED       0   2   5   1
  MRPS5 WILD-TYPE    54 133 256 101
D575V4, multiclass
       clus
vv      MRPS5 MUTATED MRPS5 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                5             256
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MRPS5 MUTATED     3   2   1   2
  MRPS5 WILD-TYPE 192 171  88  83
D575V5, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V6, binary
                 cls
clus                0   1
  MRPS5 MUTATED     7   1
  MRPS5 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      7    1
  MRPS5 WILD-TYPE  475   37
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D575V7, binary
                 cls
clus                0   1
  MRPS5 MUTATED     2   7
  MRPS5 WILD-TYPE 170 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      2    7
  MRPS5 WILD-TYPE  170  399
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  FEMALE             2             170
  MALE               7             399
[1] 2 2
[1] FALSE
D575V8, binary
                 cls
clus                0   1
  MRPS5 MUTATED     5   3
  MRPS5 WILD-TYPE 411  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      5    3
  MRPS5 WILD-TYPE  411   99
     clus
vv    MRPS5 MUTATED MRPS5 WILD-TYPE
  NO              5             411
  YES             3              99
[1] 2 2
[1] FALSE
D575V9, continuous
D575V10, continuous
[1] "Remove cluster labels:" "MRPS5 MUTATED"         
clus
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-Z6-AAPN 
"MRPS5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MRPS5 MUTATED       3                         1
  MRPS5 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRPS5 MUTATED                                           0     4
  MRPS5 WILD-TYPE                                         1   353
D575V11, multiclass
                                           clus
vv                                          MRPS5 MUTATED MRPS5 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V12, binary
                 cls
clus                0   1
  MRPS5 MUTATED     1   7
  MRPS5 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      1    7
  MRPS5 WILD-TYPE    9  391
                        clus
vv                       MRPS5 MUTATED MRPS5 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(576) Variable = SLC38A6 MUTATION ANALYSIS
D576V1, survival
                   sevent
clus2                 0   1
  SLC38A6 MUTATED     7   3
  SLC38A6 WILD-TYPE 331 213
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
               10               544 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                3               213 
$`SLC38A6 MUTATED`
TCGA-IG-A5B8 TCGA-R6-A8W8 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG 
        0.79         2.89        31.27         1.12        12.43         6.58 
TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5728 TCGA-FP-7829 
        8.05         6.02        65.10        19.53 

$`SLC38A6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
             0.79              0.00 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
             65.1             122.3 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
            7.315            13.730 
[1] "0.8 - 65.1 (7.3)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D576V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC38A6 MUTATED         0        0        2        2         2         1
  SLC38A6 WILD-TYPE      10       20       44       29        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A6 MUTATED           0          0          0          1        1
  SLC38A6 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  SLC38A6 MUTATED           0
  SLC38A6 WILD-TYPE         4
D576V3, multiclass
            clus
vv           SLC38A6 MUTATED SLC38A6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 2                29
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC38A6 MUTATED       0   2   5   2
  SLC38A6 WILD-TYPE    54 133 256 100
D576V4, multiclass
       clus
vv      SLC38A6 MUTATED SLC38A6 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  5               256
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC38A6 MUTATED     5   3   0   1
  SLC38A6 WILD-TYPE 190 170  89  84
D576V5, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  N0               5               190
  N1               3               170
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V6, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     9   0
  SLC38A6 WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      9    0
  SLC38A6 WILD-TYPE  473   38
   clus
vv  SLC38A6 MUTATED SLC38A6 WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D576V7, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     2   8
  SLC38A6 WILD-TYPE 170 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      2    8
  SLC38A6 WILD-TYPE  170  398
        clus
vv       SLC38A6 MUTATED SLC38A6 WILD-TYPE
  FEMALE               2               170
  MALE                 8               398
[1] 2 2
[1] FALSE
D576V8, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     8   1
  SLC38A6 WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      8    1
  SLC38A6 WILD-TYPE  408  101
     clus
vv    SLC38A6 MUTATED SLC38A6 WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D576V9, continuous
D576V10, continuous
[1] "Remove cluster labels:" "SLC38A6 MUTATED"       
clus
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A6QS 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" "SLC38A6 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC38A6 MUTATED       2                         0
  SLC38A6 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC38A6 MUTATED                                           0     5
  SLC38A6 WILD-TYPE                                         1   352
D576V11, multiclass
                                           clus
vv                                          SLC38A6 MUTATED SLC38A6 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V12, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     0   7
  SLC38A6 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      0    7
  SLC38A6 WILD-TYPE   10  391
                        clus
vv                       SLC38A6 MUTATED SLC38A6 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(577) Variable = PDS5A MUTATION ANALYSIS
D577V1, survival
                 sevent
clus2               0   1
  PDS5A MUTATED    19   4
  PDS5A WILD-TYPE 319 212
  PDS5A MUTATED PDS5A WILD-TYPE 
             23             531 
  PDS5A MUTATED PDS5A WILD-TYPE 
              4             212 
$`PDS5A MUTATED`
TCGA-Q9-A6FU TCGA-LN-A4A6 TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-AASW TCGA-Z6-A9VB 
        5.16        12.85        53.95         5.29         9.27         1.32 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8680 
        2.66        26.70         6.97        34.68         1.12        31.96 
TCGA-CD-8531 TCGA-CG-4462 TCGA-CG-5721 TCGA-D7-5579 TCGA-FP-A4BE TCGA-HF-7132 
       12.59         0.00         6.02        20.91        11.08        77.29 
TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A666 TCGA-VQ-A8P2 
       29.98        29.00        14.07        14.04        38.14 

$`PDS5A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         2.10        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PDS5A MUTATED PDS5A WILD-TYPE 
            0.0             0.1 
  PDS5A MUTATED PDS5A WILD-TYPE 
          77.29          122.30 
  PDS5A MUTATED PDS5A WILD-TYPE 
          12.85           13.58 
[1] "0.0 - 77.3 (12.8)"  "0.1 - 122.3 (13.6)"
[1] "hr=" "2.3"
D577V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDS5A MUTATED         0        0        1        2         6         2
  PDS5A WILD-TYPE      10       20       45       29        78        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDS5A MUTATED           0          5          1          1        3         0
  PDS5A WILD-TYPE        29         79         61         38       40         4
D577V3, multiclass
            clus
vv           PDS5A MUTATED PDS5A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PDS5A MUTATED       2   4  10   6
  PDS5A WILD-TYPE    52 131 251  96
D577V4, multiclass
       clus
vv      PDS5A MUTATED PDS5A WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3               10             251
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PDS5A MUTATED     7   9   3   2
  PDS5A WILD-TYPE 188 164  86  83
D577V5, multiclass
    clus
vv   PDS5A MUTATED PDS5A WILD-TYPE
  N0             7             188
  N1             9             164
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V6, binary
                 cls
clus                0   1
  PDS5A MUTATED    17   2
  PDS5A WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED     17    2
  PDS5A WILD-TYPE  465   36
   clus
vv  PDS5A MUTATED PDS5A WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D577V7, binary
                 cls
clus                0   1
  PDS5A MUTATED     7  17
  PDS5A WILD-TYPE 165 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED      7   17
  PDS5A WILD-TYPE  165  389
        clus
vv       PDS5A MUTATED PDS5A WILD-TYPE
  FEMALE             7             165
  MALE              17             389
[1] 2 2
[1] FALSE
D577V8, binary
                 cls
clus                0   1
  PDS5A MUTATED    17   5
  PDS5A WILD-TYPE 399  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED     17    5
  PDS5A WILD-TYPE  399   97
     clus
vv    PDS5A MUTATED PDS5A WILD-TYPE
  NO             17             399
  YES             5              97
[1] 2 2
[1] FALSE
D577V9, continuous
D577V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDS5A MUTATED       6                         1
  PDS5A WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDS5A MUTATED                                           0    13
  PDS5A WILD-TYPE                                         1   344
D577V11, multiclass
                                           clus
vv                                          PDS5A MUTATED PDS5A WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V12, binary
                 cls
clus                0   1
  PDS5A MUTATED     1  19
  PDS5A WILD-TYPE   9 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED      1   19
  PDS5A WILD-TYPE    9  379
                        clus
vv                       PDS5A MUTATED PDS5A WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(578) Variable = KLHL14 MUTATION ANALYSIS
D578V1, survival
                  sevent
clus2                0   1
  KLHL14 MUTATED    13   4
  KLHL14 WILD-TYPE 325 212
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              17              537 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               4              212 
$`KLHL14 MUTATED`
TCGA-LN-A4A2 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8485 
       12.49        34.68        29.59         0.26         4.31         9.21 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4J8 TCGA-CG-4305 TCGA-CG-5724 TCGA-CG-5733 
        1.12        28.14        13.51        15.95        12.03        21.07 
TCGA-D7-6522 TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-HU-8602 
       18.61         5.92        22.29        21.27        22.32 

$`KLHL14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KLHL14 MUTATED KLHL14 WILD-TYPE 
            0.26             0.00 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           34.68           122.30 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           15.95            13.55 
[1] "0.3 - 34.7 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D578V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHL14 MUTATED         1        0        4        1         3         3
  KLHL14 WILD-TYPE       9       20       42       30        81        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL14 MUTATED           0          2          2          2        1
  KLHL14 WILD-TYPE        29         82         60         37       42
                  vv
clus               STAGE IVA
  KLHL14 MUTATED           0
  KLHL14 WILD-TYPE         4
D578V3, multiclass
            clus
vv           KLHL14 MUTATED KLHL14 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KLHL14 MUTATED       1   6   7   5
  KLHL14 WILD-TYPE    53 129 254  97
D578V4, multiclass
       clus
vv      KLHL14 MUTATED KLHL14 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 7              254
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KLHL14 MUTATED    10   4   1   5
  KLHL14 WILD-TYPE 185 169  88  80
D578V5, multiclass
    clus
vv   KLHL14 MUTATED KLHL14 WILD-TYPE
  N0             10              185
  N1              4              169
  N2              1               88
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V6, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    18   1
  KLHL14 WILD-TYPE 464  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     18    1
  KLHL14 WILD-TYPE  464   37
   clus
vv  KLHL14 MUTATED KLHL14 WILD-TYPE
  0             18              464
  1              1               37
[1] 2 2
[1] FALSE
D578V7, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    13   7
  KLHL14 WILD-TYPE 159 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     13    7
  KLHL14 WILD-TYPE  159  399
        clus
vv       KLHL14 MUTATED KLHL14 WILD-TYPE
  FEMALE             13              159
  MALE                7              399
[1] 2 2
[1] FALSE
D578V8, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    16   2
  KLHL14 WILD-TYPE 400 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     16    2
  KLHL14 WILD-TYPE  400  100
     clus
vv    KLHL14 MUTATED KLHL14 WILD-TYPE
  NO              16              400
  YES              2              100
[1] 2 2
[1] FALSE
D578V9, continuous
[1] "Remove cluster labels:" "KLHL14 MUTATED"        
clus
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
D578V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KLHL14 MUTATED       2                         1
  KLHL14 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHL14 MUTATED                                           0    14
  KLHL14 WILD-TYPE                                         1   343
D578V11, multiclass
                                           clus
vv                                          KLHL14 MUTATED KLHL14 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V12, binary
                  cls
clus                 0   1
  KLHL14 MUTATED     1  16
  KLHL14 WILD-TYPE   9 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED      1   16
  KLHL14 WILD-TYPE    9  382
                        clus
vv                       KLHL14 MUTATED KLHL14 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(579) Variable = F8 MUTATION ANALYSIS
D579V1, survival
              sevent
clus2            0   1
  F8 MUTATED    18  16
  F8 WILD-TYPE 320 200
  F8 MUTATED F8 WILD-TYPE 
          34          520 
  F8 MUTATED F8 WILD-TYPE 
          16          200 
$`F8 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-IG-A50L TCGA-JY-A93D 
       19.99        21.99        25.78        20.05         0.53        31.56 
TCGA-L5-A4OF TCGA-L5-A4OX TCGA-LN-A8I1 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 
       26.33         7.43        13.18         6.97         6.61        34.68 
TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8366 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8690 
       29.59         2.66         0.95        25.05        31.96        10.68 
TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-5577 TCGA-D7-6521 TCGA-D7-8576 
        6.58         9.01         6.02        25.71        18.54        14.66 
TCGA-D7-A6F2 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GT 
       15.65        77.29        30.51        22.68        11.77         6.51 
TCGA-HU-A4H8 TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-VQ-A8P2 
       14.07        18.21        16.67        38.14 

$`F8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        0.23        20.15         9.86        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
       31.10         0.26        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  F8 MUTATED F8 WILD-TYPE 
        0.53         0.00 
  F8 MUTATED F8 WILD-TYPE 
       77.29       122.30 
  F8 MUTATED F8 WILD-TYPE 
      17.440       13.445 
[1] "0.5 - 77.3 (17.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D579V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  F8 MUTATED         0        1        4        1         6         4         3
  F8 WILD-TYPE      10       19       42       30        78        79        26
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F8 MUTATED            5          2          4        5         0
  F8 WILD-TYPE         79         60         35       38         4
D579V3, multiclass
            clus
vv           F8 MUTATED F8 WILD-TYPE
  STAGE I             0           10
  STAGE IA            1           19
  STAGE IB            4           42
  STAGE II            1           30
  STAGE IIA           6           78
  STAGE IIB           4           79
  STAGE III           3           26
  STAGE IIIA          5           79
  STAGE IIIB          2           60
  STAGE IIIC          4           35
  STAGE IV            5           38
  STAGE IVA           0            4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T0+T1  T2  T3  T4
  F8 MUTATED       4  10  14   9
  F8 WILD-TYPE    50 125 247  93
D579V4, multiclass
       clus
vv      F8 MUTATED F8 WILD-TYPE
  T0+T1          4           50
  T2            10          125
  T3            14          247
  T4             9           93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2  N3
  F8 MUTATED    11  14   3   9
  F8 WILD-TYPE 184 159  86  76
D579V5, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  N0         11          184
  N1         14          159
  N2          3           86
  N3          9           76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V6, binary
              cls
clus             0   1
  F8 MUTATED    31   4
  F8 WILD-TYPE 451  34
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     31    4
  F8 WILD-TYPE  451   34
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0         31          451
  1          4           34
[1] 2 2
[1] FALSE
D579V7, binary
              cls
clus             0   1
  F8 MUTATED    17  21
  F8 WILD-TYPE 155 385
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     17   21
  F8 WILD-TYPE  155  385
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE         17          155
  MALE           21          385
[1] 2 2
[1] FALSE
D579V8, binary
              cls
clus             0   1
  F8 MUTATED    27   5
  F8 WILD-TYPE 389  97
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     27    5
  F8 WILD-TYPE  389   97
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO          27          389
  YES          5           97
[1] 2 2
[1] FALSE
D579V9, continuous
D579V10, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN
  F8 MUTATED       8                         0
  F8 WILD-TYPE   125                        14
              vv
clus           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  F8 MUTATED                                           0    22
  F8 WILD-TYPE                                         1   335
D579V11, multiclass
                                           clus
vv                                          F8 MUTATED F8 WILD-TYPE
  ASIAN                                              8          125
  BLACK OR AFRICAN AMERICAN                          0           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0            1
  WHITE                                             22          335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V12, binary
              cls
clus             0   1
  F8 MUTATED     0  25
  F8 WILD-TYPE  10 373
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      0   25
  F8 WILD-TYPE   10  373
                        clus
vv                       F8 MUTATED F8 WILD-TYPE
  HISPANIC OR LATINO              0           10
  NOT HISPANIC OR LATINO         25          373
[1] 2 2
[1] FALSE

Clustering(580) Variable = PLAGL2 MUTATION ANALYSIS
D580V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     6   3
  PLAGL2 WILD-TYPE 332 213
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               9              545 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               3              213 
$`PLAGL2 MUTATED`
TCGA-L5-A8NM TCGA-LN-A49W TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-8059 TCGA-CG-5721 
        7.76        13.25        32.78        33.63        14.43         6.02 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ 
       11.08        22.32         0.10 

$`PLAGL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
             0.1              0.0 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           33.63           122.30 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           13.25            13.58 
[1] "0.1 - 33.6 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D580V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAGL2 MUTATED         0        0        0        0         3         2
  PLAGL2 WILD-TYPE      10       20       46       31        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           2          0          0          1        1
  PLAGL2 WILD-TYPE        27         84         62         38       42
                  vv
clus               STAGE IVA
  PLAGL2 MUTATED           0
  PLAGL2 WILD-TYPE         4
D580V3, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PLAGL2 MUTATED       0   1   4   4
  PLAGL2 WILD-TYPE    54 134 257  98
D580V4, multiclass
       clus
vv      PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 4              257
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PLAGL2 MUTATED     4   4   1   0
  PLAGL2 WILD-TYPE 191 169  88  85
D580V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V6, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     9   0
  PLAGL2 WILD-TYPE 473  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      9    0
  PLAGL2 WILD-TYPE  473   38
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              9              473
  1              0               38
[1] 2 2
[1] FALSE
D580V7, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   6
  PLAGL2 WILD-TYPE 169 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    6
  PLAGL2 WILD-TYPE  169  400
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  FEMALE              3              169
  MALE                6              400
[1] 2 2
[1] FALSE
D580V8, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     7   2
  PLAGL2 WILD-TYPE 409 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      7    2
  PLAGL2 WILD-TYPE  409  100
     clus
vv    PLAGL2 MUTATED PLAGL2 WILD-TYPE
  NO               7              409
  YES              2              100
[1] 2 2
[1] FALSE
D580V9, continuous
[1] "Remove cluster labels:" "PLAGL2 MUTATED"        
clus
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
D580V10, continuous
[1] "Remove cluster labels:" "PLAGL2 MUTATED"        
clus
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" "PLAGL2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PLAGL2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PLAGL2 MUTATED       3                         1
  PLAGL2 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLAGL2 MUTATED                                           0     4
  PLAGL2 WILD-TYPE                                         1   353
D580V11, multiclass
                                           clus
vv                                          PLAGL2 MUTATED PLAGL2 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V12, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     0   6
  PLAGL2 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      0    6
  PLAGL2 WILD-TYPE   10  392
                        clus
vv                       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(581) Variable = C8ORF38 MUTATION ANALYSIS
D581V1, survival
                   sevent
clus2                 0   1
  C8ORF38 MUTATED     7   1
  C8ORF38 WILD-TYPE 331 215
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                8               546 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                1               215 
$`C8ORF38 MUTATED`
TCGA-L5-A893 TCGA-BR-4201 TCGA-BR-8078 TCGA-F1-6874 TCGA-HU-A4GX TCGA-HU-A4HD 
        3.02        30.90        29.59        14.47        20.25        33.40 
TCGA-MX-A5UJ TCGA-SW-A7EA 
       19.73        19.04 

$`C8ORF38 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
             3.02              0.00 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
             33.4             122.3 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
           19.990            13.495 
[1] "3.0 - 33.4 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4"  
D581V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C8ORF38 MUTATED         1        0        2        0         0         1
  C8ORF38 WILD-TYPE       9       20       44       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C8ORF38 MUTATED           0          2          0          1        1
  C8ORF38 WILD-TYPE        29         82         62         38       42
                   vv
clus                STAGE IVA
  C8ORF38 MUTATED           0
  C8ORF38 WILD-TYPE         4
D581V3, multiclass
            clus
vv           C8ORF38 MUTATED C8ORF38 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C8ORF38 MUTATED       1   3   2   3
  C8ORF38 WILD-TYPE    53 132 259  99
D581V4, multiclass
       clus
vv      C8ORF38 MUTATED C8ORF38 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C8ORF38 MUTATED     4   0   4   0
  C8ORF38 WILD-TYPE 191 173  85  85
D581V5, multiclass
    clus
vv   C8ORF38 MUTATED C8ORF38 WILD-TYPE
  N0               4               191
  N1               0               173
  N2               4                85
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V6, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     9   0
  C8ORF38 WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      9    0
  C8ORF38 WILD-TYPE  473   38
   clus
vv  C8ORF38 MUTATED C8ORF38 WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D581V7, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     7   2
  C8ORF38 WILD-TYPE 165 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      7    2
  C8ORF38 WILD-TYPE  165  404
        clus
vv       C8ORF38 MUTATED C8ORF38 WILD-TYPE
  FEMALE               7               165
  MALE                 2               404
[1] 2 2
[1] FALSE
D581V8, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     8   0
  C8ORF38 WILD-TYPE 408 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      8    0
  C8ORF38 WILD-TYPE  408  102
     clus
vv    C8ORF38 MUTATED C8ORF38 WILD-TYPE
  NO                8               408
  YES               0               102
[1] 2 2
[1] FALSE
D581V9, continuous
D581V10, continuous
[1] "Remove cluster labels:" "C8ORF38 MUTATED"       
clus
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A8NE 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" "C8ORF38 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C8ORF38 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C8ORF38 MUTATED       2                         0
  C8ORF38 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C8ORF38 MUTATED                                           0     7
  C8ORF38 WILD-TYPE                                         1   350
D581V11, multiclass
                                           clus
vv                                          C8ORF38 MUTATED C8ORF38 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V12, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     0   8
  C8ORF38 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      0    8
  C8ORF38 WILD-TYPE   10  390
                        clus
vv                       C8ORF38 MUTATED C8ORF38 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(582) Variable = SIX3 MUTATION ANALYSIS
D582V1, survival
                sevent
clus2              0   1
  SIX3 MUTATED     6   4
  SIX3 WILD-TYPE 332 212
  SIX3 MUTATED SIX3 WILD-TYPE 
            10            544 
  SIX3 MUTATED SIX3 WILD-TYPE 
             4            212 
$`SIX3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NR TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-8372 TCGA-BR-8487 
       19.99         8.71         9.34         9.67        31.27         1.12 
TCGA-BR-A4QL TCGA-CG-5718 TCGA-HU-A4G8 TCGA-MX-A5UJ 
       16.14        36.00        22.68        19.73 

$`SIX3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        9.01        18.97         7.07        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SIX3 MUTATED SIX3 WILD-TYPE 
          1.12           0.00 
  SIX3 MUTATED SIX3 WILD-TYPE 
          36.0          122.3 
  SIX3 MUTATED SIX3 WILD-TYPE 
        17.935         13.530 
[1] "1.1 - 36.0 (17.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D582V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SIX3 MUTATED         1        0        0        1         1         1
  SIX3 WILD-TYPE       9       20       46       30        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SIX3 MUTATED           1          2          1          2        0         0
  SIX3 WILD-TYPE        28         82         61         37       43         4
D582V3, multiclass
            clus
vv           SIX3 MUTATED SIX3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SIX3 MUTATED       1   1   6   2
  SIX3 WILD-TYPE    53 134 255 100
D582V4, multiclass
       clus
vv      SIX3 MUTATED SIX3 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               6            255
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SIX3 MUTATED     2   5   1   3
  SIX3 WILD-TYPE 193 168  88  82
D582V5, multiclass
    clus
vv   SIX3 MUTATED SIX3 WILD-TYPE
  N0            2            193
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V6, binary
                cls
clus               0   1
  SIX3 MUTATED    10   0
  SIX3 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED     10    0
  SIX3 WILD-TYPE  472   38
   clus
vv  SIX3 MUTATED SIX3 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D582V7, binary
                cls
clus               0   1
  SIX3 MUTATED     8   4
  SIX3 WILD-TYPE 164 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      8    4
  SIX3 WILD-TYPE  164  402
        clus
vv       SIX3 MUTATED SIX3 WILD-TYPE
  FEMALE            8            164
  MALE              4            402
[1] 2 2
[1] FALSE
D582V8, binary
                cls
clus               0   1
  SIX3 MUTATED    11   0
  SIX3 WILD-TYPE 405 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED     11    0
  SIX3 WILD-TYPE  405  102
     clus
vv    SIX3 MUTATED SIX3 WILD-TYPE
  NO            11            405
  YES            0            102
[1] 2 2
[1] FALSE
D582V9, continuous
D582V10, continuous
[1] "Remove cluster labels:" "SIX3 MUTATED"          
clus
  SIX3 MUTATED SIX3 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" "SIX3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SIX3 MUTATED       1                         1
  SIX3 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIX3 MUTATED                                           0     8
  SIX3 WILD-TYPE                                         1   349
D582V11, multiclass
                                           clus
vv                                          SIX3 MUTATED SIX3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V12, binary
                cls
clus               0   1
  SIX3 MUTATED     0   9
  SIX3 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      0    9
  SIX3 WILD-TYPE   10  389
                        clus
vv                       SIX3 MUTATED SIX3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(583) Variable = ACAA2 MUTATION ANALYSIS
D583V1, survival
                 sevent
clus2               0   1
  ACAA2 MUTATED     5   7
  ACAA2 WILD-TYPE 333 209
  ACAA2 MUTATED ACAA2 WILD-TYPE 
             12             542 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              7             209 
$`ACAA2 MUTATED`
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-S8-A6BW TCGA-VR-AA7D TCGA-B7-A5TI TCGA-BR-4184 
       13.48         7.76        20.38         9.17        19.56         6.97 
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-IN-A6RL TCGA-VQ-A8P2 
       32.78        35.84        16.14         6.58        13.35        38.14 

$`ACAA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ACAA2 MUTATED ACAA2 WILD-TYPE 
           6.58            0.00 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
          38.14          122.30 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
         14.810          13.565 
[1] "6.6 - 38.1 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D583V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACAA2 MUTATED         0        0        2        0         2         1
  ACAA2 WILD-TYPE      10       20       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAA2 MUTATED           1          3          1          2        0         0
  ACAA2 WILD-TYPE        28         81         61         37       43         4
D583V3, multiclass
            clus
vv           ACAA2 MUTATED ACAA2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ACAA2 MUTATED       0   4   6   2
  ACAA2 WILD-TYPE    54 131 255 100
D583V4, multiclass
       clus
vv      ACAA2 MUTATED ACAA2 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACAA2 MUTATED     4   5   0   3
  ACAA2 WILD-TYPE 191 168  89  82
D583V5, multiclass
    clus
vv   ACAA2 MUTATED ACAA2 WILD-TYPE
  N0             4             191
  N1             5             168
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V6, binary
                 cls
clus                0   1
  ACAA2 MUTATED    10   0
  ACAA2 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED     10    0
  ACAA2 WILD-TYPE  472   38
   clus
vv  ACAA2 MUTATED ACAA2 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D583V7, binary
                 cls
clus                0   1
  ACAA2 MUTATED     4   8
  ACAA2 WILD-TYPE 168 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      4    8
  ACAA2 WILD-TYPE  168  398
        clus
vv       ACAA2 MUTATED ACAA2 WILD-TYPE
  FEMALE             4             168
  MALE               8             398
[1] 2 2
[1] FALSE
D583V8, binary
                 cls
clus                0   1
  ACAA2 MUTATED    10   2
  ACAA2 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED     10    2
  ACAA2 WILD-TYPE  406  100
     clus
vv    ACAA2 MUTATED ACAA2 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D583V9, continuous
[1] "Remove cluster labels:" "ACAA2 MUTATED"         
clus
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
D583V10, continuous
[1] "Remove cluster labels:" "ACAA2 MUTATED"         
clus
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7I 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" "ACAA2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ACAA2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACAA2 MUTATED       1                         0
  ACAA2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACAA2 MUTATED                                           0    10
  ACAA2 WILD-TYPE                                         1   347
D583V11, multiclass
                                           clus
vv                                          ACAA2 MUTATED ACAA2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V12, binary
                 cls
clus                0   1
  ACAA2 MUTATED     0   8
  ACAA2 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      0    8
  ACAA2 WILD-TYPE   10  390
                        clus
vv                       ACAA2 MUTATED ACAA2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(584) Variable = DDX43 MUTATION ANALYSIS
D584V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     7   6
  DDX43 WILD-TYPE 331 210
  DDX43 MUTATED DDX43 WILD-TYPE 
             13             541 
  DDX43 MUTATED DDX43 WILD-TYPE 
              6             210 
$`DDX43 MUTATED`
TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4306 
        7.76         6.97         9.34         1.12        16.14         1.02 
TCGA-CG-4441 TCGA-D7-8572 TCGA-F1-A448 TCGA-HU-A4G6 TCGA-IP-7968 TCGA-VQ-A8DT 
       14.01        16.80        21.27        24.26         2.53        48.79 
TCGA-VQ-AA6B 
       32.94 

$`DDX43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DDX43 MUTATED DDX43 WILD-TYPE 
           1.02            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          48.79          122.30 
  DDX43 MUTATED DDX43 WILD-TYPE 
          14.01           13.55 
[1] "1.0 - 48.8 (14.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D584V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX43 MUTATED         0        1        0        0         1         2
  DDX43 WILD-TYPE      10       19       46       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX43 MUTATED           0          2          5          0        1         0
  DDX43 WILD-TYPE        29         82         57         39       42         4
D584V3, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             5              57
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DDX43 MUTATED       1   3   9   0
  DDX43 WILD-TYPE    53 132 252 102
D584V4, multiclass
       clus
vv      DDX43 MUTATED DDX43 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                9             252
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX43 MUTATED     2   3   5   3
  DDX43 WILD-TYPE 193 170  84  82
D584V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             2             193
  N1             3             170
  N2             5              84
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V6, binary
                 cls
clus                0   1
  DDX43 MUTATED    10   1
  DDX43 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     10    1
  DDX43 WILD-TYPE  472   37
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D584V7, binary
                 cls
clus                0   1
  DDX43 MUTATED     4  10
  DDX43 WILD-TYPE 168 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      4   10
  DDX43 WILD-TYPE  168  396
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             4             168
  MALE              10             396
[1] 2 2
[1] FALSE
D584V8, binary
                 cls
clus                0   1
  DDX43 MUTATED     7   3
  DDX43 WILD-TYPE 409  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      7    3
  DDX43 WILD-TYPE  409   99
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              7             409
  YES             3              99
[1] 2 2
[1] FALSE
D584V9, continuous
D584V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX43 MUTATED       1                         0
  DDX43 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX43 MUTATED                                           0    10
  DDX43 WILD-TYPE                                         1   347
D584V11, multiclass
                                           clus
vv                                          DDX43 MUTATED DDX43 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V12, binary
                 cls
clus                0   1
  DDX43 MUTATED     1   8
  DDX43 WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      1    8
  DDX43 WILD-TYPE    9  390
                        clus
vv                       DDX43 MUTATED DDX43 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(585) Variable = ASTE1 MUTATION ANALYSIS
D585V1, survival
                 sevent
clus2               0   1
  ASTE1 MUTATED    15   2
  ASTE1 WILD-TYPE 323 214
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             17             537 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              2             214 
$`ASTE1 MUTATED`
TCGA-L5-A4OG TCGA-CG-4460 TCGA-JY-A939 TCGA-L5-A4OO TCGA-L5-A8NR TCGA-Q9-A6FW 
        4.70        21.99        21.70         3.32         8.71         7.82 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8680 
       34.68        35.84         6.18        31.10        17.52        31.96 
TCGA-BR-A4PD TCGA-CG-4305 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HU-A4H8 
       20.65        15.95       105.07        11.08        14.07 

$`ASTE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 
       29.42         2.66        19.96         2.20         7.40         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ASTE1 MUTATED ASTE1 WILD-TYPE 
           3.32            0.00 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
         105.07          122.30 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
          17.52           13.51 
[1] "3.3 - 105.1 (17.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4"  
D585V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASTE1 MUTATED         2        0        2        2         4         2
  ASTE1 WILD-TYPE       8       20       44       29        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASTE1 MUTATED           1          1          1          2        2         0
  ASTE1 WILD-TYPE        28         83         61         37       41         4
D585V3, multiclass
            clus
vv           ASTE1 MUTATED ASTE1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ASTE1 MUTATED       4   3   7   5
  ASTE1 WILD-TYPE    50 132 254  97
D585V4, multiclass
       clus
vv      ASTE1 MUTATED ASTE1 WILD-TYPE
  T0+T1             4              50
  T2                3             132
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ASTE1 MUTATED     8   7   3   1
  ASTE1 WILD-TYPE 187 166  86  84
D585V5, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  N0             8             187
  N1             7             166
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V6, binary
                 cls
clus                0   1
  ASTE1 MUTATED    16   2
  ASTE1 WILD-TYPE 466  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED     16    2
  ASTE1 WILD-TYPE  466   36
   clus
vv  ASTE1 MUTATED ASTE1 WILD-TYPE
  0            16             466
  1             2              36
[1] 2 2
[1] FALSE
D585V7, binary
                 cls
clus                0   1
  ASTE1 MUTATED     9  10
  ASTE1 WILD-TYPE 163 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      9   10
  ASTE1 WILD-TYPE  163  396
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  FEMALE             9             163
  MALE              10             396
[1] 2 2
[1] FALSE
D585V8, binary
                 cls
clus                0   1
  ASTE1 MUTATED    16   1
  ASTE1 WILD-TYPE 400 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED     16    1
  ASTE1 WILD-TYPE  400  101
     clus
vv    ASTE1 MUTATED ASTE1 WILD-TYPE
  NO             16             400
  YES             1             101
[1] 2 2
[1] FALSE
D585V9, continuous
D585V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASTE1 MUTATED       2                         2
  ASTE1 WILD-TYPE   131                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASTE1 MUTATED                                           0    11
  ASTE1 WILD-TYPE                                         1   346
D585V11, multiclass
                                           clus
vv                                          ASTE1 MUTATED ASTE1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V12, binary
                 cls
clus                0   1
  ASTE1 MUTATED     0  12
  ASTE1 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      0   12
  ASTE1 WILD-TYPE   10  386
                        clus
vv                       ASTE1 MUTATED ASTE1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(586) Variable = CDC42EP1 MUTATION ANALYSIS
D586V1, survival
                    sevent
clus2                  0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 335 215
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                550 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 1                215 
$`CDC42EP1 MUTATED`
TCGA-BR-8361 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-A4GU 
       31.10         5.92        30.51         6.58 

$`CDC42EP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
              5.92               0.00 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
              31.1              122.3 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
            18.545             13.565 
[1] "5.9 - 31.1 (18.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D586V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC42EP1 MUTATED         0        0        0        0         0         2
  CDC42EP1 WILD-TYPE      10       20       46       31        84        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC42EP1 MUTATED           0          0          0          2        0
  CDC42EP1 WILD-TYPE        29         84         62         37       43
                    vv
clus                 STAGE IVA
  CDC42EP1 MUTATED           0
  CDC42EP1 WILD-TYPE         4
D586V3, multiclass
            clus
vv           CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  CDC42EP1 MUTATED       0   0   2   2
  CDC42EP1 WILD-TYPE    54 135 259 100
D586V4, multiclass
       clus
vv      CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  T0+T1                0                 54
  T2                   0                135
  T3                   2                259
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  CDC42EP1 MUTATED     0   2   1   1
  CDC42EP1 WILD-TYPE 195 171  88  84
D586V5, multiclass
    clus
vv   CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  N0                0                195
  N1                2                171
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V6, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     4   0
  CDC42EP1 WILD-TYPE 478  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      4    0
  CDC42EP1 WILD-TYPE  478   38
   clus
vv  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  0                4                478
  1                0                 38
[1] 2 2
[1] FALSE
D586V7, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 169 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      3    1
  CDC42EP1 WILD-TYPE  169  405
        clus
vv       CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  FEMALE                3                169
  MALE                  1                405
[1] 2 2
[1] FALSE
D586V8, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 413 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      3    1
  CDC42EP1 WILD-TYPE  413  101
     clus
vv    CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  NO                 3                413
  YES                1                101
[1] 2 2
[1] FALSE
D586V9, continuous
D586V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  CDC42EP1 MUTATED       1                         0
  CDC42EP1 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC42EP1 MUTATED                                           0     2
  CDC42EP1 WILD-TYPE                                         1   355
D586V11, multiclass
                                           clus
vv                                          CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V12, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     0   3
  CDC42EP1 WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      0    3
  CDC42EP1 WILD-TYPE   10  395
                        clus
vv                       CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(587) Variable = KCTD3 MUTATION ANALYSIS
D587V1, survival
                 sevent
clus2               0   1
  KCTD3 MUTATED     8   4
  KCTD3 WILD-TYPE 330 212
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             12             542 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4             212 
$`KCTD3 MUTATED`
TCGA-JY-A6FD TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8360 TCGA-BR-A4IY 
       68.02         6.97        34.68        14.43         6.18        12.89 
TCGA-BR-A4QL TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-IP-7968 TCGA-MX-A5UJ 
       16.14        77.29        24.20         0.10         2.53        19.73 

$`KCTD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
            0.1             0.0 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          77.29          122.30 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         15.285          13.530 
[1] "0.1 - 77.3 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D587V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCTD3 MUTATED         0        1        0        1         3         1
  KCTD3 WILD-TYPE      10       19       46       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCTD3 MUTATED           1          3          2          2        0         0
  KCTD3 WILD-TYPE        28         81         60         37       43         4
D587V3, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCTD3 MUTATED       1   1   7   5
  KCTD3 WILD-TYPE    53 134 254  97
D587V4, multiclass
       clus
vv      KCTD3 MUTATED KCTD3 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCTD3 MUTATED     6   4   3   2
  KCTD3 WILD-TYPE 189 169  86  83
D587V5, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V6, binary
                 cls
clus                0   1
  KCTD3 MUTATED    13   0
  KCTD3 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     13    0
  KCTD3 WILD-TYPE  469   38
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D587V7, binary
                 cls
clus                0   1
  KCTD3 MUTATED     7   8
  KCTD3 WILD-TYPE 165 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      7    8
  KCTD3 WILD-TYPE  165  398
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             7             165
  MALE               8             398
[1] 2 2
[1] FALSE
D587V8, binary
                 cls
clus                0   1
  KCTD3 MUTATED    10   1
  KCTD3 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     10    1
  KCTD3 WILD-TYPE  406  101
     clus
vv    KCTD3 MUTATED KCTD3 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D587V9, continuous
D587V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCTD3 MUTATED       4                         0
  KCTD3 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCTD3 MUTATED                                           0     9
  KCTD3 WILD-TYPE                                         1   348
D587V11, multiclass
                                           clus
vv                                          KCTD3 MUTATED KCTD3 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V12, binary
                 cls
clus                0   1
  KCTD3 MUTATED     0  12
  KCTD3 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0   12
  KCTD3 WILD-TYPE   10  386
                        clus
vv                       KCTD3 MUTATED KCTD3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(588) Variable = NHLRC1 MUTATION ANALYSIS
D588V1, survival
                  sevent
clus2                0   1
  NHLRC1 MUTATED     4   6
  NHLRC1 WILD-TYPE 334 210
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              10              544 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
               6              210 
$`NHLRC1 MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-A4MI TCGA-CG-4306 
       30.90         9.34        34.68        29.59        11.77         1.02 
TCGA-CG-5733 TCGA-D7-A4YY TCGA-HJ-7597 TCGA-VQ-A8P2 
       21.07        13.78        26.47        38.14 

$`NHLRC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
            1.02             0.00 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
           38.14           122.30 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
           23.77            13.51 
[1] "1.0 - 38.1 (23.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D588V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NHLRC1 MUTATED         0        0        2        0         1         1
  NHLRC1 WILD-TYPE      10       20       44       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC1 MUTATED           0          4          1          0        1
  NHLRC1 WILD-TYPE        29         80         61         39       42
                  vv
clus               STAGE IVA
  NHLRC1 MUTATED           0
  NHLRC1 WILD-TYPE         4
D588V3, multiclass
            clus
vv           NHLRC1 MUTATED NHLRC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NHLRC1 MUTATED       0   4   5   2
  NHLRC1 WILD-TYPE    54 131 256 100
D588V4, multiclass
       clus
vv      NHLRC1 MUTATED NHLRC1 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NHLRC1 MUTATED     4   4   2   1
  NHLRC1 WILD-TYPE 191 169  87  84
D588V5, multiclass
    clus
vv   NHLRC1 MUTATED NHLRC1 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V6, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED    10   1
  NHLRC1 WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED     10    1
  NHLRC1 WILD-TYPE  472   37
   clus
vv  NHLRC1 MUTATED NHLRC1 WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D588V7, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     5   7
  NHLRC1 WILD-TYPE 167 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      5    7
  NHLRC1 WILD-TYPE  167  399
        clus
vv       NHLRC1 MUTATED NHLRC1 WILD-TYPE
  FEMALE              5              167
  MALE                7              399
[1] 2 2
[1] FALSE
D588V8, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     7   3
  NHLRC1 WILD-TYPE 409  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      7    3
  NHLRC1 WILD-TYPE  409   99
     clus
vv    NHLRC1 MUTATED NHLRC1 WILD-TYPE
  NO               7              409
  YES              3               99
[1] 2 2
[1] FALSE
D588V9, continuous
D588V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NHLRC1 MUTATED       1                         0
  NHLRC1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NHLRC1 MUTATED                                           0     7
  NHLRC1 WILD-TYPE                                         1   350
D588V11, multiclass
                                           clus
vv                                          NHLRC1 MUTATED NHLRC1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V12, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     0   7
  NHLRC1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      0    7
  NHLRC1 WILD-TYPE   10  391
                        clus
vv                       NHLRC1 MUTATED NHLRC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(589) Variable = RNASEH2B MUTATION ANALYSIS
D589V1, survival
                    sevent
clus2                  0   1
  RNASEH2B MUTATED     3   0
  RNASEH2B WILD-TYPE 335 216
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                551 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 0                216 
$`RNASEH2B MUTATED`
TCGA-B7-A5TI TCGA-BR-8369 TCGA-HF-A5NB 
       19.56        14.04        30.51 

$`RNASEH2B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
             14.04               0.00 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
             30.51             122.30 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
             19.56              13.51 
[1] "14.0 - 30.5 (19.6)" "0.0 - 122.3 (13.5)"
[1] "hr="     "3300000"
D589V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNASEH2B MUTATED         0        0        0        0         0         1
  RNASEH2B WILD-TYPE      10       20       46       31        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEH2B MUTATED           0          0          1          2        0
  RNASEH2B WILD-TYPE        29         84         61         37       43
                    vv
clus                 STAGE IVA
  RNASEH2B MUTATED           0
  RNASEH2B WILD-TYPE         4
D589V3, multiclass
            clus
vv           RNASEH2B MUTATED RNASEH2B WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  RNASEH2B MUTATED       0   0   1   3
  RNASEH2B WILD-TYPE    54 135 260  99
D589V4, multiclass
       clus
vv      RNASEH2B MUTATED RNASEH2B WILD-TYPE
  T0+T1                0                 54
  T2                   0                135
  T3                   1                260
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  RNASEH2B MUTATED     1   0   0   3
  RNASEH2B WILD-TYPE 194 173  89  82
D589V5, multiclass
    clus
vv   RNASEH2B MUTATED RNASEH2B WILD-TYPE
  N0                1                194
  N1                0                173
  N2                0                 89
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V6, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     4   0
  RNASEH2B WILD-TYPE 478  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      4    0
  RNASEH2B WILD-TYPE  478   38
   clus
vv  RNASEH2B MUTATED RNASEH2B WILD-TYPE
  0                4                478
  1                0                 38
[1] 2 2
[1] FALSE
D589V7, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     2   2
  RNASEH2B WILD-TYPE 170 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      2    2
  RNASEH2B WILD-TYPE  170  404
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  FEMALE                2                170
  MALE                  2                404
[1] 2 2
[1] FALSE
D589V8, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     3   1
  RNASEH2B WILD-TYPE 413 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      3    1
  RNASEH2B WILD-TYPE  413  101
     clus
vv    RNASEH2B MUTATED RNASEH2B WILD-TYPE
  NO                 3                413
  YES                1                101
[1] 2 2
[1] FALSE
D589V9, continuous
D589V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  RNASEH2B MUTATED       0                         0
  RNASEH2B WILD-TYPE   133                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNASEH2B MUTATED                                           0     3
  RNASEH2B WILD-TYPE                                         1   354
D589V11, multiclass
                                           clus
vv                                          RNASEH2B MUTATED RNASEH2B WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V12, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     0   3
  RNASEH2B WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      0    3
  RNASEH2B WILD-TYPE   10  395
                        clus
vv                       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(590) Variable = HRNR MUTATION ANALYSIS
D590V1, survival
                sevent
clus2              0   1
  HRNR MUTATED    30  16
  HRNR WILD-TYPE 308 200
  HRNR MUTATED HRNR WILD-TYPE 
            46            508 
  HRNR MUTATED HRNR WILD-TYPE 
            16            200 
$`HRNR MUTATED`
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A8NH TCGA-L5-A8NI TCGA-LN-A49P TCGA-LN-A8HZ 
       19.99        18.35        12.92        13.48        12.33        12.33 
TCGA-R6-A6XQ TCGA-VR-A8EX TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-7901 
        6.35        28.11        19.56        34.68        33.63         3.45 
TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A4J1 
       29.56        29.59        25.05        31.96        32.58         0.72 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8532 
       20.65        21.44         5.13        12.39        12.76        11.64 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4304 TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-6519 
       12.30         6.58        27.02         9.01       105.07        20.55 
TCGA-D7-8572 TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-FP-7916 TCGA-FP-8211 
       16.80        11.44        20.32        15.65        14.07        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GX TCGA-HU-A4H6 
        0.56        11.08        22.68         3.25        20.25        21.17 
TCGA-IN-A6RJ TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA6A 
       12.46        42.64        66.81        38.93 

$`HRNR WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32        28.73         9.07        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        24.79         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        1.15        16.14        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        12.59        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
       12.20        11.77        12.62        20.02         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       22.29         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
       19.53        22.29        17.06        59.54         5.03         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A94T 
       17.85         1.87        15.65        20.81         1.71        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HRNR MUTATED HRNR WILD-TYPE 
          0.56           0.00 
  HRNR MUTATED HRNR WILD-TYPE 
        105.07         122.30 
  HRNR MUTATED HRNR WILD-TYPE 
        17.575         13.410 
[1] "0.6 - 105.1 (17.6)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D590V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HRNR MUTATED         1        1        4        4         7         9
  HRNR WILD-TYPE       9       19       42       27        77        74
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HRNR MUTATED           1          6          3          6        3         1
  HRNR WILD-TYPE        28         78         59         33       40         3
D590V3, multiclass
            clus
vv           HRNR MUTATED HRNR WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              4             42
  STAGE II              4             27
  STAGE IIA             7             77
  STAGE IIB             9             74
  STAGE III             1             28
  STAGE IIIA            6             78
  STAGE IIIB            3             59
  STAGE IIIC            6             33
  STAGE IV              3             40
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HRNR MUTATED       6   8  21  13
  HRNR WILD-TYPE    48 127 240  89
D590V4, multiclass
       clus
vv      HRNR MUTATED HRNR WILD-TYPE
  T0+T1            6             48
  T2               8            127
  T3              21            240
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HRNR MUTATED    20  12   9   7
  HRNR WILD-TYPE 175 161  80  78
D590V5, multiclass
    clus
vv   HRNR MUTATED HRNR WILD-TYPE
  N0           20            175
  N1           12            161
  N2            9             80
  N3            7             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V6, binary
                cls
clus               0   1
  HRNR MUTATED    39   4
  HRNR WILD-TYPE 443  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     39    4
  HRNR WILD-TYPE  443   34
   clus
vv  HRNR MUTATED HRNR WILD-TYPE
  0           39            443
  1            4             34
[1] 2 2
[1] FALSE
D590V7, binary
                cls
clus               0   1
  HRNR MUTATED    14  36
  HRNR WILD-TYPE 158 370
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     14   36
  HRNR WILD-TYPE  158  370
        clus
vv       HRNR MUTATED HRNR WILD-TYPE
  FEMALE           14            158
  MALE             36            370
[1] 2 2
[1] FALSE
D590V8, binary
                cls
clus               0   1
  HRNR MUTATED    34   7
  HRNR WILD-TYPE 382  95
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     34    7
  HRNR WILD-TYPE  382   95
     clus
vv    HRNR MUTATED HRNR WILD-TYPE
  NO            34            382
  YES            7             95
[1] 2 2
[1] FALSE
D590V9, continuous
[1] "Remove cluster labels:" "HRNR MUTATED"          
clus
  HRNR MUTATED HRNR WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49R 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" "HRNR WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HRNR WILD-TYPE" "HRNR WILD-TYPE" 
D590V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HRNR MUTATED      15                         2
  HRNR WILD-TYPE   118                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HRNR MUTATED                                           0    27
  HRNR WILD-TYPE                                         1   330
D590V11, multiclass
                                           clus
vv                                          HRNR MUTATED HRNR WILD-TYPE
  ASIAN                                               15            118
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               27            330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V12, binary
                cls
clus               0   1
  HRNR MUTATED     0  38
  HRNR WILD-TYPE  10 360
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED      0   38
  HRNR WILD-TYPE   10  360
                        clus
vv                       HRNR MUTATED HRNR WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           38            360
[1] 2 2
[1] FALSE

Clustering(591) Variable = RDBP MUTATION ANALYSIS
D591V1, survival
                sevent
clus2              0   1
  RDBP MUTATED     8   4
  RDBP WILD-TYPE 330 212
  RDBP MUTATED RDBP WILD-TYPE 
            12            542 
  RDBP MUTATED RDBP WILD-TYPE 
             4            212 
$`RDBP MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NQ TCGA-Z6-A8JE TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8591 
       19.99        21.37         2.10         0.26         1.12        28.14 
TCGA-CD-8531 TCGA-CD-A4MG TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-VQ-A8P2 
       12.59         6.58         0.10        29.00        23.84        38.14 

$`RDBP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  RDBP MUTATED RDBP WILD-TYPE 
           0.1            0.0 
  RDBP MUTATED RDBP WILD-TYPE 
         38.14         122.30 
  RDBP MUTATED RDBP WILD-TYPE 
        16.290         13.565 
[1] "0.1 - 38.1 (16.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D591V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RDBP MUTATED         0        0        1        0         3         1
  RDBP WILD-TYPE      10       20       45       31        81        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RDBP MUTATED           0          3          0          4        0         0
  RDBP WILD-TYPE        29         81         62         35       43         4
D591V3, multiclass
            clus
vv           RDBP MUTATED RDBP WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            4             35
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RDBP MUTATED       0   3   5   4
  RDBP WILD-TYPE    54 132 256  98
D591V4, multiclass
       clus
vv      RDBP MUTATED RDBP WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RDBP MUTATED     4   4   2   3
  RDBP WILD-TYPE 191 169  87  82
D591V5, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  N0            4            191
  N1            4            169
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V6, binary
                cls
clus               0   1
  RDBP MUTATED    12   0
  RDBP WILD-TYPE 470  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED     12    0
  RDBP WILD-TYPE  470   38
   clus
vv  RDBP MUTATED RDBP WILD-TYPE
  0           12            470
  1            0             38
[1] 2 2
[1] FALSE
D591V7, binary
                cls
clus               0   1
  RDBP MUTATED     6   7
  RDBP WILD-TYPE 166 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      6    7
  RDBP WILD-TYPE  166  399
        clus
vv       RDBP MUTATED RDBP WILD-TYPE
  FEMALE            6            166
  MALE              7            399
[1] 2 2
[1] FALSE
D591V8, binary
                cls
clus               0   1
  RDBP MUTATED     9   2
  RDBP WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      9    2
  RDBP WILD-TYPE  407  100
     clus
vv    RDBP MUTATED RDBP WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D591V9, continuous
[1] "Remove cluster labels:" "RDBP MUTATED"          
clus
  RDBP MUTATED RDBP WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JD 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
D591V10, continuous
[1] "Remove cluster labels:" "RDBP MUTATED"          
clus
  RDBP MUTATED RDBP WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NR 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" "RDBP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RDBP MUTATED       5                         0
  RDBP WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RDBP MUTATED                                           0     8
  RDBP WILD-TYPE                                         1   349
D591V11, multiclass
                                           clus
vv                                          RDBP MUTATED RDBP WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V12, binary
                cls
clus               0   1
  RDBP MUTATED     0  10
  RDBP WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      0   10
  RDBP WILD-TYPE   10  388
                        clus
vv                       RDBP MUTATED RDBP WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(592) Variable = TNFSF13 MUTATION ANALYSIS
D592V1, survival
                   sevent
clus2                 0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 335 216
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               551 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                0               216 
$`TNFSF13 MUTATED`
TCGA-B7-5816 TCGA-CG-5723 TCGA-HU-A4G8 
       26.70       105.07        22.68 

$`TNFSF13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
            22.68              0.00 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
           105.07            122.30 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
            26.70             13.51 
[1] "22.7 - 105.1 (26.7)" "0.0 - 122.3 (13.5)" 
[1] "hr="     "9300000"
D592V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFSF13 MUTATED         0        0        0        1         0         2
  TNFSF13 WILD-TYPE      10       20       46       30        84        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFSF13 MUTATED           0          0          0          0        0
  TNFSF13 WILD-TYPE        29         84         62         39       43
                   vv
clus                STAGE IVA
  TNFSF13 MUTATED           0
  TNFSF13 WILD-TYPE         4
D592V3, multiclass
            clus
vv           TNFSF13 MUTATED TNFSF13 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TNFSF13 MUTATED       0   1   1   1
  TNFSF13 WILD-TYPE    54 134 260 101
D592V4, multiclass
       clus
vv      TNFSF13 MUTATED TNFSF13 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  1               260
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TNFSF13 MUTATED     1   2   0   0
  TNFSF13 WILD-TYPE 194 171  89  85
D592V5, multiclass
    clus
vv   TNFSF13 MUTATED TNFSF13 WILD-TYPE
  N0               1               194
  N1               2               171
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V6, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 479  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      3    0
  TNFSF13 WILD-TYPE  479   38
   clus
vv  TNFSF13 MUTATED TNFSF13 WILD-TYPE
  0               3               479
  1               0                38
[1] 2 2
[1] FALSE
D592V7, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     2   1
  TNFSF13 WILD-TYPE 170 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      2    1
  TNFSF13 WILD-TYPE  170  405
        clus
vv       TNFSF13 MUTATED TNFSF13 WILD-TYPE
  FEMALE               2               170
  MALE                 1               405
[1] 2 2
[1] FALSE
D592V8, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 413 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      3    0
  TNFSF13 WILD-TYPE  413  102
     clus
vv    TNFSF13 MUTATED TNFSF13 WILD-TYPE
  NO                3               413
  YES               0               102
[1] 2 2
[1] FALSE
D592V9, continuous
D592V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFSF13 MUTATED       1                         0
  TNFSF13 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFSF13 MUTATED                                           0     1
  TNFSF13 WILD-TYPE                                         1   356
D592V11, multiclass
[1] "Remove cluster labels:" "TNFSF13 MUTATED"       
clus
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                2               503 
       TCGA-IC-A6RF        TCGA-JY-A6FB        TCGA-JY-A938        TCGA-L5-A43I 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A43J        TCGA-L5-A4OE        TCGA-L5-A4OG        TCGA-L5-A4OI 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG        TCGA-L5-A8NT 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-Q9-A6FU        TCGA-S8-A6BV        TCGA-EQ-A4SO        TCGA-F1-6177 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-KB-A93G        TCGA-MX-A663        TCGA-IC-A6RE 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QS 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A51D        TCGA-IG-A5B8 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IG-A5S3        TCGA-IG-A625        TCGA-IG-A6QS        TCGA-IG-A7DP 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-IG-A97I        TCGA-JY-A6F8 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-JY-A6FA        TCGA-JY-A6FD        TCGA-JY-A6FE        TCGA-JY-A6FG 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-JY-A6FH        TCGA-JY-A939        TCGA-JY-A93C        TCGA-JY-A93D 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-JY-A93E        TCGA-JY-A93F        TCGA-KH-A6WC        TCGA-L5-A43C 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OF        TCGA-L5-A4OH 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A4OJ        TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OR        TCGA-L5-A4OS 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OX        TCGA-L5-A88S 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A88W        TCGA-L5-A88Z        TCGA-L5-A891 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NH 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A8NI        TCGA-L5-A8NJ        TCGA-L5-A8NK        TCGA-L5-A8NL 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A8NM        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NS 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L5-A8NU        TCGA-L5-A8NV        TCGA-L5-A8NW        TCGA-L7-A56G 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-L7-A6VZ        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-LN-A8I1        TCGA-LN-A9FO 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-LN-A9FP        TCGA-LN-A9FQ        TCGA-LN-A9FR        TCGA-Q9-A6FW 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6DQ        TCGA-R6-A6KZ        TCGA-R6-A6L4 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R6-A6L6        TCGA-R6-A6XG        TCGA-R6-A6XQ        TCGA-R6-A6Y0 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R6-A8WG        TCGA-RE-A7BO        TCGA-S8-A6BW        TCGA-V5-A7RC 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ET 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE        TCGA-Z6-A9VB 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-Z6-AAPN        TCGA-ZR-A9CJ        TCGA-B7-5818        TCGA-B7-A5TI 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-B7-A5TJ        TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4184        TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4257        TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8297 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4QM        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ        TCGA-D7-5577 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6EV        TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6F0        TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A74A        TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-KB-A93J        TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R5-A7O7        TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R5-A7ZR        TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A7BT        TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8MW        TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8N4        TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-SW-A7EA        TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DU 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91U        TCGA-VQ-A92D 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA64        TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6B        TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6J        TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
D592V12, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     0   2
  TNFSF13 WILD-TYPE  10 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      0    2
  TNFSF13 WILD-TYPE   10  396
                        clus
vv                       TNFSF13 MUTATED TNFSF13 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               2               396
[1] 2 2
[1] FALSE

Clustering(593) Variable = MCEE MUTATION ANALYSIS
D593V1, survival
                sevent
clus2              0   1
  MCEE MUTATED     2   2
  MCEE WILD-TYPE 336 214
  MCEE MUTATED MCEE WILD-TYPE 
             4            550 
  MCEE MUTATED MCEE WILD-TYPE 
             2            214 
$`MCEE MUTATED`
TCGA-LN-A9FQ TCGA-B7-5816 TCGA-BR-8382 TCGA-CG-4306 
       12.85        26.70        25.05         1.02 

$`MCEE WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MCEE MUTATED MCEE WILD-TYPE 
          1.02           0.00 
  MCEE MUTATED MCEE WILD-TYPE 
          26.7          122.3 
  MCEE MUTATED MCEE WILD-TYPE 
        18.950         13.565 
[1] "1.0 - 26.7 (18.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D593V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MCEE MUTATED         0        0        0        0         1         1
  MCEE WILD-TYPE      10       20       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCEE MUTATED           0          1          0          1        1         0
  MCEE WILD-TYPE        29         83         62         38       42         4
D593V3, multiclass
            clus
vv           MCEE MUTATED MCEE WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MCEE MUTATED       1   0   2   3
  MCEE WILD-TYPE    53 135 259  99
D593V4, multiclass
       clus
vv      MCEE MUTATED MCEE WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               2            259
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MCEE MUTATED     3   0   1   1
  MCEE WILD-TYPE 192 173  88  84
D593V5, multiclass
    clus
vv   MCEE MUTATED MCEE WILD-TYPE
  N0            3            192
  N1            0            173
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V6, binary
                cls
clus               0   1
  MCEE MUTATED     5   1
  MCEE WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCEE MUTATED      5    1
  MCEE WILD-TYPE  477   37
   clus
vv  MCEE MUTATED MCEE WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D593V7, binary
                cls
clus               0   1
  MCEE MUTATED     4   2
  MCEE WILD-TYPE 168 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCEE MUTATED      4    2
  MCEE WILD-TYPE  168  404
        clus
vv       MCEE MUTATED MCEE WILD-TYPE
  FEMALE            4            168
  MALE              2            404
[1] 2 2
[1] FALSE
D593V8, binary
                cls
clus               0   1
  MCEE MUTATED     3   0
  MCEE WILD-TYPE 413 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCEE MUTATED      3    0
  MCEE WILD-TYPE  413  102
     clus
vv    MCEE MUTATED MCEE WILD-TYPE
  NO             3            413
  YES            0            102
[1] 2 2
[1] FALSE
D593V9, continuous
D593V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MCEE MUTATED       1                         0
  MCEE WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCEE MUTATED                                           0     4
  MCEE WILD-TYPE                                         1   353
D593V11, multiclass
                                           clus
vv                                          MCEE MUTATED MCEE WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V12, binary
                cls
clus               0   1
  MCEE MUTATED     0   5
  MCEE WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCEE MUTATED      0    5
  MCEE WILD-TYPE   10  393
                        clus
vv                       MCEE MUTATED MCEE WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(594) Variable = OTX2 MUTATION ANALYSIS
D594V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     5   3
  OTX2 WILD-TYPE 333 213
  OTX2 MUTATED OTX2 WILD-TYPE 
             8            546 
  OTX2 MUTATED OTX2 WILD-TYPE 
             3            213 
$`OTX2 MUTATED`
TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 
      122.10         7.76        34.68        16.14         6.58       105.07 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`OTX2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  OTX2 MUTATED OTX2 WILD-TYPE 
          6.58           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
         122.1          122.3 
  OTX2 MUTATED OTX2 WILD-TYPE 
         25.41          13.51 
[1] "6.6 - 122.1 (25.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D594V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OTX2 MUTATED         1        0        1        1         2         1
  OTX2 WILD-TYPE       9       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTX2 MUTATED           0          2          1          0        1         0
  OTX2 WILD-TYPE        29         82         61         39       42         4
D594V3, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  OTX2 MUTATED       2   2   3   3
  OTX2 WILD-TYPE    52 133 258  99
D594V4, multiclass
       clus
vv      OTX2 MUTATED OTX2 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  OTX2 MUTATED     4   4   1   1
  OTX2 WILD-TYPE 191 169  88  84
D594V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            4            191
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V6, binary
                cls
clus               0   1
  OTX2 MUTATED    11   0
  OTX2 WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED     11    0
  OTX2 WILD-TYPE  471   38
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D594V7, binary
                cls
clus               0   1
  OTX2 MUTATED     6   5
  OTX2 WILD-TYPE 166 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      6    5
  OTX2 WILD-TYPE  166  401
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  FEMALE            6            166
  MALE              5            401
[1] 2 2
[1] FALSE
D594V8, binary
                cls
clus               0   1
  OTX2 MUTATED     7   1
  OTX2 WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      7    1
  OTX2 WILD-TYPE  409  101
     clus
vv    OTX2 MUTATED OTX2 WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D594V9, continuous
D594V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  OTX2 MUTATED       2                         0
  OTX2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OTX2 MUTATED                                           0     8
  OTX2 WILD-TYPE                                         1   349
D594V11, multiclass
                                           clus
vv                                          OTX2 MUTATED OTX2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V12, binary
                cls
clus               0   1
  OTX2 MUTATED     0   7
  OTX2 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      0    7
  OTX2 WILD-TYPE   10  391
                        clus
vv                       OTX2 MUTATED OTX2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(595) Variable = HAND2 MUTATION ANALYSIS
D595V1, survival
                 sevent
clus2               0   1
  HAND2 MUTATED     5   1
  HAND2 WILD-TYPE 333 215
  HAND2 MUTATED HAND2 WILD-TYPE 
              6             548 
  HAND2 MUTATED HAND2 WILD-TYPE 
              1             215 
$`HAND2 MUTATED`
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 TCGA-CD-8527 TCGA-CD-8528 TCGA-VQ-A8P2 
       29.59        31.10        28.14         7.17        12.33        38.14 

$`HAND2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.53        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  HAND2 MUTATED HAND2 WILD-TYPE 
           7.17            0.00 
  HAND2 MUTATED HAND2 WILD-TYPE 
          38.14          122.30 
  HAND2 MUTATED HAND2 WILD-TYPE 
         28.865          13.530 
[1] "7.2 - 38.1 (28.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D595V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAND2 MUTATED         0        0        0        1         0         1
  HAND2 WILD-TYPE      10       20       46       30        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAND2 MUTATED           0          3          0          2        0         0
  HAND2 WILD-TYPE        29         81         62         37       43         4
D595V3, multiclass
            clus
vv           HAND2 MUTATED HAND2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HAND2 MUTATED       0   1   0   6
  HAND2 WILD-TYPE    54 134 261  96
D595V4, multiclass
       clus
vv      HAND2 MUTATED HAND2 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                0             261
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HAND2 MUTATED     3   2   1   1
  HAND2 WILD-TYPE 192 171  88  84
D595V5, multiclass
    clus
vv   HAND2 MUTATED HAND2 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V6, binary
                 cls
clus                0   1
  HAND2 MUTATED     7   0
  HAND2 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAND2 MUTATED      7    0
  HAND2 WILD-TYPE  475   38
   clus
vv  HAND2 MUTATED HAND2 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D595V7, binary
                 cls
clus                0   1
  HAND2 MUTATED     5   2
  HAND2 WILD-TYPE 167 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAND2 MUTATED      5    2
  HAND2 WILD-TYPE  167  404
        clus
vv       HAND2 MUTATED HAND2 WILD-TYPE
  FEMALE             5             167
  MALE               2             404
[1] 2 2
[1] FALSE
D595V8, binary
                 cls
clus                0   1
  HAND2 MUTATED     4   2
  HAND2 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAND2 MUTATED      4    2
  HAND2 WILD-TYPE  412  100
     clus
vv    HAND2 MUTATED HAND2 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D595V9, continuous
D595V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HAND2 MUTATED       2                         0
  HAND2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAND2 MUTATED                                           0     5
  HAND2 WILD-TYPE                                         1   352
D595V11, multiclass
                                           clus
vv                                          HAND2 MUTATED HAND2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V12, binary
                 cls
clus                0   1
  HAND2 MUTATED     0   6
  HAND2 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAND2 MUTATED      0    6
  HAND2 WILD-TYPE   10  392
                        clus
vv                       HAND2 MUTATED HAND2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(596) Variable = SLC12A7 MUTATION ANALYSIS
D596V1, survival
                   sevent
clus2                 0   1
  SLC12A7 MUTATED    20   8
  SLC12A7 WILD-TYPE 318 208
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               28               526 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                8               208 
$`SLC12A7 MUTATED`
TCGA-L5-A43J TCGA-S8-A6BV TCGA-CG-4460 TCGA-FP-A8CX TCGA-JY-A939 TCGA-L5-A8NW 
        4.31        20.02        21.99         0.23        21.70        46.09 
TCGA-R6-A6Y2 TCGA-V5-A7RC TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8360 
        9.30         3.42        34.68        32.78        35.84         6.18 
TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A48A 
        0.26         1.12        28.14        12.30        12.43        12.43 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A747 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4G8 
        6.58         6.02         8.38        11.08        30.51        22.68 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       23.80        14.07        19.73        38.14 

$`SLC12A7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
        5.16        47.05        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        47.38        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29        15.65         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
             0.23              0.00 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
            46.09            122.30 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
           13.250            13.565 
[1] "0.2 - 46.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D596V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC12A7 MUTATED         0        0        6        1         7         4
  SLC12A7 WILD-TYPE      10       20       40       30        77        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A7 MUTATED           0          3          0          3        3
  SLC12A7 WILD-TYPE        29         81         62         36       40
                   vv
clus                STAGE IVA
  SLC12A7 MUTATED           0
  SLC12A7 WILD-TYPE         4
D596V3, multiclass
            clus
vv           SLC12A7 MUTATED SLC12A7 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 6                40
  STAGE II                 1                30
  STAGE IIA                7                77
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC12A7 MUTATED       2   5  13   7
  SLC12A7 WILD-TYPE    52 130 248  95
D596V4, multiclass
       clus
vv      SLC12A7 MUTATED SLC12A7 WILD-TYPE
  T0+T1               2                52
  T2                  5               130
  T3                 13               248
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC12A7 MUTATED    14   9   1   3
  SLC12A7 WILD-TYPE 181 164  88  82
D596V5, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  N0              14               181
  N1               9               164
  N2               1                88
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V6, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    23   2
  SLC12A7 WILD-TYPE 459  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     23    2
  SLC12A7 WILD-TYPE  459   36
   clus
vv  SLC12A7 MUTATED SLC12A7 WILD-TYPE
  0              23               459
  1               2                36
[1] 2 2
[1] FALSE
D596V7, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    10  20
  SLC12A7 WILD-TYPE 162 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     10   20
  SLC12A7 WILD-TYPE  162  386
        clus
vv       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  FEMALE              10               162
  MALE                20               386
[1] 2 2
[1] FALSE
D596V8, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    20   6
  SLC12A7 WILD-TYPE 396  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     20    6
  SLC12A7 WILD-TYPE  396   96
     clus
vv    SLC12A7 MUTATED SLC12A7 WILD-TYPE
  NO               20               396
  YES               6                96
[1] 2 2
[1] FALSE
D596V9, continuous
[1] "Remove cluster labels:" "SLC12A7 MUTATED"       
clus
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RE        TCGA-V5-AASV 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" "SLC12A7 WILD-TYPE" 
D596V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC12A7 MUTATED       7                         2
  SLC12A7 WILD-TYPE   126                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC12A7 MUTATED                                           0    17
  SLC12A7 WILD-TYPE                                         1   340
D596V11, multiclass
                                           clus
vv                                          SLC12A7 MUTATED SLC12A7 WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V12, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     1  21
  SLC12A7 WILD-TYPE   9 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      1   21
  SLC12A7 WILD-TYPE    9  377
                        clus
vv                       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              21               377
[1] 2 2
[1] FALSE

Clustering(597) Variable = CD1E MUTATION ANALYSIS
D597V1, survival
                sevent
clus2              0   1
  CD1E MUTATED    10   5
  CD1E WILD-TYPE 328 211
  CD1E MUTATED CD1E WILD-TYPE 
            15            539 
  CD1E MUTATED CD1E WILD-TYPE 
             5            211 
$`CD1E MUTATED`
TCGA-S8-A6BV TCGA-2H-A9GF TCGA-JY-A93D TCGA-L5-A4OJ TCGA-L5-A8NJ TCGA-R6-A6KZ 
       20.02        25.78        31.56        21.01        16.47         5.06 
TCGA-BR-6453 TCGA-BR-7723 TCGA-BR-A4PD TCGA-D7-6518 TCGA-D7-6822 TCGA-HU-A4GU 
       15.95        28.73        20.65        19.13        12.33         6.58 
TCGA-IN-A7NU TCGA-R5-A804 TCGA-VQ-A91V 
       11.70         4.60        42.64 

$`CD1E WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        34.68        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         6.08         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CD1E MUTATED CD1E WILD-TYPE 
           4.6            0.0 
  CD1E MUTATED CD1E WILD-TYPE 
         42.64         122.30 
  CD1E MUTATED CD1E WILD-TYPE 
         19.13          13.51 
[1] "4.6 - 42.6 (19.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D597V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD1E MUTATED         1        0        2        0         1         2
  CD1E WILD-TYPE       9       20       44       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD1E MUTATED           2          3          2          1        1         0
  CD1E WILD-TYPE        27         81         60         38       42         4
D597V3, multiclass
            clus
vv           CD1E MUTATED CD1E WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CD1E MUTATED       1   5   8   1
  CD1E WILD-TYPE    53 130 253 101
D597V4, multiclass
       clus
vv      CD1E MUTATED CD1E WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               8            253
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CD1E MUTATED     4   5   2   4
  CD1E WILD-TYPE 191 168  87  81
D597V5, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  N0            4            191
  N1            5            168
  N2            2             87
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V6, binary
                cls
clus               0   1
  CD1E MUTATED    14   1
  CD1E WILD-TYPE 468  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED     14    1
  CD1E WILD-TYPE  468   37
   clus
vv  CD1E MUTATED CD1E WILD-TYPE
  0           14            468
  1            1             37
[1] 2 2
[1] FALSE
D597V7, binary
                cls
clus               0   1
  CD1E MUTATED     2  15
  CD1E WILD-TYPE 170 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      2   15
  CD1E WILD-TYPE  170  391
        clus
vv       CD1E MUTATED CD1E WILD-TYPE
  FEMALE            2            170
  MALE             15            391
[1] 2 2
[1] FALSE
D597V8, binary
                cls
clus               0   1
  CD1E MUTATED    13   2
  CD1E WILD-TYPE 403 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED     13    2
  CD1E WILD-TYPE  403  100
     clus
vv    CD1E MUTATED CD1E WILD-TYPE
  NO            13            403
  YES            2            100
[1] 2 2
[1] FALSE
D597V9, continuous
D597V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD1E MUTATED       1                         1
  CD1E WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD1E MUTATED                                           0    12
  CD1E WILD-TYPE                                         1   345
D597V11, multiclass
                                           clus
vv                                          CD1E MUTATED CD1E WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V12, binary
                cls
clus               0   1
  CD1E MUTATED     0  11
  CD1E WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      0   11
  CD1E WILD-TYPE   10  387
                        clus
vv                       CD1E MUTATED CD1E WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(598) Variable = HEXDC MUTATION ANALYSIS
D598V1, survival
                 sevent
clus2               0   1
  HEXDC MUTATED     4   4
  HEXDC WILD-TYPE 334 212
  HEXDC MUTATED HEXDC WILD-TYPE 
              8             546 
  HEXDC MUTATED HEXDC WILD-TYPE 
              4             212 
$`HEXDC MUTATED`
TCGA-L5-A43J TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-5726 TCGA-HF-7132 TCGA-HJ-7597 
        4.31        31.27        11.77        28.96        77.29        26.47 
TCGA-IN-A6RN TCGA-VQ-A8P2 
       19.53        38.14 

$`HEXDC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  HEXDC MUTATED HEXDC WILD-TYPE 
           4.31            0.00 
  HEXDC MUTATED HEXDC WILD-TYPE 
          77.29          122.30 
  HEXDC MUTATED HEXDC WILD-TYPE 
         27.715          13.510 
[1] "4.3 - 77.3 (27.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D598V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HEXDC MUTATED         0        1        1        1         1         1
  HEXDC WILD-TYPE      10       19       45       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HEXDC MUTATED           0          2          0          1        0         0
  HEXDC WILD-TYPE        29         82         62         38       43         4
D598V3, multiclass
            clus
vv           HEXDC MUTATED HEXDC WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HEXDC MUTATED       3   2   2   2
  HEXDC WILD-TYPE    51 133 259 100
D598V4, multiclass
       clus
vv      HEXDC MUTATED HEXDC WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HEXDC MUTATED     3   3   1   1
  HEXDC WILD-TYPE 192 170  88  84
D598V5, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  N0             3             192
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V6, binary
                 cls
clus                0   1
  HEXDC MUTATED     7   0
  HEXDC WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      7    0
  HEXDC WILD-TYPE  475   38
   clus
vv  HEXDC MUTATED HEXDC WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D598V7, binary
                 cls
clus                0   1
  HEXDC MUTATED     3   6
  HEXDC WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      3    6
  HEXDC WILD-TYPE  169  400
        clus
vv       HEXDC MUTATED HEXDC WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D598V8, binary
                 cls
clus                0   1
  HEXDC MUTATED     4   2
  HEXDC WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      4    2
  HEXDC WILD-TYPE  412  100
     clus
vv    HEXDC MUTATED HEXDC WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D598V9, continuous
D598V10, continuous
[1] "Remove cluster labels:" "HEXDC MUTATED"         
clus
  HEXDC MUTATED HEXDC WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" "HEXDC WILD-TYPE" 
     TCGA-Z6-AAPN 
"HEXDC WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HEXDC MUTATED       1                         0
  HEXDC WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HEXDC MUTATED                                           0     6
  HEXDC WILD-TYPE                                         1   351
D598V11, multiclass
                                           clus
vv                                          HEXDC MUTATED HEXDC WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V12, binary
                 cls
clus                0   1
  HEXDC MUTATED     0   5
  HEXDC WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      0    5
  HEXDC WILD-TYPE   10  393
                        clus
vv                       HEXDC MUTATED HEXDC WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(599) Variable = C11ORF70 MUTATION ANALYSIS
D599V1, survival
                    sevent
clus2                  0   1
  C11ORF70 MUTATED     3   2
  C11ORF70 WILD-TYPE 335 214
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 5                549 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 2                214 
$`C11ORF70 MUTATED`
TCGA-JY-A6FG TCGA-B7-5816 TCGA-CD-A4MG TCGA-HU-A4GU TCGA-SW-A7EA 
       41.52        26.70         6.58         6.58        19.04 

$`C11ORF70 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
              6.58               0.00 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
             41.52             122.30 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
             19.04              13.55 
[1] "6.6 - 41.5 (19.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D599V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF70 MUTATED         0        0        1        0         1         2
  C11ORF70 WILD-TYPE      10       20       45       31        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF70 MUTATED           1          0          0          0        0
  C11ORF70 WILD-TYPE        28         84         62         39       43
                    vv
clus                 STAGE IVA
  C11ORF70 MUTATED           0
  C11ORF70 WILD-TYPE         4
D599V3, multiclass
            clus
vv           C11ORF70 MUTATED C11ORF70 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                0                 39
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C11ORF70 MUTATED       0   1   3   1
  C11ORF70 WILD-TYPE    54 134 258 101
D599V4, multiclass
       clus
vv      C11ORF70 MUTATED C11ORF70 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   3                258
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C11ORF70 MUTATED     3   2   0   0
  C11ORF70 WILD-TYPE 192 171  89  85
D599V5, multiclass
    clus
vv   C11ORF70 MUTATED C11ORF70 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                0                 89
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V6, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     5   0
  C11ORF70 WILD-TYPE 477  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      5    0
  C11ORF70 WILD-TYPE  477   38
   clus
vv  C11ORF70 MUTATED C11ORF70 WILD-TYPE
  0                5                477
  1                0                 38
[1] 2 2
[1] FALSE
D599V7, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     2   3
  C11ORF70 WILD-TYPE 170 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      2    3
  C11ORF70 WILD-TYPE  170  403
        clus
vv       C11ORF70 MUTATED C11ORF70 WILD-TYPE
  FEMALE                2                170
  MALE                  3                403
[1] 2 2
[1] FALSE
D599V8, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     5   0
  C11ORF70 WILD-TYPE 411 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      5    0
  C11ORF70 WILD-TYPE  411  102
     clus
vv    C11ORF70 MUTATED C11ORF70 WILD-TYPE
  NO                 5                411
  YES                0                102
[1] 2 2
[1] FALSE
D599V9, continuous
D599V10, continuous
[1] "Remove cluster labels:" "C11ORF70 MUTATED"      
clus
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" "C11ORF70 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C11ORF70 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF70 MUTATED       2                         0
  C11ORF70 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF70 MUTATED                                           0     3
  C11ORF70 WILD-TYPE                                         1   354
D599V11, multiclass
                                           clus
vv                                          C11ORF70 MUTATED C11ORF70 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V12, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     0   4
  C11ORF70 WILD-TYPE  10 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      0    4
  C11ORF70 WILD-TYPE   10  394
                        clus
vv                       C11ORF70 MUTATED C11ORF70 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                4                394
[1] 2 2
[1] FALSE

Clustering(600) Variable = GRXCR1 MUTATION ANALYSIS
D600V1, survival
                  sevent
clus2                0   1
  GRXCR1 MUTATED    10   7
  GRXCR1 WILD-TYPE 328 209
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
              17              537 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               7              209 
$`GRXCR1 MUTATED`
TCGA-2H-A9GK TCGA-IG-A3YB TCGA-IG-A97I TCGA-JY-A6FA TCGA-LN-A7HV TCGA-R6-A8WG 
        7.63         2.63        12.16        44.75        10.52        12.69 
TCGA-RE-A7BO TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7958 TCGA-BR-8080 TCGA-BR-8590 
        7.00        34.68        30.90        29.56         9.60         9.34 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-FP-A4BE TCGA-VQ-A8P3 TCGA-VQ-AA6G 
       12.62         6.02        11.08        37.22        26.04 

$`GRXCR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
        9.96        14.86         4.67        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
            2.63             0.00 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
           44.75           122.30 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
           12.16            13.78 
[1] "2.6 - 44.8 (12.2)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D600V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GRXCR1 MUTATED         0        0        1        0         5         2
  GRXCR1 WILD-TYPE      10       20       45       31        79        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRXCR1 MUTATED           1          3          1          2        1
  GRXCR1 WILD-TYPE        28         81         61         37       42
                  vv
clus               STAGE IVA
  GRXCR1 MUTATED           0
  GRXCR1 WILD-TYPE         4
D600V3, multiclass
            clus
vv           GRXCR1 MUTATED GRXCR1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GRXCR1 MUTATED       1   4   6   5
  GRXCR1 WILD-TYPE    53 131 255  97
D600V4, multiclass
       clus
vv      GRXCR1 MUTATED GRXCR1 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 6              255
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GRXCR1 MUTATED     7   6   2   1
  GRXCR1 WILD-TYPE 188 167  87  84
D600V5, multiclass
    clus
vv   GRXCR1 MUTATED GRXCR1 WILD-TYPE
  N0              7              188
  N1              6              167
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V6, binary
                  cls
clus                 0   1
  GRXCR1 MUTATED    17   0
  GRXCR1 WILD-TYPE 465  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRXCR1 MUTATED     17    0
  GRXCR1 WILD-TYPE  465   38
   clus
vv  GRXCR1 MUTATED GRXCR1 WILD-TYPE
  0             17              465
  1              0               38
[1] 2 2
[1] FALSE
D600V7, binary
                  cls
clus                 0   1
  GRXCR1 MUTATED     3  15
  GRXCR1 WILD-TYPE 169 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRXCR1 MUTATED      3   15
  GRXCR1 WILD-TYPE  169  391
        clus
vv       GRXCR1 MUTATED GRXCR1 WILD-TYPE
  FEMALE              3              169
  MALE               15              391
[1] 2 2
[1] FALSE
D600V8, binary
                  cls
clus                 0   1
  GRXCR1 MUTATED    12   5
  GRXCR1 WILD-TYPE 404  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRXCR1 MUTATED     12    5
  GRXCR1 WILD-TYPE  404   97
     clus
vv    GRXCR1 MUTATED GRXCR1 WILD-TYPE
  NO              12              404
  YES              5               97
[1] 2 2
[1] FALSE
D600V9, continuous
[1] "Remove cluster labels:" "GRXCR1 MUTATED"        
clus
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HW 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
D600V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GRXCR1 MUTATED       3                         1
  GRXCR1 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GRXCR1 MUTATED                                           0    12
  GRXCR1 WILD-TYPE                                         1   345
D600V11, multiclass
                                           clus
vv                                          GRXCR1 MUTATED GRXCR1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V12, binary
                  cls
clus                 0   1
  GRXCR1 MUTATED     1  12
  GRXCR1 WILD-TYPE   9 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRXCR1 MUTATED      1   12
  GRXCR1 WILD-TYPE    9  386
                        clus
vv                       GRXCR1 MUTATED GRXCR1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(601) Variable = GPR141 MUTATION ANALYSIS
D601V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     7   6
  GPR141 WILD-TYPE 331 210
  GPR141 MUTATED GPR141 WILD-TYPE 
              13              541 
  GPR141 MUTATED GPR141 WILD-TYPE 
               6              210 
$`GPR141 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OP TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7957 TCGA-BR-8363 
        4.31         7.17        26.70         6.97         9.07         0.26 
TCGA-BR-8372 TCGA-D7-6525 TCGA-D7-A4YY TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-A4GU 
       31.27        13.35        13.78        21.27        30.51         6.58 
TCGA-VQ-AA6I 
       16.14 

$`GPR141 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         3.45        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        26.04        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GPR141 MUTATED GPR141 WILD-TYPE 
            0.26             0.00 
  GPR141 MUTATED GPR141 WILD-TYPE 
           31.27           122.30 
  GPR141 MUTATED GPR141 WILD-TYPE 
           13.35            13.58 
[1] "0.3 - 31.3 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D601V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR141 MUTATED         0        1        1        0         0         3
  GPR141 WILD-TYPE      10       19       45       31        84        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR141 MUTATED           0          2          3          2        1
  GPR141 WILD-TYPE        29         82         59         37       42
                  vv
clus               STAGE IVA
  GPR141 MUTATED           0
  GPR141 WILD-TYPE         4
D601V3, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              3               59
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR141 MUTATED       1   2   7   3
  GPR141 WILD-TYPE    53 133 254  99
D601V4, multiclass
       clus
vv      GPR141 MUTATED GPR141 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 7              254
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR141 MUTATED     4   2   1   6
  GPR141 WILD-TYPE 191 171  88  79
D601V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              4              191
  N1              2              171
  N2              1               88
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V6, binary
                  cls
clus                 0   1
  GPR141 MUTATED     9   1
  GPR141 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      9    1
  GPR141 WILD-TYPE  473   37
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D601V7, binary
                  cls
clus                 0   1
  GPR141 MUTATED     5   8
  GPR141 WILD-TYPE 167 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      5    8
  GPR141 WILD-TYPE  167  398
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  FEMALE              5              167
  MALE                8              398
[1] 2 2
[1] FALSE
D601V8, binary
                  cls
clus                 0   1
  GPR141 MUTATED     8   3
  GPR141 WILD-TYPE 408  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      8    3
  GPR141 WILD-TYPE  408   99
     clus
vv    GPR141 MUTATED GPR141 WILD-TYPE
  NO               8              408
  YES              3               99
[1] 2 2
[1] FALSE
D601V9, continuous
D601V10, continuous
[1] "Remove cluster labels:" "GPR141 MUTATED"        
clus
  GPR141 MUTATED GPR141 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A4OE       TCGA-L5-A4OG 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" "GPR141 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR141 MUTATED       1                         0
  GPR141 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR141 MUTATED                                           0    11
  GPR141 WILD-TYPE                                         1   346
D601V11, multiclass
                                           clus
vv                                          GPR141 MUTATED GPR141 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V12, binary
                  cls
clus                 0   1
  GPR141 MUTATED     1   8
  GPR141 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      1    8
  GPR141 WILD-TYPE    9  390
                        clus
vv                       GPR141 MUTATED GPR141 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(602) Variable = NEK8 MUTATION ANALYSIS
D602V1, survival
                sevent
clus2              0   1
  NEK8 MUTATED    10   4
  NEK8 WILD-TYPE 328 212
  NEK8 MUTATED NEK8 WILD-TYPE 
            14            540 
  NEK8 MUTATED NEK8 WILD-TYPE 
             4            212 
$`NEK8 MUTATED`
TCGA-L5-A4OH TCGA-L5-A891 TCGA-LN-A8I1 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7715 
       32.61         3.75        13.18        30.90        34.68        33.63 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8690 TCGA-CG-5721 TCGA-CG-5733 TCGA-HJ-7597 
        4.31        25.05        10.68         6.02        21.07        26.47 
TCGA-HU-A4GX TCGA-HU-A4H3 
       20.25        29.00 

$`NEK8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88         8.22        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NEK8 MUTATED NEK8 WILD-TYPE 
          3.75           0.00 
  NEK8 MUTATED NEK8 WILD-TYPE 
         34.68         122.30 
  NEK8 MUTATED NEK8 WILD-TYPE 
         23.06          13.51 
[1] "3.8 - 34.7 (23.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D602V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEK8 MUTATED         1        0        2        0         3         0
  NEK8 WILD-TYPE       9       20       44       31        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEK8 MUTATED           0          1          1          3        1         0
  NEK8 WILD-TYPE        29         83         61         36       42         4
D602V3, multiclass
            clus
vv           NEK8 MUTATED NEK8 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NEK8 MUTATED       1   5   4   4
  NEK8 WILD-TYPE    53 130 257  98
D602V4, multiclass
       clus
vv      NEK8 MUTATED NEK8 WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NEK8 MUTATED     6   2   2   3
  NEK8 WILD-TYPE 189 171  87  82
D602V5, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  N0            6            189
  N1            2            171
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V6, binary
                cls
clus               0   1
  NEK8 MUTATED    13   0
  NEK8 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     13    0
  NEK8 WILD-TYPE  469   38
   clus
vv  NEK8 MUTATED NEK8 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D602V7, binary
                cls
clus               0   1
  NEK8 MUTATED    10   4
  NEK8 WILD-TYPE 162 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     10    4
  NEK8 WILD-TYPE  162  402
        clus
vv       NEK8 MUTATED NEK8 WILD-TYPE
  FEMALE           10            162
  MALE              4            402
[1] 2 2
[1] FALSE
D602V8, binary
                cls
clus               0   1
  NEK8 MUTATED    11   1
  NEK8 WILD-TYPE 405 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     11    1
  NEK8 WILD-TYPE  405  101
     clus
vv    NEK8 MUTATED NEK8 WILD-TYPE
  NO            11            405
  YES            1            101
[1] 2 2
[1] FALSE
D602V9, continuous
D602V10, continuous
[1] "Remove cluster labels:" "NEK8 MUTATED"          
clus
  NEK8 MUTATED NEK8 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OM 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" "NEK8 WILD-TYPE" 
    TCGA-Z6-AAPN 
"NEK8 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NEK8 MUTATED       3                         0
  NEK8 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEK8 MUTATED                                           0     9
  NEK8 WILD-TYPE                                         1   348
D602V11, multiclass
                                           clus
vv                                          NEK8 MUTATED NEK8 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V12, binary
                cls
clus               0   1
  NEK8 MUTATED     0  10
  NEK8 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED      0   10
  NEK8 WILD-TYPE   10  388
                        clus
vv                       NEK8 MUTATED NEK8 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(603) Variable = KRT222 MUTATION ANALYSIS
D603V1, survival
                  sevent
clus2                0   1
  KRT222 MUTATED     6   3
  KRT222 WILD-TYPE 332 213
  KRT222 MUTATED KRT222 WILD-TYPE 
               9              545 
  KRT222 MUTATED KRT222 WILD-TYPE 
               3              213 
$`KRT222 MUTATED`
TCGA-JY-A6FD TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8487 TCGA-D7-A6EY 
       68.02         6.97         9.34        34.68         1.12        11.44 
TCGA-HF-7132 TCGA-HU-A4GH TCGA-VQ-A8P2 
       77.29        11.77        38.14 

$`KRT222 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KRT222 MUTATED KRT222 WILD-TYPE 
            1.12             0.00 
  KRT222 MUTATED KRT222 WILD-TYPE 
           77.29           122.30 
  KRT222 MUTATED KRT222 WILD-TYPE 
           11.77            13.58 
[1] "1.1 - 77.3 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D603V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT222 MUTATED         0        1        0        1         3         0
  KRT222 WILD-TYPE      10       19       46       30        81        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT222 MUTATED           0          2          1          0        0
  KRT222 WILD-TYPE        29         82         61         39       43
                  vv
clus               STAGE IVA
  KRT222 MUTATED           0
  KRT222 WILD-TYPE         4
D603V3, multiclass
            clus
vv           KRT222 MUTATED KRT222 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KRT222 MUTATED       1   1   5   1
  KRT222 WILD-TYPE    53 134 256 101
D603V4, multiclass
       clus
vv      KRT222 MUTATED KRT222 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KRT222 MUTATED     4   4   0   1
  KRT222 WILD-TYPE 191 169  89  84
D603V5, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V6, binary
                  cls
clus                 0   1
  KRT222 MUTATED     8   0
  KRT222 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      8    0
  KRT222 WILD-TYPE  474   38
   clus
vv  KRT222 MUTATED KRT222 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D603V7, binary
                  cls
clus                 0   1
  KRT222 MUTATED     4   5
  KRT222 WILD-TYPE 168 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      4    5
  KRT222 WILD-TYPE  168  401
        clus
vv       KRT222 MUTATED KRT222 WILD-TYPE
  FEMALE              4              168
  MALE                5              401
[1] 2 2
[1] FALSE
D603V8, binary
                  cls
clus                 0   1
  KRT222 MUTATED     7   2
  KRT222 WILD-TYPE 409 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      7    2
  KRT222 WILD-TYPE  409  100
     clus
vv    KRT222 MUTATED KRT222 WILD-TYPE
  NO               7              409
  YES              2              100
[1] 2 2
[1] FALSE
D603V9, continuous
D603V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KRT222 MUTATED       2                         0
  KRT222 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRT222 MUTATED                                           0     6
  KRT222 WILD-TYPE                                         1   351
D603V11, multiclass
                                           clus
vv                                          KRT222 MUTATED KRT222 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V12, binary
                  cls
clus                 0   1
  KRT222 MUTATED     0   6
  KRT222 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      0    6
  KRT222 WILD-TYPE   10  392
                        clus
vv                       KRT222 MUTATED KRT222 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(604) Variable = GIMAP7 MUTATION ANALYSIS
D604V1, survival
                  sevent
clus2                0   1
  GIMAP7 MUTATED     4   2
  GIMAP7 WILD-TYPE 334 214
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               6              548 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               2              214 
$`GIMAP7 MUTATED`
TCGA-L5-A4OE TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-CG-5726 TCGA-HU-8602 
       24.00        34.68        32.78        36.16        28.96        22.32 

$`GIMAP7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           22.32             0.00 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           36.16           122.30 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
          30.870           13.495 
[1] "22.3 - 36.2 (30.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D604V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GIMAP7 MUTATED         0        2        0        0         2         1
  GIMAP7 WILD-TYPE      10       18       46       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP7 MUTATED           0          0          1          0        0
  GIMAP7 WILD-TYPE        29         84         61         39       43
                  vv
clus               STAGE IVA
  GIMAP7 MUTATED           0
  GIMAP7 WILD-TYPE         4
D604V3, multiclass
            clus
vv           GIMAP7 MUTATED GIMAP7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GIMAP7 MUTATED       2   0   3   1
  GIMAP7 WILD-TYPE    52 135 258 101
D604V4, multiclass
       clus
vv      GIMAP7 MUTATED GIMAP7 WILD-TYPE
  T0+T1              2               52
  T2                 0              135
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GIMAP7 MUTATED     5   0   1   0
  GIMAP7 WILD-TYPE 190 173  88  85
D604V5, multiclass
    clus
vv   GIMAP7 MUTATED GIMAP7 WILD-TYPE
  N0              5              190
  N1              0              173
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V6, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     5   0
  GIMAP7 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      5    0
  GIMAP7 WILD-TYPE  477   38
   clus
vv  GIMAP7 MUTATED GIMAP7 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D604V7, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     3   3
  GIMAP7 WILD-TYPE 169 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      3    3
  GIMAP7 WILD-TYPE  169  403
        clus
vv       GIMAP7 MUTATED GIMAP7 WILD-TYPE
  FEMALE              3              169
  MALE                3              403
[1] 2 2
[1] FALSE
D604V8, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     5   0
  GIMAP7 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      5    0
  GIMAP7 WILD-TYPE  411  102
     clus
vv    GIMAP7 MUTATED GIMAP7 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D604V9, continuous
D604V10, continuous
[1] "Remove cluster labels:" "GIMAP7 MUTATED"        
clus
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OG 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-Z6-AAPN 
"GIMAP7 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GIMAP7 MUTATED       1                         0
  GIMAP7 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GIMAP7 MUTATED                                           0     4
  GIMAP7 WILD-TYPE                                         1   353
D604V11, multiclass
                                           clus
vv                                          GIMAP7 MUTATED GIMAP7 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V12, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     0   4
  GIMAP7 WILD-TYPE  10 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      0    4
  GIMAP7 WILD-TYPE   10  394
                        clus
vv                       GIMAP7 MUTATED GIMAP7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(605) Variable = PRMT3 MUTATION ANALYSIS
D605V1, survival
                 sevent
clus2               0   1
  PRMT3 MUTATED     5   5
  PRMT3 WILD-TYPE 333 211
  PRMT3 MUTATED PRMT3 WILD-TYPE 
             10             544 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              5             211 
$`PRMT3 MUTATED`
TCGA-L7-A6VZ TCGA-LN-A49U TCGA-B7-A5TI TCGA-BR-8382 TCGA-CD-5801 TCGA-D7-A6EY 
       10.36        15.35        19.56        25.05        13.18        11.44 
TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-VQ-A8DL 
       14.47        26.47        29.98         0.92 

$`PRMT3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PRMT3 MUTATED PRMT3 WILD-TYPE 
           0.92            0.00 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
          29.98          122.30 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
          14.91           13.53 
[1] "0.9 - 30.0 (14.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D605V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRMT3 MUTATED         0        0        2        0         3         0
  PRMT3 WILD-TYPE      10       20       44       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRMT3 MUTATED           0          1          1          3        0         0
  PRMT3 WILD-TYPE        29         83         61         36       43         4
D605V3, multiclass
            clus
vv           PRMT3 MUTATED PRMT3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PRMT3 MUTATED       0   3   5   2
  PRMT3 WILD-TYPE    54 132 256 100
D605V4, multiclass
       clus
vv      PRMT3 MUTATED PRMT3 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                5             256
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PRMT3 MUTATED     4   3   0   4
  PRMT3 WILD-TYPE 191 170  89  81
D605V5, multiclass
    clus
vv   PRMT3 MUTATED PRMT3 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             0              89
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V6, binary
                 cls
clus                0   1
  PRMT3 MUTATED     9   0
  PRMT3 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      9    0
  PRMT3 WILD-TYPE  473   38
   clus
vv  PRMT3 MUTATED PRMT3 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D605V7, binary
                 cls
clus                0   1
  PRMT3 MUTATED     5   6
  PRMT3 WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      5    6
  PRMT3 WILD-TYPE  167  400
        clus
vv       PRMT3 MUTATED PRMT3 WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D605V8, binary
                 cls
clus                0   1
  PRMT3 MUTATED     8   2
  PRMT3 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      8    2
  PRMT3 WILD-TYPE  408  100
     clus
vv    PRMT3 MUTATED PRMT3 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D605V9, continuous
[1] "Remove cluster labels:" "PRMT3 MUTATED"         
clus
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49V      TCGA-LN-A49W 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
D605V10, continuous
[1] "Remove cluster labels:" "PRMT3 MUTATED"         
clus
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" "PRMT3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"PRMT3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRMT3 MUTATED       3                         0
  PRMT3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRMT3 MUTATED                                           0     8
  PRMT3 WILD-TYPE                                         1   349
D605V11, multiclass
                                           clus
vv                                          PRMT3 MUTATED PRMT3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V12, binary
                 cls
clus                0   1
  PRMT3 MUTATED     0  10
  PRMT3 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      0   10
  PRMT3 WILD-TYPE   10  388
                        clus
vv                       PRMT3 MUTATED PRMT3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(606) Variable = C20ORF160 MUTATION ANALYSIS
D606V1, survival
                     sevent
clus2                   0   1
  C20ORF160 MUTATED     6   2
  C20ORF160 WILD-TYPE 332 214
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  8                 546 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  2                 214 
$`C20ORF160 MUTATED`
TCGA-L5-A4OF TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 TCGA-D7-8572 
       26.33        34.68        44.94        29.59        31.10        16.80 
TCGA-HJ-7597 TCGA-HU-A4G8 
       26.47        22.68 

$`C20ORF160 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
               16.8                 0.0 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
              44.94              122.30 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
             28.030              13.445 
[1] "16.8 - 44.9 (28.0)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2.6"
D606V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C20ORF160 MUTATED         0        0        1        0         2         4
  C20ORF160 WILD-TYPE      10       20       45       31        82        79
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF160 MUTATED           0          0          0          1        0
  C20ORF160 WILD-TYPE        29         84         62         38       43
                     vv
clus                  STAGE IVA
  C20ORF160 MUTATED           0
  C20ORF160 WILD-TYPE         4
D606V3, multiclass
            clus
vv           C20ORF160 MUTATED C20ORF160 WILD-TYPE
  STAGE I                    0                  10
  STAGE IA                   0                  20
  STAGE IB                   1                  45
  STAGE II                   0                  31
  STAGE IIA                  2                  82
  STAGE IIB                  4                  79
  STAGE III                  0                  29
  STAGE IIIA                 0                  84
  STAGE IIIB                 0                  62
  STAGE IIIC                 1                  38
  STAGE IV                   0                  43
  STAGE IVA                  0                   4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  C20ORF160 MUTATED       1   2   3   2
  C20ORF160 WILD-TYPE    53 133 258 100
D606V4, multiclass
       clus
vv      C20ORF160 MUTATED C20ORF160 WILD-TYPE
  T0+T1                 1                  53
  T2                    2                 133
  T3                    3                 258
  T4                    2                 100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  C20ORF160 MUTATED     4   2   2   0
  C20ORF160 WILD-TYPE 191 171  87  85
D606V5, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  N0                 4                 191
  N1                 2                 171
  N2                 2                  87
  N3                 0                  85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V6, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     6   0
  C20ORF160 WILD-TYPE 476  38
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      6    0
  C20ORF160 WILD-TYPE  476   38
   clus
vv  C20ORF160 MUTATED C20ORF160 WILD-TYPE
  0                 6                 476
  1                 0                  38
[1] 2 2
[1] FALSE
D606V7, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     6   2
  C20ORF160 WILD-TYPE 166 404
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      6    2
  C20ORF160 WILD-TYPE  166  404
        clus
vv       C20ORF160 MUTATED C20ORF160 WILD-TYPE
  FEMALE                 6                 166
  MALE                   2                 404
[1] 2 2
[1] FALSE
D606V8, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     8   0
  C20ORF160 WILD-TYPE 408 102
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      8    0
  C20ORF160 WILD-TYPE  408  102
     clus
vv    C20ORF160 MUTATED C20ORF160 WILD-TYPE
  NO                  8                 408
  YES                 0                 102
[1] 2 2
[1] FALSE
D606V9, continuous
D606V10, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  C20ORF160 MUTATED       1                         0
  C20ORF160 WILD-TYPE   132                        14
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C20ORF160 MUTATED                                           0     7
  C20ORF160 WILD-TYPE                                         1   350
D606V11, multiclass
                                           clus
vv                                          C20ORF160 MUTATED
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     7
                                           clus
vv                                          C20ORF160 WILD-TYPE
  ASIAN                                                     132
  BLACK OR AFRICAN AMERICAN                                  14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V12, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     0   7
  C20ORF160 WILD-TYPE  10 391
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      0    7
  C20ORF160 WILD-TYPE   10  391
                        clus
vv                       C20ORF160 MUTATED C20ORF160 WILD-TYPE
  HISPANIC OR LATINO                     0                  10
  NOT HISPANIC OR LATINO                 7                 391
[1] 2 2
[1] FALSE

Clustering(607) Variable = ACTL6A MUTATION ANALYSIS
D607V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     5   3
  ACTL6A WILD-TYPE 333 213
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              546 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               3              213 
$`ACTL6A MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CG-5726 
       34.68        36.16        29.59        12.89        16.14        28.96 
TCGA-HF-7132 TCGA-HU-A4GQ 
       77.29         0.10 

$`ACTL6A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ACTL6A MUTATED ACTL6A WILD-TYPE 
             0.1              0.0 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
           77.29           122.30 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
          29.275           13.510 
[1] "0.1 - 77.3 (29.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D607V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACTL6A MUTATED         0        2        0        1         1         2
  ACTL6A WILD-TYPE      10       18       46       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE        29         84         61         38       43
                  vv
clus               STAGE IVA
  ACTL6A MUTATED           0
  ACTL6A WILD-TYPE         4
D607V3, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ACTL6A MUTATED       2   1   2   3
  ACTL6A WILD-TYPE    52 134 259  99
D607V4, multiclass
       clus
vv      ACTL6A MUTATED ACTL6A WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 2              259
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ACTL6A MUTATED     5   1   1   1
  ACTL6A WILD-TYPE 190 172  88  84
D607V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              5              190
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V6, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     8   0
  ACTL6A WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      8    0
  ACTL6A WILD-TYPE  474   38
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D607V7, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     3   5
  ACTL6A WILD-TYPE 169 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      3    5
  ACTL6A WILD-TYPE  169  401
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  FEMALE              3              169
  MALE                5              401
[1] 2 2
[1] FALSE
D607V8, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     6   1
  ACTL6A WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      6    1
  ACTL6A WILD-TYPE  410  101
     clus
vv    ACTL6A MUTATED ACTL6A WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D607V9, continuous
D607V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ACTL6A MUTATED       2                         0
  ACTL6A WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTL6A MUTATED                                           0     4
  ACTL6A WILD-TYPE                                         1   353
D607V11, multiclass
                                           clus
vv                                          ACTL6A MUTATED ACTL6A WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V12, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     0   6
  ACTL6A WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      0    6
  ACTL6A WILD-TYPE   10  392
                        clus
vv                       ACTL6A MUTATED ACTL6A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(608) Variable = PMEPA1 MUTATION ANALYSIS
D608V1, survival
                  sevent
clus2                0   1
  PMEPA1 MUTATED     4   2
  PMEPA1 WILD-TYPE 334 214
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               6              548 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               2              214 
$`PMEPA1 MUTATED`
TCGA-2H-A9GF TCGA-BR-6852 TCGA-BR-8363 TCGA-HU-8602 TCGA-HU-A4GT TCGA-VQ-A8P2 
       25.78        44.94         0.26        22.32         6.51        38.14 

$`PMEPA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
            0.26             0.00 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           44.94           122.30 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           24.05            13.53 
[1] "0.3 - 44.9 (24.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D608V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PMEPA1 MUTATED         0        0        1        0         2         1
  PMEPA1 WILD-TYPE      10       20       45       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PMEPA1 MUTATED           1          1          0          0        0
  PMEPA1 WILD-TYPE        28         83         62         39       43
                  vv
clus               STAGE IVA
  PMEPA1 MUTATED           0
  PMEPA1 WILD-TYPE         4
D608V3, multiclass
            clus
vv           PMEPA1 MUTATED PMEPA1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PMEPA1 MUTATED       0   1   3   2
  PMEPA1 WILD-TYPE    54 134 258 100
D608V4, multiclass
       clus
vv      PMEPA1 MUTATED PMEPA1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PMEPA1 MUTATED     4   2   0   0
  PMEPA1 WILD-TYPE 191 171  89  85
D608V5, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  N0              4              191
  N1              2              171
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V6, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     7   0
  PMEPA1 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      7    0
  PMEPA1 WILD-TYPE  475   38
   clus
vv  PMEPA1 MUTATED PMEPA1 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D608V7, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     5   2
  PMEPA1 WILD-TYPE 167 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      5    2
  PMEPA1 WILD-TYPE  167  404
        clus
vv       PMEPA1 MUTATED PMEPA1 WILD-TYPE
  FEMALE              5              167
  MALE                2              404
[1] 2 2
[1] FALSE
D608V8, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     5   1
  PMEPA1 WILD-TYPE 411 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      5    1
  PMEPA1 WILD-TYPE  411  101
     clus
vv    PMEPA1 MUTATED PMEPA1 WILD-TYPE
  NO               5              411
  YES              1              101
[1] 2 2
[1] FALSE
D608V9, continuous
D608V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PMEPA1 MUTATED       2                         0
  PMEPA1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PMEPA1 MUTATED                                           0     4
  PMEPA1 WILD-TYPE                                         1   353
D608V11, multiclass
                                           clus
vv                                          PMEPA1 MUTATED PMEPA1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V12, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     0   5
  PMEPA1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      0    5
  PMEPA1 WILD-TYPE   10  393
                        clus
vv                       PMEPA1 MUTATED PMEPA1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(609) Variable = PTPLA MUTATION ANALYSIS
D609V1, survival
                 sevent
clus2               0   1
  PTPLA MUTATED     2   5
  PTPLA WILD-TYPE 336 211
  PTPLA MUTATED PTPLA WILD-TYPE 
              7             547 
  PTPLA MUTATED PTPLA WILD-TYPE 
              5             211 
$`PTPLA MUTATED`
TCGA-IG-A625 TCGA-R6-A8WC TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-A4YV TCGA-FP-A4BE 
       12.82         2.30        16.14         6.58         5.92        11.08 
TCGA-HU-A4GQ 
        0.10 

$`PTPLA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PTPLA MUTATED PTPLA WILD-TYPE 
            0.1             0.0 
  PTPLA MUTATED PTPLA WILD-TYPE 
          16.14          122.30 
  PTPLA MUTATED PTPLA WILD-TYPE 
           6.58           13.78 
[1] "0.1 - 16.1 (6.6)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "4.5"
D609V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPLA MUTATED         0        0        0        0         2         1
  PTPLA WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPLA MUTATED           0          0          2          1        0         0
  PTPLA WILD-TYPE        29         84         60         38       43         4
D609V3, multiclass
            clus
vv           PTPLA MUTATED PTPLA WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPLA MUTATED       0   0   5   1
  PTPLA WILD-TYPE    54 135 256 101
D609V4, multiclass
       clus
vv      PTPLA MUTATED PTPLA WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                5             256
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPLA MUTATED     2   1   2   1
  PTPLA WILD-TYPE 193 172  87  84
D609V5, multiclass
    clus
vv   PTPLA MUTATED PTPLA WILD-TYPE
  N0             2             193
  N1             1             172
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V6, binary
                 cls
clus                0   1
  PTPLA MUTATED     6   0
  PTPLA WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      6    0
  PTPLA WILD-TYPE  476   38
   clus
vv  PTPLA MUTATED PTPLA WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D609V7, binary
                 cls
clus                0   1
  PTPLA MUTATED     2   5
  PTPLA WILD-TYPE 170 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      2    5
  PTPLA WILD-TYPE  170  401
        clus
vv       PTPLA MUTATED PTPLA WILD-TYPE
  FEMALE             2             170
  MALE               5             401
[1] 2 2
[1] FALSE
D609V8, binary
                 cls
clus                0   1
  PTPLA MUTATED     4   1
  PTPLA WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      4    1
  PTPLA WILD-TYPE  412  101
     clus
vv    PTPLA MUTATED PTPLA WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D609V9, continuous
D609V10, continuous
[1] "Remove cluster labels:" "PTPLA MUTATED"         
clus
  PTPLA MUTATED PTPLA WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" "PTPLA WILD-TYPE" 
     TCGA-Z6-AAPN 
"PTPLA WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPLA MUTATED       3                         1
  PTPLA WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPLA MUTATED                                           0     3
  PTPLA WILD-TYPE                                         1   354
D609V11, multiclass
                                           clus
vv                                          PTPLA MUTATED PTPLA WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V12, binary
                 cls
clus                0   1
  PTPLA MUTATED     0   7
  PTPLA WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPLA MUTATED      0    7
  PTPLA WILD-TYPE   10  391
                        clus
vv                       PTPLA MUTATED PTPLA WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(610) Variable = PNLIPRP3 MUTATION ANALYSIS
D610V1, survival
                    sevent
clus2                  0   1
  PNLIPRP3 MUTATED    10   6
  PNLIPRP3 WILD-TYPE 328 210
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
                16                538 
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
                 6                210 
$`PNLIPRP3 MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-LN-A8HZ TCGA-R6-A8WC TCGA-VR-A8EO TCGA-X8-AAAR 
        7.63         5.92        12.33         2.30        25.81        18.21 
TCGA-BR-4184 TCGA-BR-6706 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A452 
        6.97        18.05        35.84        25.05        31.96         7.53 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-HU-A4GP TCGA-R5-A7ZI 
       16.44        13.78         8.98        74.53 

$`PNLIPRP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       20.05        31.27        14.30        58.55        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
               2.3                0.0 
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
             74.53             122.30 
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
             15.11              13.53 
[1] "2.3 - 74.5 (15.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D610V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNLIPRP3 MUTATED         0        0        1        0         4         0
  PNLIPRP3 WILD-TYPE      10       20       45       31        80        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNLIPRP3 MUTATED           2          3          2          1        2
  PNLIPRP3 WILD-TYPE        27         81         60         38       41
                    vv
clus                 STAGE IVA
  PNLIPRP3 MUTATED           0
  PNLIPRP3 WILD-TYPE         4
D610V3, multiclass
            clus
vv           PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 4                 80
  STAGE IIB                 0                 83
  STAGE III                 2                 27
  STAGE IIIA                3                 81
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PNLIPRP3 MUTATED       1   3   8   4
  PNLIPRP3 WILD-TYPE    53 132 253  98
D610V4, multiclass
       clus
vv      PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                   8                253
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PNLIPRP3 MUTATED     4   8   1   3
  PNLIPRP3 WILD-TYPE 191 165  88  82
D610V5, multiclass
    clus
vv   PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  N0                4                191
  N1                8                165
  N2                1                 88
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V6, binary
                    cls
clus                   0   1
  PNLIPRP3 MUTATED    12   2
  PNLIPRP3 WILD-TYPE 470  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PNLIPRP3 MUTATED     12    2
  PNLIPRP3 WILD-TYPE  470   36
   clus
vv  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  0               12                470
  1                2                 36
[1] 2 2
[1] FALSE
D610V7, binary
                    cls
clus                   0   1
  PNLIPRP3 MUTATED     4  13
  PNLIPRP3 WILD-TYPE 168 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PNLIPRP3 MUTATED      4   13
  PNLIPRP3 WILD-TYPE  168  393
        clus
vv       PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  FEMALE                4                168
  MALE                 13                393
[1] 2 2
[1] FALSE
D610V8, binary
                    cls
clus                   0   1
  PNLIPRP3 MUTATED    12   3
  PNLIPRP3 WILD-TYPE 404  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PNLIPRP3 MUTATED     12    3
  PNLIPRP3 WILD-TYPE  404   99
     clus
vv    PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  NO                12                404
  YES                3                 99
[1] 2 2
[1] FALSE
D610V9, continuous
[1] "Remove cluster labels:" "PNLIPRP3 MUTATED"      
clus
  PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EP 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" "PNLIPRP3 WILD-TYPE" 
        TCGA-Z6-A8JE 
"PNLIPRP3 WILD-TYPE" 
D610V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PNLIPRP3 MUTATED       4                         0
  PNLIPRP3 WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PNLIPRP3 MUTATED                                           0    11
  PNLIPRP3 WILD-TYPE                                         1   346
D610V11, multiclass
                                           clus
vv                                          PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V12, binary
                    cls
clus                   0   1
  PNLIPRP3 MUTATED     1  13
  PNLIPRP3 WILD-TYPE   9 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PNLIPRP3 MUTATED      1   13
  PNLIPRP3 WILD-TYPE    9  385
                        clus
vv                       PNLIPRP3 MUTATED PNLIPRP3 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               13                385
[1] 2 2
[1] FALSE

Clustering(611) Variable = KIAA1797 MUTATION ANALYSIS
D611V1, survival
                    sevent
clus2                  0   1
  KIAA1797 MUTATED    17   6
  KIAA1797 WILD-TYPE 321 210
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                23                531 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 6                210 
$`KIAA1797 MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-L5-A4OF TCGA-L5-A4OU TCGA-LN-A49L TCGA-LN-A9FO 
       19.99         5.16        26.33        29.00        10.45         0.13 
TCGA-BR-6452 TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 
       34.68         3.45        14.43        29.59        31.10         1.12 
TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       27.12        31.96        15.95         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-D7-A4YY TCGA-HU-A4G8 TCGA-HU-A4H8 TCGA-RD-A8N9 
       65.10        13.78        22.68        14.07        35.61 

$`KIAA1797 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
        0.99        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
              0.13               0.00 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            105.07             122.30 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
             22.68              13.41 
[1] "0.1 - 105.1 (22.7)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D611V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1797 MUTATED         0        1        2        3         5         4
  KIAA1797 WILD-TYPE      10       19       44       28        79        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1797 MUTATED           1          1          3          2        2
  KIAA1797 WILD-TYPE        28         83         59         37       41
                    vv
clus                 STAGE IVA
  KIAA1797 MUTATED           0
  KIAA1797 WILD-TYPE         4
D611V3, multiclass
            clus
vv           KIAA1797 MUTATED KIAA1797 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  3                 28
  STAGE IIA                 5                 79
  STAGE IIB                 4                 79
  STAGE III                 1                 28
  STAGE IIIA                1                 83
  STAGE IIIB                3                 59
  STAGE IIIC                2                 37
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1797 MUTATED       3   6   8   7
  KIAA1797 WILD-TYPE    51 129 253  95
D611V4, multiclass
       clus
vv      KIAA1797 MUTATED KIAA1797 WILD-TYPE
  T0+T1                3                 51
  T2                   6                129
  T3                   8                253
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1797 MUTATED     9  11   3   2
  KIAA1797 WILD-TYPE 186 162  86  83
D611V5, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  N0                9                186
  N1               11                162
  N2                3                 86
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V6, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    22   1
  KIAA1797 WILD-TYPE 460  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     22    1
  KIAA1797 WILD-TYPE  460   37
   clus
vv  KIAA1797 MUTATED KIAA1797 WILD-TYPE
  0               22                460
  1                1                 37
[1] 2 2
[1] FALSE
D611V7, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    10  15
  KIAA1797 WILD-TYPE 162 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     10   15
  KIAA1797 WILD-TYPE  162  391
        clus
vv       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  FEMALE               10                162
  MALE                 15                391
[1] 2 2
[1] FALSE
D611V8, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    18   3
  KIAA1797 WILD-TYPE 398  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     18    3
  KIAA1797 WILD-TYPE  398   99
     clus
vv    KIAA1797 MUTATED KIAA1797 WILD-TYPE
  NO                18                398
  YES                3                 99
[1] 2 2
[1] FALSE
D611V9, continuous
[1] "Remove cluster labels:" "KIAA1797 MUTATED"      
clus
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49M 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" "KIAA1797 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1797 WILD-TYPE" 
D611V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1797 MUTATED       6                         0
  KIAA1797 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1797 MUTATED                                           0    14
  KIAA1797 WILD-TYPE                                         1   343
D611V11, multiclass
                                           clus
vv                                          KIAA1797 MUTATED KIAA1797 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V12, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED     0  17
  KIAA1797 WILD-TYPE  10 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED      0   17
  KIAA1797 WILD-TYPE   10  381
                        clus
vv                       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               17                381
[1] 2 2
[1] FALSE

Clustering(612) Variable = UBQLN2 MUTATION ANALYSIS
D612V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     8   1
  UBQLN2 WILD-TYPE 330 215
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               9              545 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               1              215 
$`UBQLN2 MUTATED`
TCGA-L5-A8NR TCGA-LN-A4MR TCGA-LN-A9FQ TCGA-VR-A8EZ TCGA-BR-6802 TCGA-CD-8536 
        8.71        13.22        12.85        18.18        30.90        12.43 
TCGA-CG-5723 TCGA-HU-A4G9 TCGA-IN-A7NT 
      105.07        24.20        10.62 

$`UBQLN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
            8.71             0.00 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
          105.07           122.30 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           13.22            13.58 
[1] "8.7 - 105.1 (13.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "4.5"
D612V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBQLN2 MUTATED         0        1        1        2         2         1
  UBQLN2 WILD-TYPE      10       19       45       29        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           1          2          0          1        0
  UBQLN2 WILD-TYPE        28         82         62         38       43
                  vv
clus               STAGE IVA
  UBQLN2 MUTATED           0
  UBQLN2 WILD-TYPE         4
D612V3, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  UBQLN2 MUTATED       1   3   6   1
  UBQLN2 WILD-TYPE    53 132 255 101
D612V4, multiclass
       clus
vv      UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 6              255
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  UBQLN2 MUTATED     6   3   1   1
  UBQLN2 WILD-TYPE 189 170  88  84
D612V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              6              189
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V6, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED    10   0
  UBQLN2 WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED     10    0
  UBQLN2 WILD-TYPE  472   38
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D612V7, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     5   6
  UBQLN2 WILD-TYPE 167 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      5    6
  UBQLN2 WILD-TYPE  167  400
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  FEMALE              5              167
  MALE                6              400
[1] 2 2
[1] FALSE
D612V8, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     9   1
  UBQLN2 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      9    1
  UBQLN2 WILD-TYPE  407  101
     clus
vv    UBQLN2 MUTATED UBQLN2 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D612V9, continuous
[1] "Remove cluster labels:" "UBQLN2 MUTATED"        
clus
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8Q7 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
D612V10, continuous
[1] "Remove cluster labels:" "UBQLN2 MUTATED"        
clus
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8Q7 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" "UBQLN2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UBQLN2 MUTATED       4                         0
  UBQLN2 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBQLN2 MUTATED                                           0     4
  UBQLN2 WILD-TYPE                                         1   353
D612V11, multiclass
                                           clus
vv                                          UBQLN2 MUTATED UBQLN2 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V12, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     0   7
  UBQLN2 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      0    7
  UBQLN2 WILD-TYPE   10  391
                        clus
vv                       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(613) Variable = CYP51A1 MUTATION ANALYSIS
D613V1, survival
                   sevent
clus2                 0   1
  CYP51A1 MUTATED    10   3
  CYP51A1 WILD-TYPE 328 213
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
               13               541 
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
                3               213 
$`CYP51A1 MUTATED`
TCGA-IG-A5B8 TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-8078 
        0.79        21.01         7.17         2.10         6.97        29.59 
TCGA-BR-8360 TCGA-CG-5721 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A74B TCGA-HU-A4GN 
        6.18         6.02        16.80        14.27         7.13        29.98 
TCGA-HU-A4HD 
       33.40 

$`CYP51A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34        19.96         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
             0.79              0.00 
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
             33.4             122.3 
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
             7.17             13.58 
[1] "0.8 - 33.4 (7.2)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D613V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP51A1 MUTATED         1        1        1        0         2         2
  CYP51A1 WILD-TYPE       9       19       45       31        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP51A1 MUTATED           0          4          1          0        1
  CYP51A1 WILD-TYPE        29         80         61         39       42
                   vv
clus                STAGE IVA
  CYP51A1 MUTATED           0
  CYP51A1 WILD-TYPE         4
D613V3, multiclass
            clus
vv           CYP51A1 MUTATED CYP51A1 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CYP51A1 MUTATED       2   3   6   2
  CYP51A1 WILD-TYPE    52 132 255 100
D613V4, multiclass
       clus
vv      CYP51A1 MUTATED CYP51A1 WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  6               255
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CYP51A1 MUTATED     5   4   2   2
  CYP51A1 WILD-TYPE 190 169  87  83
D613V5, multiclass
    clus
vv   CYP51A1 MUTATED CYP51A1 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V6, binary
                   cls
clus                  0   1
  CYP51A1 MUTATED    11   0
  CYP51A1 WILD-TYPE 471  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP51A1 MUTATED     11    0
  CYP51A1 WILD-TYPE  471   38
   clus
vv  CYP51A1 MUTATED CYP51A1 WILD-TYPE
  0              11               471
  1               0                38
[1] 2 2
[1] FALSE
D613V7, binary
                   cls
clus                  0   1
  CYP51A1 MUTATED     4   9
  CYP51A1 WILD-TYPE 168 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP51A1 MUTATED      4    9
  CYP51A1 WILD-TYPE  168  397
        clus
vv       CYP51A1 MUTATED CYP51A1 WILD-TYPE
  FEMALE               4               168
  MALE                 9               397
[1] 2 2
[1] FALSE
D613V8, binary
                   cls
clus                  0   1
  CYP51A1 MUTATED    12   0
  CYP51A1 WILD-TYPE 404 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP51A1 MUTATED     12    0
  CYP51A1 WILD-TYPE  404  102
     clus
vv    CYP51A1 MUTATED CYP51A1 WILD-TYPE
  NO               12               404
  YES               0               102
[1] 2 2
[1] FALSE
D613V9, continuous
[1] "Remove cluster labels:" "CYP51A1 MUTATED"       
clus
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-A8JD 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
D613V10, continuous
[1] "Remove cluster labels:" "CYP51A1 MUTATED"       
clus
  CYP51A1 MUTATED CYP51A1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A6QS 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OQ        TCGA-L5-A4OT 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" "CYP51A1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CYP51A1 MUTATED       2                         0
  CYP51A1 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP51A1 MUTATED                                           0    10
  CYP51A1 WILD-TYPE                                         1   347
D613V11, multiclass
                                           clus
vv                                          CYP51A1 MUTATED CYP51A1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V12, binary
                   cls
clus                  0   1
  CYP51A1 MUTATED     0  10
  CYP51A1 WILD-TYPE  10 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP51A1 MUTATED      0   10
  CYP51A1 WILD-TYPE   10  388
                        clus
vv                       CYP51A1 MUTATED CYP51A1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(614) Variable = AMZ2 MUTATION ANALYSIS
D614V1, survival
                sevent
clus2              0   1
  AMZ2 MUTATED     5   0
  AMZ2 WILD-TYPE 333 216
  AMZ2 MUTATED AMZ2 WILD-TYPE 
             5            549 
  AMZ2 MUTATED AMZ2 WILD-TYPE 
             0            216 
$`AMZ2 MUTATED`
TCGA-Z6-AAPN TCGA-BR-8680 TCGA-CG-4305 TCGA-FP-A4BE TCGA-VQ-A8P2 
        2.66        31.96        15.95        11.08        38.14 

$`AMZ2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMZ2 MUTATED AMZ2 WILD-TYPE 
          2.66           0.00 
  AMZ2 MUTATED AMZ2 WILD-TYPE 
         38.14         122.30 
  AMZ2 MUTATED AMZ2 WILD-TYPE 
         15.95          13.55 
[1] "2.7 - 38.1 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr="     "3300000"
D614V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMZ2 MUTATED         0        0        0        1         2         0
  AMZ2 WILD-TYPE      10       20       46       30        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMZ2 MUTATED           0          1          0          0        1         0
  AMZ2 WILD-TYPE        29         83         62         39       42         4
D614V3, multiclass
            clus
vv           AMZ2 MUTATED AMZ2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  AMZ2 MUTATED       0   1   2   2
  AMZ2 WILD-TYPE    54 134 259 100
D614V4, multiclass
       clus
vv      AMZ2 MUTATED AMZ2 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  AMZ2 MUTATED     2   2   1   0
  AMZ2 WILD-TYPE 193 171  88  85
D614V5, multiclass
    clus
vv   AMZ2 MUTATED AMZ2 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V6, binary
                cls
clus               0   1
  AMZ2 MUTATED     4   1
  AMZ2 WILD-TYPE 478  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMZ2 MUTATED      4    1
  AMZ2 WILD-TYPE  478   37
   clus
vv  AMZ2 MUTATED AMZ2 WILD-TYPE
  0            4            478
  1            1             37
[1] 2 2
[1] FALSE
D614V7, binary
                cls
clus               0   1
  AMZ2 MUTATED     0   5
  AMZ2 WILD-TYPE 172 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMZ2 MUTATED      0    5
  AMZ2 WILD-TYPE  172  401
        clus
vv       AMZ2 MUTATED AMZ2 WILD-TYPE
  FEMALE            0            172
  MALE              5            401
[1] 2 2
[1] FALSE
D614V8, binary
                cls
clus               0   1
  AMZ2 MUTATED     3   2
  AMZ2 WILD-TYPE 413 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMZ2 MUTATED      3    2
  AMZ2 WILD-TYPE  413  100
     clus
vv    AMZ2 MUTATED AMZ2 WILD-TYPE
  NO             3            413
  YES            2            100
[1] 2 2
[1] FALSE
D614V9, continuous
D614V10, continuous
[1] "Remove cluster labels:" "AMZ2 MUTATED"          
clus
  AMZ2 MUTATED AMZ2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7 
"AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" "AMZ2 WILD-TYPE" 
    TCGA-XP-A8T8 
"AMZ2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AMZ2 MUTATED       1                         1
  AMZ2 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMZ2 MUTATED                                           0     2
  AMZ2 WILD-TYPE                                         1   355
D614V11, multiclass
                                           clus
vv                                          AMZ2 MUTATED AMZ2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V12, binary
                cls
clus               0   1
  AMZ2 MUTATED     0   3
  AMZ2 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMZ2 MUTATED      0    3
  AMZ2 WILD-TYPE   10  395
                        clus
vv                       AMZ2 MUTATED AMZ2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(615) Variable = CD58 MUTATION ANALYSIS
D615V1, survival
                sevent
clus2              0   1
  CD58 MUTATED     4   4
  CD58 WILD-TYPE 334 212
  CD58 MUTATED CD58 WILD-TYPE 
             8            546 
  CD58 MUTATED CD58 WILD-TYPE 
             4            212 
$`CD58 MUTATED`
TCGA-L5-A8NI TCGA-BR-4253 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG 
       13.48         4.08        34.68        29.59         0.26         6.58 
TCGA-CG-5721 TCGA-HU-A4G8 
        6.02        22.68 

$`CD58 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CD58 MUTATED CD58 WILD-TYPE 
          0.26           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         34.68         122.30 
  CD58 MUTATED CD58 WILD-TYPE 
         10.03          13.63 
[1] "0.3 - 34.7 (10.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D615V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD58 MUTATED         0        0        1        0         2         2
  CD58 WILD-TYPE      10       20       45       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD58 MUTATED           1          1          0          0        1         0
  CD58 WILD-TYPE        28         83         62         39       42         4
D615V3, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CD58 MUTATED       0   1   5   2
  CD58 WILD-TYPE    54 134 256 100
D615V4, multiclass
       clus
vv      CD58 MUTATED CD58 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CD58 MUTATED     4   4   0   0
  CD58 WILD-TYPE 191 169  89  85
D615V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0            4            191
  N1            4            169
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V6, binary
                cls
clus               0   1
  CD58 MUTATED     8   0
  CD58 WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      8    0
  CD58 WILD-TYPE  474   38
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D615V7, binary
                cls
clus               0   1
  CD58 MUTATED     5   3
  CD58 WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      5    3
  CD58 WILD-TYPE  167  403
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D615V8, binary
                cls
clus               0   1
  CD58 MUTATED     8   0
  CD58 WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      8    0
  CD58 WILD-TYPE  408  102
     clus
vv    CD58 MUTATED CD58 WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D615V9, continuous
D615V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD58 MUTATED       2                         0
  CD58 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD58 MUTATED                                           0     5
  CD58 WILD-TYPE                                         1   352
D615V11, multiclass
                                           clus
vv                                          CD58 MUTATED CD58 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V12, binary
                cls
clus               0   1
  CD58 MUTATED     0   6
  CD58 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      0    6
  CD58 WILD-TYPE   10  392
                        clus
vv                       CD58 MUTATED CD58 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(616) Variable = SDAD1 MUTATION ANALYSIS
D616V1, survival
                 sevent
clus2               0   1
  SDAD1 MUTATED     2   4
  SDAD1 WILD-TYPE 336 212
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              6             548 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              4             212 
$`SDAD1 MUTATED`
TCGA-L5-A43H TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-5733 TCGA-D7-A6EY TCGA-FP-7916 
        0.30        31.27        12.62        21.07        11.44        14.07 

$`SDAD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SDAD1 MUTATED SDAD1 WILD-TYPE 
            0.3             0.0 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
          31.27          122.30 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
         13.345          13.565 
[1] "0.3 - 31.3 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D616V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SDAD1 MUTATED         0        0        1        0         0         1
  SDAD1 WILD-TYPE      10       20       45       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SDAD1 MUTATED           1          1          1          2        0         0
  SDAD1 WILD-TYPE        28         83         61         37       43         4
D616V3, multiclass
            clus
vv           SDAD1 MUTATED SDAD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SDAD1 MUTATED       1   2   2   3
  SDAD1 WILD-TYPE    53 133 259  99
D616V4, multiclass
       clus
vv      SDAD1 MUTATED SDAD1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SDAD1 MUTATED     2   2   1   3
  SDAD1 WILD-TYPE 193 171  88  82
D616V5, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V6, binary
                 cls
clus                0   1
  SDAD1 MUTATED     8   0
  SDAD1 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      8    0
  SDAD1 WILD-TYPE  474   38
   clus
vv  SDAD1 MUTATED SDAD1 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D616V7, binary
                 cls
clus                0   1
  SDAD1 MUTATED     4   5
  SDAD1 WILD-TYPE 168 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      4    5
  SDAD1 WILD-TYPE  168  401
        clus
vv       SDAD1 MUTATED SDAD1 WILD-TYPE
  FEMALE             4             168
  MALE               5             401
[1] 2 2
[1] FALSE
D616V8, binary
                 cls
clus                0   1
  SDAD1 MUTATED     7   0
  SDAD1 WILD-TYPE 409 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      7    0
  SDAD1 WILD-TYPE  409  102
     clus
vv    SDAD1 MUTATED SDAD1 WILD-TYPE
  NO              7             409
  YES             0             102
[1] 2 2
[1] FALSE
D616V9, continuous
D616V10, continuous
[1] "Remove cluster labels:" "SDAD1 MUTATED"         
clus
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" "SDAD1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SDAD1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SDAD1 MUTATED       2                         0
  SDAD1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SDAD1 MUTATED                                           0     6
  SDAD1 WILD-TYPE                                         1   351
D616V11, multiclass
                                           clus
vv                                          SDAD1 MUTATED SDAD1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V12, binary
                 cls
clus                0   1
  SDAD1 MUTATED     0   7
  SDAD1 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      0    7
  SDAD1 WILD-TYPE   10  391
                        clus
vv                       SDAD1 MUTATED SDAD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(617) Variable = ANKRD23 MUTATION ANALYSIS
D617V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     6   2
  ANKRD23 WILD-TYPE 332 214
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                8               546 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                2               214 
$`ANKRD23 MUTATED`
TCGA-IC-A6RF TCGA-VR-A8Q7 TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CG-5728 
       15.68        52.27         9.34        35.84        16.14        65.10 
TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.51        38.14 

$`ANKRD23 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             6.51              0.00 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             65.1             122.3 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
            25.99             13.51 
[1] "6.5 - 65.1 (26.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D617V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD23 MUTATED         0        1        2        0         1         0
  ANKRD23 WILD-TYPE      10       19       44       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          2          1          0        0
  ANKRD23 WILD-TYPE        29         82         61         39       43
                   vv
clus                STAGE IVA
  ANKRD23 MUTATED           0
  ANKRD23 WILD-TYPE         4
D617V3, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ANKRD23 MUTATED       1   2   3   1
  ANKRD23 WILD-TYPE    53 133 258 101
D617V4, multiclass
       clus
vv      ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ANKRD23 MUTATED     4   3   0   1
  ANKRD23 WILD-TYPE 191 170  89  84
D617V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V6, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     8   0
  ANKRD23 WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      8    0
  ANKRD23 WILD-TYPE  474   38
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D617V7, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     5   3
  ANKRD23 WILD-TYPE 167 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      5    3
  ANKRD23 WILD-TYPE  167  403
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  FEMALE               5               167
  MALE                 3               403
[1] 2 2
[1] FALSE
D617V8, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     6   1
  ANKRD23 WILD-TYPE 410 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      6    1
  ANKRD23 WILD-TYPE  410  101
     clus
vv    ANKRD23 MUTATED ANKRD23 WILD-TYPE
  NO                6               410
  YES               1               101
[1] 2 2
[1] FALSE
D617V9, continuous
[1] "Remove cluster labels:" "ANKRD23 MUTATED"       
clus
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
D617V10, continuous
[1] "Remove cluster labels:" "ANKRD23 MUTATED"       
clus
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                2                96 
       TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE        TCGA-L5-A4OG 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" "ANKRD23 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD23 MUTATED       1                         0
  ANKRD23 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD23 MUTATED                                           0     6
  ANKRD23 WILD-TYPE                                         1   351
D617V11, multiclass
                                           clus
vv                                          ANKRD23 MUTATED ANKRD23 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V12, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     0   5
  ANKRD23 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      0    5
  ANKRD23 WILD-TYPE   10  393
                        clus
vv                       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(618) Variable = ACTR8 MUTATION ANALYSIS
D618V1, survival
                 sevent
clus2               0   1
  ACTR8 MUTATED     7   3
  ACTR8 WILD-TYPE 331 213
  ACTR8 MUTATED ACTR8 WILD-TYPE 
             10             544 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
              3             213 
$`ACTR8 MUTATED`
TCGA-R6-A6KZ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7901 TCGA-BR-8680 
        5.06         6.97        34.68        32.78         3.45        31.96 
TCGA-BR-A4IU TCGA-FP-A4BE TCGA-HF-A5NB TCGA-VQ-A8P2 
       27.55        11.08        30.51        38.14 

$`ACTR8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ACTR8 MUTATED ACTR8 WILD-TYPE 
           3.45            0.00 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
          38.14          122.30 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
          29.03           13.53 
[1] "3.5 - 38.1 (29.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D618V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACTR8 MUTATED         0        0        0        0         3         2
  ACTR8 WILD-TYPE      10       20       46       31        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTR8 MUTATED           0          4          0          1        1         0
  ACTR8 WILD-TYPE        29         80         62         38       42         4
D618V3, multiclass
            clus
vv           ACTR8 MUTATED ACTR8 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ACTR8 MUTATED       0   0   5   6
  ACTR8 WILD-TYPE    54 135 256  96
D618V4, multiclass
       clus
vv      ACTR8 MUTATED ACTR8 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                5             256
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACTR8 MUTATED     5   4   1   1
  ACTR8 WILD-TYPE 190 169  88  84
D618V5, multiclass
    clus
vv   ACTR8 MUTATED ACTR8 WILD-TYPE
  N0             5             190
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V6, binary
                 cls
clus                0   1
  ACTR8 MUTATED     9   1
  ACTR8 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      9    1
  ACTR8 WILD-TYPE  473   37
   clus
vv  ACTR8 MUTATED ACTR8 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D618V7, binary
                 cls
clus                0   1
  ACTR8 MUTATED     5   7
  ACTR8 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      5    7
  ACTR8 WILD-TYPE  167  399
        clus
vv       ACTR8 MUTATED ACTR8 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D618V8, binary
                 cls
clus                0   1
  ACTR8 MUTATED     8   3
  ACTR8 WILD-TYPE 408  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      8    3
  ACTR8 WILD-TYPE  408   99
     clus
vv    ACTR8 MUTATED ACTR8 WILD-TYPE
  NO              8             408
  YES             3              99
[1] 2 2
[1] FALSE
D618V9, continuous
D618V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACTR8 MUTATED       2                         1
  ACTR8 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTR8 MUTATED                                           0     8
  ACTR8 WILD-TYPE                                         1   349
D618V11, multiclass
                                           clus
vv                                          ACTR8 MUTATED ACTR8 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V12, binary
                 cls
clus                0   1
  ACTR8 MUTATED     0  10
  ACTR8 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      0   10
  ACTR8 WILD-TYPE   10  388
                        clus
vv                       ACTR8 MUTATED ACTR8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(619) Variable = IFT140 MUTATION ANALYSIS
D619V1, survival
                  sevent
clus2                0   1
  IFT140 MUTATED     9  11
  IFT140 WILD-TYPE 329 205
  IFT140 MUTATED IFT140 WILD-TYPE 
              20              534 
  IFT140 MUTATED IFT140 WILD-TYPE 
              11              205 
$`IFT140 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-JY-A6FG TCGA-L5-A8NH 
        4.31        21.99        20.05        31.27        41.52        12.92 
TCGA-L5-A8NN TCGA-R6-A6XG TCGA-Z6-A9VB TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-A4QL 
        5.49        38.40         1.32        35.84        31.27        16.14 
TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-6525 TCGA-D7-A6EY 
        6.58         8.05         9.01         6.02        13.35        11.44 
TCGA-HF-A5NB TCGA-RD-A8MV 
       30.51       122.30 

$`IFT140 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ 
        0.23        20.15         9.86        25.78        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  IFT140 MUTATED IFT140 WILD-TYPE 
            1.32             0.00 
  IFT140 MUTATED IFT140 WILD-TYPE 
           122.3            122.1 
  IFT140 MUTATED IFT140 WILD-TYPE 
          14.745           13.565 
[1] "1.3 - 122.3 (14.7)" "0.0 - 122.1 (13.6)"
[1] "hr=" "1.3"
D619V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFT140 MUTATED         0        0        1        1         1         3
  IFT140 WILD-TYPE      10       20       45       30        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFT140 MUTATED           3          2          3          2        4
  IFT140 WILD-TYPE        26         82         59         37       39
                  vv
clus               STAGE IVA
  IFT140 MUTATED           0
  IFT140 WILD-TYPE         4
D619V3, multiclass
            clus
vv           IFT140 MUTATED IFT140 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               3               26
  STAGE IIIA              2               82
  STAGE IIIB              3               59
  STAGE IIIC              2               37
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  IFT140 MUTATED       3   3   9   6
  IFT140 WILD-TYPE    51 132 252  96
D619V4, multiclass
       clus
vv      IFT140 MUTATED IFT140 WILD-TYPE
  T0+T1              3               51
  T2                 3              132
  T3                 9              252
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  IFT140 MUTATED     5   8   2   5
  IFT140 WILD-TYPE 190 165  87  80
D619V5, multiclass
    clus
vv   IFT140 MUTATED IFT140 WILD-TYPE
  N0              5              190
  N1              8              165
  N2              2               87
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V6, binary
                  cls
clus                 0   1
  IFT140 MUTATED    18   3
  IFT140 WILD-TYPE 464  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFT140 MUTATED     18    3
  IFT140 WILD-TYPE  464   35
   clus
vv  IFT140 MUTATED IFT140 WILD-TYPE
  0             18              464
  1              3               35
[1] 2 2
[1] FALSE
D619V7, binary
                  cls
clus                 0   1
  IFT140 MUTATED     7  16
  IFT140 WILD-TYPE 165 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFT140 MUTATED      7   16
  IFT140 WILD-TYPE  165  390
        clus
vv       IFT140 MUTATED IFT140 WILD-TYPE
  FEMALE              7              165
  MALE               16              390
[1] 2 2
[1] FALSE
D619V8, binary
                  cls
clus                 0   1
  IFT140 MUTATED    16   2
  IFT140 WILD-TYPE 400 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFT140 MUTATED     16    2
  IFT140 WILD-TYPE  400  100
     clus
vv    IFT140 MUTATED IFT140 WILD-TYPE
  NO              16              400
  YES              2              100
[1] 2 2
[1] FALSE
D619V9, continuous
D619V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IFT140 MUTATED       1                         0
  IFT140 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFT140 MUTATED                                           0    15
  IFT140 WILD-TYPE                                         1   342
D619V11, multiclass
                                           clus
vv                                          IFT140 MUTATED IFT140 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V12, binary
                  cls
clus                 0   1
  IFT140 MUTATED     0  12
  IFT140 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFT140 MUTATED      0   12
  IFT140 WILD-TYPE   10  386
                        clus
vv                       IFT140 MUTATED IFT140 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(620) Variable = GSDMC MUTATION ANALYSIS
D620V1, survival
                 sevent
clus2               0   1
  GSDMC MUTATED    10   8
  GSDMC WILD-TYPE 328 208
  GSDMC MUTATED GSDMC WILD-TYPE 
             18             536 
  GSDMC MUTATED GSDMC WILD-TYPE 
              8             208 
$`GSDMC MUTATED`
TCGA-JY-A6FB TCGA-Q9-A6FU TCGA-JY-A93C TCGA-L5-A4OW TCGA-L5-A8NS TCGA-R6-A6XQ 
       60.39         5.16        23.18         7.13        13.41         6.35 
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7957 TCGA-BR-8382 
       11.70         6.97        34.68        18.05         9.07        25.05 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-HF-A5NB TCGA-HU-8602 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        8.22        20.65        30.51        22.32        38.14        37.22 

$`GSDMC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        25.61        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         3.45        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34         0.66        32.52        13.51        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GSDMC MUTATED GSDMC WILD-TYPE 
           5.16            0.00 
  GSDMC MUTATED GSDMC WILD-TYPE 
          60.39          122.30 
  GSDMC MUTATED GSDMC WILD-TYPE 
          19.35           13.53 
[1] "5.2 - 60.4 (19.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D620V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GSDMC MUTATED         1        0        1        0         1         4
  GSDMC WILD-TYPE       9       20       45       31        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSDMC MUTATED           0          5          2          3        1         0
  GSDMC WILD-TYPE        29         79         60         36       42         4
D620V3, multiclass
            clus
vv           GSDMC MUTATED GSDMC WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GSDMC MUTATED       1   2   7   8
  GSDMC WILD-TYPE    53 133 254  94
D620V4, multiclass
       clus
vv      GSDMC MUTATED GSDMC WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                7             254
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GSDMC MUTATED     7   5   3   3
  GSDMC WILD-TYPE 188 168  86  82
D620V5, multiclass
    clus
vv   GSDMC MUTATED GSDMC WILD-TYPE
  N0             7             188
  N1             5             168
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V6, binary
                 cls
clus                0   1
  GSDMC MUTATED    16   1
  GSDMC WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMC MUTATED     16    1
  GSDMC WILD-TYPE  466   37
   clus
vv  GSDMC MUTATED GSDMC WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D620V7, binary
                 cls
clus                0   1
  GSDMC MUTATED    10   9
  GSDMC WILD-TYPE 162 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMC MUTATED     10    9
  GSDMC WILD-TYPE  162  397
        clus
vv       GSDMC MUTATED GSDMC WILD-TYPE
  FEMALE            10             162
  MALE               9             397
[1] 2 2
[1] FALSE
D620V8, binary
                 cls
clus                0   1
  GSDMC MUTATED    14   4
  GSDMC WILD-TYPE 402  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMC MUTATED     14    4
  GSDMC WILD-TYPE  402   98
     clus
vv    GSDMC MUTATED GSDMC WILD-TYPE
  NO             14             402
  YES             4              98
[1] 2 2
[1] FALSE
D620V9, continuous
D620V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GSDMC MUTATED       2                         0
  GSDMC WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GSDMC MUTATED                                           0    15
  GSDMC WILD-TYPE                                         1   342
D620V11, multiclass
                                           clus
vv                                          GSDMC MUTATED GSDMC WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V12, binary
                 cls
clus                0   1
  GSDMC MUTATED     0  12
  GSDMC WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMC MUTATED      0   12
  GSDMC WILD-TYPE   10  386
                        clus
vv                       GSDMC MUTATED GSDMC WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(621) Variable = ANK3 MUTATION ANALYSIS
D621V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    37  21
  ANK3 WILD-TYPE 301 195
  ANK3 MUTATED ANK3 WILD-TYPE 
            58            496 
  ANK3 MUTATED ANK3 WILD-TYPE 
            21            195 
$`ANK3 MUTATED`
TCGA-JY-A6FB TCGA-2H-A9GH TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       60.39        31.27         8.94        32.45         7.69        33.27 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L7-A6VZ TCGA-LN-A4A2 TCGA-R6-A6L4 
        3.75        16.47         7.76        10.36        12.49        16.31 
TCGA-R6-A8W8 TCGA-V5-AASW TCGA-VR-A8EO TCGA-Z6-A9VB TCGA-BR-4184 TCGA-BR-4201 
        2.89         9.27        25.81         1.32         6.97        30.90 
TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8363 
        9.67        30.90        44.94        35.84        32.25         0.26 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        4.31        25.05         1.12        28.14        31.96        16.14 
TCGA-CD-5801 TCGA-CD-8535 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 
       13.18        12.82        15.95         1.02         9.01         6.02 
TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-8572 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EY 
      105.07        28.96        16.80        14.66        13.78        11.44 
TCGA-FP-7735 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
        3.48        77.29        30.51        22.32        22.68        24.20 
TCGA-HU-A4GH TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7O7 
       11.77        20.25        23.84        36.95        19.73        45.67 
TCGA-R5-A7ZI TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-AA6K 
       74.53        13.25        38.14        12.43 

$`ANK3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        4.21        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        12.92        13.48        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42        16.44        15.35         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       24.72        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        24.26         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A666 
       13.51         2.53         5.56        63.62         3.72        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        27.55        17.26 

  ANK3 MUTATED ANK3 WILD-TYPE 
          0.26           0.00 
  ANK3 MUTATED ANK3 WILD-TYPE 
        105.07         122.30 
  ANK3 MUTATED ANK3 WILD-TYPE 
         16.39          13.41 
[1] "0.3 - 105.1 (16.4)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D621V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANK3 MUTATED         1        3        6        4         6         8
  ANK3 WILD-TYPE       9       17       40       27        78        75
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ANK3 MUTATED           2          9          4          6        6         0
  ANK3 WILD-TYPE        27         75         58         33       37         4
D621V3, multiclass
            clus
vv           ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              3             17
  STAGE IB              6             40
  STAGE II              4             27
  STAGE IIA             6             78
  STAGE IIB             8             75
  STAGE III             2             27
  STAGE IIIA            9             75
  STAGE IIIB            4             58
  STAGE IIIC            6             33
  STAGE IV              6             37
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ANK3 MUTATED       6  14  24  13
  ANK3 WILD-TYPE    48 121 237  89
D621V4, multiclass
       clus
vv      ANK3 MUTATED ANK3 WILD-TYPE
  T0+T1            6             48
  T2              14            121
  T3              24            237
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ANK3 MUTATED    19  21   7  10
  ANK3 WILD-TYPE 176 152  82  75
D621V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0           19            176
  N1           21            152
  N2            7             82
  N3           10             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V6, binary
                cls
clus               0   1
  ANK3 MUTATED    52   5
  ANK3 WILD-TYPE 430  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     52    5
  ANK3 WILD-TYPE  430   33
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           52            430
  1            5             33
[1] 2 2
[1] FALSE
D621V7, binary
                cls
clus               0   1
  ANK3 MUTATED    26  37
  ANK3 WILD-TYPE 146 369
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     26   37
  ANK3 WILD-TYPE  146  369
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           26            146
  MALE             37            369
[1] 2 2
[1] FALSE
D621V8, binary
                cls
clus               0   1
  ANK3 MUTATED    44  11
  ANK3 WILD-TYPE 372  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     44   11
  ANK3 WILD-TYPE  372   91
     clus
vv    ANK3 MUTATED ANK3 WILD-TYPE
  NO            44            372
  YES           11             91
[1] 2 2
[1] FALSE
D621V9, continuous
D621V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ANK3 MUTATED      10                         1
  ANK3 WILD-TYPE   123                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANK3 MUTATED                                           0    39
  ANK3 WILD-TYPE                                         1   318
D621V11, multiclass
                                           clus
vv                                          ANK3 MUTATED ANK3 WILD-TYPE
  ASIAN                                               10            123
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               39            318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V12, binary
                cls
clus               0   1
  ANK3 MUTATED     2  39
  ANK3 WILD-TYPE   8 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      2   39
  ANK3 WILD-TYPE    8  359
                        clus
vv                       ANK3 MUTATED ANK3 WILD-TYPE
  HISPANIC OR LATINO                2              8
  NOT HISPANIC OR LATINO           39            359
[1] 2 2
[1] FALSE

Clustering(622) Variable = TMEM87B MUTATION ANALYSIS
D622V1, survival
                   sevent
clus2                 0   1
  TMEM87B MUTATED     5   1
  TMEM87B WILD-TYPE 333 215
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                6               548 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                1               215 
$`TMEM87B MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-8368 TCGA-BR-8372 TCGA-CG-5721 TCGA-VQ-A8P2 
       19.99         6.97         4.31        31.27         6.02        38.14 

$`TMEM87B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TMEM87B MUTATED TMEM87B WILD-TYPE 
             4.31              0.00 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
            38.14            122.30 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
           13.480            13.565 
[1] "4.3 - 38.1 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.3"
D622V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM87B MUTATED         0        0        1        0         0         0
  TMEM87B WILD-TYPE      10       20       45       31        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM87B MUTATED           0          2          0          2        1
  TMEM87B WILD-TYPE        29         82         62         37       42
                   vv
clus                STAGE IVA
  TMEM87B MUTATED           0
  TMEM87B WILD-TYPE         4
D622V3, multiclass
            clus
vv           TMEM87B MUTATED TMEM87B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM87B MUTATED       0   1   2   3
  TMEM87B WILD-TYPE    54 134 259  99
D622V4, multiclass
       clus
vv      TMEM87B MUTATED TMEM87B WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM87B MUTATED     1   3   0   2
  TMEM87B WILD-TYPE 194 170  89  83
D622V5, multiclass
    clus
vv   TMEM87B MUTATED TMEM87B WILD-TYPE
  N0               1               194
  N1               3               170
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V6, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     4   0
  TMEM87B WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      4    0
  TMEM87B WILD-TYPE  478   38
   clus
vv  TMEM87B MUTATED TMEM87B WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D622V7, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     1   5
  TMEM87B WILD-TYPE 171 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      1    5
  TMEM87B WILD-TYPE  171  401
        clus
vv       TMEM87B MUTATED TMEM87B WILD-TYPE
  FEMALE               1               171
  MALE                 5               401
[1] 2 2
[1] FALSE
D622V8, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     5   1
  TMEM87B WILD-TYPE 411 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      5    1
  TMEM87B WILD-TYPE  411  101
     clus
vv    TMEM87B MUTATED TMEM87B WILD-TYPE
  NO                5               411
  YES               1               101
[1] 2 2
[1] FALSE
D622V9, continuous
D622V10, continuous
[1] "Remove cluster labels:" "TMEM87B MUTATED"       
clus
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" "TMEM87B WILD-TYPE" 
       TCGA-Z6-AAPN 
"TMEM87B WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM87B MUTATED       0                         0
  TMEM87B WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM87B MUTATED                                           0     5
  TMEM87B WILD-TYPE                                         1   352
D622V11, multiclass
                                           clus
vv                                          TMEM87B MUTATED TMEM87B WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V12, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     0   3
  TMEM87B WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      0    3
  TMEM87B WILD-TYPE   10  395
                        clus
vv                       TMEM87B MUTATED TMEM87B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(623) Variable = CCDC103 MUTATION ANALYSIS
D623V1, survival
                   sevent
clus2                 0   1
  CCDC103 MUTATED     4   1
  CCDC103 WILD-TYPE 334 215
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                5               549 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                1               215 
$`CCDC103 MUTATED`
TCGA-JY-A93D TCGA-LN-A9FO TCGA-BR-7703 TCGA-CG-5723 TCGA-SW-A7EA 
       31.56         0.13        36.16       105.07        19.04 

$`CCDC103 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CCDC103 MUTATED CCDC103 WILD-TYPE 
             0.13              0.00 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
           105.07            122.30 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
            31.56             13.51 
[1] "0.1 - 105.1 (31.6)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.5"
D623V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC103 MUTATED         0        1        1        1         1         0
  CCDC103 WILD-TYPE      10       19       45       30        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC103 MUTATED           0          0          0          1        0
  CCDC103 WILD-TYPE        29         84         62         38       43
                   vv
clus                STAGE IVA
  CCDC103 MUTATED           0
  CCDC103 WILD-TYPE         4
D623V3, multiclass
            clus
vv           CCDC103 MUTATED CCDC103 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CCDC103 MUTATED       1   4   0   0
  CCDC103 WILD-TYPE    53 131 261 102
D623V4, multiclass
       clus
vv      CCDC103 MUTATED CCDC103 WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  0               261
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CCDC103 MUTATED     3   1   0   1
  CCDC103 WILD-TYPE 192 172  89  84
D623V5, multiclass
    clus
vv   CCDC103 MUTATED CCDC103 WILD-TYPE
  N0               3               192
  N1               1               172
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V6, binary
                   cls
clus                  0   1
  CCDC103 MUTATED     5   0
  CCDC103 WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      5    0
  CCDC103 WILD-TYPE  477   38
   clus
vv  CCDC103 MUTATED CCDC103 WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D623V7, binary
                   cls
clus                  0   1
  CCDC103 MUTATED     1   4
  CCDC103 WILD-TYPE 171 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      1    4
  CCDC103 WILD-TYPE  171  402
        clus
vv       CCDC103 MUTATED CCDC103 WILD-TYPE
  FEMALE               1               171
  MALE                 4               402
[1] 2 2
[1] FALSE
D623V8, binary
                   cls
clus                  0   1
  CCDC103 MUTATED     4   1
  CCDC103 WILD-TYPE 412 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      4    1
  CCDC103 WILD-TYPE  412  101
     clus
vv    CCDC103 MUTATED CCDC103 WILD-TYPE
  NO                4               412
  YES               1               101
[1] 2 2
[1] FALSE
D623V9, continuous
D623V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC103 MUTATED       1                         0
  CCDC103 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC103 MUTATED                                           0     3
  CCDC103 WILD-TYPE                                         1   354
D623V11, multiclass
                                           clus
vv                                          CCDC103 MUTATED CCDC103 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V12, binary
                   cls
clus                  0   1
  CCDC103 MUTATED     0   3
  CCDC103 WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      0    3
  CCDC103 WILD-TYPE   10  395
                        clus
vv                       CCDC103 MUTATED CCDC103 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(624) Variable = AXIN1 MUTATION ANALYSIS
D624V1, survival
                 sevent
clus2               0   1
  AXIN1 MUTATED     8   7
  AXIN1 WILD-TYPE 330 209
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             15             539 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              7             209 
$`AXIN1 MUTATED`
TCGA-L5-A8NM TCGA-LN-A4A1 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6705 
        7.76        12.59        19.56         6.97         9.67        25.61 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4J8 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-6820 
       31.10         1.12        13.51        16.14         6.58        11.31 
TCGA-HU-A4GU TCGA-IN-A6RR TCGA-VQ-A8P2 
        6.58         6.74        38.14 

$`AXIN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  AXIN1 MUTATED AXIN1 WILD-TYPE 
           1.12            0.00 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          38.14          122.30 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          11.31           13.78 
[1] "1.1 - 38.1 (11.3)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.5"
D624V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AXIN1 MUTATED         1        0        0        0         3         3
  AXIN1 WILD-TYPE       9       20       46       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AXIN1 MUTATED           0          3          3          2        0         0
  AXIN1 WILD-TYPE        29         81         59         37       43         4
D624V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AXIN1 MUTATED       1   2   9   3
  AXIN1 WILD-TYPE    53 133 252  99
D624V4, multiclass
       clus
vv      AXIN1 MUTATED AXIN1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                9             252
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AXIN1 MUTATED     3   7   1   4
  AXIN1 WILD-TYPE 192 166  88  81
D624V5, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  N0             3             192
  N1             7             166
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V6, binary
                 cls
clus                0   1
  AXIN1 MUTATED    14   0
  AXIN1 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     14    0
  AXIN1 WILD-TYPE  468   38
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D624V7, binary
                 cls
clus                0   1
  AXIN1 MUTATED     7   9
  AXIN1 WILD-TYPE 165 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      7    9
  AXIN1 WILD-TYPE  165  397
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             7             165
  MALE               9             397
[1] 2 2
[1] FALSE
D624V8, binary
                 cls
clus                0   1
  AXIN1 MUTATED    15   1
  AXIN1 WILD-TYPE 401 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     15    1
  AXIN1 WILD-TYPE  401  101
     clus
vv    AXIN1 MUTATED AXIN1 WILD-TYPE
  NO             15             401
  YES             1             101
[1] 2 2
[1] FALSE
D624V9, continuous
[1] "Remove cluster labels:" "AXIN1 MUTATED"         
clus
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A2 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" "AXIN1 WILD-TYPE" 
D624V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AXIN1 MUTATED       3                         1
  AXIN1 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AXIN1 MUTATED                                           0    12
  AXIN1 WILD-TYPE                                         1   345
D624V11, multiclass
                                           clus
vv                                          AXIN1 MUTATED AXIN1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V12, binary
                 cls
clus                0   1
  AXIN1 MUTATED     0  14
  AXIN1 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      0   14
  AXIN1 WILD-TYPE   10  384
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(625) Variable = CTSD MUTATION ANALYSIS
D625V1, survival
                sevent
clus2              0   1
  CTSD MUTATED     6   5
  CTSD WILD-TYPE 332 211
  CTSD MUTATED CTSD WILD-TYPE 
            11            543 
  CTSD MUTATED CTSD WILD-TYPE 
             5            211 
$`CTSD MUTATED`
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-R6-A6L6 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8059 
        5.92        32.45         7.04        34.68        32.78        14.43 
TCGA-BR-8368 TCGA-CD-A4MG TCGA-D7-6820 TCGA-HU-8602 TCGA-HU-A4GN 
        4.31         6.58        11.31        22.32        29.98 

$`CTSD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CTSD MUTATED CTSD WILD-TYPE 
          4.31           0.00 
  CTSD MUTATED CTSD WILD-TYPE 
         34.68         122.30 
  CTSD MUTATED CTSD WILD-TYPE 
         14.43          13.55 
[1] "4.3 - 34.7 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D625V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSD MUTATED         0        0        1        0         5         2
  CTSD WILD-TYPE      10       20       45       31        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSD MUTATED           2          0          0          0        0         0
  CTSD WILD-TYPE        27         84         62         39       43         4
D625V3, multiclass
            clus
vv           CTSD MUTATED CTSD WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTSD MUTATED       0   3   5   2
  CTSD WILD-TYPE    54 132 256 100
D625V4, multiclass
       clus
vv      CTSD MUTATED CTSD WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTSD MUTATED     6   4   0   0
  CTSD WILD-TYPE 189 169  89  85
D625V5, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  N0            6            189
  N1            4            169
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V6, binary
                cls
clus               0   1
  CTSD MUTATED    10   0
  CTSD WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED     10    0
  CTSD WILD-TYPE  472   38
   clus
vv  CTSD MUTATED CTSD WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D625V7, binary
                cls
clus               0   1
  CTSD MUTATED     4   7
  CTSD WILD-TYPE 168 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      4    7
  CTSD WILD-TYPE  168  399
        clus
vv       CTSD MUTATED CTSD WILD-TYPE
  FEMALE            4            168
  MALE              7            399
[1] 2 2
[1] FALSE
D625V8, binary
                cls
clus               0   1
  CTSD MUTATED    11   0
  CTSD WILD-TYPE 405 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED     11    0
  CTSD WILD-TYPE  405  102
     clus
vv    CTSD MUTATED CTSD WILD-TYPE
  NO            11            405
  YES            0            102
[1] 2 2
[1] FALSE
D625V9, continuous
D625V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSD MUTATED       3                         0
  CTSD WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSD MUTATED                                           0     6
  CTSD WILD-TYPE                                         1   351
D625V11, multiclass
                                           clus
vv                                          CTSD MUTATED CTSD WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V12, binary
                cls
clus               0   1
  CTSD MUTATED     0   9
  CTSD WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      0    9
  CTSD WILD-TYPE   10  389
                        clus
vv                       CTSD MUTATED CTSD WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(626) Variable = BAT4 MUTATION ANALYSIS
D626V1, survival
                sevent
clus2              0   1
  BAT4 MUTATED     3   3
  BAT4 WILD-TYPE 335 213
  BAT4 MUTATED BAT4 WILD-TYPE 
             6            548 
  BAT4 MUTATED BAT4 WILD-TYPE 
             3            213 
$`BAT4 MUTATED`
TCGA-JY-A6FH TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8370 TCGA-CD-A4MG TCGA-HU-A4GQ 
       47.38        35.84         0.26         3.32         6.58         0.10 

$`BAT4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BAT4 MUTATED BAT4 WILD-TYPE 
           0.1            0.0 
  BAT4 MUTATED BAT4 WILD-TYPE 
         47.38         122.30 
  BAT4 MUTATED BAT4 WILD-TYPE 
          4.95          13.63 
[1] "0.1 - 47.4 (5.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D626V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAT4 MUTATED         0        0        2        0         1         1
  BAT4 WILD-TYPE      10       20       44       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAT4 MUTATED           0          0          1          1        0         0
  BAT4 WILD-TYPE        29         84         61         38       43         4
D626V3, multiclass
            clus
vv           BAT4 MUTATED BAT4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BAT4 MUTATED       0   3   2   1
  BAT4 WILD-TYPE    54 132 259 101
D626V4, multiclass
       clus
vv      BAT4 MUTATED BAT4 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BAT4 MUTATED     3   1   1   1
  BAT4 WILD-TYPE 192 172  88  84
D626V5, multiclass
    clus
vv   BAT4 MUTATED BAT4 WILD-TYPE
  N0            3            192
  N1            1            172
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V6, binary
                cls
clus               0   1
  BAT4 MUTATED     6   0
  BAT4 WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      6    0
  BAT4 WILD-TYPE  476   38
   clus
vv  BAT4 MUTATED BAT4 WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D626V7, binary
                cls
clus               0   1
  BAT4 MUTATED     2   4
  BAT4 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      2    4
  BAT4 WILD-TYPE  170  402
        clus
vv       BAT4 MUTATED BAT4 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D626V8, binary
                cls
clus               0   1
  BAT4 MUTATED     6   0
  BAT4 WILD-TYPE 410 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      6    0
  BAT4 WILD-TYPE  410  102
     clus
vv    BAT4 MUTATED BAT4 WILD-TYPE
  NO             6            410
  YES            0            102
[1] 2 2
[1] FALSE
D626V9, continuous
D626V10, continuous
[1] "Remove cluster labels:" "BAT4 MUTATED"          
clus
  BAT4 MUTATED BAT4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-KH-A6WC     TCGA-L5-A43C 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" "BAT4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"BAT4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAT4 MUTATED       2                         0
  BAT4 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAT4 MUTATED                                           0     4
  BAT4 WILD-TYPE                                         1   353
D626V11, multiclass
                                           clus
vv                                          BAT4 MUTATED BAT4 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V12, binary
                cls
clus               0   1
  BAT4 MUTATED     0   5
  BAT4 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      0    5
  BAT4 WILD-TYPE   10  393
                        clus
vv                       BAT4 MUTATED BAT4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(627) Variable = OSTALPHA MUTATION ANALYSIS
D627V1, survival
                    sevent
clus2                  0   1
  OSTALPHA MUTATED     4   0
  OSTALPHA WILD-TYPE 334 216
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 4                550 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 0                216 
$`OSTALPHA MUTATED`
TCGA-VR-A8EO TCGA-BR-8487 TCGA-BR-8680 TCGA-HF-A5NB 
       25.81         1.12        31.96        30.51 

$`OSTALPHA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
              1.12               0.00 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
             31.96             122.30 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
             28.16              13.53 
[1] "1.1 - 32.0 (28.2)"  "0.0 - 122.3 (13.5)"
[1] "hr="     "3300000"
D627V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSTALPHA MUTATED         0        0        0        0         2         1
  OSTALPHA WILD-TYPE      10       20       46       31        82        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSTALPHA MUTATED           0          0          0          1        1
  OSTALPHA WILD-TYPE        29         84         62         38       42
                    vv
clus                 STAGE IVA
  OSTALPHA MUTATED           0
  OSTALPHA WILD-TYPE         4
D627V3, multiclass
            clus
vv           OSTALPHA MUTATED OSTALPHA WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  OSTALPHA MUTATED       0   0   2   3
  OSTALPHA WILD-TYPE    54 135 259  99
D627V4, multiclass
       clus
vv      OSTALPHA MUTATED OSTALPHA WILD-TYPE
  T0+T1                0                 54
  T2                   0                135
  T3                   2                259
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  OSTALPHA MUTATED     3   0   1   1
  OSTALPHA WILD-TYPE 192 173  88  84
D627V5, multiclass
    clus
vv   OSTALPHA MUTATED OSTALPHA WILD-TYPE
  N0                3                192
  N1                0                173
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V6, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     4   1
  OSTALPHA WILD-TYPE 478  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      4    1
  OSTALPHA WILD-TYPE  478   37
   clus
vv  OSTALPHA MUTATED OSTALPHA WILD-TYPE
  0                4                478
  1                1                 37
[1] 2 2
[1] FALSE
D627V7, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     2   3
  OSTALPHA WILD-TYPE 170 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      2    3
  OSTALPHA WILD-TYPE  170  403
        clus
vv       OSTALPHA MUTATED OSTALPHA WILD-TYPE
  FEMALE                2                170
  MALE                  3                403
[1] 2 2
[1] FALSE
D627V8, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     3   2
  OSTALPHA WILD-TYPE 413 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      3    2
  OSTALPHA WILD-TYPE  413  100
     clus
vv    OSTALPHA MUTATED OSTALPHA WILD-TYPE
  NO                 3                413
  YES                2                100
[1] 2 2
[1] FALSE
D627V9, continuous
[1] "Remove cluster labels:" "OSTALPHA MUTATED"      
clus
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EP 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" "OSTALPHA WILD-TYPE" 
        TCGA-Z6-A8JE 
"OSTALPHA WILD-TYPE" 
D627V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  OSTALPHA MUTATED       1                         0
  OSTALPHA WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSTALPHA MUTATED                                           0     3
  OSTALPHA WILD-TYPE                                         1   354
D627V11, multiclass
                                           clus
vv                                          OSTALPHA MUTATED OSTALPHA WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V12, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     0   3
  OSTALPHA WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      0    3
  OSTALPHA WILD-TYPE   10  395
                        clus
vv                       OSTALPHA MUTATED OSTALPHA WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(628) Variable = FNDC4 MUTATION ANALYSIS
D628V1, survival
                 sevent
clus2               0   1
  FNDC4 MUTATED     3   2
  FNDC4 WILD-TYPE 335 214
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              5             549 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              2             214 
$`FNDC4 MUTATED`
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CG-5733 TCGA-FP-A4BE TCGA-VQ-AA6F 
       16.14         5.13        21.07        11.08        54.12 

$`FNDC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15        21.44        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FNDC4 MUTATED FNDC4 WILD-TYPE 
           5.13            0.00 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
          54.12          122.30 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
          16.14           13.55 
[1] "5.1 - 54.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D628V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FNDC4 MUTATED         0        0        0        0         1         2
  FNDC4 WILD-TYPE      10       20       46       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FNDC4 MUTATED           0          2          1          0        0         0
  FNDC4 WILD-TYPE        29         82         61         39       43         4
D628V3, multiclass
            clus
vv           FNDC4 MUTATED FNDC4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FNDC4 MUTATED       0   1   4   1
  FNDC4 WILD-TYPE    54 134 257 101
D628V4, multiclass
       clus
vv      FNDC4 MUTATED FNDC4 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FNDC4 MUTATED     2   1   2   1
  FNDC4 WILD-TYPE 193 172  87  84
D628V5, multiclass
    clus
vv   FNDC4 MUTATED FNDC4 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V6, binary
                 cls
clus                0   1
  FNDC4 MUTATED     6   0
  FNDC4 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      6    0
  FNDC4 WILD-TYPE  476   38
   clus
vv  FNDC4 MUTATED FNDC4 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D628V7, binary
                 cls
clus                0   1
  FNDC4 MUTATED     2   4
  FNDC4 WILD-TYPE 170 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      2    4
  FNDC4 WILD-TYPE  170  402
        clus
vv       FNDC4 MUTATED FNDC4 WILD-TYPE
  FEMALE             2             170
  MALE               4             402
[1] 2 2
[1] FALSE
D628V8, binary
                 cls
clus                0   1
  FNDC4 MUTATED     4   2
  FNDC4 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      4    2
  FNDC4 WILD-TYPE  412  100
     clus
vv    FNDC4 MUTATED FNDC4 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D628V9, continuous
D628V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FNDC4 MUTATED       0                         1
  FNDC4 WILD-TYPE   133                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FNDC4 MUTATED                                           0     4
  FNDC4 WILD-TYPE                                         1   353
D628V11, multiclass
                                           clus
vv                                          FNDC4 MUTATED FNDC4 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V12, binary
                 cls
clus                0   1
  FNDC4 MUTATED     0   4
  FNDC4 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      0    4
  FNDC4 WILD-TYPE   10  394
                        clus
vv                       FNDC4 MUTATED FNDC4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(629) Variable = FBXO48 MUTATION ANALYSIS
D629V1, survival
                  sevent
clus2                0   1
  FBXO48 MUTATED     3   1
  FBXO48 WILD-TYPE 335 215
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               4              550 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               1              215 
$`FBXO48 MUTATED`
TCGA-BR-7704 TCGA-CG-5726 TCGA-F1-6874 TCGA-FP-A4BE 
       35.24        28.96        14.47        11.08 

$`FBXO48 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  FBXO48 MUTATED FBXO48 WILD-TYPE 
           11.08             0.00 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
           35.24           122.30 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
          21.715           13.530 
[1] "11.1 - 35.2 (21.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D629V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO48 MUTATED         0        1        2        1         1         0
  FBXO48 WILD-TYPE      10       19       44       30        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO48 MUTATED           0          0          0          0        0
  FBXO48 WILD-TYPE        29         84         62         39       43
                  vv
clus               STAGE IVA
  FBXO48 MUTATED           0
  FBXO48 WILD-TYPE         4
D629V3, multiclass
            clus
vv           FBXO48 MUTATED FBXO48 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FBXO48 MUTATED       1   2   2   0
  FBXO48 WILD-TYPE    53 133 259 102
D629V4, multiclass
       clus
vv      FBXO48 MUTATED FBXO48 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 2              259
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FBXO48 MUTATED     5   0   0   0
  FBXO48 WILD-TYPE 190 173  89  85
D629V5, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  N0              5              190
  N1              0              173
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V6, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     5   0
  FBXO48 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      5    0
  FBXO48 WILD-TYPE  477   38
   clus
vv  FBXO48 MUTATED FBXO48 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D629V7, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     1   4
  FBXO48 WILD-TYPE 171 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      1    4
  FBXO48 WILD-TYPE  171  402
        clus
vv       FBXO48 MUTATED FBXO48 WILD-TYPE
  FEMALE              1              171
  MALE                4              402
[1] 2 2
[1] FALSE
D629V8, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     2   1
  FBXO48 WILD-TYPE 414 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      2    1
  FBXO48 WILD-TYPE  414  101
     clus
vv    FBXO48 MUTATED FBXO48 WILD-TYPE
  NO               2              414
  YES              1              101
[1] 2 2
[1] FALSE
D629V9, continuous
D629V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO48 MUTATED       0                         1
  FBXO48 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO48 MUTATED                                           0     2
  FBXO48 WILD-TYPE                                         1   355
D629V11, multiclass
                                           clus
vv                                          FBXO48 MUTATED FBXO48 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V12, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     0   3
  FBXO48 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      0    3
  FBXO48 WILD-TYPE   10  395
                        clus
vv                       FBXO48 MUTATED FBXO48 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(630) Variable = UGT1A4 MUTATION ANALYSIS
D630V1, survival
                  sevent
clus2                0   1
  UGT1A4 MUTATED     6   6
  UGT1A4 WILD-TYPE 332 210
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              12              542 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
               6              210 
$`UGT1A4 MUTATED`
TCGA-2H-A9GH TCGA-R6-A6L6 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-CD-8536 
       31.27         7.04         6.97        34.68        14.43        12.43 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8DU TCGA-VQ-A8P2 
       14.27         5.92         6.51        29.00         5.46        38.14 

$`UGT1A4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        21.14        20.91        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
            5.46             0.00 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
           38.14           122.30 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
          13.350           13.565 
[1] "5.5 - 38.1 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D630V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGT1A4 MUTATED         0        0        0        1         2         2
  UGT1A4 WILD-TYPE      10       20       46       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A4 MUTATED           1          4          0          1        0
  UGT1A4 WILD-TYPE        28         80         62         38       43
                  vv
clus               STAGE IVA
  UGT1A4 MUTATED           0
  UGT1A4 WILD-TYPE         4
D630V3, multiclass
            clus
vv           UGT1A4 MUTATED UGT1A4 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  UGT1A4 MUTATED       1   1   6   3
  UGT1A4 WILD-TYPE    53 134 255  99
D630V4, multiclass
       clus
vv      UGT1A4 MUTATED UGT1A4 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 6              255
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  UGT1A4 MUTATED     3   5   1   2
  UGT1A4 WILD-TYPE 192 168  88  83
D630V5, multiclass
    clus
vv   UGT1A4 MUTATED UGT1A4 WILD-TYPE
  N0              3              192
  N1              5              168
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V6, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED    10   0
  UGT1A4 WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED     10    0
  UGT1A4 WILD-TYPE  472   38
   clus
vv  UGT1A4 MUTATED UGT1A4 WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D630V7, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     4   8
  UGT1A4 WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      4    8
  UGT1A4 WILD-TYPE  168  398
        clus
vv       UGT1A4 MUTATED UGT1A4 WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D630V8, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED    10   1
  UGT1A4 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED     10    1
  UGT1A4 WILD-TYPE  406  101
     clus
vv    UGT1A4 MUTATED UGT1A4 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D630V9, continuous
D630V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UGT1A4 MUTATED       3                         0
  UGT1A4 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGT1A4 MUTATED                                           0     8
  UGT1A4 WILD-TYPE                                         1   349
D630V11, multiclass
                                           clus
vv                                          UGT1A4 MUTATED UGT1A4 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V12, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     0   9
  UGT1A4 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      0    9
  UGT1A4 WILD-TYPE   10  389
                        clus
vv                       UGT1A4 MUTATED UGT1A4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(631) Variable = FAM113A MUTATION ANALYSIS
D631V1, survival
                   sevent
clus2                 0   1
  FAM113A MUTATED     4   5
  FAM113A WILD-TYPE 334 211
  FAM113A MUTATED FAM113A WILD-TYPE 
                9               545 
  FAM113A MUTATED FAM113A WILD-TYPE 
                5               211 
$`FAM113A MUTATED`
TCGA-CG-4460 TCGA-IG-A3Y9 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6457 
       21.99         0.85         6.97        30.90        34.68        13.68 
TCGA-BR-8363 TCGA-CG-5721 TCGA-HU-A4H8 
        0.26         6.02        14.07 

$`FAM113A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM113A MUTATED FAM113A WILD-TYPE 
             0.26              0.00 
  FAM113A MUTATED FAM113A WILD-TYPE 
            34.68            122.30 
  FAM113A MUTATED FAM113A WILD-TYPE 
            13.68             13.55 
[1] "0.3 - 34.7 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D631V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM113A MUTATED         0        0        2        0         2         0
  FAM113A WILD-TYPE      10       20       44       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM113A MUTATED           0          2          0          0        2
  FAM113A WILD-TYPE        29         82         62         39       41
                   vv
clus                STAGE IVA
  FAM113A MUTATED           0
  FAM113A WILD-TYPE         4
D631V3, multiclass
            clus
vv           FAM113A MUTATED FAM113A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM113A MUTATED       1   2   4   3
  FAM113A WILD-TYPE    53 133 257  99
D631V4, multiclass
       clus
vv      FAM113A MUTATED FAM113A WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  4               257
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM113A MUTATED     4   4   0   0
  FAM113A WILD-TYPE 191 169  89  85
D631V5, multiclass
    clus
vv   FAM113A MUTATED FAM113A WILD-TYPE
  N0               4               191
  N1               4               169
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V6, binary
                   cls
clus                  0   1
  FAM113A MUTATED     7   1
  FAM113A WILD-TYPE 475  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      7    1
  FAM113A WILD-TYPE  475   37
   clus
vv  FAM113A MUTATED FAM113A WILD-TYPE
  0               7               475
  1               1                37
[1] 2 2
[1] FALSE
D631V7, binary
                   cls
clus                  0   1
  FAM113A MUTATED     5   5
  FAM113A WILD-TYPE 167 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      5    5
  FAM113A WILD-TYPE  167  401
        clus
vv       FAM113A MUTATED FAM113A WILD-TYPE
  FEMALE               5               167
  MALE                 5               401
[1] 2 2
[1] FALSE
D631V8, binary
                   cls
clus                  0   1
  FAM113A MUTATED     9   0
  FAM113A WILD-TYPE 407 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      9    0
  FAM113A WILD-TYPE  407  102
     clus
vv    FAM113A MUTATED FAM113A WILD-TYPE
  NO                9               407
  YES               0               102
[1] 2 2
[1] FALSE
D631V9, continuous
[1] "Remove cluster labels:" "FAM113A MUTATED"       
clus
  FAM113A MUTATED FAM113A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
D631V10, continuous
[1] "Remove cluster labels:" "FAM113A MUTATED"       
clus
  FAM113A MUTATED FAM113A WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" "FAM113A WILD-TYPE" 
       TCGA-Z6-AAPN 
"FAM113A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM113A MUTATED       1                         0
  FAM113A WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM113A MUTATED                                           0     7
  FAM113A WILD-TYPE                                         1   350
D631V11, multiclass
                                           clus
vv                                          FAM113A MUTATED FAM113A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V12, binary
                   cls
clus                  0   1
  FAM113A MUTATED     0   8
  FAM113A WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      0    8
  FAM113A WILD-TYPE   10  390
                        clus
vv                       FAM113A MUTATED FAM113A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(632) Variable = BAT3 MUTATION ANALYSIS
D632V1, survival
                sevent
clus2              0   1
  BAT3 MUTATED     8   6
  BAT3 WILD-TYPE 330 210
  BAT3 MUTATED BAT3 WILD-TYPE 
            14            540 
  BAT3 MUTATED BAT3 WILD-TYPE 
             6            210 
$`BAT3 MUTATED`
TCGA-IG-A625 TCGA-R6-A8W8 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-A4QL 
       12.82         2.89        34.68        35.84        14.43        16.14 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-HF-7133 TCGA-HU-A4GQ TCGA-MX-A5UJ 
        6.02        28.96        13.78        63.06         0.10        19.73 
TCGA-MX-A666 TCGA-VQ-A8P2 
       14.04        38.14 

$`BAT3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        36.95         3.72        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  BAT3 MUTATED BAT3 WILD-TYPE 
           0.1            0.0 
  BAT3 MUTATED BAT3 WILD-TYPE 
         63.06         122.30 
  BAT3 MUTATED BAT3 WILD-TYPE 
        15.285         13.495 
[1] "0.1 - 63.1 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D632V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAT3 MUTATED         0        1        1        0         2         0
  BAT3 WILD-TYPE      10       19       45       31        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAT3 MUTATED           1          2          3          2        2         0
  BAT3 WILD-TYPE        28         82         59         37       41         4
D632V3, multiclass
            clus
vv           BAT3 MUTATED BAT3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            3             59
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BAT3 MUTATED       1   3   5   5
  BAT3 WILD-TYPE    53 132 256  97
D632V4, multiclass
       clus
vv      BAT3 MUTATED BAT3 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               5            256
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BAT3 MUTATED     3   3   3   4
  BAT3 WILD-TYPE 192 170  86  81
D632V5, multiclass
    clus
vv   BAT3 MUTATED BAT3 WILD-TYPE
  N0            3            192
  N1            3            170
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V6, binary
                cls
clus               0   1
  BAT3 MUTATED    13   0
  BAT3 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED     13    0
  BAT3 WILD-TYPE  469   38
   clus
vv  BAT3 MUTATED BAT3 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D632V7, binary
                cls
clus               0   1
  BAT3 MUTATED     5  10
  BAT3 WILD-TYPE 167 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      5   10
  BAT3 WILD-TYPE  167  396
        clus
vv       BAT3 MUTATED BAT3 WILD-TYPE
  FEMALE            5            167
  MALE             10            396
[1] 2 2
[1] FALSE
D632V8, binary
                cls
clus               0   1
  BAT3 MUTATED     9   3
  BAT3 WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      9    3
  BAT3 WILD-TYPE  407   99
     clus
vv    BAT3 MUTATED BAT3 WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D632V9, continuous
D632V10, continuous
[1] "Remove cluster labels:" "BAT3 MUTATED"          
clus
  BAT3 MUTATED BAT3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" "BAT3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"BAT3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAT3 MUTATED       2                         0
  BAT3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAT3 MUTATED                                           0     9
  BAT3 WILD-TYPE                                         1   348
D632V11, multiclass
                                           clus
vv                                          BAT3 MUTATED BAT3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V12, binary
                cls
clus               0   1
  BAT3 MUTATED     0  10
  BAT3 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      0   10
  BAT3 WILD-TYPE   10  388
                        clus
vv                       BAT3 MUTATED BAT3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(633) Variable = TRIML2 MUTATION ANALYSIS
D633V1, survival
                  sevent
clus2                0   1
  TRIML2 MUTATED    14   7
  TRIML2 WILD-TYPE 324 209
  TRIML2 MUTATED TRIML2 WILD-TYPE 
              21              533 
  TRIML2 MUTATED TRIML2 WILD-TYPE 
               7              209 
$`TRIML2 MUTATED`
TCGA-JY-A938 TCGA-2H-A9GK TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OW TCGA-LN-A49Y 
       34.85         7.63        25.22        30.25         7.13        12.46 
TCGA-BR-4280 TCGA-BR-7196 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8687 TCGA-CD-A487 
        6.61        21.90        28.14        31.96         8.22        12.30 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4305 TCGA-D7-A4Z0 TCGA-HF-A5NB TCGA-HU-A4G3 
       11.61         6.58        15.95        14.76        30.51         5.59 
TCGA-IN-8663 TCGA-IN-A6RP TCGA-VQ-A8P2 
        3.39         6.44        38.14 

$`TRIML2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       23.18        31.56        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82        12.43         6.31        11.31        12.43 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TRIML2 MUTATED TRIML2 WILD-TYPE 
            3.39             0.00 
  TRIML2 MUTATED TRIML2 WILD-TYPE 
           38.14           122.30 
  TRIML2 MUTATED TRIML2 WILD-TYPE 
           12.46            13.58 
[1] "3.4 - 38.1 (12.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D633V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIML2 MUTATED         2        0        0        1         2         7
  TRIML2 WILD-TYPE       8       20       46       30        82        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIML2 MUTATED           2          3          0          4        2
  TRIML2 WILD-TYPE        27         81         62         35       41
                  vv
clus               STAGE IVA
  TRIML2 MUTATED           0
  TRIML2 WILD-TYPE         4
D633V3, multiclass
            clus
vv           TRIML2 MUTATED TRIML2 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               7               76
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              4               35
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TRIML2 MUTATED       3   6   9   5
  TRIML2 WILD-TYPE    51 129 252  97
D633V4, multiclass
       clus
vv      TRIML2 MUTATED TRIML2 WILD-TYPE
  T0+T1              3               51
  T2                 6              129
  T3                 9              252
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TRIML2 MUTATED     4  11   5   4
  TRIML2 WILD-TYPE 191 162  84  81
D633V5, multiclass
    clus
vv   TRIML2 MUTATED TRIML2 WILD-TYPE
  N0              4              191
  N1             11              162
  N2              5               84
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V6, binary
                  cls
clus                 0   1
  TRIML2 MUTATED    21   2
  TRIML2 WILD-TYPE 461  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIML2 MUTATED     21    2
  TRIML2 WILD-TYPE  461   36
   clus
vv  TRIML2 MUTATED TRIML2 WILD-TYPE
  0             21              461
  1              2               36
[1] 2 2
[1] FALSE
D633V7, binary
                  cls
clus                 0   1
  TRIML2 MUTATED     7  17
  TRIML2 WILD-TYPE 165 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIML2 MUTATED      7   17
  TRIML2 WILD-TYPE  165  389
        clus
vv       TRIML2 MUTATED TRIML2 WILD-TYPE
  FEMALE              7              165
  MALE               17              389
[1] 2 2
[1] FALSE
D633V8, binary
                  cls
clus                 0   1
  TRIML2 MUTATED    18   5
  TRIML2 WILD-TYPE 398  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIML2 MUTATED     18    5
  TRIML2 WILD-TYPE  398   97
     clus
vv    TRIML2 MUTATED TRIML2 WILD-TYPE
  NO              18              398
  YES              5               97
[1] 2 2
[1] FALSE
D633V9, continuous
[1] "Remove cluster labels:" "TRIML2 MUTATED"        
clus
  TRIML2 MUTATED TRIML2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A4A1       TCGA-LN-A4A2 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
D633V10, continuous
[1] "Remove cluster labels:" "TRIML2 MUTATED"        
clus
  TRIML2 MUTATED TRIML2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OX       TCGA-L5-A88S 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" "TRIML2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIML2 MUTATED       6                         1
  TRIML2 WILD-TYPE   127                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIML2 MUTATED                                           0    12
  TRIML2 WILD-TYPE                                         1   345
D633V11, multiclass
                                           clus
vv                                          TRIML2 MUTATED TRIML2 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V12, binary
                  cls
clus                 0   1
  TRIML2 MUTATED     0  15
  TRIML2 WILD-TYPE  10 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIML2 MUTATED      0   15
  TRIML2 WILD-TYPE   10  383
                        clus
vv                       TRIML2 MUTATED TRIML2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(634) Variable = CTSA MUTATION ANALYSIS
D634V1, survival
                sevent
clus2              0   1
  CTSA MUTATED     3   2
  CTSA WILD-TYPE 335 214
  CTSA MUTATED CTSA WILD-TYPE 
             5            549 
  CTSA MUTATED CTSA WILD-TYPE 
             2            214 
$`CTSA MUTATED`
TCGA-BR-4184 TCGA-CG-4305 TCGA-CG-5723 TCGA-D7-A6EY TCGA-FP-A4BE 
        6.97        15.95       105.07        11.44        11.08 

$`CTSA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CTSA MUTATED CTSA WILD-TYPE 
          6.97           0.00 
  CTSA MUTATED CTSA WILD-TYPE 
        105.07         122.30 
  CTSA MUTATED CTSA WILD-TYPE 
         11.44          13.58 
[1] "7.0 - 105.1 (11.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D634V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSA MUTATED         0        0        0        2         1         0
  CTSA WILD-TYPE      10       20       46       29        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSA MUTATED           0          1          1          0        0         0
  CTSA WILD-TYPE        29         83         61         39       43         4
D634V3, multiclass
            clus
vv           CTSA MUTATED CTSA WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CTSA MUTATED       0   2   3   0
  CTSA WILD-TYPE    54 133 258 102
D634V4, multiclass
       clus
vv      CTSA MUTATED CTSA WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               3            258
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CTSA MUTATED     1   3   0   1
  CTSA WILD-TYPE 194 170  89  84
D634V5, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  N0            1            194
  N1            3            170
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V6, binary
                cls
clus               0   1
  CTSA MUTATED     4   0
  CTSA WILD-TYPE 478  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    0
  CTSA WILD-TYPE  478   38
   clus
vv  CTSA MUTATED CTSA WILD-TYPE
  0            4            478
  1            0             38
[1] 2 2
[1] FALSE
D634V7, binary
                cls
clus               0   1
  CTSA MUTATED     1   4
  CTSA WILD-TYPE 171 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      1    4
  CTSA WILD-TYPE  171  402
        clus
vv       CTSA MUTATED CTSA WILD-TYPE
  FEMALE            1            171
  MALE              4            402
[1] 2 2
[1] FALSE
D634V8, binary
                cls
clus               0   1
  CTSA MUTATED     4   1
  CTSA WILD-TYPE 412 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    1
  CTSA WILD-TYPE  412  101
     clus
vv    CTSA MUTATED CTSA WILD-TYPE
  NO             4            412
  YES            1            101
[1] 2 2
[1] FALSE
D634V9, continuous
D634V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSA MUTATED       0                         1
  CTSA WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSA MUTATED                                           0     2
  CTSA WILD-TYPE                                         1   355
D634V11, multiclass
                                           clus
vv                                          CTSA MUTATED CTSA WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V12, binary
                cls
clus               0   1
  CTSA MUTATED     0   3
  CTSA WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      0    3
  CTSA WILD-TYPE   10  395
                        clus
vv                       CTSA MUTATED CTSA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(635) Variable = ATP6V1C2 MUTATION ANALYSIS
D635V1, survival
                    sevent
clus2                  0   1
  ATP6V1C2 MUTATED     9   5
  ATP6V1C2 WILD-TYPE 329 211
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                14                540 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 5                211 
$`ATP6V1C2 MUTATED`
TCGA-LN-A49V TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6453 TCGA-BR-8360 TCGA-BR-8363 
       12.59        19.56         6.97        15.95         6.18         0.26 
TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5723 TCGA-HU-A4G3 TCGA-HU-A4GN TCGA-HU-A4GQ 
        1.12         6.58       105.07         5.59        29.98         0.10 
TCGA-IN-8663 TCGA-VQ-A8P2 
        3.39        38.14 

$`ATP6V1C2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
               0.1                0.0 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
            105.07             122.30 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
             6.775             13.730 
[1] "0.1 - 105.1 (6.8)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D635V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1C2 MUTATED         1        0        1        1         6         2
  ATP6V1C2 WILD-TYPE       9       20       45       30        78        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1C2 MUTATED           0          2          0          2        0
  ATP6V1C2 WILD-TYPE        29         82         62         37       43
                    vv
clus                 STAGE IVA
  ATP6V1C2 MUTATED           0
  ATP6V1C2 WILD-TYPE         4
D635V3, multiclass
            clus
vv           ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 6                 78
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ATP6V1C2 MUTATED       1   6   5   3
  ATP6V1C2 WILD-TYPE    53 129 256  99
D635V4, multiclass
       clus
vv      ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  T0+T1                1                 53
  T2                   6                129
  T3                   5                256
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ATP6V1C2 MUTATED     5   7   3   1
  ATP6V1C2 WILD-TYPE 190 166  86  84
D635V5, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  N0                5                190
  N1                7                166
  N2                3                 86
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V6, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED    14   0
  ATP6V1C2 WILD-TYPE 468  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED     14    0
  ATP6V1C2 WILD-TYPE  468   38
   clus
vv  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  0               14                468
  1                0                 38
[1] 2 2
[1] FALSE
D635V7, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     3  13
  ATP6V1C2 WILD-TYPE 169 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      3   13
  ATP6V1C2 WILD-TYPE  169  393
        clus
vv       ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  FEMALE                3                169
  MALE                 13                393
[1] 2 2
[1] FALSE
D635V8, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED    13   2
  ATP6V1C2 WILD-TYPE 403 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED     13    2
  ATP6V1C2 WILD-TYPE  403  100
     clus
vv    ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  NO                13                403
  YES                2                100
[1] 2 2
[1] FALSE
D635V9, continuous
[1] "Remove cluster labels:" "ATP6V1C2 MUTATED"      
clus
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49W         TCGA-LN-A49X 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-Z6-A8JE 
"ATP6V1C2 WILD-TYPE" 
D635V10, continuous
[1] "Remove cluster labels:" "ATP6V1C2 MUTATED"      
clus
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" "ATP6V1C2 WILD-TYPE" 
        TCGA-Z6-AAPN 
"ATP6V1C2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1C2 MUTATED       5                         1
  ATP6V1C2 WILD-TYPE   128                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1C2 MUTATED                                           0     9
  ATP6V1C2 WILD-TYPE                                         1   348
D635V11, multiclass
                                           clus
vv                                          ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V12, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     0  14
  ATP6V1C2 WILD-TYPE  10 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      0   14
  ATP6V1C2 WILD-TYPE   10  384
                        clus
vv                       ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               14                384
[1] 2 2
[1] FALSE

Clustering(636) Variable = AKAP11 MUTATION ANALYSIS
D636V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    12   5
  AKAP11 WILD-TYPE 326 211
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              17              537 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               5              211 
$`AKAP11 MUTATED`
TCGA-Q9-A6FU TCGA-2H-A9GM TCGA-L7-A6VZ TCGA-LN-A49S TCGA-BR-4184 TCGA-BR-4256 
        5.16        13.94        10.36        13.15         6.97         9.34 
TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8678 TCGA-CG-4465 TCGA-CG-5721 TCGA-HU-A4GF 
       34.68         4.31        24.79         9.01         6.02        25.81 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       29.98         6.51         6.58        20.25        29.00 

$`AKAP11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        21.37         8.98         0.10         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
            4.31             0.00 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           34.68           122.30 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           10.36            13.68 
[1] "4.3 - 34.7 (10.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D636V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP11 MUTATED         0        0        2        0         5         3
  AKAP11 WILD-TYPE      10       20       44       31        79        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           0          2          1          3        2
  AKAP11 WILD-TYPE        29         82         61         36       41
                  vv
clus               STAGE IVA
  AKAP11 MUTATED           0
  AKAP11 WILD-TYPE         4
D636V3, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  AKAP11 MUTATED       1   3   8   6
  AKAP11 WILD-TYPE    53 132 253  96
D636V4, multiclass
       clus
vv      AKAP11 MUTATED AKAP11 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 8              253
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  AKAP11 MUTATED     8   6   2   3
  AKAP11 WILD-TYPE 187 167  87  82
D636V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0              8              187
  N1              6              167
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V6, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    16   1
  AKAP11 WILD-TYPE 466  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     16    1
  AKAP11 WILD-TYPE  466   37
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             16              466
  1              1               37
[1] 2 2
[1] FALSE
D636V7, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     8  11
  AKAP11 WILD-TYPE 164 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      8   11
  AKAP11 WILD-TYPE  164  395
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE              8              164
  MALE               11              395
[1] 2 2
[1] FALSE
D636V8, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    14   2
  AKAP11 WILD-TYPE 402 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     14    2
  AKAP11 WILD-TYPE  402  100
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO              14              402
  YES              2              100
[1] 2 2
[1] FALSE
D636V9, continuous
[1] "Remove cluster labels:" "AKAP11 MUTATED"        
clus
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
D636V10, continuous
[1] "Remove cluster labels:" "AKAP11 MUTATED"        
clus
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-IC-A6RE       TCGA-IG-A3QL 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AKAP11 MUTATED       7                         0
  AKAP11 WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AKAP11 MUTATED                                           0     9
  AKAP11 WILD-TYPE                                         1   348
D636V11, multiclass
                                           clus
vv                                          AKAP11 MUTATED AKAP11 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V12, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     0  16
  AKAP11 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      0   16
  AKAP11 WILD-TYPE   10  382
                        clus
vv                       AKAP11 MUTATED AKAP11 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(637) Variable = RBMX MUTATION ANALYSIS
D637V1, survival
                sevent
clus2              0   1
  RBMX MUTATED     5   4
  RBMX WILD-TYPE 333 212
  RBMX MUTATED RBMX WILD-TYPE 
             9            545 
  RBMX MUTATED RBMX WILD-TYPE 
             4            212 
$`RBMX MUTATED`
TCGA-BR-4184 TCGA-BR-8080 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5723 TCGA-HF-7134 
        6.97         9.60         6.58        11.77       105.07        52.21 
TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-MX-A5UJ 
       30.51        24.20        19.73 

$`RBMX WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RBMX MUTATED RBMX WILD-TYPE 
          6.58           0.00 
  RBMX MUTATED RBMX WILD-TYPE 
        105.07         122.30 
  RBMX MUTATED RBMX WILD-TYPE 
         19.73          13.55 
[1] "6.6 - 105.1 (19.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D637V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBMX MUTATED         0        2        0        1         1         0
  RBMX WILD-TYPE      10       18       46       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBMX MUTATED           0          3          0          2        0         0
  RBMX WILD-TYPE        29         81         62         37       43         4
D637V3, multiclass
            clus
vv           RBMX MUTATED RBMX WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RBMX MUTATED       2   1   4   2
  RBMX WILD-TYPE    52 134 257 100
D637V4, multiclass
       clus
vv      RBMX MUTATED RBMX WILD-TYPE
  T0+T1            2             52
  T2               1            134
  T3               4            257
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RBMX MUTATED     3   3   1   2
  RBMX WILD-TYPE 192 170  88  83
D637V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  N0            3            192
  N1            3            170
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V6, binary
                cls
clus               0   1
  RBMX MUTATED     9   0
  RBMX WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      9    0
  RBMX WILD-TYPE  473   38
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D637V7, binary
                cls
clus               0   1
  RBMX MUTATED     5   5
  RBMX WILD-TYPE 167 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      5    5
  RBMX WILD-TYPE  167  401
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            5            167
  MALE              5            401
[1] 2 2
[1] FALSE
D637V8, binary
                cls
clus               0   1
  RBMX MUTATED     8   1
  RBMX WILD-TYPE 408 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      8    1
  RBMX WILD-TYPE  408  101
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO             8            408
  YES            1            101
[1] 2 2
[1] FALSE
D637V9, continuous
D637V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RBMX MUTATED       3                         0
  RBMX WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBMX MUTATED                                           0     4
  RBMX WILD-TYPE                                         1   353
D637V11, multiclass
                                           clus
vv                                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V12, binary
                cls
clus               0   1
  RBMX MUTATED     0   7
  RBMX WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    7
  RBMX WILD-TYPE   10  391
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(638) Variable = GNPNAT1 MUTATION ANALYSIS
D638V1, survival
                   sevent
clus2                 0   1
  GNPNAT1 MUTATED     4   1
  GNPNAT1 WILD-TYPE 334 215
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                5               549 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                1               215 
$`GNPNAT1 MUTATED`
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A6F2 TCGA-IN-8462 TCGA-IN-A6RL 
        6.02        65.10        15.65        18.81        13.35 

$`GNPNAT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       14.07        15.68        33.40        36.36         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
             6.02              0.00 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
             65.1             122.3 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
            15.65             13.55 
[1] "6.0 - 65.1 (15.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.3"
D638V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNPNAT1 MUTATED         0        0        2        0         0         1
  GNPNAT1 WILD-TYPE      10       20       44       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNPNAT1 MUTATED           0          2          0          0        1
  GNPNAT1 WILD-TYPE        29         82         62         39       42
                   vv
clus                STAGE IVA
  GNPNAT1 MUTATED           0
  GNPNAT1 WILD-TYPE         4
D638V3, multiclass
            clus
vv           GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GNPNAT1 MUTATED       0   4   0   2
  GNPNAT1 WILD-TYPE    54 131 261 100
D638V4, multiclass
       clus
vv      GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  T0+T1               0                54
  T2                  4               131
  T3                  0               261
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GNPNAT1 MUTATED     3   3   0   0
  GNPNAT1 WILD-TYPE 192 170  89  85
D638V5, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  N0               3               192
  N1               3               170
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V6, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     6   0
  GNPNAT1 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      6    0
  GNPNAT1 WILD-TYPE  476   38
   clus
vv  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D638V7, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     2   4
  GNPNAT1 WILD-TYPE 170 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      2    4
  GNPNAT1 WILD-TYPE  170  402
        clus
vv       GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  FEMALE               2               170
  MALE                 4               402
[1] 2 2
[1] FALSE
D638V8, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     4   0
  GNPNAT1 WILD-TYPE 412 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      4    0
  GNPNAT1 WILD-TYPE  412  102
     clus
vv    GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  NO                4               412
  YES               0               102
[1] 2 2
[1] FALSE
D638V9, continuous
D638V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GNPNAT1 MUTATED       0                         0
  GNPNAT1 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNPNAT1 MUTATED                                           0     4
  GNPNAT1 WILD-TYPE                                         1   353
D638V11, multiclass
                                           clus
vv                                          GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V12, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     0   4
  GNPNAT1 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      0    4
  GNPNAT1 WILD-TYPE   10  394
                        clus
vv                       GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(639) Variable = PTPN23 MUTATION ANALYSIS
D639V1, survival
                  sevent
clus2                0   1
  PTPN23 MUTATED    17   5
  PTPN23 WILD-TYPE 321 211
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              22              532 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
               5              211 
$`PTPN23 MUTATED`
TCGA-IC-A6RF TCGA-IC-A6RE TCGA-L5-A4OO TCGA-L5-A8NF TCGA-VR-A8EZ TCGA-B7-5818 
       15.68         7.69         3.32         2.66        18.18        11.70 
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
        6.97        44.94        29.59        31.27         1.12        28.14 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB 
        6.02        28.96         5.92        11.08        77.29        30.51 
TCGA-HU-A4G8 TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-VQ-AA6F 
       22.68        29.00        19.73        54.12 

$`PTPN23 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        32.94        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PTPN23 MUTATED PTPN23 WILD-TYPE 
            1.12             0.00 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
           77.29           122.30 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
          18.955           13.510 
[1] "1.1 - 77.3 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D639V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN23 MUTATED         0        2        2        1         3         6
  PTPN23 WILD-TYPE      10       18       44       30        81        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN23 MUTATED           0          3          0          6        2
  PTPN23 WILD-TYPE        29         81         62         33       41
                  vv
clus               STAGE IVA
  PTPN23 MUTATED           1
  PTPN23 WILD-TYPE         3
D639V3, multiclass
            clus
vv           PTPN23 MUTATED PTPN23 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               6               77
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              6               33
  STAGE IV                2               41
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PTPN23 MUTATED       4   3  10   9
  PTPN23 WILD-TYPE    50 132 251  93
D639V4, multiclass
       clus
vv      PTPN23 MUTATED PTPN23 WILD-TYPE
  T0+T1              4               50
  T2                 3              132
  T3                10              251
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTPN23 MUTATED    11   7   2   6
  PTPN23 WILD-TYPE 184 166  87  79
D639V5, multiclass
    clus
vv   PTPN23 MUTATED PTPN23 WILD-TYPE
  N0             11              184
  N1              7              166
  N2              2               87
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V6, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    24   1
  PTPN23 WILD-TYPE 458  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     24    1
  PTPN23 WILD-TYPE  458   37
   clus
vv  PTPN23 MUTATED PTPN23 WILD-TYPE
  0             24              458
  1              1               37
[1] 2 2
[1] FALSE
D639V7, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    11  15
  PTPN23 WILD-TYPE 161 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     11   15
  PTPN23 WILD-TYPE  161  391
        clus
vv       PTPN23 MUTATED PTPN23 WILD-TYPE
  FEMALE             11              161
  MALE               15              391
[1] 2 2
[1] FALSE
D639V8, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    16   4
  PTPN23 WILD-TYPE 400  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     16    4
  PTPN23 WILD-TYPE  400   98
     clus
vv    PTPN23 MUTATED PTPN23 WILD-TYPE
  NO              16              400
  YES              4               98
[1] 2 2
[1] FALSE
D639V9, continuous
[1] "Remove cluster labels:" "PTPN23 MUTATED"        
clus
  PTPN23 MUTATED PTPN23 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" "PTPN23 WILD-TYPE" 
D639V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN23 MUTATED       2                         1
  PTPN23 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN23 MUTATED                                           0    18
  PTPN23 WILD-TYPE                                         1   339
D639V11, multiclass
                                           clus
vv                                          PTPN23 MUTATED PTPN23 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V12, binary
                  cls
clus                 0   1
  PTPN23 MUTATED     0  17
  PTPN23 WILD-TYPE  10 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED      0   17
  PTPN23 WILD-TYPE   10  381
                        clus
vv                       PTPN23 MUTATED PTPN23 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             17              381
[1] 2 2
[1] FALSE

Clustering(640) Variable = AGAP6 MUTATION ANALYSIS
D640V1, survival
                 sevent
clus2               0   1
  AGAP6 MUTATED     6   5
  AGAP6 WILD-TYPE 332 211
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             11             543 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             211 
$`AGAP6 MUTATED`
TCGA-VR-A8EQ TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8487 
       22.82         6.18        34.68        35.84         6.18         1.12 
TCGA-BR-A4QL TCGA-CD-8527 TCGA-CG-5726 TCGA-F1-A448 TCGA-R5-A7ZI 
       16.14         7.17        28.96        21.27        74.53 

$`AGAP6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
           1.12            0.00 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          74.53          122.30 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          21.27           13.51 
[1] "1.1 - 74.5 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D640V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AGAP6 MUTATED         0        1        2        1         3         0
  AGAP6 WILD-TYPE      10       19       44       30        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGAP6 MUTATED           1          0          2          0        1         0
  AGAP6 WILD-TYPE        28         84         60         39       42         4
D640V3, multiclass
            clus
vv           AGAP6 MUTATED AGAP6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AGAP6 MUTATED       1   3   6   1
  AGAP6 WILD-TYPE    53 132 255 101
D640V4, multiclass
       clus
vv      AGAP6 MUTATED AGAP6 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AGAP6 MUTATED     6   3   0   2
  AGAP6 WILD-TYPE 189 170  89  83
D640V5, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V6, binary
                 cls
clus                0   1
  AGAP6 MUTATED    10   1
  AGAP6 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED     10    1
  AGAP6 WILD-TYPE  472   37
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D640V7, binary
                 cls
clus                0   1
  AGAP6 MUTATED     6   5
  AGAP6 WILD-TYPE 166 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      6    5
  AGAP6 WILD-TYPE  166  401
        clus
vv       AGAP6 MUTATED AGAP6 WILD-TYPE
  FEMALE             6             166
  MALE               5             401
[1] 2 2
[1] FALSE
D640V8, binary
                 cls
clus                0   1
  AGAP6 MUTATED     8   2
  AGAP6 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      8    2
  AGAP6 WILD-TYPE  408  100
     clus
vv    AGAP6 MUTATED AGAP6 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D640V9, continuous
[1] "Remove cluster labels:" "AGAP6 MUTATED"         
clus
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
D640V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AGAP6 MUTATED       1                         0
  AGAP6 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGAP6 MUTATED                                           0     9
  AGAP6 WILD-TYPE                                         1   348
D640V11, multiclass
                                           clus
vv                                          AGAP6 MUTATED AGAP6 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V12, binary
                 cls
clus                0   1
  AGAP6 MUTATED     2   7
  AGAP6 WILD-TYPE   8 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      2    7
  AGAP6 WILD-TYPE    8  391
                        clus
vv                       AGAP6 MUTATED AGAP6 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(641) Variable = PPARGC1B MUTATION ANALYSIS
D641V1, survival
                    sevent
clus2                  0   1
  PPARGC1B MUTATED     6   3
  PPARGC1B WILD-TYPE 332 213
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 9                545 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                213 
$`PPARGC1B MUTATED`
TCGA-CG-4460 TCGA-2H-A9GQ TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-D7-A6EZ 
       21.99         4.21        31.10         1.12        28.14        20.32 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GN 
       30.51        22.32        29.98 

$`PPARGC1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              1.12               0.00 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              31.1              122.3 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             22.32              13.51 
[1] "1.1 - 31.1 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D641V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPARGC1B MUTATED         0        0        0        0         2         2
  PPARGC1B WILD-TYPE      10       20       46       31        82        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1B MUTATED           1          1          0          3        1
  PPARGC1B WILD-TYPE        28         83         62         36       42
                    vv
clus                 STAGE IVA
  PPARGC1B MUTATED           0
  PPARGC1B WILD-TYPE         4
D641V3, multiclass
            clus
vv           PPARGC1B MUTATED PPARGC1B WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 2                 81
  STAGE III                 1                 28
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PPARGC1B MUTATED       0   1   3   6
  PPARGC1B WILD-TYPE    54 134 258  96
D641V4, multiclass
       clus
vv      PPARGC1B MUTATED PPARGC1B WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   3                258
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PPARGC1B MUTATED     3   3   2   2
  PPARGC1B WILD-TYPE 192 170  87  83
D641V5, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  N0                3                192
  N1                3                170
  N2                2                 87
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V6, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED    10   1
  PPARGC1B WILD-TYPE 472  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED     10    1
  PPARGC1B WILD-TYPE  472   37
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0               10                472
  1                1                 37
[1] 2 2
[1] FALSE
D641V7, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     6   5
  PPARGC1B WILD-TYPE 166 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      6    5
  PPARGC1B WILD-TYPE  166  401
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                6                166
  MALE                  5                401
[1] 2 2
[1] FALSE
D641V8, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     9   1
  PPARGC1B WILD-TYPE 407 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      9    1
  PPARGC1B WILD-TYPE  407  101
     clus
vv    PPARGC1B MUTATED PPARGC1B WILD-TYPE
  NO                 9                407
  YES                1                101
[1] 2 2
[1] FALSE
D641V9, continuous
D641V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPARGC1B MUTATED       2                         0
  PPARGC1B WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPARGC1B MUTATED                                           0     6
  PPARGC1B WILD-TYPE                                         1   351
D641V11, multiclass
                                           clus
vv                                          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V12, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     0   8
  PPARGC1B WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      0    8
  PPARGC1B WILD-TYPE   10  390
                        clus
vv                       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(642) Variable = ACTG2 MUTATION ANALYSIS
D642V1, survival
                 sevent
clus2               0   1
  ACTG2 MUTATED     7   3
  ACTG2 WILD-TYPE 331 213
  ACTG2 MUTATED ACTG2 WILD-TYPE 
             10             544 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
              3             213 
$`ACTG2 MUTATED`
TCGA-L5-A4OH TCGA-X8-AAAR TCGA-BR-4184 TCGA-BR-6455 TCGA-BR-8690 TCGA-CG-4306 
       32.61        18.21         6.97        13.87        10.68         1.02 
TCGA-CG-4437 TCGA-HU-A4G8 TCGA-MX-A5UJ TCGA-R5-A7O7 
        8.05        22.68        19.73        45.67 

$`ACTG2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 
       20.02         3.02        27.02        15.95         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        14.04        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ACTG2 MUTATED ACTG2 WILD-TYPE 
           1.02            0.00 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
          45.67          122.30 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
          16.04           13.53 
[1] "1.0 - 45.7 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D642V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACTG2 MUTATED         1        0        0        1         0         2
  ACTG2 WILD-TYPE       9       20       46       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTG2 MUTATED           0          3          1          0        2         0
  ACTG2 WILD-TYPE        29         81         61         39       41         4
D642V3, multiclass
            clus
vv           ACTG2 MUTATED ACTG2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ACTG2 MUTATED       2   1   7   1
  ACTG2 WILD-TYPE    52 134 254 101
D642V4, multiclass
       clus
vv      ACTG2 MUTATED ACTG2 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                7             254
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ACTG2 MUTATED     2   7   2   1
  ACTG2 WILD-TYPE 193 166  87  84
D642V5, multiclass
    clus
vv   ACTG2 MUTATED ACTG2 WILD-TYPE
  N0             2             193
  N1             7             166
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V6, binary
                 cls
clus                0   1
  ACTG2 MUTATED     8   2
  ACTG2 WILD-TYPE 474  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      8    2
  ACTG2 WILD-TYPE  474   36
   clus
vv  ACTG2 MUTATED ACTG2 WILD-TYPE
  0             8             474
  1             2              36
[1] 2 2
[1] FALSE
D642V7, binary
                 cls
clus                0   1
  ACTG2 MUTATED     5   7
  ACTG2 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      5    7
  ACTG2 WILD-TYPE  167  399
        clus
vv       ACTG2 MUTATED ACTG2 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D642V8, binary
                 cls
clus                0   1
  ACTG2 MUTATED     9   0
  ACTG2 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      9    0
  ACTG2 WILD-TYPE  407  102
     clus
vv    ACTG2 MUTATED ACTG2 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D642V9, continuous
D642V10, continuous
[1] "Remove cluster labels:" "ACTG2 MUTATED"         
clus
  ACTG2 MUTATED ACTG2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OM 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" "ACTG2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACTG2 MUTATED       1                         0
  ACTG2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTG2 MUTATED                                           0     9
  ACTG2 WILD-TYPE                                         1   348
D642V11, multiclass
                                           clus
vv                                          ACTG2 MUTATED ACTG2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V12, binary
                 cls
clus                0   1
  ACTG2 MUTATED     1   8
  ACTG2 WILD-TYPE   9 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      1    8
  ACTG2 WILD-TYPE    9  390
                        clus
vv                       ACTG2 MUTATED ACTG2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(643) Variable = SMTN MUTATION ANALYSIS
D643V1, survival
                sevent
clus2              0   1
  SMTN MUTATED    13   6
  SMTN WILD-TYPE 325 210
  SMTN MUTATED SMTN WILD-TYPE 
            19            535 
  SMTN MUTATED SMTN WILD-TYPE 
             6            210 
$`SMTN MUTATED`
TCGA-L5-A8NQ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6852 TCGA-BR-7707 
       21.37         9.44         6.97         9.34        44.94        35.84 
TCGA-BR-7715 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4J2 
       33.63         0.26         4.31         1.12        31.96        14.17 
TCGA-CD-A4MG TCGA-D7-A6EY TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 
        6.58        11.44         6.51        20.25        29.00        38.14 
TCGA-VQ-A92D 
       66.81 

$`SMTN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.47         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SMTN MUTATED SMTN WILD-TYPE 
          0.26           0.00 
  SMTN MUTATED SMTN WILD-TYPE 
         66.81         122.30 
  SMTN MUTATED SMTN WILD-TYPE 
         14.17          13.55 
[1] "0.3 - 66.8 (14.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D643V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMTN MUTATED         1        0        4        0         6         2
  SMTN WILD-TYPE       9       20       42       31        78        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMTN MUTATED           0          2          1          2        2         0
  SMTN WILD-TYPE        29         82         61         37       41         4
D643V3, multiclass
            clus
vv           SMTN MUTATED SMTN WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              0             31
  STAGE IIA             6             78
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SMTN MUTATED       1   5   7   7
  SMTN WILD-TYPE    53 130 254  95
D643V4, multiclass
       clus
vv      SMTN MUTATED SMTN WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               7            254
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SMTN MUTATED    11   4   3   2
  SMTN WILD-TYPE 184 169  86  83
D643V5, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  N0           11            184
  N1            4            169
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V6, binary
                cls
clus               0   1
  SMTN MUTATED    18   1
  SMTN WILD-TYPE 464  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     18    1
  SMTN WILD-TYPE  464   37
   clus
vv  SMTN MUTATED SMTN WILD-TYPE
  0           18            464
  1            1             37
[1] 2 2
[1] FALSE
D643V7, binary
                cls
clus               0   1
  SMTN MUTATED    10  11
  SMTN WILD-TYPE 162 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     10   11
  SMTN WILD-TYPE  162  395
        clus
vv       SMTN MUTATED SMTN WILD-TYPE
  FEMALE           10            162
  MALE             11            395
[1] 2 2
[1] FALSE
D643V8, binary
                cls
clus               0   1
  SMTN MUTATED    18   1
  SMTN WILD-TYPE 398 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     18    1
  SMTN WILD-TYPE  398  101
     clus
vv    SMTN MUTATED SMTN WILD-TYPE
  NO            18            398
  YES            1            101
[1] 2 2
[1] FALSE
D643V9, continuous
D643V10, continuous
[1] "Remove cluster labels:" "SMTN MUTATED"          
clus
  SMTN MUTATED SMTN WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" "SMTN WILD-TYPE" 
    TCGA-Z6-AAPN 
"SMTN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SMTN MUTATED       6                         1
  SMTN WILD-TYPE   127                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMTN MUTATED                                           0    14
  SMTN WILD-TYPE                                         1   343
D643V11, multiclass
                                           clus
vv                                          SMTN MUTATED SMTN WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V12, binary
                cls
clus               0   1
  SMTN MUTATED     0  18
  SMTN WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED      0   18
  SMTN WILD-TYPE   10  380
                        clus
vv                       SMTN MUTATED SMTN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(644) Variable = C9ORF46 MUTATION ANALYSIS
D644V1, survival
                   sevent
clus2                 0   1
  C9ORF46 MUTATED     3   1
  C9ORF46 WILD-TYPE 335 215
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                4               550 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                1               215 
$`C9ORF46 MUTATED`
TCGA-L5-A4OU TCGA-BR-A4QL TCGA-CG-4437 TCGA-HF-7132 
       29.00        16.14         8.05        77.29 

$`C9ORF46 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
             8.05              0.00 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
            77.29            122.30 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
            22.57             13.53 
[1] "8.1 - 77.3 (22.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D644V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF46 MUTATED         0        0        1        2         1         0
  C9ORF46 WILD-TYPE      10       20       45       29        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF46 MUTATED           0          0          1          0        0
  C9ORF46 WILD-TYPE        29         84         61         39       43
                   vv
clus                STAGE IVA
  C9ORF46 MUTATED           0
  C9ORF46 WILD-TYPE         4
D644V3, multiclass
            clus
vv           C9ORF46 MUTATED C9ORF46 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 2                29
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C9ORF46 MUTATED       0   3   2   0
  C9ORF46 WILD-TYPE    54 132 259 102
D644V4, multiclass
       clus
vv      C9ORF46 MUTATED C9ORF46 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  2               259
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C9ORF46 MUTATED     2   2   0   1
  C9ORF46 WILD-TYPE 193 171  89  84
D644V5, multiclass
    clus
vv   C9ORF46 MUTATED C9ORF46 WILD-TYPE
  N0               2               193
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V6, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     5   0
  C9ORF46 WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      5    0
  C9ORF46 WILD-TYPE  477   38
   clus
vv  C9ORF46 MUTATED C9ORF46 WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D644V7, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     1   4
  C9ORF46 WILD-TYPE 171 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      1    4
  C9ORF46 WILD-TYPE  171  402
        clus
vv       C9ORF46 MUTATED C9ORF46 WILD-TYPE
  FEMALE               1               171
  MALE                 4               402
[1] 2 2
[1] FALSE
D644V8, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     3   1
  C9ORF46 WILD-TYPE 413 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      3    1
  C9ORF46 WILD-TYPE  413  101
     clus
vv    C9ORF46 MUTATED C9ORF46 WILD-TYPE
  NO                3               413
  YES               1               101
[1] 2 2
[1] FALSE
D644V9, continuous
D644V10, continuous
[1] "Remove cluster labels:" "C9ORF46 MUTATED"       
clus
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C9ORF46 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF46 MUTATED       0                         0
  C9ORF46 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF46 MUTATED                                           0     2
  C9ORF46 WILD-TYPE                                         1   355
D644V11, multiclass
[1] "Remove cluster labels:" "C9ORF46 MUTATED"       
clus
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                2               503 
       TCGA-IC-A6RF        TCGA-JY-A6FB        TCGA-JY-A938        TCGA-L5-A43I 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A43J        TCGA-L5-A4OE        TCGA-L5-A4OG        TCGA-L5-A4OI 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG        TCGA-L5-A8NT 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-Q9-A6FU        TCGA-S8-A6BV        TCGA-EQ-A4SO        TCGA-F1-6177 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-KB-A93G        TCGA-MX-A663        TCGA-IC-A6RE 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QS 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A51D        TCGA-IG-A5B8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A5S3        TCGA-IG-A625        TCGA-IG-A6QS        TCGA-IG-A7DP 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-IG-A97I        TCGA-JY-A6F8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-JY-A6FA        TCGA-JY-A6FD        TCGA-JY-A6FE        TCGA-JY-A6FG 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-JY-A6FH        TCGA-JY-A939        TCGA-JY-A93C        TCGA-JY-A93D 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-JY-A93E        TCGA-JY-A93F        TCGA-KH-A6WC        TCGA-L5-A43C 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OF        TCGA-L5-A4OH 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OJ        TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OR        TCGA-L5-A4OS 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A88W        TCGA-L5-A88Z        TCGA-L5-A891        TCGA-L5-A893 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NH        TCGA-L5-A8NI 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NJ        TCGA-L5-A8NK        TCGA-L5-A8NL        TCGA-L5-A8NM 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NS        TCGA-L5-A8NU 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-L5-A8NV        TCGA-L5-A8NW        TCGA-L7-A56G        TCGA-L7-A6VZ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M        TCGA-LN-A49N 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A49X 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2        TCGA-LN-A4A3 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6        TCGA-LN-A4A8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR        TCGA-LN-A5U5 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-LN-A8I1        TCGA-LN-A9FO        TCGA-LN-A9FP 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-LN-A9FQ        TCGA-LN-A9FR        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R6-A6DQ        TCGA-R6-A6KZ        TCGA-R6-A6L4        TCGA-R6-A6L6 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R6-A6XG        TCGA-R6-A6XQ        TCGA-R6-A6Y0        TCGA-R6-A6Y2 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-R6-A8WG 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-RE-A7BO        TCGA-S8-A6BW        TCGA-V5-A7RC        TCGA-V5-A7RE 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7I 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE        TCGA-Z6-A9VB        TCGA-Z6-AAPN 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-ZR-A9CJ        TCGA-B7-5816        TCGA-B7-5818        TCGA-B7-A5TI 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-B7-A5TJ        TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4184        TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4257        TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8297 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QM 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487        TCGA-CD-A489 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG        TCGA-CD-A4MH 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-CD-A4MI        TCGA-CD-A4MJ        TCGA-D7-5577        TCGA-D7-5578 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM        TCGA-HJ-7597 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244        TCGA-HU-8249 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-KB-A93J        TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R5-A7O7        TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-R5-A7ZR        TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-RD-A7BT        TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-RD-A8MW        TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-RD-A8N4        TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-SW-A7EA        TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DU 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91U        TCGA-VQ-A92D 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-AA64        TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-AA6B        TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-VQ-AA6J        TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
D644V12, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     0   1
  C9ORF46 WILD-TYPE  10 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      0    1
  C9ORF46 WILD-TYPE   10  397
                        clus
vv                       C9ORF46 MUTATED C9ORF46 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               1               397
[1] 2 2
[1] FALSE

Clustering(645) Variable = KCNMB2 MUTATION ANALYSIS
D645V1, survival
                  sevent
clus2                0   1
  KCNMB2 MUTATED     7   1
  KCNMB2 WILD-TYPE 331 215
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
               8              546 
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
               1              215 
$`KCNMB2 MUTATED`
TCGA-X8-AAAR TCGA-BR-7197 TCGA-D7-6818 TCGA-D7-8579 TCGA-D7-A4Z0 TCGA-HU-A4GP 
       18.21         9.21        12.36        20.91        14.76         8.98 
TCGA-RD-A8MV TCGA-VQ-A8P2 
      122.30        38.14 

$`KCNMB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        13.78        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
            8.98             0.00 
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
           122.3            122.1 
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
          16.485           13.530 
[1] "9.0 - 122.3 (16.5)" "0.0 - 122.1 (13.5)"
[1] "hr=" "4.2"
D645V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNMB2 MUTATED         0        0        1        1         1         2
  KCNMB2 WILD-TYPE      10       20       45       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNMB2 MUTATED           0          2          1          0        0
  KCNMB2 WILD-TYPE        29         82         61         39       43
                  vv
clus               STAGE IVA
  KCNMB2 MUTATED           0
  KCNMB2 WILD-TYPE         4
D645V3, multiclass
            clus
vv           KCNMB2 MUTATED KCNMB2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KCNMB2 MUTATED       1   5   2   1
  KCNMB2 WILD-TYPE    53 130 259 101
D645V4, multiclass
       clus
vv      KCNMB2 MUTATED KCNMB2 WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 2              259
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KCNMB2 MUTATED     2   3   3   1
  KCNMB2 WILD-TYPE 193 170  86  84
D645V5, multiclass
    clus
vv   KCNMB2 MUTATED KCNMB2 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V6, binary
                  cls
clus                 0   1
  KCNMB2 MUTATED     9   0
  KCNMB2 WILD-TYPE 473  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNMB2 MUTATED      9    0
  KCNMB2 WILD-TYPE  473   38
   clus
vv  KCNMB2 MUTATED KCNMB2 WILD-TYPE
  0              9              473
  1              0               38
[1] 2 2
[1] FALSE
D645V7, binary
                  cls
clus                 0   1
  KCNMB2 MUTATED     4   6
  KCNMB2 WILD-TYPE 168 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNMB2 MUTATED      4    6
  KCNMB2 WILD-TYPE  168  400
        clus
vv       KCNMB2 MUTATED KCNMB2 WILD-TYPE
  FEMALE              4              168
  MALE                6              400
[1] 2 2
[1] FALSE
D645V8, binary
                  cls
clus                 0   1
  KCNMB2 MUTATED     4   5
  KCNMB2 WILD-TYPE 412  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNMB2 MUTATED      4    5
  KCNMB2 WILD-TYPE  412   97
     clus
vv    KCNMB2 MUTATED KCNMB2 WILD-TYPE
  NO               4              412
  YES              5               97
[1] 2 2
[1] FALSE
D645V9, continuous
D645V10, continuous
[1] "Remove cluster labels:" "KCNMB2 MUTATED"        
clus
  KCNMB2 MUTATED KCNMB2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" "KCNMB2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"KCNMB2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KCNMB2 MUTATED       1                         0
  KCNMB2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNMB2 MUTATED                                           0     9
  KCNMB2 WILD-TYPE                                         1   348
D645V11, multiclass
                                           clus
vv                                          KCNMB2 MUTATED KCNMB2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V12, binary
                  cls
clus                 0   1
  KCNMB2 MUTATED     0   9
  KCNMB2 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNMB2 MUTATED      0    9
  KCNMB2 WILD-TYPE   10  389
                        clus
vv                       KCNMB2 MUTATED KCNMB2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(646) Variable = C9ORF152 MUTATION ANALYSIS
D646V1, survival
                    sevent
clus2                  0   1
  C9ORF152 MUTATED     0   4
  C9ORF152 WILD-TYPE 338 212
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 4                550 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 4                212 
$`C9ORF152 MUTATED`
TCGA-L5-A4OW TCGA-BR-4257 TCGA-BR-8284 TCGA-D7-A6EZ 
        7.13         9.67         8.05        20.32 

$`C9ORF152 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
              7.13               0.00 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
             20.32             122.30 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
              8.86              13.63 
[1] "7.1 - 20.3 (8.9)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "4"  
D646V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF152 MUTATED         0        0        0        0         0         1
  C9ORF152 WILD-TYPE      10       20       46       31        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF152 MUTATED           0          1          0          1        0
  C9ORF152 WILD-TYPE        29         83         62         38       43
                    vv
clus                 STAGE IVA
  C9ORF152 MUTATED           0
  C9ORF152 WILD-TYPE         4
D646V3, multiclass
            clus
vv           C9ORF152 MUTATED C9ORF152 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C9ORF152 MUTATED       0   1   1   1
  C9ORF152 WILD-TYPE    54 134 260 101
D646V4, multiclass
       clus
vv      C9ORF152 MUTATED C9ORF152 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   1                260
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C9ORF152 MUTATED     0   1   1   1
  C9ORF152 WILD-TYPE 195 172  88  84
D646V5, multiclass
    clus
vv   C9ORF152 MUTATED C9ORF152 WILD-TYPE
  N0                0                195
  N1                1                172
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V6, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     4   0
  C9ORF152 WILD-TYPE 478  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      4    0
  C9ORF152 WILD-TYPE  478   38
   clus
vv  C9ORF152 MUTATED C9ORF152 WILD-TYPE
  0                4                478
  1                0                 38
[1] 2 2
[1] FALSE
D646V7, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     3   1
  C9ORF152 WILD-TYPE 169 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      3    1
  C9ORF152 WILD-TYPE  169  405
        clus
vv       C9ORF152 MUTATED C9ORF152 WILD-TYPE
  FEMALE                3                169
  MALE                  1                405
[1] 2 2
[1] FALSE
D646V8, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     4   0
  C9ORF152 WILD-TYPE 412 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      4    0
  C9ORF152 WILD-TYPE  412  102
     clus
vv    C9ORF152 MUTATED C9ORF152 WILD-TYPE
  NO                 4                412
  YES                0                102
[1] 2 2
[1] FALSE
D646V9, continuous
D646V10, continuous
[1] "Remove cluster labels:" "C9ORF152 MUTATED"      
clus
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C9ORF152 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF152 MUTATED       0                         0
  C9ORF152 WILD-TYPE   133                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF152 MUTATED                                           0     3
  C9ORF152 WILD-TYPE                                         1   354
D646V11, multiclass
                                           clus
vv                                          C9ORF152 MUTATED C9ORF152 WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V12, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     0   3
  C9ORF152 WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      0    3
  C9ORF152 WILD-TYPE   10  395
                        clus
vv                       C9ORF152 MUTATED C9ORF152 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(647) Variable = ZFP36L1 MUTATION ANALYSIS
D647V1, survival
                   sevent
clus2                 0   1
  ZFP36L1 MUTATED     3   1
  ZFP36L1 WILD-TYPE 335 215
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                4               550 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                1               215 
$`ZFP36L1 MUTATED`
TCGA-BR-6852 TCGA-CD-A4MI TCGA-R5-A7ZI TCGA-VQ-A8P2 
       44.94        11.77        74.53        38.14 

$`ZFP36L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            11.77              0.00 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            74.53            122.30 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
            41.54             13.53 
[1] "11.8 - 74.5 (41.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.2"
D647V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFP36L1 MUTATED         0        0        0        0         1         1
  ZFP36L1 WILD-TYPE      10       20       46       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L1 MUTATED           0          2          0          0        1
  ZFP36L1 WILD-TYPE        29         82         62         39       42
                   vv
clus                STAGE IVA
  ZFP36L1 MUTATED           0
  ZFP36L1 WILD-TYPE         4
D647V3, multiclass
            clus
vv           ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZFP36L1 MUTATED       0   0   2   3
  ZFP36L1 WILD-TYPE    54 135 259  99
D647V4, multiclass
       clus
vv      ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZFP36L1 MUTATED     2   3   0   0
  ZFP36L1 WILD-TYPE 193 170  89  85
D647V5, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V6, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     4   1
  ZFP36L1 WILD-TYPE 478  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      4    1
  ZFP36L1 WILD-TYPE  478   37
   clus
vv  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  0               4               478
  1               1                37
[1] 2 2
[1] FALSE
D647V7, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     2   3
  ZFP36L1 WILD-TYPE 170 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      2    3
  ZFP36L1 WILD-TYPE  170  403
        clus
vv       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  FEMALE               2               170
  MALE                 3               403
[1] 2 2
[1] FALSE
D647V8, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     4   1
  ZFP36L1 WILD-TYPE 412 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      4    1
  ZFP36L1 WILD-TYPE  412  101
     clus
vv    ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  NO                4               412
  YES               1               101
[1] 2 2
[1] FALSE
D647V9, continuous
D647V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZFP36L1 MUTATED       1                         0
  ZFP36L1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFP36L1 MUTATED                                           0     4
  ZFP36L1 WILD-TYPE                                         1   353
D647V11, multiclass
                                           clus
vv                                          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V12, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     1   3
  ZFP36L1 WILD-TYPE   9 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      1    3
  ZFP36L1 WILD-TYPE    9  395
                        clus
vv                       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(648) Variable = HTR1F MUTATION ANALYSIS
D648V1, survival
                 sevent
clus2               0   1
  HTR1F MUTATED     5   3
  HTR1F WILD-TYPE 333 213
  HTR1F MUTATED HTR1F WILD-TYPE 
              8             546 
  HTR1F MUTATED HTR1F WILD-TYPE 
              3             213 
$`HTR1F MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GR TCGA-IG-A8O2 TCGA-B7-A5TJ TCGA-BR-6566 TCGA-BR-7716 
       31.27        32.45         4.67        11.01        32.78        39.78 
TCGA-BR-8297 TCGA-BR-8487 
        7.40         1.12 

$`HTR1F WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  HTR1F MUTATED HTR1F WILD-TYPE 
           1.12            0.00 
  HTR1F MUTATED HTR1F WILD-TYPE 
          39.78          122.30 
  HTR1F MUTATED HTR1F WILD-TYPE 
         21.140          13.565 
[1] "1.1 - 39.8 (21.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D648V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTR1F MUTATED         0        0        0        0         3         3
  HTR1F WILD-TYPE      10       20       46       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR1F MUTATED           0          0          1          1        0         0
  HTR1F WILD-TYPE        29         84         61         38       43         4
D648V3, multiclass
            clus
vv           HTR1F MUTATED HTR1F WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HTR1F MUTATED       1   0   5   2
  HTR1F WILD-TYPE    53 135 256 100
D648V4, multiclass
       clus
vv      HTR1F MUTATED HTR1F WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                5             256
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HTR1F MUTATED     3   2   1   1
  HTR1F WILD-TYPE 192 171  88  84
D648V5, multiclass
    clus
vv   HTR1F MUTATED HTR1F WILD-TYPE
  N0             3             192
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V6, binary
                 cls
clus                0   1
  HTR1F MUTATED     9   0
  HTR1F WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1F MUTATED      9    0
  HTR1F WILD-TYPE  473   38
   clus
vv  HTR1F MUTATED HTR1F WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D648V7, binary
                 cls
clus                0   1
  HTR1F MUTATED     3   6
  HTR1F WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1F MUTATED      3    6
  HTR1F WILD-TYPE  169  400
        clus
vv       HTR1F MUTATED HTR1F WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D648V8, binary
                 cls
clus                0   1
  HTR1F MUTATED     7   0
  HTR1F WILD-TYPE 409 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1F MUTATED      7    0
  HTR1F WILD-TYPE  409  102
     clus
vv    HTR1F MUTATED HTR1F WILD-TYPE
  NO              7             409
  YES             0             102
[1] 2 2
[1] FALSE
D648V9, continuous
D648V10, continuous
[1] "Remove cluster labels:" "HTR1F MUTATED"         
clus
  HTR1F MUTATED HTR1F WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" "HTR1F WILD-TYPE" 
     TCGA-Z6-AAPN 
"HTR1F WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HTR1F MUTATED       1                         0
  HTR1F WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTR1F MUTATED                                           0     6
  HTR1F WILD-TYPE                                         1   351
D648V11, multiclass
                                           clus
vv                                          HTR1F MUTATED HTR1F WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V12, binary
                 cls
clus                0   1
  HTR1F MUTATED     0   7
  HTR1F WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1F MUTATED      0    7
  HTR1F WILD-TYPE   10  391
                        clus
vv                       HTR1F MUTATED HTR1F WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(649) Variable = CDH24 MUTATION ANALYSIS
D649V1, survival
                 sevent
clus2               0   1
  CDH24 MUTATED     9   3
  CDH24 WILD-TYPE 329 213
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             542 
  CDH24 MUTATED CDH24 WILD-TYPE 
              3             213 
$`CDH24 MUTATED`
TCGA-BR-4191 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8487 
       18.35         6.61        35.84        14.43        31.10         1.12 
TCGA-BR-A4CQ TCGA-F1-6874 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ 
       34.98        14.47        24.20        29.98        20.25        19.73 

$`CDH24 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CDH24 MUTATED CDH24 WILD-TYPE 
           1.12            0.00 
  CDH24 MUTATED CDH24 WILD-TYPE 
          35.84          122.30 
  CDH24 MUTATED CDH24 WILD-TYPE 
         19.990          13.445 
[1] "1.1 - 35.8 (20.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.9"
D649V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH24 MUTATED         0        1        2        0         2         1
  CDH24 WILD-TYPE      10       19       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH24 MUTATED           2          2          0          2        0         0
  CDH24 WILD-TYPE        27         82         62         37       43         4
D649V3, multiclass
            clus
vv           CDH24 MUTATED CDH24 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CDH24 MUTATED       1   4   2   5
  CDH24 WILD-TYPE    53 131 259  97
D649V4, multiclass
       clus
vv      CDH24 MUTATED CDH24 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                2             259
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CDH24 MUTATED     5   6   3   0
  CDH24 WILD-TYPE 190 167  86  85
D649V5, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  N0             5             190
  N1             6             167
  N2             3              86
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V6, binary
                 cls
clus                0   1
  CDH24 MUTATED    14   0
  CDH24 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     14    0
  CDH24 WILD-TYPE  468   38
   clus
vv  CDH24 MUTATED CDH24 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D649V7, binary
                 cls
clus                0   1
  CDH24 MUTATED     8   6
  CDH24 WILD-TYPE 164 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      8    6
  CDH24 WILD-TYPE  164  400
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  FEMALE             8             164
  MALE               6             400
[1] 2 2
[1] FALSE
D649V8, binary
                 cls
clus                0   1
  CDH24 MUTATED    13   0
  CDH24 WILD-TYPE 403 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     13    0
  CDH24 WILD-TYPE  403  102
     clus
vv    CDH24 MUTATED CDH24 WILD-TYPE
  NO             13             403
  YES             0             102
[1] 2 2
[1] FALSE
D649V9, continuous
D649V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDH24 MUTATED       3                         0
  CDH24 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH24 MUTATED                                           0    11
  CDH24 WILD-TYPE                                         1   346
D649V11, multiclass
                                           clus
vv                                          CDH24 MUTATED CDH24 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V12, binary
                 cls
clus                0   1
  CDH24 MUTATED     0  14
  CDH24 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      0   14
  CDH24 WILD-TYPE   10  384
                        clus
vv                       CDH24 MUTATED CDH24 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(650) Variable = HERC1 MUTATION ANALYSIS
D650V1, survival
                 sevent
clus2               0   1
  HERC1 MUTATED    33  14
  HERC1 WILD-TYPE 305 202
  HERC1 MUTATED HERC1 WILD-TYPE 
             47             507 
  HERC1 MUTATED HERC1 WILD-TYPE 
             14             202 
$`HERC1 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-IC-A6RE TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A8NJ 
       21.99         5.92         7.69         7.13         7.40        16.47 
TCGA-L7-A56G TCGA-LN-A8HZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-AASW 
       10.85        12.33         6.35        53.95        12.69         9.27 
TCGA-VR-A8EW TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-4280 
        8.12         9.17         2.10        19.56        30.90         6.61 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8297 
       34.68        35.84        14.43        29.59        32.25         7.40 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4IY TCGA-CD-A4MI 
       31.10        31.27         1.12        31.96        12.89        11.77 
TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6528 TCGA-D7-8572 TCGA-HF-A5NB 
       30.97         6.02       105.07        15.22        16.80        30.51 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GT TCGA-MX-A5UJ 
       22.32        24.20         3.25        11.77         6.51        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8P2 
       18.21        74.53        16.67        19.04        38.14 

$`HERC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
       29.00         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       38.40         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        27.55        28.57         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97         7.07         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HERC1 MUTATED HERC1 WILD-TYPE 
           1.12            0.00 
  HERC1 MUTATED HERC1 WILD-TYPE 
         105.07          122.30 
  HERC1 MUTATED HERC1 WILD-TYPE 
          16.47           13.51 
[1] "1.1 - 105.1 (16.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D650V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HERC1 MUTATED         0        2        5        1         5         7
  HERC1 WILD-TYPE      10       18       41       30        79        76
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC1 MUTATED           4          6          2          6        4         0
  HERC1 WILD-TYPE        25         78         60         33       39         4
D650V3, multiclass
            clus
vv           HERC1 MUTATED HERC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              7              76
  STAGE III              4              25
  STAGE IIIA             6              78
  STAGE IIIB             2              60
  STAGE IIIC             6              33
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HERC1 MUTATED       4  11  11  17
  HERC1 WILD-TYPE    50 124 250  85
D650V4, multiclass
       clus
vv      HERC1 MUTATED HERC1 WILD-TYPE
  T0+T1             4              50
  T2               11             124
  T3               11             250
  T4               17              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HERC1 MUTATED    16  14   7   5
  HERC1 WILD-TYPE 179 159  82  80
D650V5, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  N0            16             179
  N1            14             159
  N2             7              82
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V6, binary
                 cls
clus                0   1
  HERC1 MUTATED    41   3
  HERC1 WILD-TYPE 441  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     41    3
  HERC1 WILD-TYPE  441   35
   clus
vv  HERC1 MUTATED HERC1 WILD-TYPE
  0            41             441
  1             3              35
[1] 2 2
[1] FALSE
D650V7, binary
                 cls
clus                0   1
  HERC1 MUTATED    23  26
  HERC1 WILD-TYPE 149 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     23   26
  HERC1 WILD-TYPE  149  380
        clus
vv       HERC1 MUTATED HERC1 WILD-TYPE
  FEMALE            23             149
  MALE              26             380
[1] 2 2
[1] FALSE
D650V8, binary
                 cls
clus                0   1
  HERC1 MUTATED    40   7
  HERC1 WILD-TYPE 376  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     40    7
  HERC1 WILD-TYPE  376   95
     clus
vv    HERC1 MUTATED HERC1 WILD-TYPE
  NO             40             376
  YES             7              95
[1] 2 2
[1] FALSE
D650V9, continuous
D650V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HERC1 MUTATED      10                         1
  HERC1 WILD-TYPE   123                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HERC1 MUTATED                                           0    30
  HERC1 WILD-TYPE                                         1   327
D650V11, multiclass
                                           clus
vv                                          HERC1 MUTATED HERC1 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                30             327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V12, binary
                 cls
clus                0   1
  HERC1 MUTATED     2  35
  HERC1 WILD-TYPE   8 363
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED      2   35
  HERC1 WILD-TYPE    8  363
                        clus
vv                       HERC1 MUTATED HERC1 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            35             363
[1] 2 2
[1] FALSE

Clustering(651) Variable = C1ORF14 MUTATION ANALYSIS
D651V1, survival
                   sevent
clus2                 0   1
  C1ORF14 MUTATED     8   6
  C1ORF14 WILD-TYPE 330 210
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               14               540 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
                6               210 
$`C1ORF14 MUTATED`
TCGA-L5-A8NM TCGA-LN-A9FP TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8081 
        7.76        12.03         6.97         6.61        35.84        32.25 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-F1-6874 TCGA-HU-A4GQ 
       28.14        31.96        21.44        16.14        14.47         0.10 
TCGA-HU-A4GX TCGA-HU-A4H8 
       20.25        14.07 

$`C1ORF14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
              0.1               0.0 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
            35.84            122.30 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
           15.305            13.510 
[1] "0.1 - 35.8 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D651V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF14 MUTATED         0        0        4        0         2         3
  C1ORF14 WILD-TYPE      10       20       42       31        82        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF14 MUTATED           1          1          1          3        1
  C1ORF14 WILD-TYPE        28         83         61         36       42
                   vv
clus                STAGE IVA
  C1ORF14 MUTATED           0
  C1ORF14 WILD-TYPE         4
D651V3, multiclass
            clus
vv           C1ORF14 MUTATED C1ORF14 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               3                36
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C1ORF14 MUTATED       1   6   3   6
  C1ORF14 WILD-TYPE    53 129 258  96
D651V4, multiclass
       clus
vv      C1ORF14 MUTATED C1ORF14 WILD-TYPE
  T0+T1               1                53
  T2                  6               129
  T3                  3               258
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C1ORF14 MUTATED     7   4   3   2
  C1ORF14 WILD-TYPE 188 169  86  83
D651V5, multiclass
    clus
vv   C1ORF14 MUTATED C1ORF14 WILD-TYPE
  N0               7               188
  N1               4               169
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V6, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED    14   1
  C1ORF14 WILD-TYPE 468  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED     14    1
  C1ORF14 WILD-TYPE  468   37
   clus
vv  C1ORF14 MUTATED C1ORF14 WILD-TYPE
  0              14               468
  1               1                37
[1] 2 2
[1] FALSE
D651V7, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED     8   8
  C1ORF14 WILD-TYPE 164 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED      8    8
  C1ORF14 WILD-TYPE  164  398
        clus
vv       C1ORF14 MUTATED C1ORF14 WILD-TYPE
  FEMALE               8               164
  MALE                 8               398
[1] 2 2
[1] FALSE
D651V8, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED    14   1
  C1ORF14 WILD-TYPE 402 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED     14    1
  C1ORF14 WILD-TYPE  402  101
     clus
vv    C1ORF14 MUTATED C1ORF14 WILD-TYPE
  NO               14               402
  YES               1               101
[1] 2 2
[1] FALSE
D651V9, continuous
D651V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF14 MUTATED       5                         0
  C1ORF14 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF14 MUTATED                                           0    10
  C1ORF14 WILD-TYPE                                         1   347
D651V11, multiclass
                                           clus
vv                                          C1ORF14 MUTATED C1ORF14 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V12, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED     0  14
  C1ORF14 WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED      0   14
  C1ORF14 WILD-TYPE   10  384
                        clus
vv                       C1ORF14 MUTATED C1ORF14 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(652) Variable = PRPF40B MUTATION ANALYSIS
D652V1, survival
                   sevent
clus2                 0   1
  PRPF40B MUTATED    12   7
  PRPF40B WILD-TYPE 326 209
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               19               535 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
                7               209 
$`PRPF40B MUTATED`
TCGA-IC-A6RF TCGA-IC-A6RE TCGA-L5-A8NM TCGA-R6-A6L4 TCGA-B7-5816 TCGA-BR-4201 
       15.68         7.69         7.76        16.31        26.70        30.90 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        34.68        30.90        31.96        11.77        12.62 
TCGA-CG-4306 TCGA-D7-6815 TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-HU-A4GQ 
        1.02        15.98        14.47        11.08        29.98         0.10 
TCGA-VQ-A8P2 
       38.14 

$`PRPF40B WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
       11.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PRPF40B MUTATED PRPF40B WILD-TYPE 
              0.1               0.0 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
            38.14            122.30 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
            15.68             13.51 
[1] "0.1 - 38.1 (15.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D652V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRPF40B MUTATED         0        2        2        0         3         4
  PRPF40B WILD-TYPE      10       18       44       31        81        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF40B MUTATED           0          3          0          1        2
  PRPF40B WILD-TYPE        29         81         62         38       41
                   vv
clus                STAGE IVA
  PRPF40B MUTATED           0
  PRPF40B WILD-TYPE         4
D652V3, multiclass
            clus
vv           PRPF40B MUTATED PRPF40B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                18
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PRPF40B MUTATED       4   6   5   4
  PRPF40B WILD-TYPE    50 129 256  98
D652V4, multiclass
       clus
vv      PRPF40B MUTATED PRPF40B WILD-TYPE
  T0+T1               4                50
  T2                  6               129
  T3                  5               256
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PRPF40B MUTATED     7   6   5   0
  PRPF40B WILD-TYPE 188 167  84  85
D652V5, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  N0               7               188
  N1               6               167
  N2               5                84
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V6, binary
                   cls
clus                  0   1
  PRPF40B MUTATED    18   2
  PRPF40B WILD-TYPE 464  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED     18    2
  PRPF40B WILD-TYPE  464   36
   clus
vv  PRPF40B MUTATED PRPF40B WILD-TYPE
  0              18               464
  1               2                36
[1] 2 2
[1] FALSE
D652V7, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     7  14
  PRPF40B WILD-TYPE 165 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      7   14
  PRPF40B WILD-TYPE  165  392
        clus
vv       PRPF40B MUTATED PRPF40B WILD-TYPE
  FEMALE               7               165
  MALE                14               392
[1] 2 2
[1] FALSE
D652V8, binary
                   cls
clus                  0   1
  PRPF40B MUTATED    16   3
  PRPF40B WILD-TYPE 400  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED     16    3
  PRPF40B WILD-TYPE  400   99
     clus
vv    PRPF40B MUTATED PRPF40B WILD-TYPE
  NO               16               400
  YES               3                99
[1] 2 2
[1] FALSE
D652V9, continuous
D652V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PRPF40B MUTATED       6                         1
  PRPF40B WILD-TYPE   127                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRPF40B MUTATED                                           0    13
  PRPF40B WILD-TYPE                                         1   344
D652V11, multiclass
                                           clus
vv                                          PRPF40B MUTATED PRPF40B WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V12, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     0  18
  PRPF40B WILD-TYPE  10 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      0   18
  PRPF40B WILD-TYPE   10  380
                        clus
vv                       PRPF40B MUTATED PRPF40B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(653) Variable = SERPINA1 MUTATION ANALYSIS
D653V1, survival
                    sevent
clus2                  0   1
  SERPINA1 MUTATED     3   4
  SERPINA1 WILD-TYPE 335 212
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 7                547 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 4                212 
$`SERPINA1 MUTATED`
TCGA-IG-A4P3 TCGA-JY-A6F8 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8683 TCGA-CD-8536 
       18.64       122.10         6.97         9.34         9.86        12.43 
TCGA-MX-A5UJ 
       19.73 

$`SERPINA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
              6.97               0.00 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
             122.1              122.3 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
             12.43              13.58 
[1] "7.0 - 122.1 (12.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D653V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINA1 MUTATED         1        0        0        1         0         1
  SERPINA1 WILD-TYPE       9       20       46       30        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA1 MUTATED           0          3          1          0        1
  SERPINA1 WILD-TYPE        29         81         61         39       42
                    vv
clus                 STAGE IVA
  SERPINA1 MUTATED           0
  SERPINA1 WILD-TYPE         4
D653V3, multiclass
            clus
vv           SERPINA1 MUTATED SERPINA1 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SERPINA1 MUTATED       1   1   3   3
  SERPINA1 WILD-TYPE    53 134 258  99
D653V4, multiclass
       clus
vv      SERPINA1 MUTATED SERPINA1 WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   3                258
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SERPINA1 MUTATED     3   3   3   0
  SERPINA1 WILD-TYPE 192 170  86  85
D653V5, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  N0                3                192
  N1                3                170
  N2                3                 86
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V6, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     7   1
  SERPINA1 WILD-TYPE 475  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      7    1
  SERPINA1 WILD-TYPE  475   37
   clus
vv  SERPINA1 MUTATED SERPINA1 WILD-TYPE
  0                7                475
  1                1                 37
[1] 2 2
[1] FALSE
D653V7, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     3   6
  SERPINA1 WILD-TYPE 169 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      3    6
  SERPINA1 WILD-TYPE  169  400
        clus
vv       SERPINA1 MUTATED SERPINA1 WILD-TYPE
  FEMALE                3                169
  MALE                  6                400
[1] 2 2
[1] FALSE
D653V8, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     6   1
  SERPINA1 WILD-TYPE 410 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      6    1
  SERPINA1 WILD-TYPE  410  101
     clus
vv    SERPINA1 MUTATED SERPINA1 WILD-TYPE
  NO                 6                410
  YES                1                101
[1] 2 2
[1] FALSE
D653V9, continuous
D653V10, continuous
[1] "Remove cluster labels:" "SERPINA1 MUTATED"      
clus
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4QT         TCGA-IG-A50L 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" "SERPINA1 WILD-TYPE" 
        TCGA-Z6-AAPN 
"SERPINA1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINA1 MUTATED       2                         0
  SERPINA1 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINA1 MUTATED                                           0     6
  SERPINA1 WILD-TYPE                                         1   351
D653V11, multiclass
                                           clus
vv                                          SERPINA1 MUTATED SERPINA1 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V12, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     0   7
  SERPINA1 WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      0    7
  SERPINA1 WILD-TYPE   10  391
                        clus
vv                       SERPINA1 MUTATED SERPINA1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(654) Variable = FZR1 MUTATION ANALYSIS
D654V1, survival
                sevent
clus2              0   1
  FZR1 MUTATED     9   3
  FZR1 WILD-TYPE 329 213
  FZR1 MUTATED FZR1 WILD-TYPE 
            12            542 
  FZR1 MUTATED FZR1 WILD-TYPE 
             3            213 
$`FZR1 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FG TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-B7-5816 TCGA-B7-A5TJ 
       19.99        41.52        13.22        21.37        26.70        11.01 
TCGA-BR-4280 TCGA-CG-4437 TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-VQ-A8P2 
        6.61         8.05        11.08        24.20        20.25        38.14 

$`FZR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        1.32         2.66        19.73        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FZR1 MUTATED FZR1 WILD-TYPE 
          6.61           0.00 
  FZR1 MUTATED FZR1 WILD-TYPE 
         41.52         122.30 
  FZR1 MUTATED FZR1 WILD-TYPE 
         20.12          13.53 
[1] "6.6 - 41.5 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D654V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FZR1 MUTATED         0        1        0        1         2         2
  FZR1 WILD-TYPE      10       19       46       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FZR1 MUTATED           3          1          0          2        0         0
  FZR1 WILD-TYPE        26         83         62         37       43         4
D654V3, multiclass
            clus
vv           FZR1 MUTATED FZR1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             3             26
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FZR1 MUTATED       1   3   4   4
  FZR1 WILD-TYPE    53 132 257  98
D654V4, multiclass
       clus
vv      FZR1 MUTATED FZR1 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FZR1 MUTATED     4   5   1   1
  FZR1 WILD-TYPE 191 168  88  84
D654V5, multiclass
    clus
vv   FZR1 MUTATED FZR1 WILD-TYPE
  N0            4            191
  N1            5            168
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V6, binary
                cls
clus               0   1
  FZR1 MUTATED    11   0
  FZR1 WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED     11    0
  FZR1 WILD-TYPE  471   38
   clus
vv  FZR1 MUTATED FZR1 WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D654V7, binary
                cls
clus               0   1
  FZR1 MUTATED     4   8
  FZR1 WILD-TYPE 168 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      4    8
  FZR1 WILD-TYPE  168  398
        clus
vv       FZR1 MUTATED FZR1 WILD-TYPE
  FEMALE            4            168
  MALE              8            398
[1] 2 2
[1] FALSE
D654V8, binary
                cls
clus               0   1
  FZR1 MUTATED     9   2
  FZR1 WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      9    2
  FZR1 WILD-TYPE  407  100
     clus
vv    FZR1 MUTATED FZR1 WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D654V9, continuous
D654V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FZR1 MUTATED       2                         1
  FZR1 WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FZR1 MUTATED                                           0     8
  FZR1 WILD-TYPE                                         1   349
D654V11, multiclass
                                           clus
vv                                          FZR1 MUTATED FZR1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V12, binary
                cls
clus               0   1
  FZR1 MUTATED     0   6
  FZR1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      0    6
  FZR1 WILD-TYPE   10  392
                        clus
vv                       FZR1 MUTATED FZR1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(655) Variable = BRF1 MUTATION ANALYSIS
D655V1, survival
                sevent
clus2              0   1
  BRF1 MUTATED     5   5
  BRF1 WILD-TYPE 333 211
  BRF1 MUTATED BRF1 WILD-TYPE 
            10            544 
  BRF1 MUTATED BRF1 WILD-TYPE 
             5            211 
$`BRF1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 TCGA-D7-A6EX TCGA-D7-A6EY 
        6.97        30.90         9.34        32.78        11.31        11.44 
TCGA-HU-A4GH TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.77        13.35        19.73        38.14 

$`BRF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BRF1 MUTATED BRF1 WILD-TYPE 
          6.97           0.00 
  BRF1 MUTATED BRF1 WILD-TYPE 
         38.14         122.30 
  BRF1 MUTATED BRF1 WILD-TYPE 
         12.56          13.63 
[1] "7.0 - 38.1 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D655V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRF1 MUTATED         0        1        0        0         1         0
  BRF1 WILD-TYPE      10       19       46       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRF1 MUTATED           0          5          1          0        0         0
  BRF1 WILD-TYPE        29         79         61         39       43         4
D655V3, multiclass
            clus
vv           BRF1 MUTATED BRF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            5             79
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BRF1 MUTATED       1   2   5   1
  BRF1 WILD-TYPE    53 133 256 101
D655V4, multiclass
       clus
vv      BRF1 MUTATED BRF1 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               5            256
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BRF1 MUTATED     2   4   2   1
  BRF1 WILD-TYPE 193 169  87  84
D655V5, multiclass
    clus
vv   BRF1 MUTATED BRF1 WILD-TYPE
  N0            2            193
  N1            4            169
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V6, binary
                cls
clus               0   1
  BRF1 MUTATED    10   0
  BRF1 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED     10    0
  BRF1 WILD-TYPE  472   38
   clus
vv  BRF1 MUTATED BRF1 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D655V7, binary
                cls
clus               0   1
  BRF1 MUTATED     6   5
  BRF1 WILD-TYPE 166 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      6    5
  BRF1 WILD-TYPE  166  401
        clus
vv       BRF1 MUTATED BRF1 WILD-TYPE
  FEMALE            6            166
  MALE              5            401
[1] 2 2
[1] FALSE
D655V8, binary
                cls
clus               0   1
  BRF1 MUTATED     9   1
  BRF1 WILD-TYPE 407 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      9    1
  BRF1 WILD-TYPE  407  101
     clus
vv    BRF1 MUTATED BRF1 WILD-TYPE
  NO             9            407
  YES            1            101
[1] 2 2
[1] FALSE
D655V9, continuous
D655V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRF1 MUTATED       1                         0
  BRF1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRF1 MUTATED                                           0    10
  BRF1 WILD-TYPE                                         1   347
D655V11, multiclass
                                           clus
vv                                          BRF1 MUTATED BRF1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V12, binary
                cls
clus               0   1
  BRF1 MUTATED     0  10
  BRF1 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      0   10
  BRF1 WILD-TYPE   10  388
                        clus
vv                       BRF1 MUTATED BRF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(656) Variable = ESRP1 MUTATION ANALYSIS
D656V1, survival
                 sevent
clus2               0   1
  ESRP1 MUTATED     5   5
  ESRP1 WILD-TYPE 333 211
  ESRP1 MUTATED ESRP1 WILD-TYPE 
             10             544 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              5             211 
$`ESRP1 MUTATED`
TCGA-2H-A9GL TCGA-L5-A4OH TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8382 TCGA-CD-A4MG 
        5.92        32.61         6.97         0.26        25.05         6.58 
TCGA-CG-4477 TCGA-CG-5721 TCGA-HU-A4H3 TCGA-VQ-AA6B 
       30.97         6.02        29.00        32.94 

$`ESRP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97         7.07         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ESRP1 MUTATED ESRP1 WILD-TYPE 
           0.26            0.00 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
          32.94          122.30 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
         16.010          13.565 
[1] "0.3 - 32.9 (16.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D656V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ESRP1 MUTATED         1        0        2        0         1         0
  ESRP1 WILD-TYPE       9       20       44       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESRP1 MUTATED           1          1          1          2        1         0
  ESRP1 WILD-TYPE        28         83         61         37       42         4
D656V3, multiclass
            clus
vv           ESRP1 MUTATED ESRP1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ESRP1 MUTATED       2   2   4   3
  ESRP1 WILD-TYPE    52 133 257  99
D656V4, multiclass
       clus
vv      ESRP1 MUTATED ESRP1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                4             257
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ESRP1 MUTATED     4   3   1   2
  ESRP1 WILD-TYPE 191 170  88  83
D656V5, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V6, binary
                 cls
clus                0   1
  ESRP1 MUTATED    10   0
  ESRP1 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED     10    0
  ESRP1 WILD-TYPE  472   38
   clus
vv  ESRP1 MUTATED ESRP1 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D656V7, binary
                 cls
clus                0   1
  ESRP1 MUTATED     5   6
  ESRP1 WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      5    6
  ESRP1 WILD-TYPE  167  400
        clus
vv       ESRP1 MUTATED ESRP1 WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D656V8, binary
                 cls
clus                0   1
  ESRP1 MUTATED     7   2
  ESRP1 WILD-TYPE 409 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      7    2
  ESRP1 WILD-TYPE  409  100
     clus
vv    ESRP1 MUTATED ESRP1 WILD-TYPE
  NO              7             409
  YES             2             100
[1] 2 2
[1] FALSE
D656V9, continuous
D656V10, continuous
[1] "Remove cluster labels:" "ESRP1 MUTATED"         
clus
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OM 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ESRP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ESRP1 MUTATED       2                         0
  ESRP1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ESRP1 MUTATED                                           0     6
  ESRP1 WILD-TYPE                                         1   351
D656V11, multiclass
                                           clus
vv                                          ESRP1 MUTATED ESRP1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V12, binary
                 cls
clus                0   1
  ESRP1 MUTATED     0   6
  ESRP1 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      0    6
  ESRP1 WILD-TYPE   10  392
                        clus
vv                       ESRP1 MUTATED ESRP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(657) Variable = P2RY4 MUTATION ANALYSIS
D657V1, survival
                 sevent
clus2               0   1
  P2RY4 MUTATED     6   7
  P2RY4 WILD-TYPE 332 209
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             13             541 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
              7             209 
$`P2RY4 MUTATED`
TCGA-IG-A3Y9 TCGA-BR-4184 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8487 
        0.85         6.97         0.69         8.05         2.20         1.12 
TCGA-CD-8524 TCGA-CG-5726 TCGA-D7-8576 TCGA-FP-8209 TCGA-HU-A4GX TCGA-HU-A4GY 
       12.76        28.96        14.66        59.54        20.25         0.26 
TCGA-HU-A4H4 
       23.84 

$`P2RY4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        17.06         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         6.58         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  P2RY4 MUTATED P2RY4 WILD-TYPE 
           0.26            0.00 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
          59.54          122.30 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
           8.05           13.68 
[1] "0.3 - 59.5 (8.1)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.9"
D657V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P2RY4 MUTATED         0        1        1        1         1         2
  P2RY4 WILD-TYPE      10       19       45       30        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P2RY4 MUTATED           0          3          2          2        0         0
  P2RY4 WILD-TYPE        29         81         60         37       43         4
D657V3, multiclass
            clus
vv           P2RY4 MUTATED P2RY4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  P2RY4 MUTATED       1   2   4   6
  P2RY4 WILD-TYPE    53 133 257  96
D657V4, multiclass
       clus
vv      P2RY4 MUTATED P2RY4 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  P2RY4 MUTATED     6   3   2   2
  P2RY4 WILD-TYPE 189 170  87  83
D657V5, multiclass
    clus
vv   P2RY4 MUTATED P2RY4 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V6, binary
                 cls
clus                0   1
  P2RY4 MUTATED    12   0
  P2RY4 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED     12    0
  P2RY4 WILD-TYPE  470   38
   clus
vv  P2RY4 MUTATED P2RY4 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D657V7, binary
                 cls
clus                0   1
  P2RY4 MUTATED     9   4
  P2RY4 WILD-TYPE 163 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED      9    4
  P2RY4 WILD-TYPE  163  402
        clus
vv       P2RY4 MUTATED P2RY4 WILD-TYPE
  FEMALE             9             163
  MALE               4             402
[1] 2 2
[1] FALSE
D657V8, binary
                 cls
clus                0   1
  P2RY4 MUTATED    10   1
  P2RY4 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED     10    1
  P2RY4 WILD-TYPE  406  101
     clus
vv    P2RY4 MUTATED P2RY4 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D657V9, continuous
[1] "Remove cluster labels:" "P2RY4 MUTATED"         
clus
  P2RY4 MUTATED P2RY4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
D657V10, continuous
[1] "Remove cluster labels:" "P2RY4 MUTATED"         
clus
  P2RY4 MUTATED P2RY4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" "P2RY4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"P2RY4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P2RY4 MUTATED       4                         0
  P2RY4 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P2RY4 MUTATED                                           0     8
  P2RY4 WILD-TYPE                                         1   349
D657V11, multiclass
                                           clus
vv                                          P2RY4 MUTATED P2RY4 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V12, binary
                 cls
clus                0   1
  P2RY4 MUTATED     0  12
  P2RY4 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED      0   12
  P2RY4 WILD-TYPE   10  386
                        clus
vv                       P2RY4 MUTATED P2RY4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(658) Variable = EPHA3 MUTATION ANALYSIS
D658V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    24  12
  EPHA3 WILD-TYPE 314 204
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             36             518 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             12             204 
$`EPHA3 MUTATED`
TCGA-CG-4444 TCGA-2H-A9GH TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A97H TCGA-L5-A8NE 
       47.05        31.27        32.45         0.85        14.50        55.50 
TCGA-L5-A8NJ TCGA-L5-A8NW TCGA-VR-A8EY TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 
       16.47        46.09        33.70         6.97         9.34        34.68 
TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
       30.90        31.27         1.12        27.12        28.14        31.96 
TCGA-BR-8690 TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4436 
       10.68         5.13        13.18        12.43        11.61         7.99 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6527 TCGA-D7-6820 TCGA-F1-6875 TCGA-F1-A448 
      105.07        65.10        10.26        11.31        72.23        21.27 
TCGA-FP-A9TM TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A6RR TCGA-VQ-A8DU TCGA-VQ-A8P2 
        6.21        23.84        23.80         6.74         5.46        38.14 

$`EPHA3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       16.24         4.21         7.69        33.27        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       20.22        12.79         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       24.79        32.58         9.86        20.88         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44        16.14        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        14.47        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        29.00        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           0.85            0.00 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         105.07          122.30 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         22.535          13.495 
[1] "0.8 - 105.1 (22.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D658V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA3 MUTATED         0        1        4        2         6         5
  EPHA3 WILD-TYPE      10       19       42       29        78        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA3 MUTATED           1          9          3          2        1         0
  EPHA3 WILD-TYPE        28         75         59         37       42         4
D658V3, multiclass
            clus
vv           EPHA3 MUTATED EPHA3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             9              75
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPHA3 MUTATED       2  11  16   6
  EPHA3 WILD-TYPE    52 124 245  96
D658V4, multiclass
       clus
vv      EPHA3 MUTATED EPHA3 WILD-TYPE
  T0+T1             2              52
  T2               11             124
  T3               16             245
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPHA3 MUTATED    10  15   6   4
  EPHA3 WILD-TYPE 185 158  83  81
D658V5, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            10             185
  N1            15             158
  N2             6              83
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V6, binary
                 cls
clus                0   1
  EPHA3 MUTATED    34   1
  EPHA3 WILD-TYPE 448  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     34    1
  EPHA3 WILD-TYPE  448   37
   clus
vv  EPHA3 MUTATED EPHA3 WILD-TYPE
  0            34             448
  1             1              37
[1] 2 2
[1] FALSE
D658V7, binary
                 cls
clus                0   1
  EPHA3 MUTATED     7  29
  EPHA3 WILD-TYPE 165 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      7   29
  EPHA3 WILD-TYPE  165  377
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE             7             165
  MALE              29             377
[1] 2 2
[1] FALSE
D658V8, binary
                 cls
clus                0   1
  EPHA3 MUTATED    28   6
  EPHA3 WILD-TYPE 388  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     28    6
  EPHA3 WILD-TYPE  388   96
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             28             388
  YES             6              96
[1] 2 2
[1] FALSE
D658V9, continuous
[1] "Remove cluster labels:" "EPHA3 MUTATED"         
clus
  EPHA3 MUTATED EPHA3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EPHA3 WILD-TYPE" "EPHA3 WILD-TYPE" 
D658V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHA3 MUTATED       7                         1
  EPHA3 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHA3 MUTATED                                           0    22
  EPHA3 WILD-TYPE                                         1   335
D658V11, multiclass
                                           clus
vv                                          EPHA3 MUTATED EPHA3 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                22             335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V12, binary
                 cls
clus                0   1
  EPHA3 MUTATED     1  23
  EPHA3 WILD-TYPE   9 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      1   23
  EPHA3 WILD-TYPE    9  375
                        clus
vv                       EPHA3 MUTATED EPHA3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            23             375
[1] 2 2
[1] FALSE

Clustering(659) Variable = IDE MUTATION ANALYSIS
D659V1, survival
               sevent
clus2             0   1
  IDE MUTATED     7   7
  IDE WILD-TYPE 331 209
  IDE MUTATED IDE WILD-TYPE 
           14           540 
  IDE MUTATED IDE WILD-TYPE 
            7           209 
$`IDE MUTATED`
TCGA-LN-A49N TCGA-LN-A7HX TCGA-R6-A6XQ TCGA-Z6-A8JD TCGA-BR-7703 TCGA-BR-8680 
       12.43        12.23         6.35         3.42        36.16        31.96 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-HJ-7597 TCGA-HU-A4GH 
       16.14         6.58        11.77         1.02        26.47        11.77 
TCGA-HU-A4GQ TCGA-HU-A4GT 
        0.10         6.51 

$`IDE WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        21.37        29.98         8.98         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  IDE MUTATED IDE WILD-TYPE 
          0.1           0.0 
  IDE MUTATED IDE WILD-TYPE 
        36.16        122.30 
  IDE MUTATED IDE WILD-TYPE 
       11.770        13.825 
[1] "0.1 - 36.2 (11.8)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.8"
D659V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDE MUTATED         0        2        1        0         3         2
  IDE WILD-TYPE      10       18       45       31        81        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDE MUTATED           0          2          1          1        2         0
  IDE WILD-TYPE        29         82         61         38       41         4
D659V3, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              0            10
  STAGE IA             2            18
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            3            81
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           1            38
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  IDE MUTATED       2   3   6   3
  IDE WILD-TYPE    52 132 255  99
D659V4, multiclass
       clus
vv      IDE MUTATED IDE WILD-TYPE
  T0+T1           2            52
  T2              3           132
  T3              6           255
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  IDE MUTATED     8   2   3   1
  IDE WILD-TYPE 187 171  86  84
D659V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0           8           187
  N1           2           171
  N2           3            86
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V6, binary
               cls
clus              0   1
  IDE MUTATED    11   2
  IDE WILD-TYPE 471  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     11    2
  IDE WILD-TYPE  471   36
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0          11           471
  1           2            36
[1] 2 2
[1] FALSE
D659V7, binary
               cls
clus              0   1
  IDE MUTATED     4  11
  IDE WILD-TYPE 168 395
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      4   11
  IDE WILD-TYPE  168  395
        clus
vv       IDE MUTATED IDE WILD-TYPE
  FEMALE           4           168
  MALE            11           395
[1] 2 2
[1] FALSE
D659V8, binary
               cls
clus              0   1
  IDE MUTATED    12   1
  IDE WILD-TYPE 404 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     12    1
  IDE WILD-TYPE  404  101
     clus
vv    IDE MUTATED IDE WILD-TYPE
  NO           12           404
  YES           1           101
[1] 2 2
[1] FALSE
D659V9, continuous
D659V10, continuous
[1] "Remove cluster labels:" "IDE MUTATED"           
clus
  IDE MUTATED IDE WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A4OX    TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A8NF    TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-L5-A8NS    TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-LN-A4A6    TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-LN-A7HW    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" "IDE WILD-TYPE" 
   TCGA-Z6-AAPN 
"IDE WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  IDE MUTATED       8                         0
  IDE WILD-TYPE   125                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IDE MUTATED                                           0     6
  IDE WILD-TYPE                                         1   351
D659V11, multiclass
                                           clus
vv                                          IDE MUTATED IDE WILD-TYPE
  ASIAN                                               8           125
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               6           351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V12, binary
               cls
clus              0   1
  IDE MUTATED     0  14
  IDE WILD-TYPE  10 384
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      0   14
  IDE WILD-TYPE   10  384
                        clus
vv                       IDE MUTATED IDE WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          14           384
[1] 2 2
[1] FALSE

Clustering(660) Variable = C15ORF52 MUTATION ANALYSIS
D660V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     4   2
  C15ORF52 WILD-TYPE 334 214
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 6                548 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 2                214 
$`C15ORF52 MUTATED`
TCGA-JY-A6FG TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-HF-7132 TCGA-HU-A4GT 
       41.52         1.12        28.14         6.58        77.29         6.51 

$`C15ORF52 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
              1.12               0.00 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             77.29             122.30 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
            17.360             13.565 
[1] "1.1 - 77.3 (17.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D660V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C15ORF52 MUTATED         0        0        0        1         3         0
  C15ORF52 WILD-TYPE      10       20       46       30        81        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           1          0          0          1        0
  C15ORF52 WILD-TYPE        28         84         62         38       43
                    vv
clus                 STAGE IVA
  C15ORF52 MUTATED           0
  C15ORF52 WILD-TYPE         4
D660V3, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 0                 83
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C15ORF52 MUTATED       0   1   4   1
  C15ORF52 WILD-TYPE    54 134 257 101
D660V4, multiclass
       clus
vv      C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   4                257
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C15ORF52 MUTATED     3   2   0   1
  C15ORF52 WILD-TYPE 192 171  89  84
D660V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0                3                192
  N1                2                171
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V6, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     7   0
  C15ORF52 WILD-TYPE 475  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      7    0
  C15ORF52 WILD-TYPE  475   38
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0                7                475
  1                0                 38
[1] 2 2
[1] FALSE
D660V7, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     3   4
  C15ORF52 WILD-TYPE 169 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      3    4
  C15ORF52 WILD-TYPE  169  402
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  FEMALE                3                169
  MALE                  4                402
[1] 2 2
[1] FALSE
D660V8, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     5   1
  C15ORF52 WILD-TYPE 411 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      5    1
  C15ORF52 WILD-TYPE  411  101
     clus
vv    C15ORF52 MUTATED C15ORF52 WILD-TYPE
  NO                 5                411
  YES                1                101
[1] 2 2
[1] FALSE
D660V9, continuous
D660V10, continuous
[1] "Remove cluster labels:" "C15ORF52 MUTATED"      
clus
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FH         TCGA-KH-A6WC 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" "C15ORF52 WILD-TYPE" 
        TCGA-Z6-AAPN 
"C15ORF52 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C15ORF52 MUTATED       2                         0
  C15ORF52 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C15ORF52 MUTATED                                           0     4
  C15ORF52 WILD-TYPE                                         1   353
D660V11, multiclass
                                           clus
vv                                          C15ORF52 MUTATED C15ORF52 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V12, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     0   5
  C15ORF52 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      0    5
  C15ORF52 WILD-TYPE   10  393
                        clus
vv                       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(661) Variable = MARVELD3 MUTATION ANALYSIS
D661V1, survival
                    sevent
clus2                  0   1
  MARVELD3 MUTATED     8   5
  MARVELD3 WILD-TYPE 330 211
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                13                541 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                 5                211 
$`MARVELD3 MUTATED`
TCGA-LN-A49M TCGA-VR-A8EQ TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8487 
       12.66        22.82         9.34         9.67        34.68         1.12 
TCGA-BR-A4QL TCGA-CG-5733 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4H5 
       16.14        21.07        11.08        30.51        23.84        23.80 
TCGA-VQ-A8E2 
       43.36 

$`MARVELD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        4.08         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        29.00        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
              1.12               0.00 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
             43.36             122.30 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
             21.07              13.51 
[1] "1.1 - 43.4 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D661V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MARVELD3 MUTATED         1        0        1        0         4         1
  MARVELD3 WILD-TYPE       9       20       45       31        80        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARVELD3 MUTATED           1          1          2          1        0
  MARVELD3 WILD-TYPE        28         83         60         38       43
                    vv
clus                 STAGE IVA
  MARVELD3 MUTATED           0
  MARVELD3 WILD-TYPE         4
D661V3, multiclass
            clus
vv           MARVELD3 MUTATED MARVELD3 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 4                 80
  STAGE IIB                 1                 82
  STAGE III                 1                 28
  STAGE IIIA                1                 83
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  MARVELD3 MUTATED       1   4   6   1
  MARVELD3 WILD-TYPE    53 131 255 101
D661V4, multiclass
       clus
vv      MARVELD3 MUTATED MARVELD3 WILD-TYPE
  T0+T1                1                 53
  T2                   4                131
  T3                   6                255
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  MARVELD3 MUTATED     5   3   3   2
  MARVELD3 WILD-TYPE 190 170  86  83
D661V5, multiclass
    clus
vv   MARVELD3 MUTATED MARVELD3 WILD-TYPE
  N0                5                190
  N1                3                170
  N2                3                 86
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V6, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED    13   0
  MARVELD3 WILD-TYPE 469  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED     13    0
  MARVELD3 WILD-TYPE  469   38
   clus
vv  MARVELD3 MUTATED MARVELD3 WILD-TYPE
  0               13                469
  1                0                 38
[1] 2 2
[1] FALSE
D661V7, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     7   7
  MARVELD3 WILD-TYPE 165 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      7    7
  MARVELD3 WILD-TYPE  165  399
        clus
vv       MARVELD3 MUTATED MARVELD3 WILD-TYPE
  FEMALE                7                165
  MALE                  7                399
[1] 2 2
[1] FALSE
D661V8, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     9   5
  MARVELD3 WILD-TYPE 407  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      9    5
  MARVELD3 WILD-TYPE  407   97
     clus
vv    MARVELD3 MUTATED MARVELD3 WILD-TYPE
  NO                 9                407
  YES                5                 97
[1] 2 2
[1] FALSE
D661V9, continuous
[1] "Remove cluster labels:" "MARVELD3 MUTATED"      
clus
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" "MARVELD3 WILD-TYPE" 
D661V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  MARVELD3 MUTATED       4                         2
  MARVELD3 WILD-TYPE   129                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MARVELD3 MUTATED                                           0     6
  MARVELD3 WILD-TYPE                                         1   351
D661V11, multiclass
                                           clus
vv                                          MARVELD3 MUTATED MARVELD3 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V12, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     0  10
  MARVELD3 WILD-TYPE  10 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      0   10
  MARVELD3 WILD-TYPE   10  388
                        clus
vv                       MARVELD3 MUTATED MARVELD3 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               10                388
[1] 2 2
[1] FALSE

Clustering(662) Variable = C1ORF141 MUTATION ANALYSIS
D662V1, survival
                    sevent
clus2                  0   1
  C1ORF141 MUTATED     8   2
  C1ORF141 WILD-TYPE 330 214
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                10                544 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                 2                214 
$`C1ORF141 MUTATED`
TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-8533 TCGA-CD-A4MG 
       31.10         4.31        31.27        31.96        15.39         6.58 
TCGA-CG-5728 TCGA-HF-A5NB TCGA-IN-7808 TCGA-RD-A8N1 
       65.10        30.51         3.45       115.69 

$`C1ORF141 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
              3.45               0.00 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
            115.69             122.30 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
            30.805             13.510 
[1] "3.5 - 115.7 (30.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.1"
D662V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF141 MUTATED         0        0        2        1         1         1
  C1ORF141 WILD-TYPE      10       20       44       30        83        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF141 MUTATED           0          0          1          3        1
  C1ORF141 WILD-TYPE        29         84         61         36       42
                    vv
clus                 STAGE IVA
  C1ORF141 MUTATED           0
  C1ORF141 WILD-TYPE         4
D662V3, multiclass
            clus
vv           C1ORF141 MUTATED C1ORF141 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 1                 83
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C1ORF141 MUTATED       0   3   4   5
  C1ORF141 WILD-TYPE    54 132 257  97
D662V4, multiclass
       clus
vv      C1ORF141 MUTATED C1ORF141 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   4                257
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C1ORF141 MUTATED     5   0   3   3
  C1ORF141 WILD-TYPE 190 173  86  82
D662V5, multiclass
    clus
vv   C1ORF141 MUTATED C1ORF141 WILD-TYPE
  N0                5                190
  N1                0                173
  N2                3                 86
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V6, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED    10   2
  C1ORF141 WILD-TYPE 472  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED     10    2
  C1ORF141 WILD-TYPE  472   36
   clus
vv  C1ORF141 MUTATED C1ORF141 WILD-TYPE
  0               10                472
  1                2                 36
[1] 2 2
[1] FALSE
D662V7, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     5   7
  C1ORF141 WILD-TYPE 167 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      5    7
  C1ORF141 WILD-TYPE  167  399
        clus
vv       C1ORF141 MUTATED C1ORF141 WILD-TYPE
  FEMALE                5                167
  MALE                  7                399
[1] 2 2
[1] FALSE
D662V8, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     8   2
  C1ORF141 WILD-TYPE 408 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      8    2
  C1ORF141 WILD-TYPE  408  100
     clus
vv    C1ORF141 MUTATED C1ORF141 WILD-TYPE
  NO                 8                408
  YES                2                100
[1] 2 2
[1] FALSE
D662V9, continuous
D662V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF141 MUTATED       3                         0
  C1ORF141 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF141 MUTATED                                           0     7
  C1ORF141 WILD-TYPE                                         1   350
D662V11, multiclass
                                           clus
vv                                          C1ORF141 MUTATED C1ORF141 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V12, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     0  10
  C1ORF141 WILD-TYPE  10 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      0   10
  C1ORF141 WILD-TYPE   10  388
                        clus
vv                       C1ORF141 MUTATED C1ORF141 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               10                388
[1] 2 2
[1] FALSE

Clustering(663) Variable = PKN1 MUTATION ANALYSIS
D663V1, survival
                sevent
clus2              0   1
  PKN1 MUTATED     7   2
  PKN1 WILD-TYPE 331 214
  PKN1 MUTATED PKN1 WILD-TYPE 
             9            545 
  PKN1 MUTATED PKN1 WILD-TYPE 
             2            214 
$`PKN1 MUTATED`
TCGA-LN-A7HY TCGA-BR-4184 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CG-4449 TCGA-CG-5721 
       12.03         6.97        31.27        16.14        19.07         6.02 
TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-MX-A5UJ 
        6.51        14.07        19.73 

$`PKN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PKN1 MUTATED PKN1 WILD-TYPE 
          6.02           0.00 
  PKN1 MUTATED PKN1 WILD-TYPE 
         31.27         122.30 
  PKN1 MUTATED PKN1 WILD-TYPE 
         14.07          13.55 
[1] "6.0 - 31.3 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D663V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKN1 MUTATED         0        0        2        1         1         0
  PKN1 WILD-TYPE      10       20       44       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKN1 MUTATED           1          2          1          1        2         0
  PKN1 WILD-TYPE        28         82         61         38       41         4
D663V3, multiclass
            clus
vv           PKN1 MUTATED PKN1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PKN1 MUTATED       1   2   5   3
  PKN1 WILD-TYPE    53 133 256  99
D663V4, multiclass
       clus
vv      PKN1 MUTATED PKN1 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               5            256
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PKN1 MUTATED     2   5   2   2
  PKN1 WILD-TYPE 193 168  87  83
D663V5, multiclass
    clus
vv   PKN1 MUTATED PKN1 WILD-TYPE
  N0            2            193
  N1            5            168
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V6, binary
                cls
clus               0   1
  PKN1 MUTATED    10   0
  PKN1 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED     10    0
  PKN1 WILD-TYPE  472   38
   clus
vv  PKN1 MUTATED PKN1 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D663V7, binary
                cls
clus               0   1
  PKN1 MUTATED     4   7
  PKN1 WILD-TYPE 168 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      4    7
  PKN1 WILD-TYPE  168  399
        clus
vv       PKN1 MUTATED PKN1 WILD-TYPE
  FEMALE            4            168
  MALE              7            399
[1] 2 2
[1] FALSE
D663V8, binary
                cls
clus               0   1
  PKN1 MUTATED     9   0
  PKN1 WILD-TYPE 407 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      9    0
  PKN1 WILD-TYPE  407  102
     clus
vv    PKN1 MUTATED PKN1 WILD-TYPE
  NO             9            407
  YES            0            102
[1] 2 2
[1] FALSE
D663V9, continuous
[1] "Remove cluster labels:" "PKN1 MUTATED"          
clus
  PKN1 MUTATED PKN1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PKN1 WILD-TYPE" "PKN1 WILD-TYPE" "PKN1 WILD-TYPE" 
D663V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKN1 MUTATED       3                         0
  PKN1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKN1 MUTATED                                           0     5
  PKN1 WILD-TYPE                                         1   352
D663V11, multiclass
                                           clus
vv                                          PKN1 MUTATED PKN1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V12, binary
                cls
clus               0   1
  PKN1 MUTATED     0   8
  PKN1 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      0    8
  PKN1 WILD-TYPE   10  390
                        clus
vv                       PKN1 MUTATED PKN1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(664) Variable = PCF11 MUTATION ANALYSIS
D664V1, survival
                 sevent
clus2               0   1
  PCF11 MUTATED    17   5
  PCF11 WILD-TYPE 321 211
  PCF11 MUTATED PCF11 WILD-TYPE 
             22             532 
  PCF11 MUTATED PCF11 WILD-TYPE 
              5             211 
$`PCF11 MUTATED`
TCGA-LN-A8I0 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8058 TCGA-BR-8077 
       13.38        30.90        34.68        35.84        37.25         0.69 
TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 
        6.18        31.96        11.77        15.95         1.02         6.02 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-A4G2 TCGA-HU-A4GQ 
       11.31        22.29        52.21        30.51        24.30         0.10 
TCGA-R5-A804 TCGA-VQ-A8P2 TCGA-VQ-A92D TCGA-VQ-AA6B 
        4.60        38.14        66.81        32.94 

$`PCF11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        14.43        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       12.20        12.62        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         6.08         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        42.64        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PCF11 MUTATED PCF11 WILD-TYPE 
            0.1             0.0 
  PCF11 MUTATED PCF11 WILD-TYPE 
          66.81          122.30 
  PCF11 MUTATED PCF11 WILD-TYPE 
         23.295          13.510 
[1] "0.1 - 66.8 (23.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D664V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCF11 MUTATED         0        1        3        1         3         1
  PCF11 WILD-TYPE      10       19       43       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCF11 MUTATED           0          3          3          2        4         0
  PCF11 WILD-TYPE        29         81         59         37       39         4
D664V3, multiclass
            clus
vv           PCF11 MUTATED PCF11 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PCF11 MUTATED       1   6   9   7
  PCF11 WILD-TYPE    53 129 252  95
D664V4, multiclass
       clus
vv      PCF11 MUTATED PCF11 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                9             252
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PCF11 MUTATED     7   6   7   1
  PCF11 WILD-TYPE 188 167  82  84
D664V5, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             7              82
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V6, binary
                 cls
clus                0   1
  PCF11 MUTATED    19   3
  PCF11 WILD-TYPE 463  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED     19    3
  PCF11 WILD-TYPE  463   35
   clus
vv  PCF11 MUTATED PCF11 WILD-TYPE
  0            19             463
  1             3              35
[1] 2 2
[1] FALSE
D664V7, binary
                 cls
clus                0   1
  PCF11 MUTATED     9  14
  PCF11 WILD-TYPE 163 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      9   14
  PCF11 WILD-TYPE  163  392
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  FEMALE             9             163
  MALE              14             392
[1] 2 2
[1] FALSE
D664V8, binary
                 cls
clus                0   1
  PCF11 MUTATED    17   3
  PCF11 WILD-TYPE 399  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED     17    3
  PCF11 WILD-TYPE  399   99
     clus
vv    PCF11 MUTATED PCF11 WILD-TYPE
  NO             17             399
  YES             3              99
[1] 2 2
[1] FALSE
D664V9, continuous
D664V10, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Z6-AAPN 
"PCF11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PCF11 MUTATED       5                         1
  PCF11 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCF11 MUTATED                                           0    12
  PCF11 WILD-TYPE                                         1   345
D664V11, multiclass
                                           clus
vv                                          PCF11 MUTATED PCF11 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V12, binary
                 cls
clus                0   1
  PCF11 MUTATED     0  15
  PCF11 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      0   15
  PCF11 WILD-TYPE   10  383
                        clus
vv                       PCF11 MUTATED PCF11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(665) Variable = RASSF5 MUTATION ANALYSIS
D665V1, survival
                  sevent
clus2                0   1
  RASSF5 MUTATED     3   3
  RASSF5 WILD-TYPE 335 213
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               6              548 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               3              213 
$`RASSF5 MUTATED`
TCGA-IG-A7DP TCGA-JY-A6FA TCGA-B7-5816 TCGA-BR-8372 TCGA-CD-A4MG TCGA-HU-A4GQ 
       14.86        44.75        26.70        31.27         6.58         0.10 

$`RASSF5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  RASSF5 MUTATED RASSF5 WILD-TYPE 
             0.1              0.0 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
           44.75           122.30 
  RASSF5 MUTATED RASSF5 WILD-TYPE 
           20.78            13.53 
[1] "0.1 - 44.8 (20.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D665V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASSF5 MUTATED         0        0        0        0         1         2
  RASSF5 WILD-TYPE      10       20       46       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASSF5 MUTATED           0          1          0          2        0
  RASSF5 WILD-TYPE        29         83         62         37       43
                  vv
clus               STAGE IVA
  RASSF5 MUTATED           0
  RASSF5 WILD-TYPE         4
D665V3, multiclass
            clus
vv           RASSF5 MUTATED RASSF5 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RASSF5 MUTATED       0   1   1   4
  RASSF5 WILD-TYPE    54 134 260  98
D665V4, multiclass
       clus
vv      RASSF5 MUTATED RASSF5 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 1              260
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RASSF5 MUTATED     2   1   1   1
  RASSF5 WILD-TYPE 193 172  88  84
D665V5, multiclass
    clus
vv   RASSF5 MUTATED RASSF5 WILD-TYPE
  N0              2              193
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V6, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     5   0
  RASSF5 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      5    0
  RASSF5 WILD-TYPE  477   38
   clus
vv  RASSF5 MUTATED RASSF5 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D665V7, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     2   4
  RASSF5 WILD-TYPE 170 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      2    4
  RASSF5 WILD-TYPE  170  402
        clus
vv       RASSF5 MUTATED RASSF5 WILD-TYPE
  FEMALE              2              170
  MALE                4              402
[1] 2 2
[1] FALSE
D665V8, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     6   0
  RASSF5 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      6    0
  RASSF5 WILD-TYPE  410  102
     clus
vv    RASSF5 MUTATED RASSF5 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D665V9, continuous
[1] "Remove cluster labels:" "RASSF5 MUTATED"        
clus
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
D665V10, continuous
[1] "Remove cluster labels:" "RASSF5 MUTATED"        
clus
  RASSF5 MUTATED RASSF5 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FE 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" "RASSF5 WILD-TYPE" 
      TCGA-Z6-AAPN 
"RASSF5 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RASSF5 MUTATED       3                         0
  RASSF5 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASSF5 MUTATED                                           0     3
  RASSF5 WILD-TYPE                                         1   354
D665V11, multiclass
                                           clus
vv                                          RASSF5 MUTATED RASSF5 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V12, binary
                  cls
clus                 0   1
  RASSF5 MUTATED     0   5
  RASSF5 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASSF5 MUTATED      0    5
  RASSF5 WILD-TYPE   10  393
                        clus
vv                       RASSF5 MUTATED RASSF5 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(666) Variable = SLC10A6 MUTATION ANALYSIS
D666V1, survival
                   sevent
clus2                 0   1
  SLC10A6 MUTATED     7   2
  SLC10A6 WILD-TYPE 331 214
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                9               545 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                2               214 
$`SLC10A6 MUTATED`
TCGA-2H-A9GK TCGA-L7-A6VZ TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-8536 
        7.63        10.36        35.84         4.31        31.96        12.43 
TCGA-CD-A4MG TCGA-FP-A4BE TCGA-SW-A7EB 
        6.58        11.08         5.79 

$`SLC10A6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
             4.31              0.00 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
            35.84            122.30 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
            10.36             13.78 
[1] "4.3 - 35.8 (10.4)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.3"
D666V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC10A6 MUTATED         0        0        2        1         2         0
  SLC10A6 WILD-TYPE      10       20       44       30        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC10A6 MUTATED           1          1          0          1        1
  SLC10A6 WILD-TYPE        28         83         62         38       42
                   vv
clus                STAGE IVA
  SLC10A6 MUTATED           0
  SLC10A6 WILD-TYPE         4
D666V3, multiclass
            clus
vv           SLC10A6 MUTATED SLC10A6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC10A6 MUTATED       1   2   6   1
  SLC10A6 WILD-TYPE    53 133 255 101
D666V4, multiclass
       clus
vv      SLC10A6 MUTATED SLC10A6 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  6               255
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC10A6 MUTATED     5   1   2   1
  SLC10A6 WILD-TYPE 190 172  87  84
D666V5, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  N0               5               190
  N1               1               172
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V6, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     8   1
  SLC10A6 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      8    1
  SLC10A6 WILD-TYPE  474   37
   clus
vv  SLC10A6 MUTATED SLC10A6 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D666V7, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     3   7
  SLC10A6 WILD-TYPE 169 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      3    7
  SLC10A6 WILD-TYPE  169  399
        clus
vv       SLC10A6 MUTATED SLC10A6 WILD-TYPE
  FEMALE               3               169
  MALE                 7               399
[1] 2 2
[1] FALSE
D666V8, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     7   2
  SLC10A6 WILD-TYPE 409 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      7    2
  SLC10A6 WILD-TYPE  409  100
     clus
vv    SLC10A6 MUTATED SLC10A6 WILD-TYPE
  NO                7               409
  YES               2               100
[1] 2 2
[1] FALSE
D666V9, continuous
D666V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC10A6 MUTATED       3                         1
  SLC10A6 WILD-TYPE   130                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC10A6 MUTATED                                           0     5
  SLC10A6 WILD-TYPE                                         1   352
D666V11, multiclass
                                           clus
vv                                          SLC10A6 MUTATED SLC10A6 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V12, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     0   9
  SLC10A6 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      0    9
  SLC10A6 WILD-TYPE   10  389
                        clus
vv                       SLC10A6 MUTATED SLC10A6 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(667) Variable = OSGEPL1 MUTATION ANALYSIS
D667V1, survival
                   sevent
clus2                 0   1
  OSGEPL1 MUTATED     2   2
  OSGEPL1 WILD-TYPE 336 214
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               550 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                2               214 
$`OSGEPL1 MUTATED`
TCGA-B7-5816 TCGA-CD-A4MG TCGA-CG-5728 TCGA-VQ-A8DU 
       26.70         6.58        65.10         5.46 

$`OSGEPL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
             5.46              0.00 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
             65.1             122.3 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
           16.640            13.565 
[1] "5.5 - 65.1 (16.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D667V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSGEPL1 MUTATED         0        0        1        0         1         1
  OSGEPL1 WILD-TYPE      10       20       45       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSGEPL1 MUTATED           0          1          0          0        0
  OSGEPL1 WILD-TYPE        29         83         62         39       43
                   vv
clus                STAGE IVA
  OSGEPL1 MUTATED           0
  OSGEPL1 WILD-TYPE         4
D667V3, multiclass
            clus
vv           OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  OSGEPL1 MUTATED       0   1   2   1
  OSGEPL1 WILD-TYPE    54 134 259 101
D667V4, multiclass
       clus
vv      OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  OSGEPL1 MUTATED     3   0   1   0
  OSGEPL1 WILD-TYPE 192 173  88  85
D667V5, multiclass
    clus
vv   OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  N0               3               192
  N1               0               173
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V6, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     4   0
  OSGEPL1 WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      4    0
  OSGEPL1 WILD-TYPE  478   38
   clus
vv  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D667V7, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     2   2
  OSGEPL1 WILD-TYPE 170 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      2    2
  OSGEPL1 WILD-TYPE  170  404
        clus
vv       OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  FEMALE               2               170
  MALE                 2               404
[1] 2 2
[1] FALSE
D667V8, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     3   0
  OSGEPL1 WILD-TYPE 413 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      3    0
  OSGEPL1 WILD-TYPE  413  102
     clus
vv    OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  NO                3               413
  YES               0               102
[1] 2 2
[1] FALSE
D667V9, continuous
D667V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  OSGEPL1 MUTATED       1                         0
  OSGEPL1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSGEPL1 MUTATED                                           0     2
  OSGEPL1 WILD-TYPE                                         1   355
D667V11, multiclass
                                           clus
vv                                          OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V12, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     0   2
  OSGEPL1 WILD-TYPE  10 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      0    2
  OSGEPL1 WILD-TYPE   10  396
                        clus
vv                       OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               2               396
[1] 2 2
[1] FALSE

Clustering(668) Variable = TSSK2 MUTATION ANALYSIS
D668V1, survival
                 sevent
clus2               0   1
  TSSK2 MUTATED     5   4
  TSSK2 WILD-TYPE 333 212
  TSSK2 MUTATED TSSK2 WILD-TYPE 
              9             545 
  TSSK2 MUTATED TSSK2 WILD-TYPE 
              4             212 
$`TSSK2 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OW TCGA-BR-4256 TCGA-CD-A4MI TCGA-CG-4306 TCGA-HU-A4G8 
       19.99         7.13         9.34        11.77         1.02        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-MX-A5UJ 
       24.20         6.58        19.73 

$`TSSK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        24.26         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TSSK2 MUTATED TSSK2 WILD-TYPE 
           1.02            0.00 
  TSSK2 MUTATED TSSK2 WILD-TYPE 
           24.2           122.3 
  TSSK2 MUTATED TSSK2 WILD-TYPE 
          11.77           13.58 
[1] "1.0 - 24.2 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D668V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TSSK2 MUTATED         0        1        0        0         0         3
  TSSK2 WILD-TYPE      10       19       46       31        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSSK2 MUTATED           0          3          0          1        1         0
  TSSK2 WILD-TYPE        29         81         62         38       42         4
D668V3, multiclass
            clus
vv           TSSK2 MUTATED TSSK2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TSSK2 MUTATED       1   1   6   1
  TSSK2 WILD-TYPE    53 134 255 101
D668V4, multiclass
       clus
vv      TSSK2 MUTATED TSSK2 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TSSK2 MUTATED     2   5   2   1
  TSSK2 WILD-TYPE 193 168  87  84
D668V5, multiclass
    clus
vv   TSSK2 MUTATED TSSK2 WILD-TYPE
  N0             2             193
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V6, binary
                 cls
clus                0   1
  TSSK2 MUTATED     8   1
  TSSK2 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSSK2 MUTATED      8    1
  TSSK2 WILD-TYPE  474   37
   clus
vv  TSSK2 MUTATED TSSK2 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D668V7, binary
                 cls
clus                0   1
  TSSK2 MUTATED     5   5
  TSSK2 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSSK2 MUTATED      5    5
  TSSK2 WILD-TYPE  167  401
        clus
vv       TSSK2 MUTATED TSSK2 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D668V8, binary
                 cls
clus                0   1
  TSSK2 MUTATED     8   0
  TSSK2 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSSK2 MUTATED      8    0
  TSSK2 WILD-TYPE  408  102
     clus
vv    TSSK2 MUTATED TSSK2 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D668V9, continuous
D668V10, continuous
[1] "Remove cluster labels:" "TSSK2 MUTATED"         
clus
  TSSK2 MUTATED TSSK2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX      TCGA-L5-A88S 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" "TSSK2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TSSK2 MUTATED       4                         0
  TSSK2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TSSK2 MUTATED                                           0     4
  TSSK2 WILD-TYPE                                         1   353
D668V11, multiclass
                                           clus
vv                                          TSSK2 MUTATED TSSK2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V12, binary
                 cls
clus                0   1
  TSSK2 MUTATED     0   7
  TSSK2 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSSK2 MUTATED      0    7
  TSSK2 WILD-TYPE   10  391
                        clus
vv                       TSSK2 MUTATED TSSK2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(669) Variable = DNAJC1 MUTATION ANALYSIS
D669V1, survival
                  sevent
clus2                0   1
  DNAJC1 MUTATED    10   3
  DNAJC1 WILD-TYPE 328 213
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              13              541 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
               3              213 
$`DNAJC1 MUTATED`
TCGA-JY-A6FG TCGA-LN-A49R TCGA-R6-A6XG TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8487 
       41.52        13.38        38.40        34.68        44.94         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4G8 
       28.14        31.96        11.77         6.02        14.47        22.68 
TCGA-HU-A4GQ 
        0.10 

$`DNAJC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
             0.1              0.0 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
           44.94           122.30 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
           22.68            13.51 
[1] "0.1 - 44.9 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D669V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJC1 MUTATED         0        0        1        0         3         1
  DNAJC1 WILD-TYPE      10       20       45       31        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC1 MUTATED           2          2          0          2        2
  DNAJC1 WILD-TYPE        27         82         62         37       41
                  vv
clus               STAGE IVA
  DNAJC1 MUTATED           0
  DNAJC1 WILD-TYPE         4
D669V3, multiclass
            clus
vv           DNAJC1 MUTATED DNAJC1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DNAJC1 MUTATED       0   1   7   5
  DNAJC1 WILD-TYPE    54 134 254  97
D669V4, multiclass
       clus
vv      DNAJC1 MUTATED DNAJC1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 7              254
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DNAJC1 MUTATED     5   5   2   1
  DNAJC1 WILD-TYPE 190 168  87  84
D669V5, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  N0              5              190
  N1              5              168
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V6, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED    12   1
  DNAJC1 WILD-TYPE 470  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED     12    1
  DNAJC1 WILD-TYPE  470   37
   clus
vv  DNAJC1 MUTATED DNAJC1 WILD-TYPE
  0             12              470
  1              1               37
[1] 2 2
[1] FALSE
D669V7, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     5   9
  DNAJC1 WILD-TYPE 167 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      5    9
  DNAJC1 WILD-TYPE  167  397
        clus
vv       DNAJC1 MUTATED DNAJC1 WILD-TYPE
  FEMALE              5              167
  MALE                9              397
[1] 2 2
[1] FALSE
D669V8, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED    12   1
  DNAJC1 WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED     12    1
  DNAJC1 WILD-TYPE  404  101
     clus
vv    DNAJC1 MUTATED DNAJC1 WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D669V9, continuous
[1] "Remove cluster labels:" "DNAJC1 MUTATED"        
clus
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
D669V10, continuous
[1] "Remove cluster labels:" "DNAJC1 MUTATED"        
clus
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" "DNAJC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DNAJC1 MUTATED       5                         0
  DNAJC1 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJC1 MUTATED                                           0     8
  DNAJC1 WILD-TYPE                                         1   349
D669V11, multiclass
                                           clus
vv                                          DNAJC1 MUTATED DNAJC1 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V12, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     0  12
  DNAJC1 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      0   12
  DNAJC1 WILD-TYPE   10  386
                        clus
vv                       DNAJC1 MUTATED DNAJC1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(670) Variable = KPNA3 MUTATION ANALYSIS
D670V1, survival
                 sevent
clus2               0   1
  KPNA3 MUTATED     4   5
  KPNA3 WILD-TYPE 334 211
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              9             545 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              5             211 
$`KPNA3 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A8NS TCGA-LN-A4MR TCGA-BR-4184 TCGA-BR-4257 
       19.99        21.99        13.41        13.22         6.97         9.67 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-A4QL 
        6.61        34.68        16.14 

$`KPNA3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KPNA3 MUTATED KPNA3 WILD-TYPE 
           6.61            0.00 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
          34.68          122.30 
  KPNA3 MUTATED KPNA3 WILD-TYPE 
          13.41           13.58 
[1] "6.6 - 34.7 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D670V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KPNA3 MUTATED         0        0        0        0         3         1
  KPNA3 WILD-TYPE      10       20       46       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNA3 MUTATED           1          1          1          1        1         0
  KPNA3 WILD-TYPE        28         83         61         38       42         4
D670V3, multiclass
            clus
vv           KPNA3 MUTATED KPNA3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KPNA3 MUTATED       0   2   6   1
  KPNA3 WILD-TYPE    54 133 255 101
D670V4, multiclass
       clus
vv      KPNA3 MUTATED KPNA3 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KPNA3 MUTATED     4   3   0   2
  KPNA3 WILD-TYPE 191 170  89  83
D670V5, multiclass
    clus
vv   KPNA3 MUTATED KPNA3 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V6, binary
                 cls
clus                0   1
  KPNA3 MUTATED     7   1
  KPNA3 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      7    1
  KPNA3 WILD-TYPE  475   37
   clus
vv  KPNA3 MUTATED KPNA3 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D670V7, binary
                 cls
clus                0   1
  KPNA3 MUTATED     5   5
  KPNA3 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      5    5
  KPNA3 WILD-TYPE  167  401
        clus
vv       KPNA3 MUTATED KPNA3 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D670V8, binary
                 cls
clus                0   1
  KPNA3 MUTATED     8   1
  KPNA3 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      8    1
  KPNA3 WILD-TYPE  408  101
     clus
vv    KPNA3 MUTATED KPNA3 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D670V9, continuous
[1] "Remove cluster labels:" "KPNA3 MUTATED"         
clus
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
D670V10, continuous
[1] "Remove cluster labels:" "KPNA3 MUTATED"         
clus
  KPNA3 MUTATED KPNA3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" "KPNA3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KPNA3 MUTATED       1                         0
  KPNA3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KPNA3 MUTATED                                           0     8
  KPNA3 WILD-TYPE                                         1   349
D670V11, multiclass
                                           clus
vv                                          KPNA3 MUTATED KPNA3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V12, binary
                 cls
clus                0   1
  KPNA3 MUTATED     0   7
  KPNA3 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA3 MUTATED      0    7
  KPNA3 WILD-TYPE   10  391
                        clus
vv                       KPNA3 MUTATED KPNA3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(671) Variable = RRH MUTATION ANALYSIS
D671V1, survival
               sevent
clus2             0   1
  RRH MUTATED     2   2
  RRH WILD-TYPE 336 214
  RRH MUTATED RRH WILD-TYPE 
            4           550 
  RRH MUTATED RRH WILD-TYPE 
            2           214 
$`RRH MUTATED`
TCGA-L5-A43I TCGA-IC-A6RE TCGA-BR-4279 TCGA-HU-8602 
       18.28         7.69         9.57        22.32 

$`RRH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RRH MUTATED RRH WILD-TYPE 
         7.69          0.00 
  RRH MUTATED RRH WILD-TYPE 
        22.32        122.30 
  RRH MUTATED RRH WILD-TYPE 
       13.925        13.565 
[1] "7.7 - 22.3 (13.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D671V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRH MUTATED         0        0        0        1         0         3
  RRH WILD-TYPE      10       20       46       30        84        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRH MUTATED           0          1          0          0        0         0
  RRH WILD-TYPE        29         83         62         39       43         4
D671V3, multiclass
            clus
vv           RRH MUTATED RRH WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             1            30
  STAGE IIA            0            84
  STAGE IIB            3            80
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           0            62
  STAGE IIIC           0            39
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  RRH MUTATED       1   1   1   2
  RRH WILD-TYPE    53 134 260 100
D671V4, multiclass
       clus
vv      RRH MUTATED RRH WILD-TYPE
  T0+T1           1            53
  T2              1           134
  T3              1           260
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  RRH MUTATED     2   3   0   0
  RRH WILD-TYPE 193 170  89  85
D671V5, multiclass
    clus
vv   RRH MUTATED RRH WILD-TYPE
  N0           2           193
  N1           3           170
  N2           0            89
  N3           0            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V6, binary
               cls
clus              0   1
  RRH MUTATED     4   0
  RRH WILD-TYPE 478  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  RRH MUTATED      4    0
  RRH WILD-TYPE  478   38
   clus
vv  RRH MUTATED RRH WILD-TYPE
  0           4           478
  1           0            38
[1] 2 2
[1] FALSE
D671V7, binary
               cls
clus              0   1
  RRH MUTATED     1   4
  RRH WILD-TYPE 171 402
[1] "tbl2"
               cls
clus            [,1] [,2]
  RRH MUTATED      1    4
  RRH WILD-TYPE  171  402
        clus
vv       RRH MUTATED RRH WILD-TYPE
  FEMALE           1           171
  MALE             4           402
[1] 2 2
[1] FALSE
D671V8, binary
               cls
clus              0   1
  RRH MUTATED     4   1
  RRH WILD-TYPE 412 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  RRH MUTATED      4    1
  RRH WILD-TYPE  412  101
     clus
vv    RRH MUTATED RRH WILD-TYPE
  NO            4           412
  YES           1           101
[1] 2 2
[1] FALSE
D671V9, continuous
D671V10, continuous
[1] "Remove cluster labels:" "RRH MUTATED"           
clus
  RRH MUTATED RRH WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG    TCGA-L5-A4OI 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC    TCGA-IG-A4P3 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS    TCGA-IG-A8O2 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG    TCGA-JY-A6FH 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H    TCGA-L5-A4OH 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP    TCGA-L5-A4OQ 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX    TCGA-L5-A88S 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF    TCGA-L5-A8NK 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS    TCGA-L5-A8NW 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6    TCGA-LN-A4A9 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8    TCGA-Q9-A6FW 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" "RRH WILD-TYPE" 
   TCGA-Z6-AAPN 
"RRH WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  RRH MUTATED       1                         0
  RRH WILD-TYPE   132                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRH MUTATED                                           0     4
  RRH WILD-TYPE                                         1   353
D671V11, multiclass
                                           clus
vv                                          RRH MUTATED RRH WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V12, binary
               cls
clus              0   1
  RRH MUTATED     0   4
  RRH WILD-TYPE  10 394
[1] "tbl2"
               cls
clus            [,1] [,2]
  RRH MUTATED      0    4
  RRH WILD-TYPE   10  394
                        clus
vv                       RRH MUTATED RRH WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           4           394
[1] 2 2
[1] FALSE

Clustering(672) Variable = SRP14 MUTATION ANALYSIS
D672V1, survival
                 sevent
clus2               0   1
  SRP14 MUTATED     1   2
  SRP14 WILD-TYPE 337 214
  SRP14 MUTATED SRP14 WILD-TYPE 
              3             551 
  SRP14 MUTATED SRP14 WILD-TYPE 
              2             214 
$`SRP14 MUTATED`
TCGA-L5-A43J TCGA-BR-8487 TCGA-HU-A4GQ 
        4.31         1.12         0.10 

$`SRP14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SRP14 MUTATED SRP14 WILD-TYPE 
            0.1             0.0 
  SRP14 MUTATED SRP14 WILD-TYPE 
           4.31          122.30 
  SRP14 MUTATED SRP14 WILD-TYPE 
           1.12           13.68 
[1] "0.1 - 4.3 (1.1)"    "0.0 - 122.3 (13.7)"
[1] "hr=" "23" 
D672V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRP14 MUTATED         0        0        0        0         1         1
  SRP14 WILD-TYPE      10       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRP14 MUTATED           0          0          0          1        0         0
  SRP14 WILD-TYPE        29         84         62         38       43         4
D672V3, multiclass
            clus
vv           SRP14 MUTATED SRP14 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SRP14 MUTATED       0   0   2   1
  SRP14 WILD-TYPE    54 135 259 101
D672V4, multiclass
       clus
vv      SRP14 MUTATED SRP14 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SRP14 MUTATED     2   0   1   0
  SRP14 WILD-TYPE 193 173  88  85
D672V5, multiclass
    clus
vv   SRP14 MUTATED SRP14 WILD-TYPE
  N0             2             193
  N1             0             173
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V6, binary
                 cls
clus                0   1
  SRP14 MUTATED     2   0
  SRP14 WILD-TYPE 480  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      2    0
  SRP14 WILD-TYPE  480   38
   clus
vv  SRP14 MUTATED SRP14 WILD-TYPE
  0             2             480
  1             0              38
[1] 2 2
[1] FALSE
D672V7, binary
                 cls
clus                0   1
  SRP14 MUTATED     1   2
  SRP14 WILD-TYPE 171 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      1    2
  SRP14 WILD-TYPE  171  404
        clus
vv       SRP14 MUTATED SRP14 WILD-TYPE
  FEMALE             1             171
  MALE               2             404
[1] 2 2
[1] FALSE
D672V8, binary
                 cls
clus                0   1
  SRP14 MUTATED     2   0
  SRP14 WILD-TYPE 414 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      2    0
  SRP14 WILD-TYPE  414  102
     clus
vv    SRP14 MUTATED SRP14 WILD-TYPE
  NO              2             414
  YES             0             102
[1] 2 2
[1] FALSE
D672V9, continuous
D672V10, continuous
[1] "Remove cluster labels:" "SRP14 MUTATED"         
clus
  SRP14 MUTATED SRP14 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SRP14 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SRP14 MUTATED       1                         0
  SRP14 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRP14 MUTATED                                           0     2
  SRP14 WILD-TYPE                                         1   355
D672V11, multiclass
                                           clus
vv                                          SRP14 MUTATED SRP14 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V12, binary
                 cls
clus                0   1
  SRP14 MUTATED     0   2
  SRP14 WILD-TYPE  10 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      0    2
  SRP14 WILD-TYPE   10  396
                        clus
vv                       SRP14 MUTATED SRP14 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             2             396
[1] 2 2
[1] FALSE

Clustering(673) Variable = PDE8A MUTATION ANALYSIS
D673V1, survival
                 sevent
clus2               0   1
  PDE8A MUTATED     9   3
  PDE8A WILD-TYPE 329 213
  PDE8A MUTATED PDE8A WILD-TYPE 
             12             542 
  PDE8A MUTATED PDE8A WILD-TYPE 
              3             213 
$`PDE8A MUTATED`
TCGA-L5-A4OJ TCGA-LN-A5U6 TCGA-VR-AA4G TCGA-BR-7707 TCGA-BR-8589 TCGA-BR-8591 
       21.01        12.33        18.05        35.84        27.12        28.14 
TCGA-CG-4440 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6818 TCGA-D7-A6EY TCGA-VQ-A8P2 
        4.01         6.02       105.07        12.36        11.44        38.14 

$`PDE8A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PDE8A MUTATED PDE8A WILD-TYPE 
           4.01            0.00 
  PDE8A MUTATED PDE8A WILD-TYPE 
         105.07          122.30 
  PDE8A MUTATED PDE8A WILD-TYPE 
          19.53           13.53 
[1] "4.0 - 105.1 (19.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D673V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDE8A MUTATED         1        0        1        1         0         1
  PDE8A WILD-TYPE       9       20       45       30        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDE8A MUTATED           0          4          2          1        2         0
  PDE8A WILD-TYPE        29         80         60         38       41         4
D673V3, multiclass
            clus
vv           PDE8A MUTATED PDE8A WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PDE8A MUTATED       2   5   2   5
  PDE8A WILD-TYPE    52 130 259  97
D673V4, multiclass
       clus
vv      PDE8A MUTATED PDE8A WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3                2             259
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PDE8A MUTATED     3   5   1   4
  PDE8A WILD-TYPE 192 168  88  81
D673V5, multiclass
    clus
vv   PDE8A MUTATED PDE8A WILD-TYPE
  N0             3             192
  N1             5             168
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V6, binary
                 cls
clus                0   1
  PDE8A MUTATED    13   1
  PDE8A WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED     13    1
  PDE8A WILD-TYPE  469   37
   clus
vv  PDE8A MUTATED PDE8A WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D673V7, binary
                 cls
clus                0   1
  PDE8A MUTATED     7   7
  PDE8A WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      7    7
  PDE8A WILD-TYPE  165  399
        clus
vv       PDE8A MUTATED PDE8A WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D673V8, binary
                 cls
clus                0   1
  PDE8A MUTATED     8   3
  PDE8A WILD-TYPE 408  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      8    3
  PDE8A WILD-TYPE  408   99
     clus
vv    PDE8A MUTATED PDE8A WILD-TYPE
  NO              8             408
  YES             3              99
[1] 2 2
[1] FALSE
D673V9, continuous
[1] "Remove cluster labels:" "PDE8A MUTATED"         
clus
  PDE8A MUTATED PDE8A WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B      TCGA-VR-AA7D 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
D673V10, continuous
[1] "Remove cluster labels:" "PDE8A MUTATED"         
clus
  PDE8A MUTATED PDE8A WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" "PDE8A WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDE8A MUTATED       1                         0
  PDE8A WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDE8A MUTATED                                           0    10
  PDE8A WILD-TYPE                                         1   347
D673V11, multiclass
                                           clus
vv                                          PDE8A MUTATED PDE8A WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V12, binary
                 cls
clus                0   1
  PDE8A MUTATED     0   8
  PDE8A WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE8A MUTATED      0    8
  PDE8A WILD-TYPE   10  390
                        clus
vv                       PDE8A MUTATED PDE8A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(674) Variable = ARPC5L MUTATION ANALYSIS
D674V1, survival
                  sevent
clus2                0   1
  ARPC5L MUTATED     1   1
  ARPC5L WILD-TYPE 337 215
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              552 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               1              215 
$`ARPC5L MUTATED`
TCGA-BR-8078 TCGA-R5-A804 
       29.59         4.60 

$`ARPC5L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         6.08         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ARPC5L MUTATED ARPC5L WILD-TYPE 
             4.6              0.0 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
           29.59           122.30 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
          17.095           13.565 
[1] "4.6 - 29.6 (17.1)"  "0.0 - 122.3 (13.6)"
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
D674V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARPC5L MUTATED         0        0        0        0         0         1
  ARPC5L WILD-TYPE      10       20       46       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARPC5L MUTATED           0          0          0          0        1
  ARPC5L WILD-TYPE        29         84         62         39       42
                  vv
clus               STAGE IVA
  ARPC5L MUTATED           0
  ARPC5L WILD-TYPE         4
D674V3, multiclass
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              533 
      TCGA-IC-A6RF       TCGA-JY-A6FB       TCGA-JY-A938       TCGA-L5-A43I 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A43J       TCGA-L5-A4OE       TCGA-L5-A4OG       TCGA-L5-A4OI 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A88T       TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-S8-A6BV       TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4476       TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-F1-6177       TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-MX-A663       TCGA-2H-A9GF       TCGA-2H-A9GG       TCGA-2H-A9GH 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GI       TCGA-2H-A9GJ       TCGA-2H-A9GK       TCGA-2H-A9GL 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GM       TCGA-2H-A9GN       TCGA-2H-A9GO       TCGA-2H-A9GQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GR       TCGA-IC-A6RE       TCGA-IG-A3I8       TCGA-IG-A3QL 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YB       TCGA-IG-A3YC 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QS       TCGA-IG-A4QT       TCGA-IG-A50L 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A51D       TCGA-IG-A5B8       TCGA-IG-A5S3       TCGA-IG-A625 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A7DP       TCGA-IG-A8O2       TCGA-IG-A97H 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A97I       TCGA-JY-A6F8       TCGA-JY-A6FA       TCGA-JY-A6FD 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-JY-A939 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-JY-A93C       TCGA-JY-A93D       TCGA-JY-A93E       TCGA-JY-A93F 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OH       TCGA-L5-A4OJ       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OS       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A88W 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A88Z       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NH       TCGA-L5-A8NI       TCGA-L5-A8NJ       TCGA-L5-A8NK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NL       TCGA-L5-A8NM       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NU       TCGA-L5-A8NV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NW       TCGA-L7-A6VZ       TCGA-LN-A49K       TCGA-LN-A49L 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-LN-A8I1 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A9FO       TCGA-LN-A9FP       TCGA-LN-A9FQ       TCGA-LN-A9FR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A8W5       TCGA-RE-A7BO 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-S8-A6BW       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-VR-A8EO 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-Z6-A9VB       TCGA-Z6-AAPN       TCGA-ZR-A9CJ       TCGA-B7-5816 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-5818       TCGA-B7-A5TI       TCGA-B7-A5TJ       TCGA-B7-A5TK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-A5TN       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4253 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4361       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5803       TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6520 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV       TCGA-D7-A6EX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0       TCGA-D7-A6F2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A       TCGA-D7-A74B 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874       TCGA-F1-6875 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735       TCGA-FP-7829 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-HF-7132       TCGA-HF-7133       TCGA-HF-7134 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597       TCGA-HU-8243 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-7806       TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RJ       TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RP       TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A7NT       TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IP-7968       TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-MX-A666       TCGA-R5-A7O7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT       TCGA-RD-A7BW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW       TCGA-RD-A8N0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4       TCGA-RD-A8N5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA       TCGA-SW-A7EB 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU       TCGA-VQ-A8DV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U       TCGA-VQ-A91V 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64       TCGA-VQ-AA68 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B       TCGA-VQ-AA6F 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J       TCGA-VQ-AA6K 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" 
                  vv
clus               T0+T1  T2  T3  T4
  ARPC5L MUTATED       1   0   1   1
  ARPC5L WILD-TYPE    53 135 260 101
D674V4, multiclass
       clus
vv      ARPC5L MUTATED ARPC5L WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 1              260
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARPC5L MUTATED     1   0   1   0
  ARPC5L WILD-TYPE 194 173  88  85
D674V5, multiclass
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              540 
      TCGA-IC-A6RF       TCGA-JY-A6FB       TCGA-JY-A938       TCGA-L5-A43I 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A43J       TCGA-L5-A43M       TCGA-L5-A4OE       TCGA-L5-A4OG 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-S8-A6BV       TCGA-CG-4444 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476       TCGA-CG-5716 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663       TCGA-2H-A9GF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GG       TCGA-2H-A9GH       TCGA-2H-A9GI       TCGA-2H-A9GJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GK       TCGA-2H-A9GL       TCGA-2H-A9GM       TCGA-2H-A9GN 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-2H-A9GO       TCGA-2H-A9GQ       TCGA-2H-A9GR       TCGA-IC-A6RE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A4P3       TCGA-IG-A4QS 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A51D       TCGA-IG-A5B8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A5S3       TCGA-IG-A625       TCGA-IG-A6QS       TCGA-IG-A8O2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IG-A97I       TCGA-JY-A6F8       TCGA-JY-A6FA       TCGA-JY-A6FD 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-JY-A939 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-JY-A93C       TCGA-JY-A93D       TCGA-JY-A93E       TCGA-JY-A93F 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OH       TCGA-L5-A4OJ       TCGA-L5-A4OM       TCGA-L5-A4ON 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OS       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A88W 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A88Z       TCGA-L5-A891       TCGA-L5-A893       TCGA-L5-A8NE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NH       TCGA-L5-A8NI       TCGA-L5-A8NJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NL       TCGA-L5-A8NM       TCGA-L5-A8NN 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-L5-A8NV       TCGA-L5-A8NW       TCGA-L7-A6VZ       TCGA-LN-A49K 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49L       TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A8I1       TCGA-LN-A9FO       TCGA-LN-A9FP       TCGA-LN-A9FQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-LN-A9FR       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A8W5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RE-A7BO       TCGA-S8-A6BW       TCGA-V5-A7RB       TCGA-V5-A7RE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE       TCGA-Z6-A9VB 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-Z6-AAPN       TCGA-ZR-A9CJ       TCGA-B7-5816       TCGA-B7-5818 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-A5TI       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-FP-A9TM 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7132       TCGA-HF-7133       TCGA-HF-7134       TCGA-HF-7136 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-A5NB       TCGA-HJ-7597       TCGA-HU-8238       TCGA-HU-8243 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462       TCGA-IN-8663 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL       TCGA-IN-A6RN 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR       TCGA-IN-A6RS 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU       TCGA-IN-AB1V 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A6F5       TCGA-KB-A6F7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KB-A93J       TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-R5-A7O7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A805 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7BS       TCGA-RD-A7BT       TCGA-RD-A7BW       TCGA-RD-A7C1 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8MV       TCGA-RD-A8MW       TCGA-RD-A8N0       TCGA-RD-A8N1 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N2       TCGA-RD-A8N4       TCGA-RD-A8N5       TCGA-RD-A8N6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N9       TCGA-SW-A7EA       TCGA-SW-A7EB       TCGA-VQ-A8DL 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DT       TCGA-VQ-A8DU       TCGA-VQ-A8DV       TCGA-VQ-A8DZ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2       TCGA-VQ-A8P3 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM       TCGA-VQ-A8PQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A91Q       TCGA-VQ-A91U       TCGA-VQ-A91V       TCGA-VQ-A92D 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A94T       TCGA-VQ-AA64       TCGA-VQ-AA68       TCGA-VQ-AA69 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6A       TCGA-VQ-AA6B       TCGA-VQ-AA6F       TCGA-VQ-AA6G 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6I       TCGA-VQ-AA6J       TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
D674V6, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   1
  ARPC5L WILD-TYPE 480  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    1
  ARPC5L WILD-TYPE  480   37
   clus
vv  ARPC5L MUTATED ARPC5L WILD-TYPE
  0              2              480
  1              1               37
[1] 2 2
[1] FALSE
D674V7, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   1
  ARPC5L WILD-TYPE 170 405
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    1
  ARPC5L WILD-TYPE  170  405
        clus
vv       ARPC5L MUTATED ARPC5L WILD-TYPE
  FEMALE              2              170
  MALE                1              405
[1] 2 2
[1] FALSE
D674V8, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   0
  ARPC5L WILD-TYPE 414 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    0
  ARPC5L WILD-TYPE  414  102
     clus
vv    ARPC5L MUTATED ARPC5L WILD-TYPE
  NO               2              414
  YES              0              102
[1] 2 2
[1] FALSE
D674V9, continuous
D674V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARPC5L MUTATED       0                         1
  ARPC5L WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARPC5L MUTATED                                           0     2
  ARPC5L WILD-TYPE                                         1   355
D674V11, multiclass
                                           clus
vv                                          ARPC5L MUTATED ARPC5L WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V12, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     0   3
  ARPC5L WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      0    3
  ARPC5L WILD-TYPE   10  395
                        clus
vv                       ARPC5L MUTATED ARPC5L WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(675) Variable = UPK2 MUTATION ANALYSIS
D675V1, survival
                sevent
clus2              0   1
  UPK2 MUTATED     2   3
  UPK2 WILD-TYPE 336 213
  UPK2 MUTATED UPK2 WILD-TYPE 
             5            549 
  UPK2 MUTATED UPK2 WILD-TYPE 
             3            213 
$`UPK2 MUTATED`
TCGA-R6-A8WG TCGA-BR-8081 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-4465 
       12.69        32.25         6.18         6.58         9.01 

$`UPK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  UPK2 MUTATED UPK2 WILD-TYPE 
          6.18           0.00 
  UPK2 MUTATED UPK2 WILD-TYPE 
         32.25         122.30 
  UPK2 MUTATED UPK2 WILD-TYPE 
          9.01          13.68 
[1] "6.2 - 32.2 (9.0)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "2.1"
D675V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UPK2 MUTATED         0        0        0        0         2         1
  UPK2 WILD-TYPE      10       20       46       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UPK2 MUTATED           0          0          0          0        1         0
  UPK2 WILD-TYPE        29         84         62         39       42         4
D675V3, multiclass
            clus
vv           UPK2 MUTATED UPK2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  UPK2 MUTATED       0   0   2   2
  UPK2 WILD-TYPE    54 135 259 100
D675V4, multiclass
       clus
vv      UPK2 MUTATED UPK2 WILD-TYPE
  T0+T1            0             54
  T2               0            135
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  UPK2 MUTATED     3   0   0   1
  UPK2 WILD-TYPE 192 173  89  84
D675V5, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  N0            3            192
  N1            0            173
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V6, binary
                cls
clus               0   1
  UPK2 MUTATED     3   1
  UPK2 WILD-TYPE 479  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      3    1
  UPK2 WILD-TYPE  479   37
   clus
vv  UPK2 MUTATED UPK2 WILD-TYPE
  0            3            479
  1            1             37
[1] 2 2
[1] FALSE
D675V7, binary
                cls
clus               0   1
  UPK2 MUTATED     2   3
  UPK2 WILD-TYPE 170 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      2    3
  UPK2 WILD-TYPE  170  403
        clus
vv       UPK2 MUTATED UPK2 WILD-TYPE
  FEMALE            2            170
  MALE              3            403
[1] 2 2
[1] FALSE
D675V8, binary
                cls
clus               0   1
  UPK2 MUTATED     4   0
  UPK2 WILD-TYPE 412 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      4    0
  UPK2 WILD-TYPE  412  102
     clus
vv    UPK2 MUTATED UPK2 WILD-TYPE
  NO             4            412
  YES            0            102
[1] 2 2
[1] FALSE
D675V9, continuous
D675V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UPK2 MUTATED       1                         0
  UPK2 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UPK2 MUTATED                                           0     3
  UPK2 WILD-TYPE                                         1   354
D675V11, multiclass
                                           clus
vv                                          UPK2 MUTATED UPK2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V12, binary
                cls
clus               0   1
  UPK2 MUTATED     1   3
  UPK2 WILD-TYPE   9 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      1    3
  UPK2 WILD-TYPE    9  395
                        clus
vv                       UPK2 MUTATED UPK2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(676) Variable = NEUROD6 MUTATION ANALYSIS
D676V1, survival
                   sevent
clus2                 0   1
  NEUROD6 MUTATED     4   3
  NEUROD6 WILD-TYPE 334 213
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                7               547 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                3               213 
$`NEUROD6 MUTATED`
TCGA-IG-A3YA TCGA-BR-4184 TCGA-BR-6566 TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-A4GD 
       20.78         6.97        32.78        15.95         1.02        22.75 
TCGA-HU-A4GQ 
        0.10 

$`NEUROD6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       11.77        12.62        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
              0.1               0.0 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
            32.78            122.30 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
            15.95             13.55 
[1] "0.1 - 32.8 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D676V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEUROD6 MUTATED         0        0        0        1         1         1
  NEUROD6 WILD-TYPE      10       20       46       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEUROD6 MUTATED           0          2          0          1        1
  NEUROD6 WILD-TYPE        29         82         62         38       42
                   vv
clus                STAGE IVA
  NEUROD6 MUTATED           0
  NEUROD6 WILD-TYPE         4
D676V3, multiclass
            clus
vv           NEUROD6 MUTATED NEUROD6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  NEUROD6 MUTATED       0   1   4   2
  NEUROD6 WILD-TYPE    54 134 257 100
D676V4, multiclass
       clus
vv      NEUROD6 MUTATED NEUROD6 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  NEUROD6 MUTATED     2   3   2   0
  NEUROD6 WILD-TYPE 193 170  87  85
D676V5, multiclass
    clus
vv   NEUROD6 MUTATED NEUROD6 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V6, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     5   1
  NEUROD6 WILD-TYPE 477  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      5    1
  NEUROD6 WILD-TYPE  477   37
   clus
vv  NEUROD6 MUTATED NEUROD6 WILD-TYPE
  0               5               477
  1               1                37
[1] 2 2
[1] FALSE
D676V7, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     1   6
  NEUROD6 WILD-TYPE 171 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      1    6
  NEUROD6 WILD-TYPE  171  400
        clus
vv       NEUROD6 MUTATED NEUROD6 WILD-TYPE
  FEMALE               1               171
  MALE                 6               400
[1] 2 2
[1] FALSE
D676V8, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     6   0
  NEUROD6 WILD-TYPE 410 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      6    0
  NEUROD6 WILD-TYPE  410  102
     clus
vv    NEUROD6 MUTATED NEUROD6 WILD-TYPE
  NO                6               410
  YES               0               102
[1] 2 2
[1] FALSE
D676V9, continuous
[1] "Remove cluster labels:" "NEUROD6 MUTATED"       
clus
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YB 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
D676V10, continuous
[1] "Remove cluster labels:" "NEUROD6 MUTATED"       
clus
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YC        TCGA-IG-A4P3 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" "NEUROD6 WILD-TYPE" 
       TCGA-Z6-AAPN 
"NEUROD6 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  NEUROD6 MUTATED       2                         0
  NEUROD6 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEUROD6 MUTATED                                           0     3
  NEUROD6 WILD-TYPE                                         1   354
D676V11, multiclass
                                           clus
vv                                          NEUROD6 MUTATED NEUROD6 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V12, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     0   5
  NEUROD6 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      0    5
  NEUROD6 WILD-TYPE   10  393
                        clus
vv                       NEUROD6 MUTATED NEUROD6 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(677) Variable = KIF20B MUTATION ANALYSIS
D677V1, survival
                  sevent
clus2                0   1
  KIF20B MUTATED    12   7
  KIF20B WILD-TYPE 326 209
  KIF20B MUTATED KIF20B WILD-TYPE 
              19              535 
  KIF20B MUTATED KIF20B WILD-TYPE 
               7              209 
$`KIF20B MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-S8-A6BV TCGA-2H-A9GH TCGA-IG-A5B8 TCGA-KH-A6WC 
        4.31        19.99        20.02        31.27         0.79         6.28 
TCGA-L5-A88W TCGA-L5-A8NK TCGA-LN-A4A6 TCGA-B7-A5TJ TCGA-BR-4201 TCGA-BR-8078 
       25.12        13.55        12.85        11.01        30.90        29.59 
TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-5728 TCGA-F1-A448 TCGA-VQ-A8PE 
       31.96        12.43        12.62        65.10        21.27        22.19 
TCGA-VQ-AA64 
       18.41 

$`KIF20B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15         9.86        25.78        20.05        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        22.39        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIF20B MUTATED KIF20B WILD-TYPE 
            0.79             0.00 
  KIF20B MUTATED KIF20B WILD-TYPE 
            65.1            122.3 
  KIF20B MUTATED KIF20B WILD-TYPE 
           19.99            13.51 
[1] "0.8 - 65.1 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D677V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF20B MUTATED         1        1        3        2         2         4
  KIF20B WILD-TYPE       9       19       43       29        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF20B MUTATED           0          1          3          1        1
  KIF20B WILD-TYPE        29         83         59         38       42
                  vv
clus               STAGE IVA
  KIF20B MUTATED           0
  KIF20B WILD-TYPE         4
D677V3, multiclass
            clus
vv           KIF20B MUTATED KIF20B WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KIF20B MUTATED       4   4  11   3
  KIF20B WILD-TYPE    50 131 250  99
D677V4, multiclass
       clus
vv      KIF20B MUTATED KIF20B WILD-TYPE
  T0+T1              4               50
  T2                 4              131
  T3                11              250
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KIF20B MUTATED    10   3   2   3
  KIF20B WILD-TYPE 185 170  87  82
D677V5, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  N0             10              185
  N1              3              170
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V6, binary
                  cls
clus                 0   1
  KIF20B MUTATED    15   1
  KIF20B WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED     15    1
  KIF20B WILD-TYPE  467   37
   clus
vv  KIF20B MUTATED KIF20B WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D677V7, binary
                  cls
clus                 0   1
  KIF20B MUTATED     6  16
  KIF20B WILD-TYPE 166 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      6   16
  KIF20B WILD-TYPE  166  390
        clus
vv       KIF20B MUTATED KIF20B WILD-TYPE
  FEMALE              6              166
  MALE               16              390
[1] 2 2
[1] FALSE
D677V8, binary
                  cls
clus                 0   1
  KIF20B MUTATED    13   4
  KIF20B WILD-TYPE 403  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED     13    4
  KIF20B WILD-TYPE  403   98
     clus
vv    KIF20B MUTATED KIF20B WILD-TYPE
  NO              13              403
  YES              4               98
[1] 2 2
[1] FALSE
D677V9, continuous
[1] "Remove cluster labels:" "KIF20B MUTATED"        
clus
  KIF20B MUTATED KIF20B WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A8 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
D677V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF20B MUTATED       4                         1
  KIF20B WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF20B MUTATED                                           0    15
  KIF20B WILD-TYPE                                         1   342
D677V11, multiclass
                                           clus
vv                                          KIF20B MUTATED KIF20B WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V12, binary
                  cls
clus                 0   1
  KIF20B MUTATED     1  13
  KIF20B WILD-TYPE   9 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      1   13
  KIF20B WILD-TYPE    9  385
                        clus
vv                       KIF20B MUTATED KIF20B WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(678) Variable = NPHS1 MUTATION ANALYSIS
D678V1, survival
                 sevent
clus2               0   1
  NPHS1 MUTATED    12   9
  NPHS1 WILD-TYPE 326 207
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             21             533 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
              9             207 
$`NPHS1 MUTATED`
TCGA-2H-A9GK TCGA-JY-A6FG TCGA-L5-A8NN TCGA-R6-A6XG TCGA-VR-A8EX TCGA-BR-8080 
        7.63        41.52         5.49        38.40        28.11         9.60 
TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8534 
        4.31        11.80        16.14        12.30        11.64        12.07 
TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-8573 TCGA-D7-A6EY TCGA-FP-8209 TCGA-FP-A4BE 
       15.95         6.02        19.50        11.44        59.54        11.08 
TCGA-HU-A4GU TCGA-IN-A6RJ TCGA-VQ-A8P2 
        6.58        12.46        38.14 

$`NPHS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 
       12.53         7.17        12.33        12.39        12.59        15.39 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8210 TCGA-FP-8211 
       19.53        14.07        22.29        17.06         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NPHS1 MUTATED NPHS1 WILD-TYPE 
           4.31            0.00 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
          59.54          122.30 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
          12.07           13.78 
[1] "4.3 - 59.5 (12.1)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D678V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NPHS1 MUTATED         0        1        2        3         2         1
  NPHS1 WILD-TYPE      10       19       44       28        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NPHS1 MUTATED           3          1          3          1        2         1
  NPHS1 WILD-TYPE        26         83         59         38       41         3
D678V3, multiclass
            clus
vv           NPHS1 MUTATED NPHS1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              3              26
  STAGE IIIA             1              83
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NPHS1 MUTATED       2   3  11   4
  NPHS1 WILD-TYPE    52 132 250  98
D678V4, multiclass
       clus
vv      NPHS1 MUTATED NPHS1 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3               11             250
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NPHS1 MUTATED     8   8   0   4
  NPHS1 WILD-TYPE 187 165  89  81
D678V5, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  N0             8             187
  N1             8             165
  N2             0              89
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V6, binary
                 cls
clus                0   1
  NPHS1 MUTATED    18   2
  NPHS1 WILD-TYPE 464  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     18    2
  NPHS1 WILD-TYPE  464   36
   clus
vv  NPHS1 MUTATED NPHS1 WILD-TYPE
  0            18             464
  1             2              36
[1] 2 2
[1] FALSE
D678V7, binary
                 cls
clus                0   1
  NPHS1 MUTATED     4  17
  NPHS1 WILD-TYPE 168 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      4   17
  NPHS1 WILD-TYPE  168  389
        clus
vv       NPHS1 MUTATED NPHS1 WILD-TYPE
  FEMALE             4             168
  MALE              17             389
[1] 2 2
[1] FALSE
D678V8, binary
                 cls
clus                0   1
  NPHS1 MUTATED    17   4
  NPHS1 WILD-TYPE 399  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     17    4
  NPHS1 WILD-TYPE  399   98
     clus
vv    NPHS1 MUTATED NPHS1 WILD-TYPE
  NO             17             399
  YES             4              98
[1] 2 2
[1] FALSE
D678V9, continuous
[1] "Remove cluster labels:" "NPHS1 MUTATED"         
clus
  NPHS1 MUTATED NPHS1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" "NPHS1 WILD-TYPE" 
D678V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NPHS1 MUTATED       4                         1
  NPHS1 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPHS1 MUTATED                                           0    12
  NPHS1 WILD-TYPE                                         1   345
D678V11, multiclass
                                           clus
vv                                          NPHS1 MUTATED NPHS1 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V12, binary
                 cls
clus                0   1
  NPHS1 MUTATED     0  14
  NPHS1 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      0   14
  NPHS1 WILD-TYPE   10  384
                        clus
vv                       NPHS1 MUTATED NPHS1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(679) Variable = NUFIP2 MUTATION ANALYSIS
D679V1, survival
                  sevent
clus2                0   1
  NUFIP2 MUTATED     4   3
  NUFIP2 WILD-TYPE 334 213
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               7              547 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               3              213 
$`NUFIP2 MUTATED`
TCGA-BR-4257 TCGA-BR-8372 TCGA-D7-5578 TCGA-D7-8570 TCGA-D7-A4YV TCGA-HF-7132 
        9.67        31.27        12.66        24.72         5.92        77.29 
TCGA-HU-A4GQ 
        0.10 

$`NUFIP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
             0.1              0.0 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
           77.29           122.30 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
           12.66            13.58 
[1] "0.1 - 77.3 (12.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D679V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUFIP2 MUTATED         0        0        0        1         0         1
  NUFIP2 WILD-TYPE      10       20       46       30        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP2 MUTATED           0          1          1          2        0
  NUFIP2 WILD-TYPE        29         83         61         37       43
                  vv
clus               STAGE IVA
  NUFIP2 MUTATED           0
  NUFIP2 WILD-TYPE         4
D679V3, multiclass
            clus
vv           NUFIP2 MUTATED NUFIP2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NUFIP2 MUTATED       0   2   3   2
  NUFIP2 WILD-TYPE    54 133 258 100
D679V4, multiclass
       clus
vv      NUFIP2 MUTATED NUFIP2 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NUFIP2 MUTATED     0   2   2   2
  NUFIP2 WILD-TYPE 195 171  87  83
D679V5, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  N0              0              195
  N1              2              171
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V6, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     8   0
  NUFIP2 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      8    0
  NUFIP2 WILD-TYPE  474   38
   clus
vv  NUFIP2 MUTATED NUFIP2 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D679V7, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     3   5
  NUFIP2 WILD-TYPE 169 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      3    5
  NUFIP2 WILD-TYPE  169  401
        clus
vv       NUFIP2 MUTATED NUFIP2 WILD-TYPE
  FEMALE              3              169
  MALE                5              401
[1] 2 2
[1] FALSE
D679V8, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     6   1
  NUFIP2 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      6    1
  NUFIP2 WILD-TYPE  410  101
     clus
vv    NUFIP2 MUTATED NUFIP2 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D679V9, continuous
D679V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NUFIP2 MUTATED       1                         0
  NUFIP2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUFIP2 MUTATED                                           0     6
  NUFIP2 WILD-TYPE                                         1   351
D679V11, multiclass
                                           clus
vv                                          NUFIP2 MUTATED NUFIP2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V12, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     0   7
  NUFIP2 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      0    7
  NUFIP2 WILD-TYPE   10  391
                        clus
vv                       NUFIP2 MUTATED NUFIP2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(680) Variable = MED23 MUTATION ANALYSIS
D680V1, survival
                 sevent
clus2               0   1
  MED23 MUTATED    14   8
  MED23 WILD-TYPE 324 208
  MED23 MUTATED MED23 WILD-TYPE 
             22             532 
  MED23 MUTATED MED23 WILD-TYPE 
              8             208 
$`MED23 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-IG-A50L 
       19.99        21.99        25.78        31.27        58.55         0.53 
TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 
        6.97         6.18        34.68         0.26        28.14        31.96 
TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-F1-6874 
       15.95         8.05         6.02       105.07        11.44        14.47 
TCGA-HU-A4GT TCGA-IN-8462 TCGA-IN-A6RN TCGA-KB-A6F5 
        6.51        18.81        19.53         5.56 

$`MED23 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GK 
        0.23        20.15         9.86        20.05        14.30         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        5.92        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
        3.45         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MED23 MUTATED MED23 WILD-TYPE 
           0.26            0.00 
  MED23 MUTATED MED23 WILD-TYPE 
         105.07          122.30 
  MED23 MUTATED MED23 WILD-TYPE 
          17.38           13.51 
[1] "0.3 - 105.1 (17.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D680V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MED23 MUTATED         1        0        3        3         3         2
  MED23 WILD-TYPE       9       20       43       28        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED23 MUTATED           1          3          1          2        3         0
  MED23 WILD-TYPE        28         81         61         37       40         4
D680V3, multiclass
            clus
vv           MED23 MUTATED MED23 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               3              28
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MED23 MUTATED       3   7   9   4
  MED23 WILD-TYPE    51 128 252  98
D680V4, multiclass
       clus
vv      MED23 MUTATED MED23 WILD-TYPE
  T0+T1             3              51
  T2                7             128
  T3                9             252
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MED23 MUTATED     6  10   3   3
  MED23 WILD-TYPE 189 163  86  82
D680V5, multiclass
    clus
vv   MED23 MUTATED MED23 WILD-TYPE
  N0             6             189
  N1            10             163
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V6, binary
                 cls
clus                0   1
  MED23 MUTATED    18   2
  MED23 WILD-TYPE 464  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED     18    2
  MED23 WILD-TYPE  464   36
   clus
vv  MED23 MUTATED MED23 WILD-TYPE
  0            18             464
  1             2              36
[1] 2 2
[1] FALSE
D680V7, binary
                 cls
clus                0   1
  MED23 MUTATED     7  16
  MED23 WILD-TYPE 165 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      7   16
  MED23 WILD-TYPE  165  390
        clus
vv       MED23 MUTATED MED23 WILD-TYPE
  FEMALE             7             165
  MALE              16             390
[1] 2 2
[1] FALSE
D680V8, binary
                 cls
clus                0   1
  MED23 MUTATED    21   0
  MED23 WILD-TYPE 395 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED     21    0
  MED23 WILD-TYPE  395  102
     clus
vv    MED23 MUTATED MED23 WILD-TYPE
  NO             21             395
  YES             0             102
[1] 2 2
[1] FALSE
D680V9, continuous
D680V10, continuous
[1] "Remove cluster labels:" "MED23 MUTATED"         
clus
  MED23 MUTATED MED23 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" "MED23 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MED23 MUTATED       3                         0
  MED23 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MED23 MUTATED                                           0    11
  MED23 WILD-TYPE                                         1   346
D680V11, multiclass
                                           clus
vv                                          MED23 MUTATED MED23 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V12, binary
                 cls
clus                0   1
  MED23 MUTATED     0  13
  MED23 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      0   13
  MED23 WILD-TYPE   10  385
                        clus
vv                       MED23 MUTATED MED23 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(681) Variable = FBXO34 MUTATION ANALYSIS
D681V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     7   5
  FBXO34 WILD-TYPE 331 211
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              12              542 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               5              211 
$`FBXO34 MUTATED`
TCGA-JY-A6FG TCGA-L5-A8NN TCGA-LN-A7HZ TCGA-V5-A7RC TCGA-B7-5816 TCGA-BR-8078 
       41.52         5.49        13.18         3.42        26.70        29.59 
TCGA-BR-8487 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5723 TCGA-D7-6525 TCGA-HU-A4GN 
        1.12         6.97         0.99       105.07        13.35        29.98 

$`FBXO34 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97         7.07        30.97        36.00         1.02 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
            0.99             0.00 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          105.07           122.30 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          13.265           13.630 
[1] "1.0 - 105.1 (13.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D681V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO34 MUTATED         1        0        1        2         3         2
  FBXO34 WILD-TYPE       9       20       45       29        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO34 MUTATED           2          1          0          0        0
  FBXO34 WILD-TYPE        27         83         62         39       43
                  vv
clus               STAGE IVA
  FBXO34 MUTATED           0
  FBXO34 WILD-TYPE         4
D681V3, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FBXO34 MUTATED       1   6   3   2
  FBXO34 WILD-TYPE    53 129 258 100
D681V4, multiclass
       clus
vv      FBXO34 MUTATED FBXO34 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FBXO34 MUTATED     5   6   1   0
  FBXO34 WILD-TYPE 190 167  88  85
D681V5, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  N0              5              190
  N1              6              167
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V6, binary
                  cls
clus                 0   1
  FBXO34 MUTATED    11   0
  FBXO34 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED     11    0
  FBXO34 WILD-TYPE  471   38
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D681V7, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     3  10
  FBXO34 WILD-TYPE 169 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      3   10
  FBXO34 WILD-TYPE  169  396
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  FEMALE              3              169
  MALE               10              396
[1] 2 2
[1] FALSE
D681V8, binary
                  cls
clus                 0   1
  FBXO34 MUTATED    11   1
  FBXO34 WILD-TYPE 405 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED     11    1
  FBXO34 WILD-TYPE  405  101
     clus
vv    FBXO34 MUTATED FBXO34 WILD-TYPE
  NO              11              405
  YES              1              101
[1] 2 2
[1] FALSE
D681V9, continuous
[1] "Remove cluster labels:" "FBXO34 MUTATED"        
clus
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FBXO34 WILD-TYPE" "FBXO34 WILD-TYPE" 
D681V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO34 MUTATED       2                         2
  FBXO34 WILD-TYPE   131                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO34 MUTATED                                           0     6
  FBXO34 WILD-TYPE                                         1   351
D681V11, multiclass
                                           clus
vv                                          FBXO34 MUTATED FBXO34 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V12, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     0   8
  FBXO34 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      0    8
  FBXO34 WILD-TYPE   10  390
                        clus
vv                       FBXO34 MUTATED FBXO34 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(682) Variable = SH2B1 MUTATION ANALYSIS
D682V1, survival
                 sevent
clus2               0   1
  SH2B1 MUTATED     7   4
  SH2B1 WILD-TYPE 331 212
  SH2B1 MUTATED SH2B1 WILD-TYPE 
             11             543 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
              4             212 
$`SH2B1 MUTATED`
TCGA-IG-A5B8 TCGA-V5-AASX TCGA-BR-6852 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG 
        0.79         8.98        44.94         1.12        12.43         6.58 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-A5NB 
      105.07        21.07         5.92        11.08        30.51 

$`SH2B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SH2B1 MUTATED SH2B1 WILD-TYPE 
           0.79            0.00 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
         105.07          122.30 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
          11.08           13.68 
[1] "0.8 - 105.1 (11.1)" "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D682V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH2B1 MUTATED         0        0        2        2         4         1
  SH2B1 WILD-TYPE      10       20       44       29        80        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SH2B1 MUTATED           0          1          0          1        0         0
  SH2B1 WILD-TYPE        29         83         62         38       43         4
D682V3, multiclass
            clus
vv           SH2B1 MUTATED SH2B1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              4              80
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SH2B1 MUTATED       1   3   7   1
  SH2B1 WILD-TYPE    53 132 254 101
D682V4, multiclass
       clus
vv      SH2B1 MUTATED SH2B1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SH2B1 MUTATED     7   2   1   1
  SH2B1 WILD-TYPE 188 171  88  84
D682V5, multiclass
    clus
vv   SH2B1 MUTATED SH2B1 WILD-TYPE
  N0             7             188
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V6, binary
                 cls
clus                0   1
  SH2B1 MUTATED    12   0
  SH2B1 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED     12    0
  SH2B1 WILD-TYPE  470   38
   clus
vv  SH2B1 MUTATED SH2B1 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D682V7, binary
                 cls
clus                0   1
  SH2B1 MUTATED     6   7
  SH2B1 WILD-TYPE 166 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      6    7
  SH2B1 WILD-TYPE  166  399
        clus
vv       SH2B1 MUTATED SH2B1 WILD-TYPE
  FEMALE             6             166
  MALE               7             399
[1] 2 2
[1] FALSE
D682V8, binary
                 cls
clus                0   1
  SH2B1 MUTATED     8   2
  SH2B1 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      8    2
  SH2B1 WILD-TYPE  408  100
     clus
vv    SH2B1 MUTATED SH2B1 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D682V9, continuous
[1] "Remove cluster labels:" "SH2B1 MUTATED"         
clus
  SH2B1 MUTATED SH2B1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
D682V10, continuous
[1] "Remove cluster labels:" "SH2B1 MUTATED"         
clus
  SH2B1 MUTATED SH2B1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A6QS 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" "SH2B1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SH2B1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SH2B1 MUTATED       2                         1
  SH2B1 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH2B1 MUTATED                                           0     6
  SH2B1 WILD-TYPE                                         1   351
D682V11, multiclass
                                           clus
vv                                          SH2B1 MUTATED SH2B1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V12, binary
                 cls
clus                0   1
  SH2B1 MUTATED     0   9
  SH2B1 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      0    9
  SH2B1 WILD-TYPE   10  389
                        clus
vv                       SH2B1 MUTATED SH2B1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(683) Variable = P2RX1 MUTATION ANALYSIS
D683V1, survival
                 sevent
clus2               0   1
  P2RX1 MUTATED     5   0
  P2RX1 WILD-TYPE 333 216
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              5             549 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              0             216 
$`P2RX1 MUTATED`
TCGA-R6-A6XG TCGA-B7-5816 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4G8 
       38.40        26.70        65.10        22.32        22.68 

$`P2RX1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  P2RX1 MUTATED P2RX1 WILD-TYPE 
          22.32            0.00 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
           65.1           122.3 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
          26.70           13.51 
[1] "22.3 - 65.1 (26.7)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9200000"
D683V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P2RX1 MUTATED         0        0        1        0         0         3
  P2RX1 WILD-TYPE      10       20       45       31        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P2RX1 MUTATED           0          0          0          0        0         0
  P2RX1 WILD-TYPE        29         84         62         39       43         4
D683V3, multiclass
            clus
vv           P2RX1 MUTATED P2RX1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  P2RX1 MUTATED       0   1   1   2
  P2RX1 WILD-TYPE    54 134 260 100
D683V4, multiclass
       clus
vv      P2RX1 MUTATED P2RX1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  P2RX1 MUTATED     3   1   0   0
  P2RX1 WILD-TYPE 192 172  89  85
D683V5, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  N0             3             192
  N1             1             172
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V6, binary
                 cls
clus                0   1
  P2RX1 MUTATED     4   0
  P2RX1 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      4    0
  P2RX1 WILD-TYPE  478   38
   clus
vv  P2RX1 MUTATED P2RX1 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D683V7, binary
                 cls
clus                0   1
  P2RX1 MUTATED     4   1
  P2RX1 WILD-TYPE 168 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      4    1
  P2RX1 WILD-TYPE  168  405
        clus
vv       P2RX1 MUTATED P2RX1 WILD-TYPE
  FEMALE             4             168
  MALE               1             405
[1] 2 2
[1] FALSE
D683V8, binary
                 cls
clus                0   1
  P2RX1 MUTATED     4   0
  P2RX1 WILD-TYPE 412 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      4    0
  P2RX1 WILD-TYPE  412  102
     clus
vv    P2RX1 MUTATED P2RX1 WILD-TYPE
  NO              4             412
  YES             0             102
[1] 2 2
[1] FALSE
D683V9, continuous
D683V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P2RX1 MUTATED       2                         0
  P2RX1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P2RX1 MUTATED                                           0     2
  P2RX1 WILD-TYPE                                         1   355
D683V11, multiclass
                                           clus
vv                                          P2RX1 MUTATED P2RX1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V12, binary
                 cls
clus                0   1
  P2RX1 MUTATED     0   4
  P2RX1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      0    4
  P2RX1 WILD-TYPE   10  394
                        clus
vv                       P2RX1 MUTATED P2RX1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(684) Variable = SAP30BP MUTATION ANALYSIS
D684V1, survival
                   sevent
clus2                 0   1
  SAP30BP MUTATED     6   1
  SAP30BP WILD-TYPE 332 215
  SAP30BP MUTATED SAP30BP WILD-TYPE 
                7               547 
  SAP30BP MUTATED SAP30BP WILD-TYPE 
                1               215 
$`SAP30BP MUTATED`
TCGA-L5-A4OI TCGA-FP-A8CX TCGA-LN-A9FQ TCGA-CG-5728 TCGA-HU-A4GH TCGA-HU-A4GQ 
       19.99         0.23        12.85        65.10        11.77         0.10 
TCGA-VQ-A8P2 
       38.14 

$`SAP30BP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SAP30BP MUTATED SAP30BP WILD-TYPE 
              0.1               0.0 
  SAP30BP MUTATED SAP30BP WILD-TYPE 
             65.1             122.3 
  SAP30BP MUTATED SAP30BP WILD-TYPE 
            12.85             13.58 
[1] "0.1 - 65.1 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.9"
D684V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAP30BP MUTATED         0        1        1        0         1         0
  SAP30BP WILD-TYPE      10       19       45       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAP30BP MUTATED           0          1          0          3        0
  SAP30BP WILD-TYPE        29         83         62         36       43
                   vv
clus                STAGE IVA
  SAP30BP MUTATED           0
  SAP30BP WILD-TYPE         4
D684V3, multiclass
            clus
vv           SAP30BP MUTATED SAP30BP WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SAP30BP MUTATED       1   1   2   3
  SAP30BP WILD-TYPE    53 134 259  99
D684V4, multiclass
       clus
vv      SAP30BP MUTATED SAP30BP WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SAP30BP MUTATED     3   1   1   2
  SAP30BP WILD-TYPE 192 172  88  83
D684V5, multiclass
    clus
vv   SAP30BP MUTATED SAP30BP WILD-TYPE
  N0               3               192
  N1               1               172
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V6, binary
                   cls
clus                  0   1
  SAP30BP MUTATED     5   0
  SAP30BP WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SAP30BP MUTATED      5    0
  SAP30BP WILD-TYPE  477   38
   clus
vv  SAP30BP MUTATED SAP30BP WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D684V7, binary
                   cls
clus                  0   1
  SAP30BP MUTATED     1   6
  SAP30BP WILD-TYPE 171 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SAP30BP MUTATED      1    6
  SAP30BP WILD-TYPE  171  400
        clus
vv       SAP30BP MUTATED SAP30BP WILD-TYPE
  FEMALE               1               171
  MALE                 6               400
[1] 2 2
[1] FALSE
D684V8, binary
                   cls
clus                  0   1
  SAP30BP MUTATED     4   1
  SAP30BP WILD-TYPE 412 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SAP30BP MUTATED      4    1
  SAP30BP WILD-TYPE  412  101
     clus
vv    SAP30BP MUTATED SAP30BP WILD-TYPE
  NO                4               412
  YES               1               101
[1] 2 2
[1] FALSE
D684V9, continuous
D684V10, continuous
[1] "Remove cluster labels:" "SAP30BP MUTATED"       
clus
  SAP30BP MUTATED SAP30BP WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" "SAP30BP WILD-TYPE" 
       TCGA-Z6-AAPN 
"SAP30BP WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SAP30BP MUTATED       3                         0
  SAP30BP WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SAP30BP MUTATED                                           0     3
  SAP30BP WILD-TYPE                                         1   354
D684V11, multiclass
                                           clus
vv                                          SAP30BP MUTATED SAP30BP WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V12, binary
                   cls
clus                  0   1
  SAP30BP MUTATED     0   4
  SAP30BP WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SAP30BP MUTATED      0    4
  SAP30BP WILD-TYPE   10  394
                        clus
vv                       SAP30BP MUTATED SAP30BP WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(685) Variable = NCEH1 MUTATION ANALYSIS
D685V1, survival
                 sevent
clus2               0   1
  NCEH1 MUTATED     5   3
  NCEH1 WILD-TYPE 333 213
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              8             546 
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              3             213 
$`NCEH1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A891 TCGA-VR-A8ER TCGA-BR-8368 TCGA-FP-A4BE TCGA-HJ-7597 
       19.99         3.75        12.43         4.31        11.08        26.47 
TCGA-HU-A4GQ TCGA-HU-A4GU 
        0.10         6.58 

$`NCEH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NCEH1 MUTATED NCEH1 WILD-TYPE 
            0.1             0.0 
  NCEH1 MUTATED NCEH1 WILD-TYPE 
          26.47          122.30 
  NCEH1 MUTATED NCEH1 WILD-TYPE 
           8.83           13.73 
[1] "0.1 - 26.5 (8.8)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.6"
D685V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCEH1 MUTATED         0        0        2        0         1         1
  NCEH1 WILD-TYPE      10       20       44       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCEH1 MUTATED           1          0          0          2        0         0
  NCEH1 WILD-TYPE        28         84         62         37       43         4
D685V3, multiclass
            clus
vv           NCEH1 MUTATED NCEH1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NCEH1 MUTATED       0   2   4   2
  NCEH1 WILD-TYPE    54 133 257 100
D685V4, multiclass
       clus
vv      NCEH1 MUTATED NCEH1 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NCEH1 MUTATED     3   3   1   1
  NCEH1 WILD-TYPE 192 170  88  84
D685V5, multiclass
    clus
vv   NCEH1 MUTATED NCEH1 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V6, binary
                 cls
clus                0   1
  NCEH1 MUTATED     6   0
  NCEH1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCEH1 MUTATED      6    0
  NCEH1 WILD-TYPE  476   38
   clus
vv  NCEH1 MUTATED NCEH1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D685V7, binary
                 cls
clus                0   1
  NCEH1 MUTATED     2   6
  NCEH1 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCEH1 MUTATED      2    6
  NCEH1 WILD-TYPE  170  400
        clus
vv       NCEH1 MUTATED NCEH1 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D685V8, binary
                 cls
clus                0   1
  NCEH1 MUTATED     5   2
  NCEH1 WILD-TYPE 411 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCEH1 MUTATED      5    2
  NCEH1 WILD-TYPE  411  100
     clus
vv    NCEH1 MUTATED NCEH1 WILD-TYPE
  NO              5             411
  YES             2             100
[1] 2 2
[1] FALSE
D685V9, continuous
[1] "Remove cluster labels:" "NCEH1 MUTATED"         
clus
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
D685V10, continuous
[1] "Remove cluster labels:" "NCEH1 MUTATED"         
clus
  NCEH1 MUTATED NCEH1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8EU 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" "NCEH1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NCEH1 MUTATED       2                         1
  NCEH1 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCEH1 MUTATED                                           0     4
  NCEH1 WILD-TYPE                                         1   353
D685V11, multiclass
                                           clus
vv                                          NCEH1 MUTATED NCEH1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V12, binary
                 cls
clus                0   1
  NCEH1 MUTATED     0   5
  NCEH1 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCEH1 MUTATED      0    5
  NCEH1 WILD-TYPE   10  393
                        clus
vv                       NCEH1 MUTATED NCEH1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(686) Variable = ANTXR1 MUTATION ANALYSIS
D686V1, survival
                  sevent
clus2                0   1
  ANTXR1 MUTATED     8   4
  ANTXR1 WILD-TYPE 330 212
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              12              542 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               4              212 
$`ANTXR1 MUTATED`
TCGA-L5-A4OS TCGA-V5-AASX TCGA-BR-6452 TCGA-BR-8369 TCGA-BR-8680 TCGA-CG-4306 
       58.59         8.98        34.68        14.04        31.96         1.02 
TCGA-CG-5726 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HU-A4GU TCGA-R5-A7ZI TCGA-RD-A8N6 
       28.96        11.44        21.27         6.58        74.53         8.94 

$`ANTXR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
            1.02             0.00 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
           74.53           122.30 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          17.655           13.530 
[1] "1.0 - 74.5 (17.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D686V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANTXR1 MUTATED         0        1        0        0         1         2
  ANTXR1 WILD-TYPE      10       19       46       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANTXR1 MUTATED           0          1          3          0        3
  ANTXR1 WILD-TYPE        29         83         59         39       40
                  vv
clus               STAGE IVA
  ANTXR1 MUTATED           0
  ANTXR1 WILD-TYPE         4
D686V3, multiclass
            clus
vv           ANTXR1 MUTATED ANTXR1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              3               59
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ANTXR1 MUTATED       1   2   6   2
  ANTXR1 WILD-TYPE    53 133 255 100
D686V4, multiclass
       clus
vv      ANTXR1 MUTATED ANTXR1 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 6              255
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ANTXR1 MUTATED     2   3   3   3
  ANTXR1 WILD-TYPE 193 170  86  82
D686V5, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V6, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     8   3
  ANTXR1 WILD-TYPE 474  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      8    3
  ANTXR1 WILD-TYPE  474   35
   clus
vv  ANTXR1 MUTATED ANTXR1 WILD-TYPE
  0              8              474
  1              3               35
[1] 2 2
[1] FALSE
D686V7, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     6   6
  ANTXR1 WILD-TYPE 166 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      6    6
  ANTXR1 WILD-TYPE  166  400
        clus
vv       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  FEMALE              6              166
  MALE                6              400
[1] 2 2
[1] FALSE
D686V8, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     8   1
  ANTXR1 WILD-TYPE 408 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      8    1
  ANTXR1 WILD-TYPE  408  101
     clus
vv    ANTXR1 MUTATED ANTXR1 WILD-TYPE
  NO               8              408
  YES              1              101
[1] 2 2
[1] FALSE
D686V9, continuous
[1] "Remove cluster labels:" "ANTXR1 MUTATED"        
clus
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" "ANTXR1 WILD-TYPE" 
D686V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ANTXR1 MUTATED       2                         0
  ANTXR1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANTXR1 MUTATED                                           0     8
  ANTXR1 WILD-TYPE                                         1   349
D686V11, multiclass
                                           clus
vv                                          ANTXR1 MUTATED ANTXR1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V12, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     2   7
  ANTXR1 WILD-TYPE   8 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      2    7
  ANTXR1 WILD-TYPE    8  391
                        clus
vv                       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(687) Variable = BLMH MUTATION ANALYSIS
D687V1, survival
                sevent
clus2              0   1
  BLMH MUTATED     3   2
  BLMH WILD-TYPE 335 214
  BLMH MUTATED BLMH WILD-TYPE 
             5            549 
  BLMH MUTATED BLMH WILD-TYPE 
             2            214 
$`BLMH MUTATED`
TCGA-BR-8060 TCGA-CD-A4MG TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-HU-A4H8 
       11.44         6.58         6.51        23.84        14.07 

$`BLMH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        2.10        12.95        29.00        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BLMH MUTATED BLMH WILD-TYPE 
          6.51           0.00 
  BLMH MUTATED BLMH WILD-TYPE 
         23.84         122.30 
  BLMH MUTATED BLMH WILD-TYPE 
         11.44          13.58 
[1] "6.5 - 23.8 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D687V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BLMH MUTATED         0        0        1        0         2         2
  BLMH WILD-TYPE      10       20       45       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BLMH MUTATED           0          0          0          0        0         0
  BLMH WILD-TYPE        29         84         62         39       43         4
D687V3, multiclass
            clus
vv           BLMH MUTATED BLMH WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BLMH MUTATED       1   2   2   0
  BLMH WILD-TYPE    53 133 259 102
D687V4, multiclass
       clus
vv      BLMH MUTATED BLMH WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               2            259
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BLMH MUTATED     2   1   2   0
  BLMH WILD-TYPE 193 172  87  85
D687V5, multiclass
    clus
vv   BLMH MUTATED BLMH WILD-TYPE
  N0            2            193
  N1            1            172
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V6, binary
                cls
clus               0   1
  BLMH MUTATED     5   0
  BLMH WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      5    0
  BLMH WILD-TYPE  477   38
   clus
vv  BLMH MUTATED BLMH WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D687V7, binary
                cls
clus               0   1
  BLMH MUTATED     3   2
  BLMH WILD-TYPE 169 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      3    2
  BLMH WILD-TYPE  169  404
        clus
vv       BLMH MUTATED BLMH WILD-TYPE
  FEMALE            3            169
  MALE              2            404
[1] 2 2
[1] FALSE
D687V8, binary
                cls
clus               0   1
  BLMH MUTATED     5   0
  BLMH WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      5    0
  BLMH WILD-TYPE  411  102
     clus
vv    BLMH MUTATED BLMH WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D687V9, continuous
D687V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BLMH MUTATED       4                         0
  BLMH WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BLMH MUTATED                                           0     1
  BLMH WILD-TYPE                                         1   356
D687V11, multiclass
                                           clus
vv                                          BLMH MUTATED BLMH WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                1            356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V12, binary
                cls
clus               0   1
  BLMH MUTATED     0   5
  BLMH WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      0    5
  BLMH WILD-TYPE   10  393
                        clus
vv                       BLMH MUTATED BLMH WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(688) Variable = ZNF207 MUTATION ANALYSIS
D688V1, survival
                  sevent
clus2                0   1
  ZNF207 MUTATED     8   2
  ZNF207 WILD-TYPE 330 214
  ZNF207 MUTATED ZNF207 WILD-TYPE 
              10              544 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               2              214 
$`ZNF207 MUTATED`
TCGA-L5-A4OS TCGA-L5-A8NS TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 
       58.59        13.41        34.68        36.16        14.43        29.59 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-HF-A5NB 
       31.96        16.14        12.62        30.51 

$`ZNF207 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZNF207 MUTATED ZNF207 WILD-TYPE 
           12.62             0.00 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
           58.59           122.30 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
          30.050           13.495 
[1] "12.6 - 58.6 (30.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3"  
D688V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF207 MUTATED         0        1        1        0         1         3
  ZNF207 WILD-TYPE      10       19       45       31        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF207 MUTATED           1          0          1          1        1
  ZNF207 WILD-TYPE        28         84         61         38       42
                  vv
clus               STAGE IVA
  ZNF207 MUTATED           0
  ZNF207 WILD-TYPE         4
D688V3, multiclass
            clus
vv           ZNF207 MUTATED ZNF207 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF207 MUTATED       1   2   3   4
  ZNF207 WILD-TYPE    53 133 258  98
D688V4, multiclass
       clus
vv      ZNF207 MUTATED ZNF207 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF207 MUTATED     5   2   1   2
  ZNF207 WILD-TYPE 190 171  88  83
D688V5, multiclass
    clus
vv   ZNF207 MUTATED ZNF207 WILD-TYPE
  N0              5              190
  N1              2              171
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V6, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     9   1
  ZNF207 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      9    1
  ZNF207 WILD-TYPE  473   37
   clus
vv  ZNF207 MUTATED ZNF207 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D688V7, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     5   5
  ZNF207 WILD-TYPE 167 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      5    5
  ZNF207 WILD-TYPE  167  401
        clus
vv       ZNF207 MUTATED ZNF207 WILD-TYPE
  FEMALE              5              167
  MALE                5              401
[1] 2 2
[1] FALSE
D688V8, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     8   2
  ZNF207 WILD-TYPE 408 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      8    2
  ZNF207 WILD-TYPE  408  100
     clus
vv    ZNF207 MUTATED ZNF207 WILD-TYPE
  NO               8              408
  YES              2              100
[1] 2 2
[1] FALSE
D688V9, continuous
D688V10, continuous
[1] "Remove cluster labels:" "ZNF207 MUTATED"        
clus
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZNF207 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF207 MUTATED       2                         0
  ZNF207 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF207 MUTATED                                           0     7
  ZNF207 WILD-TYPE                                         1   350
D688V11, multiclass
                                           clus
vv                                          ZNF207 MUTATED ZNF207 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V12, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     0   7
  ZNF207 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      0    7
  ZNF207 WILD-TYPE   10  391
                        clus
vv                       ZNF207 MUTATED ZNF207 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(689) Variable = SIGLEC10 MUTATION ANALYSIS
D689V1, survival
                    sevent
clus2                  0   1
  SIGLEC10 MUTATED    12   4
  SIGLEC10 WILD-TYPE 326 212
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                16                538 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                 4                212 
$`SIGLEC10 MUTATED`
TCGA-JY-A6FD TCGA-L5-A43H TCGA-LN-A8HZ TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-7197 
       68.02         0.30        12.33        19.56         9.34         9.21 
TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-8610 
       29.59        31.96        12.43         6.58         6.02         0.76 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-IN-8462 
       22.68        29.98         0.10        18.81 

$`SIGLEC10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        6.31        12.30        11.31        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       14.07        15.68        33.40        36.36         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
               0.1                0.0 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
             68.02             122.30 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
             12.38              13.63 
[1] "0.1 - 68.0 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D689V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SIGLEC10 MUTATED         0        1        0        1         5         3
  SIGLEC10 WILD-TYPE      10       19       46       30        79        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC10 MUTATED           1          0          0          2        2
  SIGLEC10 WILD-TYPE        28         84         62         37       41
                    vv
clus                 STAGE IVA
  SIGLEC10 MUTATED           0
  SIGLEC10 WILD-TYPE         4
D689V3, multiclass
            clus
vv           SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 5                 79
  STAGE IIB                 3                 80
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  2                 41
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SIGLEC10 MUTATED       1   3   6   5
  SIGLEC10 WILD-TYPE    53 132 255  97
D689V4, multiclass
       clus
vv      SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                   6                255
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SIGLEC10 MUTATED     7   6   2   1
  SIGLEC10 WILD-TYPE 188 167  87  84
D689V5, multiclass
    clus
vv   SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  N0                7                188
  N1                6                167
  N2                2                 87
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V6, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED    15   1
  SIGLEC10 WILD-TYPE 467  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED     15    1
  SIGLEC10 WILD-TYPE  467   37
   clus
vv  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  0               15                467
  1                1                 37
[1] 2 2
[1] FALSE
D689V7, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED     3  13
  SIGLEC10 WILD-TYPE 169 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED      3   13
  SIGLEC10 WILD-TYPE  169  393
        clus
vv       SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  FEMALE                3                169
  MALE                 13                393
[1] 2 2
[1] FALSE
D689V8, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED    14   2
  SIGLEC10 WILD-TYPE 402 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED     14    2
  SIGLEC10 WILD-TYPE  402  100
     clus
vv    SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  NO                14                402
  YES                2                100
[1] 2 2
[1] FALSE
D689V9, continuous
D689V10, continuous
[1] "Remove cluster labels:" "SIGLEC10 MUTATED"      
clus
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" "SIGLEC10 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SIGLEC10 MUTATED       9                         0
  SIGLEC10 WILD-TYPE   124                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIGLEC10 MUTATED                                           0     6
  SIGLEC10 WILD-TYPE                                         1   351
D689V11, multiclass
                                           clus
vv                                          SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  ASIAN                                                    9                124
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V12, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED     0  13
  SIGLEC10 WILD-TYPE  10 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED      0   13
  SIGLEC10 WILD-TYPE   10  385
                        clus
vv                       SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               13                385
[1] 2 2
[1] FALSE

Clustering(690) Variable = FAHD2A MUTATION ANALYSIS
D690V1, survival
                  sevent
clus2                0   1
  FAHD2A MUTATED     4   4
  FAHD2A WILD-TYPE 334 212
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               8              546 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               4              212 
$`FAHD2A MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8487 TCGA-HU-A4G8 
       19.99        21.99         6.97         0.26         1.12        22.68 
TCGA-HU-A4GQ TCGA-VQ-A8P2 
        0.10        38.14 

$`FAHD2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FAHD2A MUTATED FAHD2A WILD-TYPE 
             0.1              0.0 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           38.14           122.30 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
          13.480           13.565 
[1] "0.1 - 38.1 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D690V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAHD2A MUTATED         0        0        1        0         1         1
  FAHD2A WILD-TYPE      10       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2A MUTATED           0          3          0          2        1
  FAHD2A WILD-TYPE        29         81         62         37       42
                  vv
clus               STAGE IVA
  FAHD2A MUTATED           0
  FAHD2A WILD-TYPE         4
D690V3, multiclass
            clus
vv           FAHD2A MUTATED FAHD2A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAHD2A MUTATED       0   1   4   4
  FAHD2A WILD-TYPE    54 134 257  98
D690V4, multiclass
       clus
vv      FAHD2A MUTATED FAHD2A WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 4              257
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAHD2A MUTATED     3   4   1   1
  FAHD2A WILD-TYPE 192 169  88  84
D690V5, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  N0              3              192
  N1              4              169
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V6, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   1
  FAHD2A WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    1
  FAHD2A WILD-TYPE  476   37
   clus
vv  FAHD2A MUTATED FAHD2A WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D690V7, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   4
  FAHD2A WILD-TYPE 167 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    4
  FAHD2A WILD-TYPE  167  402
        clus
vv       FAHD2A MUTATED FAHD2A WILD-TYPE
  FEMALE              5              167
  MALE                4              402
[1] 2 2
[1] FALSE
D690V8, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     7   1
  FAHD2A WILD-TYPE 409 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      7    1
  FAHD2A WILD-TYPE  409  101
     clus
vv    FAHD2A MUTATED FAHD2A WILD-TYPE
  NO               7              409
  YES              1              101
[1] 2 2
[1] FALSE
D690V9, continuous
D690V10, continuous
[1] "Remove cluster labels:" "FAHD2A MUTATED"        
clus
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" "FAHD2A WILD-TYPE" 
      TCGA-Z6-AAPN 
"FAHD2A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAHD2A MUTATED       2                         0
  FAHD2A WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAHD2A MUTATED                                           0     6
  FAHD2A WILD-TYPE                                         1   351
D690V11, multiclass
                                           clus
vv                                          FAHD2A MUTATED FAHD2A WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V12, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     0   6
  FAHD2A WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      0    6
  FAHD2A WILD-TYPE   10  392
                        clus
vv                       FAHD2A MUTATED FAHD2A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(691) Variable = NUFIP1 MUTATION ANALYSIS
D691V1, survival
                  sevent
clus2                0   1
  NUFIP1 MUTATED     8   5
  NUFIP1 WILD-TYPE 330 211
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
              13              541 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               5              211 
$`NUFIP1 MUTATED`
TCGA-L5-A43J TCGA-S8-A6BV TCGA-JY-A6FA TCGA-LN-A49R TCGA-BR-4256 TCGA-BR-6452 
        4.31        20.02        44.75        13.38         9.34        34.68 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4437 TCGA-F1-6874 TCGA-IN-7806 TCGA-RD-A8N9 
       16.14         6.58         8.05        14.47        36.36        35.61 
TCGA-VQ-A8P2 
       38.14 

$`NUFIP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
            4.31             0.00 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           44.75           122.30 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           16.14            13.51 
[1] "4.3 - 44.8 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D691V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUFIP1 MUTATED         0        0        1        2         2         3
  NUFIP1 WILD-TYPE      10       20       45       29        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP1 MUTATED           1          2          1          0        0
  NUFIP1 WILD-TYPE        28         82         61         39       43
                  vv
clus               STAGE IVA
  NUFIP1 MUTATED           0
  NUFIP1 WILD-TYPE         4
D691V3, multiclass
            clus
vv           NUFIP1 MUTATED NUFIP1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NUFIP1 MUTATED       0   4   7   1
  NUFIP1 WILD-TYPE    54 131 254 101
D691V4, multiclass
       clus
vv      NUFIP1 MUTATED NUFIP1 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 7              254
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NUFIP1 MUTATED     4   8   0   1
  NUFIP1 WILD-TYPE 191 165  89  84
D691V5, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  N0              4              191
  N1              8              165
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V6, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED    11   0
  NUFIP1 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED     11    0
  NUFIP1 WILD-TYPE  471   38
   clus
vv  NUFIP1 MUTATED NUFIP1 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D691V7, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     3  10
  NUFIP1 WILD-TYPE 169 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      3   10
  NUFIP1 WILD-TYPE  169  396
        clus
vv       NUFIP1 MUTATED NUFIP1 WILD-TYPE
  FEMALE              3              169
  MALE               10              396
[1] 2 2
[1] FALSE
D691V8, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     9   3
  NUFIP1 WILD-TYPE 407  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      9    3
  NUFIP1 WILD-TYPE  407   99
     clus
vv    NUFIP1 MUTATED NUFIP1 WILD-TYPE
  NO               9              407
  YES              3               99
[1] 2 2
[1] FALSE
D691V9, continuous
[1] "Remove cluster labels:" "NUFIP1 MUTATED"        
clus
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" "NUFIP1 WILD-TYPE" 
D691V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NUFIP1 MUTATED       4                         0
  NUFIP1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUFIP1 MUTATED                                           0     8
  NUFIP1 WILD-TYPE                                         1   349
D691V11, multiclass
                                           clus
vv                                          NUFIP1 MUTATED NUFIP1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V12, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     0   9
  NUFIP1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      0    9
  NUFIP1 WILD-TYPE   10  389
                        clus
vv                       NUFIP1 MUTATED NUFIP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(692) Variable = PYHIN1 MUTATION ANALYSIS
D692V1, survival
                  sevent
clus2                0   1
  PYHIN1 MUTATED     9   5
  PYHIN1 WILD-TYPE 329 211
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              14              540 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
               5              211 
$`PYHIN1 MUTATED`
TCGA-L5-A43M TCGA-L5-A43E TCGA-R6-A6L4 TCGA-BR-8297 TCGA-BR-8372 TCGA-CD-8529 
        8.94        30.25        16.31         7.40        31.27        12.30 
TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-HF-7132 TCGA-HU-A4GU 
        1.02        28.96         5.92        11.31        77.29         6.58 
TCGA-VQ-A91U TCGA-VQ-A91V 
        1.71        42.64 

$`PYHIN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A92D 
       22.19        17.85         1.87        15.65        20.81        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
            1.02             0.00 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
           77.29           122.30 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
          11.805           13.630 
[1] "1.0 - 77.3 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D692V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PYHIN1 MUTATED         1        1        0        1         0         2
  PYHIN1 WILD-TYPE       9       19       46       30        84        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PYHIN1 MUTATED           0          3          0          2        2
  PYHIN1 WILD-TYPE        29         81         62         37       41
                  vv
clus               STAGE IVA
  PYHIN1 MUTATED           0
  PYHIN1 WILD-TYPE         4
D692V3, multiclass
            clus
vv           PYHIN1 MUTATED PYHIN1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PYHIN1 MUTATED       2   1   7   3
  PYHIN1 WILD-TYPE    52 134 254  99
D692V4, multiclass
       clus
vv      PYHIN1 MUTATED PYHIN1 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 7              254
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PYHIN1 MUTATED     3   4   4   2
  PYHIN1 WILD-TYPE 192 169  85  83
D692V5, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V6, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED    10   2
  PYHIN1 WILD-TYPE 472  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED     10    2
  PYHIN1 WILD-TYPE  472   36
   clus
vv  PYHIN1 MUTATED PYHIN1 WILD-TYPE
  0             10              472
  1              2               36
[1] 2 2
[1] FALSE
D692V7, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     3  11
  PYHIN1 WILD-TYPE 169 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      3   11
  PYHIN1 WILD-TYPE  169  395
        clus
vv       PYHIN1 MUTATED PYHIN1 WILD-TYPE
  FEMALE              3              169
  MALE               11              395
[1] 2 2
[1] FALSE
D692V8, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     9   3
  PYHIN1 WILD-TYPE 407  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      9    3
  PYHIN1 WILD-TYPE  407   99
     clus
vv    PYHIN1 MUTATED PYHIN1 WILD-TYPE
  NO               9              407
  YES              3               99
[1] 2 2
[1] FALSE
D692V9, continuous
D692V10, continuous
[1] "Remove cluster labels:" "PYHIN1 MUTATED"        
clus
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" "PYHIN1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PYHIN1 MUTATED       3                         0
  PYHIN1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PYHIN1 MUTATED                                           0     6
  PYHIN1 WILD-TYPE                                         1   351
D692V11, multiclass
                                           clus
vv                                          PYHIN1 MUTATED PYHIN1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V12, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     0   7
  PYHIN1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      0    7
  PYHIN1 WILD-TYPE   10  391
                        clus
vv                       PYHIN1 MUTATED PYHIN1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(693) Variable = KIAA1462 MUTATION ANALYSIS
D693V1, survival
                    sevent
clus2                  0   1
  KIAA1462 MUTATED    14   9
  KIAA1462 WILD-TYPE 324 207
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                23                531 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                 9                207 
$`KIAA1462 MUTATED`
TCGA-JY-A6FD TCGA-V5-AASW TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 
       68.02         9.27         9.67        34.68         6.18        31.10 
TCGA-BR-A4J1 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-A489 TCGA-CG-4436 TCGA-CG-5721 
        0.72        16.14         7.17        11.31         7.99         6.02 
TCGA-CG-5733 TCGA-EQ-8122 TCGA-F1-A448 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 
       21.07         7.99        21.27        77.29        26.47        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4H8 TCGA-IN-8663 TCGA-VQ-A8P2 
       22.68        25.81        14.07         3.39        38.14 

$`KIAA1462 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
       19.96         7.13         0.62        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.26        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
              0.72               0.00 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
             77.29             122.30 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
             16.14              13.51 
[1] "0.7 - 77.3 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D693V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1462 MUTATED         0        0        3        2         5         5
  KIAA1462 WILD-TYPE      10       20       43       29        79        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1462 MUTATED           0          4          2          1        1
  KIAA1462 WILD-TYPE        29         80         60         38       42
                    vv
clus                 STAGE IVA
  KIAA1462 MUTATED           0
  KIAA1462 WILD-TYPE         4
D693V3, multiclass
            clus
vv           KIAA1462 MUTATED KIAA1462 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  3                 43
  STAGE II                  2                 29
  STAGE IIA                 5                 79
  STAGE IIB                 5                 78
  STAGE III                 0                 29
  STAGE IIIA                4                 80
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1462 MUTATED       1   6   9   7
  KIAA1462 WILD-TYPE    53 129 252  95
D693V4, multiclass
       clus
vv      KIAA1462 MUTATED KIAA1462 WILD-TYPE
  T0+T1                1                 53
  T2                   6                129
  T3                   9                252
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1462 MUTATED    10   9   3   2
  KIAA1462 WILD-TYPE 185 164  86  83
D693V5, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  N0               10                185
  N1                9                164
  N2                3                 86
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V6, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    23   0
  KIAA1462 WILD-TYPE 459  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     23    0
  KIAA1462 WILD-TYPE  459   38
   clus
vv  KIAA1462 MUTATED KIAA1462 WILD-TYPE
  0               23                459
  1                0                 38
[1] 2 2
[1] FALSE
D693V7, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    13  13
  KIAA1462 WILD-TYPE 159 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     13   13
  KIAA1462 WILD-TYPE  159  393
        clus
vv       KIAA1462 MUTATED KIAA1462 WILD-TYPE
  FEMALE               13                159
  MALE                 13                393
[1] 2 2
[1] FALSE
D693V8, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    18   5
  KIAA1462 WILD-TYPE 398  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     18    5
  KIAA1462 WILD-TYPE  398   97
     clus
vv    KIAA1462 MUTATED KIAA1462 WILD-TYPE
  NO                18                398
  YES                5                 97
[1] 2 2
[1] FALSE
D693V9, continuous
[1] "Remove cluster labels:" "KIAA1462 MUTATED"      
clus
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" "KIAA1462 WILD-TYPE" 
        TCGA-Z6-A8JE 
"KIAA1462 WILD-TYPE" 
D693V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1462 MUTATED       8                         0
  KIAA1462 WILD-TYPE   125                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1462 MUTATED                                           0    14
  KIAA1462 WILD-TYPE                                         1   343
D693V11, multiclass
                                           clus
vv                                          KIAA1462 MUTATED KIAA1462 WILD-TYPE
  ASIAN                                                    8                125
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V12, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED     1  19
  KIAA1462 WILD-TYPE   9 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED      1   19
  KIAA1462 WILD-TYPE    9  379
                        clus
vv                       KIAA1462 MUTATED KIAA1462 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               19                379
[1] 2 2
[1] FALSE

Clustering(694) Variable = MGST2 MUTATION ANALYSIS
D694V1, survival
                 sevent
clus2               0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 335 216
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             551 
  MGST2 MUTATED MGST2 WILD-TYPE 
              0             216 
$`MGST2 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-A4MJ 
       44.94        29.59        12.62 

$`MGST2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MGST2 MUTATED MGST2 WILD-TYPE 
          12.62            0.00 
  MGST2 MUTATED MGST2 WILD-TYPE 
          44.94          122.30 
  MGST2 MUTATED MGST2 WILD-TYPE 
          29.59           13.55 
[1] "12.6 - 44.9 (29.6)" "0.0 - 122.3 (13.6)"
[1] "hr="     "3300000"
D694V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGST2 MUTATED         0        0        1        0         1         1
  MGST2 WILD-TYPE      10       20       45       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGST2 MUTATED           0          0          0          0        0         0
  MGST2 WILD-TYPE        29         84         62         39       43         4
D694V3, multiclass
            clus
vv           MGST2 MUTATED MGST2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MGST2 MUTATED       0   1   1   1
  MGST2 WILD-TYPE    54 134 260 101
D694V4, multiclass
       clus
vv      MGST2 MUTATED MGST2 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                1             260
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MGST2 MUTATED     3   0   0   0
  MGST2 WILD-TYPE 192 173  89  85
D694V5, multiclass
    clus
vv   MGST2 MUTATED MGST2 WILD-TYPE
  N0             3             192
  N1             0             173
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V6, binary
                 cls
clus                0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 479  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      3    0
  MGST2 WILD-TYPE  479   38
   clus
vv  MGST2 MUTATED MGST2 WILD-TYPE
  0             3             479
  1             0              38
[1] 2 2
[1] FALSE
D694V7, binary
                 cls
clus                0   1
  MGST2 MUTATED     2   1
  MGST2 WILD-TYPE 170 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      2    1
  MGST2 WILD-TYPE  170  405
        clus
vv       MGST2 MUTATED MGST2 WILD-TYPE
  FEMALE             2             170
  MALE               1             405
[1] 2 2
[1] FALSE
D694V8, binary
                 cls
clus                0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 413 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      3    0
  MGST2 WILD-TYPE  413  102
     clus
vv    MGST2 MUTATED MGST2 WILD-TYPE
  NO              3             413
  YES             0             102
[1] 2 2
[1] FALSE
D694V9, continuous
D694V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MGST2 MUTATED       1                         0
  MGST2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MGST2 MUTATED                                           0     2
  MGST2 WILD-TYPE                                         1   355
D694V11, multiclass
                                           clus
vv                                          MGST2 MUTATED MGST2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V12, binary
                 cls
clus                0   1
  MGST2 MUTATED     0   3
  MGST2 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      0    3
  MGST2 WILD-TYPE   10  395
                        clus
vv                       MGST2 MUTATED MGST2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(695) Variable = ZNF285 MUTATION ANALYSIS
D695V1, survival
                  sevent
clus2                0   1
  ZNF285 MUTATED     8   4
  ZNF285 WILD-TYPE 330 212
  ZNF285 MUTATED ZNF285 WILD-TYPE 
              12              542 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               4              212 
$`ZNF285 MUTATED`
TCGA-2H-A9GJ TCGA-L5-A4OU TCGA-L5-A8NN TCGA-V5-AASW TCGA-VR-A8EZ TCGA-BR-6452 
       58.55        29.00         5.49         9.27        18.18        34.68 
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-8369 TCGA-BR-8382 TCGA-CD-A4MH TCGA-VQ-A8P3 
       19.33        33.63        14.04        25.05        12.20        37.22 

$`ZNF285 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZNF285 MUTATED ZNF285 WILD-TYPE 
            5.49             0.00 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
           58.55           122.30 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
          22.190           13.495 
[1] "5.5 - 58.5 (22.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D695V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF285 MUTATED         1        0        0        0         4         1
  ZNF285 WILD-TYPE       9       20       46       31        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF285 MUTATED           1          1          1          2        0
  ZNF285 WILD-TYPE        28         83         61         37       43
                  vv
clus               STAGE IVA
  ZNF285 MUTATED           0
  ZNF285 WILD-TYPE         4
D695V3, multiclass
            clus
vv           ZNF285 MUTATED ZNF285 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF285 MUTATED       1   0   9   2
  ZNF285 WILD-TYPE    53 135 252 100
D695V4, multiclass
       clus
vv      ZNF285 MUTATED ZNF285 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 9              252
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF285 MUTATED     5   4   0   3
  ZNF285 WILD-TYPE 190 169  89  82
D695V5, multiclass
    clus
vv   ZNF285 MUTATED ZNF285 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              0               89
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V6, binary
                  cls
clus                 0   1
  ZNF285 MUTATED    12   0
  ZNF285 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED     12    0
  ZNF285 WILD-TYPE  470   38
   clus
vv  ZNF285 MUTATED ZNF285 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D695V7, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     7   7
  ZNF285 WILD-TYPE 165 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      7    7
  ZNF285 WILD-TYPE  165  399
        clus
vv       ZNF285 MUTATED ZNF285 WILD-TYPE
  FEMALE              7              165
  MALE                7              399
[1] 2 2
[1] FALSE
D695V8, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     9   3
  ZNF285 WILD-TYPE 407  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      9    3
  ZNF285 WILD-TYPE  407   99
     clus
vv    ZNF285 MUTATED ZNF285 WILD-TYPE
  NO               9              407
  YES              3               99
[1] 2 2
[1] FALSE
D695V9, continuous
[1] "Remove cluster labels:" "ZNF285 MUTATED"        
clus
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8Q7 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
D695V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF285 MUTATED       1                         0
  ZNF285 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF285 MUTATED                                           0    12
  ZNF285 WILD-TYPE                                         1   345
D695V11, multiclass
                                           clus
vv                                          ZNF285 MUTATED ZNF285 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V12, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     0   9
  ZNF285 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      0    9
  ZNF285 WILD-TYPE   10  389
                        clus
vv                       ZNF285 MUTATED ZNF285 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(696) Variable = OPLAH MUTATION ANALYSIS
D696V1, survival
                 sevent
clus2               0   1
  OPLAH MUTATED    11  10
  OPLAH WILD-TYPE 327 206
  OPLAH MUTATED OPLAH WILD-TYPE 
             21             533 
  OPLAH MUTATED OPLAH WILD-TYPE 
             10             206 
$`OPLAH MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GJ TCGA-IG-A4QS TCGA-BR-7703 TCGA-BR-7959 
       19.99        21.99        58.55         3.88        36.16        33.21 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-A4J1 TCGA-BR-A4QL 
       29.59         6.18         4.31        31.27         0.72        16.14 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-D7-A6EZ 
        6.58         1.02         6.02        13.78        11.44        20.32 
TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-VQ-A8P2 
        0.10        19.73        38.14 

$`OPLAH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.31        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  OPLAH MUTATED OPLAH WILD-TYPE 
            0.1             0.0 
  OPLAH MUTATED OPLAH WILD-TYPE 
          58.55          122.30 
  OPLAH MUTATED OPLAH WILD-TYPE 
          16.14           13.51 
[1] "0.1 - 58.5 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D696V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPLAH MUTATED         2        1        2        0         2         2
  OPLAH WILD-TYPE       8       19       44       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OPLAH MUTATED           0          6          4          3        3         0
  OPLAH WILD-TYPE        29         78         58         36       40         4
D696V3, multiclass
            clus
vv           OPLAH MUTATED OPLAH WILD-TYPE
  STAGE I                2               8
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             6              78
  STAGE IIIB             4              58
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OPLAH MUTATED       3   2  10  10
  OPLAH WILD-TYPE    51 133 251  92
D696V4, multiclass
       clus
vv      OPLAH MUTATED OPLAH WILD-TYPE
  T0+T1             3              51
  T2                2             133
  T3               10             251
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OPLAH MUTATED     9   7   5   5
  OPLAH WILD-TYPE 186 166  84  80
D696V5, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  N0             9             186
  N1             7             166
  N2             5              84
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V6, binary
                 cls
clus                0   1
  OPLAH MUTATED    22   2
  OPLAH WILD-TYPE 460  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED     22    2
  OPLAH WILD-TYPE  460   36
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0            22             460
  1             2              36
[1] 2 2
[1] FALSE
D696V7, binary
                 cls
clus                0   1
  OPLAH MUTATED     8  18
  OPLAH WILD-TYPE 164 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      8   18
  OPLAH WILD-TYPE  164  388
        clus
vv       OPLAH MUTATED OPLAH WILD-TYPE
  FEMALE             8             164
  MALE              18             388
[1] 2 2
[1] FALSE
D696V8, binary
                 cls
clus                0   1
  OPLAH MUTATED    19   2
  OPLAH WILD-TYPE 397 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED     19    2
  OPLAH WILD-TYPE  397  100
     clus
vv    OPLAH MUTATED OPLAH WILD-TYPE
  NO             19             397
  YES             2             100
[1] 2 2
[1] FALSE
D696V9, continuous
D696V10, continuous
[1] "Remove cluster labels:" "OPLAH MUTATED"         
clus
  OPLAH MUTATED OPLAH WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" "OPLAH WILD-TYPE" 
     TCGA-Z6-AAPN 
"OPLAH WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OPLAH MUTATED       3                         1
  OPLAH WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OPLAH MUTATED                                           0    17
  OPLAH WILD-TYPE                                         1   340
D696V11, multiclass
                                           clus
vv                                          OPLAH MUTATED OPLAH WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V12, binary
                 cls
clus                0   1
  OPLAH MUTATED     0  19
  OPLAH WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      0   19
  OPLAH WILD-TYPE   10  379
                        clus
vv                       OPLAH MUTATED OPLAH WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(697) Variable = NRK MUTATION ANALYSIS
D697V1, survival
               sevent
clus2             0   1
  NRK MUTATED    15  11
  NRK WILD-TYPE 323 205
  NRK MUTATED NRK WILD-TYPE 
           26           528 
  NRK MUTATED NRK WILD-TYPE 
           11           205 
$`NRK MUTATED`
TCGA-CG-4444 TCGA-2H-A9GR TCGA-IG-A4QS TCGA-L5-A88W TCGA-LN-A49Y TCGA-R6-A6Y0 
       47.05        32.45         3.88        25.12        12.46        53.95 
TCGA-B7-A5TJ TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8363 
       11.01        44.94        29.59         2.66        31.10         0.26 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-4469 TCGA-D7-6818 TCGA-D7-A4YV 
        4.31         1.12        27.12         7.07        12.36         5.92 
TCGA-FP-8211 TCGA-HF-A5NB TCGA-IN-8663 TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-SW-A7EA 
       13.58        30.51         3.39        74.53         8.61        19.04 
TCGA-VQ-A8PK TCGA-VQ-A91V 
       17.85        42.64 

$`NRK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         6.18        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       22.19         1.87        15.65        20.81         1.71        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NRK MUTATED NRK WILD-TYPE 
         0.26          0.00 
  NRK MUTATED NRK WILD-TYPE 
        74.53        122.30 
  NRK MUTATED NRK WILD-TYPE 
       15.715        13.530 
[1] "0.3 - 74.5 (15.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D697V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRK MUTATED         0        1        3        0         5         5
  NRK WILD-TYPE      10       19       43       31        79        78
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRK MUTATED           0          4          3          2        4         0
  NRK WILD-TYPE        29         80         59         37       39         4
D697V3, multiclass
            clus
vv           NRK MUTATED NRK WILD-TYPE
  STAGE I              0            10
  STAGE IA             1            19
  STAGE IB             3            43
  STAGE II             0            31
  STAGE IIA            5            79
  STAGE IIB            5            78
  STAGE III            0            29
  STAGE IIIA           4            80
  STAGE IIIB           3            59
  STAGE IIIC           2            37
  STAGE IV             4            39
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  NRK MUTATED       2   6  13   8
  NRK WILD-TYPE    52 129 248  94
D697V4, multiclass
       clus
vv      NRK MUTATED NRK WILD-TYPE
  T0+T1           2            52
  T2              6           129
  T3             13           248
  T4              8            94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NRK MUTATED    11   5   5   6
  NRK WILD-TYPE 184 168  84  79
D697V5, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          11           184
  N1           5           168
  N2           5            84
  N3           6            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V6, binary
               cls
clus              0   1
  NRK MUTATED    25   2
  NRK WILD-TYPE 457  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     25    2
  NRK WILD-TYPE  457   36
   clus
vv  NRK MUTATED NRK WILD-TYPE
  0          25           457
  1           2            36
[1] 2 2
[1] FALSE
D697V7, binary
               cls
clus              0   1
  NRK MUTATED    13  18
  NRK WILD-TYPE 159 388
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     13   18
  NRK WILD-TYPE  159  388
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          13           159
  MALE            18           388
[1] 2 2
[1] FALSE
D697V8, binary
               cls
clus              0   1
  NRK MUTATED    19   7
  NRK WILD-TYPE 397  95
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     19    7
  NRK WILD-TYPE  397   95
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           19           397
  YES           7            95
[1] 2 2
[1] FALSE
D697V9, continuous
[1] "Remove cluster labels:" "NRK MUTATED"           
clus
  NRK MUTATED NRK WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" "NRK WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"NRK WILD-TYPE" "NRK WILD-TYPE" 
D697V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NRK MUTATED       2                         0
  NRK WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRK MUTATED                                           1    23
  NRK WILD-TYPE                                         0   334
D697V11, multiclass
                                           clus
vv                                          NRK MUTATED NRK WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             0
  WHITE                                              23           334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V12, binary
               cls
clus              0   1
  NRK MUTATED     1  23
  NRK WILD-TYPE   9 375
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      1   23
  NRK WILD-TYPE    9  375
                        clus
vv                       NRK MUTATED NRK WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          23           375
[1] 2 2
[1] FALSE

Clustering(698) Variable = AP3M2 MUTATION ANALYSIS
D698V1, survival
                 sevent
clus2               0   1
  AP3M2 MUTATED     9   4
  AP3M2 WILD-TYPE 329 212
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             13             541 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
              4             212 
$`AP3M2 MUTATED`
TCGA-LN-A4A4 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8589 
       12.59        30.90         9.57        34.68        18.15        27.12 
TCGA-CG-4305 TCGA-CG-5734 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GX 
       15.95         7.99        30.51        24.20         6.51        20.25 
TCGA-MX-A5UJ 
       19.73 

$`AP3M2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  AP3M2 MUTATED AP3M2 WILD-TYPE 
           6.51            0.00 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          34.68          122.30 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          19.73           13.51 
[1] "6.5 - 34.7 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D698V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AP3M2 MUTATED         0        1        0        2         2         0
  AP3M2 WILD-TYPE      10       19       46       29        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP3M2 MUTATED           1          2          1          2        1         0
  AP3M2 WILD-TYPE        28         82         61         37       42         4
D698V3, multiclass
            clus
vv           AP3M2 MUTATED AP3M2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AP3M2 MUTATED       1   3   5   4
  AP3M2 WILD-TYPE    53 132 256  98
D698V4, multiclass
       clus
vv      AP3M2 MUTATED AP3M2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AP3M2 MUTATED     3   6   2   1
  AP3M2 WILD-TYPE 192 167  87  84
D698V5, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  N0             3             192
  N1             6             167
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V6, binary
                 cls
clus                0   1
  AP3M2 MUTATED    13   0
  AP3M2 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED     13    0
  AP3M2 WILD-TYPE  469   38
   clus
vv  AP3M2 MUTATED AP3M2 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D698V7, binary
                 cls
clus                0   1
  AP3M2 MUTATED     7   6
  AP3M2 WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      7    6
  AP3M2 WILD-TYPE  165  400
        clus
vv       AP3M2 MUTATED AP3M2 WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D698V8, binary
                 cls
clus                0   1
  AP3M2 MUTATED    10   2
  AP3M2 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED     10    2
  AP3M2 WILD-TYPE  406  100
     clus
vv    AP3M2 MUTATED AP3M2 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D698V9, continuous
[1] "Remove cluster labels:" "AP3M2 MUTATED"         
clus
  AP3M2 MUTATED AP3M2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A5      TCGA-LN-A4A6 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" "AP3M2 WILD-TYPE" 
D698V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AP3M2 MUTATED       4                         0
  AP3M2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AP3M2 MUTATED                                           0     6
  AP3M2 WILD-TYPE                                         1   351
D698V11, multiclass
                                           clus
vv                                          AP3M2 MUTATED AP3M2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V12, binary
                 cls
clus                0   1
  AP3M2 MUTATED     0  10
  AP3M2 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      0   10
  AP3M2 WILD-TYPE   10  388
                        clus
vv                       AP3M2 MUTATED AP3M2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(699) Variable = CD93 MUTATION ANALYSIS
D699V1, survival
                sevent
clus2              0   1
  CD93 MUTATED    13   8
  CD93 WILD-TYPE 325 208
  CD93 MUTATED CD93 WILD-TYPE 
            21            533 
  CD93 MUTATED CD93 WILD-TYPE 
             8            208 
$`CD93 MUTATED`
TCGA-CG-4460 TCGA-IG-A3YC TCGA-L5-A4OJ TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-V5-AASX 
       21.99        20.12        21.01        16.47         7.76         8.98 
TCGA-VR-A8EX TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8360 
       28.11         6.97         9.34        34.68        36.16         6.18 
TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8678 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-A4GT 
        0.26        25.05        24.79         5.92        30.51         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-VQ-AA6J 
        6.58        29.00        27.55 

$`CD93 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        17.26 

  CD93 MUTATED CD93 WILD-TYPE 
          0.26           0.00 
  CD93 MUTATED CD93 WILD-TYPE 
         36.16         122.30 
  CD93 MUTATED CD93 WILD-TYPE 
         20.12          13.51 
[1] "0.3 - 36.2 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D699V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD93 MUTATED         1        2        2        0         3         3
  CD93 WILD-TYPE       9       18       44       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD93 MUTATED           1          2          1          3        1         1
  CD93 WILD-TYPE        28         82         61         36       42         3
D699V3, multiclass
            clus
vv           CD93 MUTATED CD93 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CD93 MUTATED       4   3   8   5
  CD93 WILD-TYPE    50 132 253  97
D699V4, multiclass
       clus
vv      CD93 MUTATED CD93 WILD-TYPE
  T0+T1            4             50
  T2               3            132
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CD93 MUTATED     8  10   1   3
  CD93 WILD-TYPE 187 163  88  82
D699V5, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  N0            8            187
  N1           10            163
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V6, binary
                cls
clus               0   1
  CD93 MUTATED    20   2
  CD93 WILD-TYPE 462  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     20    2
  CD93 WILD-TYPE  462   36
   clus
vv  CD93 MUTATED CD93 WILD-TYPE
  0           20            462
  1            2             36
[1] 2 2
[1] FALSE
D699V7, binary
                cls
clus               0   1
  CD93 MUTATED    12  12
  CD93 WILD-TYPE 160 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     12   12
  CD93 WILD-TYPE  160  394
        clus
vv       CD93 MUTATED CD93 WILD-TYPE
  FEMALE           12            160
  MALE             12            394
[1] 2 2
[1] FALSE
D699V8, binary
                cls
clus               0   1
  CD93 MUTATED    18   2
  CD93 WILD-TYPE 398 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     18    2
  CD93 WILD-TYPE  398  100
     clus
vv    CD93 MUTATED CD93 WILD-TYPE
  NO            18            398
  YES            2            100
[1] 2 2
[1] FALSE
D699V9, continuous
D699V10, continuous
[1] "Remove cluster labels:" "CD93 MUTATED"          
clus
  CD93 MUTATED CD93 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A4P3 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD93 MUTATED       4                         1
  CD93 WILD-TYPE   129                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD93 MUTATED                                           0    16
  CD93 WILD-TYPE                                         1   341
D699V11, multiclass
                                           clus
vv                                          CD93 MUTATED CD93 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V12, binary
                cls
clus               0   1
  CD93 MUTATED     0  17
  CD93 WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      0   17
  CD93 WILD-TYPE   10  381
                        clus
vv                       CD93 MUTATED CD93 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(700) Variable = ZBTB38 MUTATION ANALYSIS
D700V1, survival
                  sevent
clus2                0   1
  ZBTB38 MUTATED    15   7
  ZBTB38 WILD-TYPE 323 209
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              22              532 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
               7              209 
$`ZBTB38 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-M9-A5M8 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4256 
       19.99        21.99        33.11        26.70        19.56         9.34 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-A4J5 
       34.68        13.87        29.59         0.26         1.12        28.34 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5733 TCGA-HU-8249 TCGA-HU-A4G3 
       20.42        16.14         6.02        21.07        28.96         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-VQ-A8PK 
       22.68         6.51        23.84        17.85 

$`ZBTB38 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        2.10         1.32         2.66        19.73        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57         6.61        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
            0.26             0.00 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
           34.68           122.30 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
          20.205           13.410 
[1] "0.3 - 34.7 (20.2)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D700V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB38 MUTATED         0        0        2        0         4         6
  ZBTB38 WILD-TYPE      10       20       44       31        80        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB38 MUTATED           0          3          2          2        2
  ZBTB38 WILD-TYPE        29         81         60         37       41
                  vv
clus               STAGE IVA
  ZBTB38 MUTATED           0
  ZBTB38 WILD-TYPE         4
D700V3, multiclass
            clus
vv           ZBTB38 MUTATED ZBTB38 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               6               77
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZBTB38 MUTATED       0   5  10   6
  ZBTB38 WILD-TYPE    54 130 251  96
D700V4, multiclass
       clus
vv      ZBTB38 MUTATED ZBTB38 WILD-TYPE
  T0+T1              0               54
  T2                 5              130
  T3                10              251
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB38 MUTATED     8   6   4   4
  ZBTB38 WILD-TYPE 187 167  85  81
D700V5, multiclass
    clus
vv   ZBTB38 MUTATED ZBTB38 WILD-TYPE
  N0              8              187
  N1              6              167
  N2              4               85
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V6, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    20   1
  ZBTB38 WILD-TYPE 462  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     20    1
  ZBTB38 WILD-TYPE  462   37
   clus
vv  ZBTB38 MUTATED ZBTB38 WILD-TYPE
  0             20              462
  1              1               37
[1] 2 2
[1] FALSE
D700V7, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    12  10
  ZBTB38 WILD-TYPE 160 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     12   10
  ZBTB38 WILD-TYPE  160  396
        clus
vv       ZBTB38 MUTATED ZBTB38 WILD-TYPE
  FEMALE             12              160
  MALE               10              396
[1] 2 2
[1] FALSE
D700V8, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    22   0
  ZBTB38 WILD-TYPE 394 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     22    0
  ZBTB38 WILD-TYPE  394  102
     clus
vv    ZBTB38 MUTATED ZBTB38 WILD-TYPE
  NO              22              394
  YES              0              102
[1] 2 2
[1] FALSE
D700V9, continuous
D700V10, continuous
[1] "Remove cluster labels:" "ZBTB38 MUTATED"        
clus
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" "ZBTB38 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB38 MUTATED       6                         0
  ZBTB38 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB38 MUTATED                                           0    12
  ZBTB38 WILD-TYPE                                         1   345
D700V11, multiclass
                                           clus
vv                                          ZBTB38 MUTATED ZBTB38 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V12, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED     0  16
  ZBTB38 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED      0   16
  ZBTB38 WILD-TYPE   10  382
                        clus
vv                       ZBTB38 MUTATED ZBTB38 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(701) Variable = PRAMEF14 MUTATION ANALYSIS
D701V1, survival
                    sevent
clus2                  0   1
  PRAMEF14 MUTATED     3   2
  PRAMEF14 WILD-TYPE 335 214
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 5                549 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 2                214 
$`PRAMEF14 MUTATED`
TCGA-L5-A4OG TCGA-BR-8284 TCGA-BR-8360 TCGA-CD-A48A TCGA-HU-A4GQ 
        4.70         8.05         6.18        12.43         0.10 

$`PRAMEF14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        29.59         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
               0.1                0.0 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
             12.43             122.30 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
              6.18              13.78 
[1] "0.1 - 12.4 (6.2)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "3.2"
D701V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRAMEF14 MUTATED         2        0        0        0         2         0
  PRAMEF14 WILD-TYPE       8       20       46       31        82        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF14 MUTATED           0          0          0          2        0
  PRAMEF14 WILD-TYPE        29         84         62         37       43
                    vv
clus                 STAGE IVA
  PRAMEF14 MUTATED           0
  PRAMEF14 WILD-TYPE         4
D701V3, multiclass
            clus
vv           PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PRAMEF14 MUTATED       2   0   2   2
  PRAMEF14 WILD-TYPE    52 135 259 100
D701V4, multiclass
       clus
vv      PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  T0+T1                2                 52
  T2                   0                135
  T3                   2                259
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PRAMEF14 MUTATED     3   1   1   1
  PRAMEF14 WILD-TYPE 192 172  88  84
D701V5, multiclass
    clus
vv   PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  N0                3                192
  N1                1                172
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V6, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     5   0
  PRAMEF14 WILD-TYPE 477  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      5    0
  PRAMEF14 WILD-TYPE  477   38
   clus
vv  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  0                5                477
  1                0                 38
[1] 2 2
[1] FALSE
D701V7, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     2   4
  PRAMEF14 WILD-TYPE 170 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      2    4
  PRAMEF14 WILD-TYPE  170  402
        clus
vv       PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  FEMALE                2                170
  MALE                  4                402
[1] 2 2
[1] FALSE
D701V8, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     5   1
  PRAMEF14 WILD-TYPE 411 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      5    1
  PRAMEF14 WILD-TYPE  411  101
     clus
vv    PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  NO                 5                411
  YES                1                101
[1] 2 2
[1] FALSE
D701V9, continuous
D701V10, continuous
[1] "Remove cluster labels:" "PRAMEF14 MUTATED"      
clus
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OI         TCGA-L5-A88T 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" "PRAMEF14 WILD-TYPE" 
        TCGA-Z6-AAPN 
"PRAMEF14 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PRAMEF14 MUTATED       2                         1
  PRAMEF14 WILD-TYPE   131                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRAMEF14 MUTATED                                           0     3
  PRAMEF14 WILD-TYPE                                         1   354
D701V11, multiclass
                                           clus
vv                                          PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V12, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     0   5
  PRAMEF14 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      0    5
  PRAMEF14 WILD-TYPE   10  393
                        clus
vv                       PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(702) Variable = ANKRD28 MUTATION ANALYSIS
D702V1, survival
                   sevent
clus2                 0   1
  ANKRD28 MUTATED     9   8
  ANKRD28 WILD-TYPE 329 208
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               17               537 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                8               208 
$`ANKRD28 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-2H-A9GI TCGA-JY-A6FD TCGA-LN-A9FR TCGA-BR-4256 
        4.31        21.99        14.30        68.02        12.26         9.34 
TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8487 TCGA-BR-A4QL 
       34.68        18.15        31.10         0.95         1.12        16.14 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-MX-A5UG TCGA-MX-A5UJ 
        6.02       105.07         0.10         3.72        19.73 

$`ANKRD28 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A666 
       13.51         2.53         5.56        63.62        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
              0.1               0.0 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
           105.07            122.30 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
            14.30             13.55 
[1] "0.1 - 105.1 (14.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D702V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD28 MUTATED         0        0        0        1         4         2
  ANKRD28 WILD-TYPE      10       20       46       30        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD28 MUTATED           1          2          1          2        3
  ANKRD28 WILD-TYPE        28         82         61         37       40
                   vv
clus                STAGE IVA
  ANKRD28 MUTATED           0
  ANKRD28 WILD-TYPE         4
D702V3, multiclass
            clus
vv           ANKRD28 MUTATED ANKRD28 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                4                80
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ANKRD28 MUTATED       0   2   9   5
  ANKRD28 WILD-TYPE    54 133 252  97
D702V4, multiclass
       clus
vv      ANKRD28 MUTATED ANKRD28 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  9               252
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ANKRD28 MUTATED     5   8   3   1
  ANKRD28 WILD-TYPE 190 165  86  84
D702V5, multiclass
    clus
vv   ANKRD28 MUTATED ANKRD28 WILD-TYPE
  N0               5               190
  N1               8               165
  N2               3                86
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V6, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED    15   1
  ANKRD28 WILD-TYPE 467  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED     15    1
  ANKRD28 WILD-TYPE  467   37
   clus
vv  ANKRD28 MUTATED ANKRD28 WILD-TYPE
  0              15               467
  1               1                37
[1] 2 2
[1] FALSE
D702V7, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED     8   9
  ANKRD28 WILD-TYPE 164 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      8    9
  ANKRD28 WILD-TYPE  164  397
        clus
vv       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  FEMALE               8               164
  MALE                 9               397
[1] 2 2
[1] FALSE
D702V8, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED    15   1
  ANKRD28 WILD-TYPE 401 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED     15    1
  ANKRD28 WILD-TYPE  401  101
     clus
vv    ANKRD28 MUTATED ANKRD28 WILD-TYPE
  NO               15               401
  YES               1               101
[1] 2 2
[1] FALSE
D702V9, continuous
D702V10, continuous
[1] "Remove cluster labels:" "ANKRD28 MUTATED"       
clus
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-Z6-AAPN 
"ANKRD28 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD28 MUTATED       4                         0
  ANKRD28 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD28 MUTATED                                           0     9
  ANKRD28 WILD-TYPE                                         1   348
D702V11, multiclass
                                           clus
vv                                          ANKRD28 MUTATED ANKRD28 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V12, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED     0  11
  ANKRD28 WILD-TYPE  10 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      0   11
  ANKRD28 WILD-TYPE   10  387
                        clus
vv                       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(703) Variable = MKRN3 MUTATION ANALYSIS
D703V1, survival
                 sevent
clus2               0   1
  MKRN3 MUTATED    15   7
  MKRN3 WILD-TYPE 323 209
  MKRN3 MUTATED MKRN3 WILD-TYPE 
             22             532 
  MKRN3 MUTATED MKRN3 WILD-TYPE 
              7             209 
$`MKRN3 MUTATED`
TCGA-2H-A9GF TCGA-IG-A4P3 TCGA-JY-A6FH TCGA-L5-A8NJ TCGA-LN-A49Y TCGA-R6-A8W8 
       25.78        18.64        47.38        16.47        12.46         2.89 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8077 TCGA-BR-8080 
        6.97        30.90        34.68        32.78         0.69         9.60 
TCGA-BR-8361 TCGA-BR-8369 TCGA-CD-8529 TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4H0 
       31.10        14.04        12.30        29.98         8.98         2.10 
TCGA-HU-A4H3 TCGA-IN-A6RI TCGA-IN-AB1X TCGA-RD-A7BT 
       29.00        18.38        13.51         8.61 

$`MKRN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       33.21        37.25        14.43        11.44        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77        21.37         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.58        20.25         0.26        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MKRN3 MUTATED MKRN3 WILD-TYPE 
           0.69            0.00 
  MKRN3 MUTATED MKRN3 WILD-TYPE 
          47.38          122.30 
  MKRN3 MUTATED MKRN3 WILD-TYPE 
         15.255          13.530 
[1] "0.7 - 47.4 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D703V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MKRN3 MUTATED         1        0        1        0         6         2
  MKRN3 WILD-TYPE       9       20       45       31        78        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKRN3 MUTATED           2          1          2          4        2         0
  MKRN3 WILD-TYPE        27         83         60         35       41         4
D703V3, multiclass
            clus
vv           MKRN3 MUTATED MKRN3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              6              78
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MKRN3 MUTATED       1   7   9   6
  MKRN3 WILD-TYPE    53 128 252  96
D703V4, multiclass
       clus
vv      MKRN3 MUTATED MKRN3 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MKRN3 MUTATED     7   8   1   5
  MKRN3 WILD-TYPE 188 165  88  80
D703V5, multiclass
    clus
vv   MKRN3 MUTATED MKRN3 WILD-TYPE
  N0             7             188
  N1             8             165
  N2             1              88
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V6, binary
                 cls
clus                0   1
  MKRN3 MUTATED    21   1
  MKRN3 WILD-TYPE 461  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKRN3 MUTATED     21    1
  MKRN3 WILD-TYPE  461   37
   clus
vv  MKRN3 MUTATED MKRN3 WILD-TYPE
  0            21             461
  1             1              37
[1] 2 2
[1] FALSE
D703V7, binary
                 cls
clus                0   1
  MKRN3 MUTATED    11  13
  MKRN3 WILD-TYPE 161 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKRN3 MUTATED     11   13
  MKRN3 WILD-TYPE  161  393
        clus
vv       MKRN3 MUTATED MKRN3 WILD-TYPE
  FEMALE            11             161
  MALE              13             393
[1] 2 2
[1] FALSE
D703V8, binary
                 cls
clus                0   1
  MKRN3 MUTATED    18   2
  MKRN3 WILD-TYPE 398 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKRN3 MUTATED     18    2
  MKRN3 WILD-TYPE  398  100
     clus
vv    MKRN3 MUTATED MKRN3 WILD-TYPE
  NO             18             398
  YES             2             100
[1] 2 2
[1] FALSE
D703V9, continuous
[1] "Remove cluster labels:" "MKRN3 MUTATED"         
clus
  MKRN3 MUTATED MKRN3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A4A1      TCGA-LN-A4A2 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" "MKRN3 WILD-TYPE" 
D703V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MKRN3 MUTATED       6                         0
  MKRN3 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKRN3 MUTATED                                           1    15
  MKRN3 WILD-TYPE                                         0   342
D703V11, multiclass
                                           clus
vv                                          MKRN3 MUTATED MKRN3 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V12, binary
                 cls
clus                0   1
  MKRN3 MUTATED     0  20
  MKRN3 WILD-TYPE  10 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKRN3 MUTATED      0   20
  MKRN3 WILD-TYPE   10  378
                        clus
vv                       MKRN3 MUTATED MKRN3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(704) Variable = MAN1C1 MUTATION ANALYSIS
D704V1, survival
                  sevent
clus2                0   1
  MAN1C1 MUTATED     4   4
  MAN1C1 WILD-TYPE 334 212
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               8              546 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               4              212 
$`MAN1C1 MUTATED`
TCGA-LN-A49S TCGA-BR-4256 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-5726 TCGA-D7-5577 
       13.15         9.34        29.59         6.58        28.96        25.71 
TCGA-FP-A4BE TCGA-HU-A4G8 
       11.08        22.68 

$`MAN1C1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
            6.58             0.00 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
           29.59           122.30 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
          17.915           13.565 
[1] "6.6 - 29.6 (17.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D704V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAN1C1 MUTATED         1        1        0        0         3         3
  MAN1C1 WILD-TYPE       9       19       46       31        81        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAN1C1 MUTATED           0          2          0          0        0
  MAN1C1 WILD-TYPE        29         82         62         39       43
                  vv
clus               STAGE IVA
  MAN1C1 MUTATED           0
  MAN1C1 WILD-TYPE         4
D704V3, multiclass
            clus
vv           MAN1C1 MUTATED MAN1C1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAN1C1 MUTATED       2   1   4   3
  MAN1C1 WILD-TYPE    52 134 257  99
D704V4, multiclass
       clus
vv      MAN1C1 MUTATED MAN1C1 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAN1C1 MUTATED     7   3   0   1
  MAN1C1 WILD-TYPE 188 170  89  84
D704V5, multiclass
    clus
vv   MAN1C1 MUTATED MAN1C1 WILD-TYPE
  N0              7              188
  N1              3              170
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V6, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED    10   0
  MAN1C1 WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED     10    0
  MAN1C1 WILD-TYPE  472   38
   clus
vv  MAN1C1 MUTATED MAN1C1 WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D704V7, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     4   7
  MAN1C1 WILD-TYPE 168 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      4    7
  MAN1C1 WILD-TYPE  168  399
        clus
vv       MAN1C1 MUTATED MAN1C1 WILD-TYPE
  FEMALE              4              168
  MALE                7              399
[1] 2 2
[1] FALSE
D704V8, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     7   2
  MAN1C1 WILD-TYPE 409 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      7    2
  MAN1C1 WILD-TYPE  409  100
     clus
vv    MAN1C1 MUTATED MAN1C1 WILD-TYPE
  NO               7              409
  YES              2              100
[1] 2 2
[1] FALSE
D704V9, continuous
[1] "Remove cluster labels:" "MAN1C1 MUTATED"        
clus
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
D704V10, continuous
[1] "Remove cluster labels:" "MAN1C1 MUTATED"        
clus
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49U 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" "MAN1C1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"MAN1C1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAN1C1 MUTATED       3                         2
  MAN1C1 WILD-TYPE   130                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAN1C1 MUTATED                                           0     5
  MAN1C1 WILD-TYPE                                         1   352
D704V11, multiclass
                                           clus
vv                                          MAN1C1 MUTATED MAN1C1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V12, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     0  10
  MAN1C1 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      0   10
  MAN1C1 WILD-TYPE   10  388
                        clus
vv                       MAN1C1 MUTATED MAN1C1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(705) Variable = STK11 MUTATION ANALYSIS
D705V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED     8   2
  STK11 WILD-TYPE 330 214
  STK11 MUTATED STK11 WILD-TYPE 
             10             544 
  STK11 MUTATED STK11 WILD-TYPE 
              2             214 
$`STK11 MUTATED`
TCGA-JY-A6FD TCGA-L5-A8NM TCGA-LN-A7HV TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-BR-A4J6 
       68.02         7.76        10.52         3.42         2.66         0.66 
TCGA-D7-A4YT TCGA-HU-8602 TCGA-VQ-A91V TCGA-VQ-A94T 
       14.27        22.32        42.64        11.24 

$`STK11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53        28.34        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA64 
        1.87        15.65        20.81         1.71        66.81        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  STK11 MUTATED STK11 WILD-TYPE 
           0.66            0.00 
  STK11 MUTATED STK11 WILD-TYPE 
          68.02          122.30 
  STK11 MUTATED STK11 WILD-TYPE 
          10.88           13.63 
[1] "0.7 - 68.0 (10.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D705V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK11 MUTATED         0        0        0        0         4         3
  STK11 WILD-TYPE      10       20       46       31        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK11 MUTATED           0          2          1          0        0         0
  STK11 WILD-TYPE        29         82         61         39       43         4
D705V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  STK11 MUTATED       0   3   7   1
  STK11 WILD-TYPE    54 132 254 101
D705V4, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                7             254
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK11 MUTATED     6   1   2   1
  STK11 WILD-TYPE 189 172  87  84
D705V5, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  N0             6             189
  N1             1             172
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V6, binary
                 cls
clus                0   1
  STK11 MUTATED    10   0
  STK11 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     10    0
  STK11 WILD-TYPE  472   38
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D705V7, binary
                 cls
clus                0   1
  STK11 MUTATED     5   6
  STK11 WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      5    6
  STK11 WILD-TYPE  167  400
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D705V8, binary
                 cls
clus                0   1
  STK11 MUTATED     8   2
  STK11 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      8    2
  STK11 WILD-TYPE  408  100
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D705V9, continuous
[1] "Remove cluster labels:" "STK11 MUTATED"         
clus
  STK11 MUTATED STK11 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JE 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" 
D705V10, continuous
[1] "Remove cluster labels:" "STK11 MUTATED"         
clus
  STK11 MUTATED STK11 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" "STK11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STK11 MUTATED       3                         0
  STK11 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STK11 MUTATED                                           0     6
  STK11 WILD-TYPE                                         1   351
D705V11, multiclass
                                           clus
vv                                          STK11 MUTATED STK11 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V12, binary
                 cls
clus                0   1
  STK11 MUTATED     0   7
  STK11 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      0    7
  STK11 WILD-TYPE   10  391
                        clus
vv                       STK11 MUTATED STK11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(706) Variable = VPS13A MUTATION ANALYSIS
D706V1, survival
                  sevent
clus2                0   1
  VPS13A MUTATED    26  12
  VPS13A WILD-TYPE 312 204
  VPS13A MUTATED VPS13A WILD-TYPE 
              38              516 
  VPS13A MUTATED VPS13A WILD-TYPE 
              12              204 
$`VPS13A MUTATED`
TCGA-IC-A6RF TCGA-2H-A9GM TCGA-IG-A4P3 TCGA-L5-A8NS TCGA-BR-4184 TCGA-BR-4256 
       15.68        13.94        18.64        13.41         6.97         9.34 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 
        6.61        34.68        32.78        36.16        35.24        39.78 
TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
       29.59         2.66        31.10        27.12        28.14        31.96 
TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ 
       12.89        16.14        12.43        12.30         6.58        12.62 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-5577 
        1.02         8.05         6.02       105.07        65.10        25.71 
TCGA-D7-5579 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 
       20.91         5.92        14.47        29.98        20.25        29.00 
TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       38.14        26.04 

$`VPS13A WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       69.04        21.07         7.99        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        16.14        27.55        12.43        17.26 

  VPS13A MUTATED VPS13A WILD-TYPE 
            1.02             0.00 
  VPS13A MUTATED VPS13A WILD-TYPE 
          105.07           122.30 
  VPS13A MUTATED VPS13A WILD-TYPE 
          19.445           13.410 
[1] "1.0 - 105.1 (19.4)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D706V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS13A MUTATED         1        2        4        4         5         8
  VPS13A WILD-TYPE       9       18       42       27        79        75
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13A MUTATED           1          4          2          4        4
  VPS13A WILD-TYPE        28         80         60         35       39
                  vv
clus               STAGE IVA
  VPS13A MUTATED           0
  VPS13A WILD-TYPE         4
D706V3, multiclass
            clus
vv           VPS13A MUTATED VPS13A WILD-TYPE
  STAGE I                 1                9
  STAGE IA                2               18
  STAGE IB                4               42
  STAGE II                4               27
  STAGE IIA               5               79
  STAGE IIB               8               75
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              2               60
  STAGE IIIC              4               35
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  VPS13A MUTATED       4  10  14  11
  VPS13A WILD-TYPE    50 125 247  91
D706V4, multiclass
       clus
vv      VPS13A MUTATED VPS13A WILD-TYPE
  T0+T1              4               50
  T2                10              125
  T3                14              247
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  VPS13A MUTATED    15  16   5   5
  VPS13A WILD-TYPE 180 157  84  80
D706V5, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  N0             15              180
  N1             16              157
  N2              5               84
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V6, binary
                  cls
clus                 0   1
  VPS13A MUTATED    37   3
  VPS13A WILD-TYPE 445  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     37    3
  VPS13A WILD-TYPE  445   35
   clus
vv  VPS13A MUTATED VPS13A WILD-TYPE
  0             37              445
  1              3               35
[1] 2 2
[1] FALSE
D706V7, binary
                  cls
clus                 0   1
  VPS13A MUTATED    16  26
  VPS13A WILD-TYPE 156 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     16   26
  VPS13A WILD-TYPE  156  380
        clus
vv       VPS13A MUTATED VPS13A WILD-TYPE
  FEMALE             16              156
  MALE               26              380
[1] 2 2
[1] FALSE
D706V8, binary
                  cls
clus                 0   1
  VPS13A MUTATED    33   3
  VPS13A WILD-TYPE 383  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     33    3
  VPS13A WILD-TYPE  383   99
     clus
vv    VPS13A MUTATED VPS13A WILD-TYPE
  NO              33              383
  YES              3               99
[1] 2 2
[1] FALSE
D706V9, continuous
D706V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  VPS13A MUTATED       9                         1
  VPS13A WILD-TYPE   124                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS13A MUTATED                                           0    25
  VPS13A WILD-TYPE                                         1   332
D706V11, multiclass
                                           clus
vv                                          VPS13A MUTATED VPS13A WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 25              332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V12, binary
                  cls
clus                 0   1
  VPS13A MUTATED     0  32
  VPS13A WILD-TYPE  10 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED      0   32
  VPS13A WILD-TYPE   10  366
                        clus
vv                       VPS13A MUTATED VPS13A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             32              366
[1] 2 2
[1] FALSE

Clustering(707) Variable = BEND5 MUTATION ANALYSIS
D707V1, survival
                 sevent
clus2               0   1
  BEND5 MUTATED     2   4
  BEND5 WILD-TYPE 336 212
  BEND5 MUTATED BEND5 WILD-TYPE 
              6             548 
  BEND5 MUTATED BEND5 WILD-TYPE 
              4             212 
$`BEND5 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-IG-A4P3 TCGA-LN-A4A9 TCGA-Z6-AAPN TCGA-HJ-7597 
       21.99        79.07        18.64        11.54         2.66        26.47 

$`BEND5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO 
       27.12         5.16        20.02        47.05        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BEND5 MUTATED BEND5 WILD-TYPE 
           2.66            0.00 
  BEND5 MUTATED BEND5 WILD-TYPE 
          79.07          122.30 
  BEND5 MUTATED BEND5 WILD-TYPE 
         20.315          13.530 
[1] "2.7 - 79.1 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D707V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEND5 MUTATED         0        0        2        1         2         2
  BEND5 WILD-TYPE      10       20       44       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BEND5 MUTATED           0          0          0          0        1         0
  BEND5 WILD-TYPE        29         84         62         39       42         4
D707V3, multiclass
            clus
vv           BEND5 MUTATED BEND5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BEND5 MUTATED       0   4   2   2
  BEND5 WILD-TYPE    54 131 259 100
D707V4, multiclass
       clus
vv      BEND5 MUTATED BEND5 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BEND5 MUTATED     6   2   0   0
  BEND5 WILD-TYPE 189 171  89  85
D707V5, multiclass
    clus
vv   BEND5 MUTATED BEND5 WILD-TYPE
  N0             6             189
  N1             2             171
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V6, binary
                 cls
clus                0   1
  BEND5 MUTATED     7   1
  BEND5 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      7    1
  BEND5 WILD-TYPE  475   37
   clus
vv  BEND5 MUTATED BEND5 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D707V7, binary
                 cls
clus                0   1
  BEND5 MUTATED     3   6
  BEND5 WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      3    6
  BEND5 WILD-TYPE  169  400
        clus
vv       BEND5 MUTATED BEND5 WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D707V8, binary
                 cls
clus                0   1
  BEND5 MUTATED     6   1
  BEND5 WILD-TYPE 410 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      6    1
  BEND5 WILD-TYPE  410  101
     clus
vv    BEND5 MUTATED BEND5 WILD-TYPE
  NO              6             410
  YES             1             101
[1] 2 2
[1] FALSE
D707V9, continuous
[1] "Remove cluster labels:" "BEND5 MUTATED"         
clus
  BEND5 MUTATED BEND5 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BEND5 WILD-TYPE" "BEND5 WILD-TYPE" "BEND5 WILD-TYPE" 
D707V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BEND5 MUTATED       1                         0
  BEND5 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BEND5 MUTATED                                           0     5
  BEND5 WILD-TYPE                                         1   352
D707V11, multiclass
                                           clus
vv                                          BEND5 MUTATED BEND5 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V12, binary
                 cls
clus                0   1
  BEND5 MUTATED     0   6
  BEND5 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      0    6
  BEND5 WILD-TYPE   10  392
                        clus
vv                       BEND5 MUTATED BEND5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(708) Variable = TPTE2 MUTATION ANALYSIS
D708V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED    12   9
  TPTE2 WILD-TYPE 326 207
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             21             533 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              9             207 
$`TPTE2 MUTATED`
TCGA-L5-A43E TCGA-L5-A88W TCGA-L5-A8NF TCGA-R6-A6XG TCGA-Z6-AAPN TCGA-BR-4184 
       30.25        25.12         2.66        38.40         2.66         6.97 
TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-8680 TCGA-BR-8690 TCGA-CG-5721 
       34.68         9.17        35.24        31.96        10.68         6.02 
TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GU 
       14.76         7.99        52.21        26.47         5.92         6.58 
TCGA-HU-A4H6 TCGA-RD-A7BT TCGA-VQ-A8PK 
       21.17         8.61        17.85 

$`TPTE2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        6.21        77.29        63.06        30.51         1.51        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM 
       43.36        37.41        38.14        37.22        22.19         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           2.66            0.00 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          52.21          122.30 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          14.76           13.55 
[1] "2.7 - 52.2 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D708V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPTE2 MUTATED         1        1        1        1         3         4
  TPTE2 WILD-TYPE       9       19       45       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPTE2 MUTATED           0          2          2          1        3         1
  TPTE2 WILD-TYPE        29         82         60         38       40         3
D708V3, multiclass
            clus
vv           TPTE2 MUTATED TPTE2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TPTE2 MUTATED       3   3  11   4
  TPTE2 WILD-TYPE    51 132 250  98
D708V4, multiclass
       clus
vv      TPTE2 MUTATED TPTE2 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3               11             250
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TPTE2 MUTATED     9   4   3   4
  TPTE2 WILD-TYPE 186 169  86  81
D708V5, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  N0             9             186
  N1             4             169
  N2             3              86
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED    15   2
  TPTE2 WILD-TYPE 467  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED     15    2
  TPTE2 WILD-TYPE  467   36
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0            15             467
  1             2              36
[1] 2 2
[1] FALSE
D708V7, binary
                 cls
clus                0   1
  TPTE2 MUTATED     8  14
  TPTE2 WILD-TYPE 164 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      8   14
  TPTE2 WILD-TYPE  164  392
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             8             164
  MALE              14             392
[1] 2 2
[1] FALSE
D708V8, binary
                 cls
clus                0   1
  TPTE2 MUTATED    18   3
  TPTE2 WILD-TYPE 398  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED     18    3
  TPTE2 WILD-TYPE  398   99
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO             18             398
  YES             3              99
[1] 2 2
[1] FALSE
D708V9, continuous
D708V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TPTE2 MUTATED       4                         0
  TPTE2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TPTE2 MUTATED                                           1    15
  TPTE2 WILD-TYPE                                         0   342
D708V11, multiclass
                                           clus
vv                                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V12, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0  16
  TPTE2 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0   16
  TPTE2 WILD-TYPE   10  382
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(709) Variable = NFE2L1 MUTATION ANALYSIS
D709V1, survival
                  sevent
clus2                0   1
  NFE2L1 MUTATED     7   6
  NFE2L1 WILD-TYPE 331 210
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
              13              541 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               6              210 
$`NFE2L1 MUTATED`
TCGA-EQ-A4SO TCGA-IG-A97H TCGA-JY-A939 TCGA-LN-A4A5 TCGA-R6-A8W5 TCGA-BR-4191 
       16.24        14.50        21.70        22.39        15.78        18.35 
TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-A4MI TCGA-D7-A6EY TCGA-F1-6874 
       30.90         1.12        12.30        11.77        11.44        14.47 
TCGA-HU-A4GN 
       29.98 

$`NFE2L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
            1.12             0.00 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
            30.9            122.3 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
           15.78            13.51 
[1] "1.1 - 30.9 (15.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D709V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFE2L1 MUTATED         0        0        1        0         4         1
  NFE2L1 WILD-TYPE      10       20       45       31        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFE2L1 MUTATED           0          1          2          0        1
  NFE2L1 WILD-TYPE        29         83         60         39       42
                  vv
clus               STAGE IVA
  NFE2L1 MUTATED           1
  NFE2L1 WILD-TYPE         3
D709V3, multiclass
            clus
vv           NFE2L1 MUTATED NFE2L1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NFE2L1 MUTATED       2   4   5   2
  NFE2L1 WILD-TYPE    52 131 256 100
D709V4, multiclass
       clus
vv      NFE2L1 MUTATED NFE2L1 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NFE2L1 MUTATED     4   7   0   1
  NFE2L1 WILD-TYPE 191 166  89  84
D709V5, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  N0              4              191
  N1              7              166
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V6, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED    12   2
  NFE2L1 WILD-TYPE 470  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED     12    2
  NFE2L1 WILD-TYPE  470   36
   clus
vv  NFE2L1 MUTATED NFE2L1 WILD-TYPE
  0             12              470
  1              2               36
[1] 2 2
[1] FALSE
D709V7, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     5  10
  NFE2L1 WILD-TYPE 167 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      5   10
  NFE2L1 WILD-TYPE  167  396
        clus
vv       NFE2L1 MUTATED NFE2L1 WILD-TYPE
  FEMALE              5              167
  MALE               10              396
[1] 2 2
[1] FALSE
D709V8, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED    10   2
  NFE2L1 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED     10    2
  NFE2L1 WILD-TYPE  406  100
     clus
vv    NFE2L1 MUTATED NFE2L1 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D709V9, continuous
[1] "Remove cluster labels:" "NFE2L1 MUTATED"        
clus
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A6 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
D709V10, continuous
[1] "Remove cluster labels:" "NFE2L1 MUTATED"        
clus
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-JY-A6FA       TCGA-JY-A6FE 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W8 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" "NFE2L1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NFE2L1 MUTATED       5                         0
  NFE2L1 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L1 MUTATED                                           0    10
  NFE2L1 WILD-TYPE                                         1   347
D709V11, multiclass
                                           clus
vv                                          NFE2L1 MUTATED NFE2L1 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V12, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     0  14
  NFE2L1 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      0   14
  NFE2L1 WILD-TYPE   10  384
                        clus
vv                       NFE2L1 MUTATED NFE2L1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(710) Variable = ITGAV MUTATION ANALYSIS
D710V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    16   5
  ITGAV WILD-TYPE 322 211
  ITGAV MUTATED ITGAV WILD-TYPE 
             21             533 
  ITGAV MUTATED ITGAV WILD-TYPE 
              5             211 
$`ITGAV MUTATED`
TCGA-L5-A43J TCGA-JY-A6FD TCGA-JY-A93E TCGA-LN-A4A9 TCGA-LN-A7HX TCGA-BR-6458 
        4.31        68.02        25.22        11.54        12.23        19.33 
TCGA-BR-7197 TCGA-BR-7722 TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-5730 
        9.21        15.32        29.59         1.12        15.95         4.01 
TCGA-D7-6528 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-KB-A93J 
       15.22        22.32        25.81         6.51        14.07        36.95 
TCGA-VQ-A8P2 TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.14        12.43        17.26 

$`ITGAV WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        54.12        26.04        16.14        27.55 

  ITGAV MUTATED ITGAV WILD-TYPE 
           1.12            0.00 
  ITGAV MUTATED ITGAV WILD-TYPE 
          68.02          122.30 
  ITGAV MUTATED ITGAV WILD-TYPE 
          15.32           13.51 
[1] "1.1 - 68.0 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D710V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAV MUTATED         0        1        3        3         6         5
  ITGAV WILD-TYPE      10       19       43       28        78        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAV MUTATED           0          2          0          1        2         0
  ITGAV WILD-TYPE        29         82         62         38       41         4
D710V3, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               3              28
  STAGE IIA              6              78
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGAV MUTATED       2   7   9   5
  ITGAV WILD-TYPE    52 128 252  97
D710V4, multiclass
       clus
vv      ITGAV MUTATED ITGAV WILD-TYPE
  T0+T1             2              52
  T2                7             128
  T3                9             252
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGAV MUTATED    13   8   1   1
  ITGAV WILD-TYPE 182 165  88  84
D710V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0            13             182
  N1             8             165
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V6, binary
                 cls
clus                0   1
  ITGAV MUTATED    20   1
  ITGAV WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     20    1
  ITGAV WILD-TYPE  462   37
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D710V7, binary
                 cls
clus                0   1
  ITGAV MUTATED     9  14
  ITGAV WILD-TYPE 163 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      9   14
  ITGAV WILD-TYPE  163  392
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  FEMALE             9             163
  MALE              14             392
[1] 2 2
[1] FALSE
D710V8, binary
                 cls
clus                0   1
  ITGAV MUTATED    15   5
  ITGAV WILD-TYPE 401  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     15    5
  ITGAV WILD-TYPE  401   97
     clus
vv    ITGAV MUTATED ITGAV WILD-TYPE
  NO             15             401
  YES             5              97
[1] 2 2
[1] FALSE
D710V9, continuous
[1] "Remove cluster labels:" "ITGAV MUTATED"         
clus
  ITGAV MUTATED ITGAV WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ITGAV WILD-TYPE" "ITGAV WILD-TYPE" 
D710V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGAV MUTATED       8                         0
  ITGAV WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGAV MUTATED                                           0    13
  ITGAV WILD-TYPE                                         1   344
D710V11, multiclass
                                           clus
vv                                          ITGAV MUTATED ITGAV WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V12, binary
                 cls
clus                0   1
  ITGAV MUTATED     0  15
  ITGAV WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      0   15
  ITGAV WILD-TYPE   10  383
                        clus
vv                       ITGAV MUTATED ITGAV WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(711) Variable = BRCA2 MUTATION ANALYSIS
D711V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED    25  13
  BRCA2 WILD-TYPE 313 203
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             38             516 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             13             203 
$`BRCA2 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-JY-A6FA TCGA-L5-A8NF 
        4.31        19.99         5.92         0.85        44.75         2.66 
TCGA-L5-A8NS TCGA-LN-A4A2 TCGA-R6-A8W8 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 
       13.41        12.49         2.89         6.97        34.68        44.94 
TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8384 TCGA-BR-8680 
       29.59         6.18        31.10         4.31         3.72        31.96 
TCGA-CD-8529 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
       12.30        11.61         6.58        11.77        12.62        15.95 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6520 TCGA-D7-A4YT TCGA-D7-A6EZ 
        6.02        65.10        21.07        18.84        14.27        20.32 
TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-IN-A6RL 
       77.29        22.32        22.68        29.98         6.58        13.35 
TCGA-IN-A6RP TCGA-VQ-A8P2 
        6.44        38.14 

$`BRCA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.43         6.31        12.30        11.31        12.43        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           0.85            0.00 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          77.29          122.30 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          13.38           13.63 
[1] "0.8 - 77.3 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D711V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRCA2 MUTATED         0        1        3        2         6         8
  BRCA2 WILD-TYPE      10       19       43       29        78        75
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA2 MUTATED           1         10          0          4        4         1
  BRCA2 WILD-TYPE        28         74         62         35       39         3
D711V3, multiclass
            clus
vv           BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              8              75
  STAGE III              1              28
  STAGE IIIA            10              74
  STAGE IIIB             0              62
  STAGE IIIC             4              35
  STAGE IV               4              39
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BRCA2 MUTATED       3  11  15  11
  BRCA2 WILD-TYPE    51 124 246  91
D711V4, multiclass
       clus
vv      BRCA2 MUTATED BRCA2 WILD-TYPE
  T0+T1             3              51
  T2               11             124
  T3               15             246
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BRCA2 MUTATED    17  14   7   3
  BRCA2 WILD-TYPE 178 159  82  82
D711V5, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  N0            17             178
  N1            14             159
  N2             7              82
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V6, binary
                 cls
clus                0   1
  BRCA2 MUTATED    35   3
  BRCA2 WILD-TYPE 447  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     35    3
  BRCA2 WILD-TYPE  447   35
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0            35             447
  1             3              35
[1] 2 2
[1] FALSE
D711V7, binary
                 cls
clus                0   1
  BRCA2 MUTATED    13  29
  BRCA2 WILD-TYPE 159 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     13   29
  BRCA2 WILD-TYPE  159  377
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE            13             159
  MALE              29             377
[1] 2 2
[1] FALSE
D711V8, binary
                 cls
clus                0   1
  BRCA2 MUTATED    30   7
  BRCA2 WILD-TYPE 386  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     30    7
  BRCA2 WILD-TYPE  386   95
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO             30             386
  YES             7              95
[1] 2 2
[1] FALSE
D711V9, continuous
[1] "Remove cluster labels:" "BRCA2 MUTATED"         
clus
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A3 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
D711V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRCA2 MUTATED      13                         0
  BRCA2 WILD-TYPE   120                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRCA2 MUTATED                                           0    23
  BRCA2 WILD-TYPE                                         1   334
D711V11, multiclass
                                           clus
vv                                          BRCA2 MUTATED BRCA2 WILD-TYPE
  ASIAN                                                13             120
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V12, binary
                 cls
clus                0   1
  BRCA2 MUTATED     0  30
  BRCA2 WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0   30
  BRCA2 WILD-TYPE   10  368
                        clus
vv                       BRCA2 MUTATED BRCA2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(712) Variable = CWF19L2 MUTATION ANALYSIS
D712V1, survival
                   sevent
clus2                 0   1
  CWF19L2 MUTATED    13   4
  CWF19L2 WILD-TYPE 325 212
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               17               537 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                4               212 
$`CWF19L2 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4QS TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A8NQ TCGA-V5-AASX 
       19.99         3.88        21.01        18.35        21.37         8.98 
TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YY 
       35.84        29.59        12.43         6.02        65.10        13.78 
TCGA-FP-7916 TCGA-HU-A4GT TCGA-HU-A4H5 TCGA-MX-A5UJ TCGA-R5-A7ZI 
       14.07         6.51        23.80        19.73        74.53 

$`CWF19L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO 
       30.25         0.30        26.33        32.61        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
             3.88              0.00 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            74.53            122.30 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            19.73             13.48 
[1] "3.9 - 74.5 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D712V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CWF19L2 MUTATED         2        0        3        1         2         2
  CWF19L2 WILD-TYPE       8       20       43       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CWF19L2 MUTATED           0          1          2          2        3
  CWF19L2 WILD-TYPE        29         83         60         37       40
                   vv
clus                STAGE IVA
  CWF19L2 MUTATED           0
  CWF19L2 WILD-TYPE         4
D712V3, multiclass
            clus
vv           CWF19L2 MUTATED CWF19L2 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CWF19L2 MUTATED       3   4   6   5
  CWF19L2 WILD-TYPE    51 131 255  97
D712V4, multiclass
       clus
vv      CWF19L2 MUTATED CWF19L2 WILD-TYPE
  T0+T1               3                51
  T2                  4               131
  T3                  6               255
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CWF19L2 MUTATED     8   4   3   3
  CWF19L2 WILD-TYPE 187 169  86  82
D712V5, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  N0               8               187
  N1               4               169
  N2               3                86
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V6, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    13   2
  CWF19L2 WILD-TYPE 469  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     13    2
  CWF19L2 WILD-TYPE  469   36
   clus
vv  CWF19L2 MUTATED CWF19L2 WILD-TYPE
  0              13               469
  1               2                36
[1] 2 2
[1] FALSE
D712V7, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     8  12
  CWF19L2 WILD-TYPE 164 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      8   12
  CWF19L2 WILD-TYPE  164  394
        clus
vv       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  FEMALE               8               164
  MALE                12               394
[1] 2 2
[1] FALSE
D712V8, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    14   1
  CWF19L2 WILD-TYPE 402 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     14    1
  CWF19L2 WILD-TYPE  402  101
     clus
vv    CWF19L2 MUTATED CWF19L2 WILD-TYPE
  NO               14               402
  YES               1               101
[1] 2 2
[1] FALSE
D712V9, continuous
[1] "Remove cluster labels:" "CWF19L2 MUTATED"       
clus
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-VR-A8EO        TCGA-VR-A8EP 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" "CWF19L2 WILD-TYPE" 
D712V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CWF19L2 MUTATED       4                         1
  CWF19L2 WILD-TYPE   129                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CWF19L2 MUTATED                                           0    12
  CWF19L2 WILD-TYPE                                         1   345
D712V11, multiclass
                                           clus
vv                                          CWF19L2 MUTATED CWF19L2 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V12, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     1  12
  CWF19L2 WILD-TYPE   9 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      1   12
  CWF19L2 WILD-TYPE    9  386
                        clus
vv                       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(713) Variable = GBP3 MUTATION ANALYSIS
D713V1, survival
                sevent
clus2              0   1
  GBP3 MUTATED     6   0
  GBP3 WILD-TYPE 332 216
  GBP3 MUTATED GBP3 WILD-TYPE 
             6            548 
  GBP3 MUTATED GBP3 WILD-TYPE 
             0            216 
$`GBP3 MUTATED`
TCGA-L5-A4OI TCGA-BR-8081 TCGA-HU-8602 TCGA-HU-A4GX TCGA-IN-A6RN TCGA-VQ-A8P2 
       19.99        32.25        22.32        20.25        19.53        38.14 

$`GBP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GBP3 MUTATED GBP3 WILD-TYPE 
         19.53           0.00 
  GBP3 MUTATED GBP3 WILD-TYPE 
         38.14         122.30 
  GBP3 MUTATED GBP3 WILD-TYPE 
        21.285         13.495 
[1] "19.5 - 38.1 (21.3)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9200000"
D713V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GBP3 MUTATED         0        0        0        0         1         2
  GBP3 WILD-TYPE      10       20       46       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GBP3 MUTATED           0          1          0          2        0         0
  GBP3 WILD-TYPE        29         83         62         37       43         4
D713V3, multiclass
            clus
vv           GBP3 MUTATED GBP3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GBP3 MUTATED       1   0   1   4
  GBP3 WILD-TYPE    53 135 260  98
D713V4, multiclass
       clus
vv      GBP3 MUTATED GBP3 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               1            260
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GBP3 MUTATED     2   1   2   1
  GBP3 WILD-TYPE 193 172  87  84
D713V5, multiclass
    clus
vv   GBP3 MUTATED GBP3 WILD-TYPE
  N0            2            193
  N1            1            172
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V6, binary
                cls
clus               0   1
  GBP3 MUTATED     5   0
  GBP3 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP3 MUTATED      5    0
  GBP3 WILD-TYPE  477   38
   clus
vv  GBP3 MUTATED GBP3 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D713V7, binary
                cls
clus               0   1
  GBP3 MUTATED     4   2
  GBP3 WILD-TYPE 168 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP3 MUTATED      4    2
  GBP3 WILD-TYPE  168  404
        clus
vv       GBP3 MUTATED GBP3 WILD-TYPE
  FEMALE            4            168
  MALE              2            404
[1] 2 2
[1] FALSE
D713V8, binary
                cls
clus               0   1
  GBP3 MUTATED     5   1
  GBP3 WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP3 MUTATED      5    1
  GBP3 WILD-TYPE  411  101
     clus
vv    GBP3 MUTATED GBP3 WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D713V9, continuous
D713V10, continuous
[1] "Remove cluster labels:" "GBP3 MUTATED"          
clus
  GBP3 MUTATED GBP3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" "GBP3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"GBP3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GBP3 MUTATED       2                         0
  GBP3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GBP3 MUTATED                                           0     4
  GBP3 WILD-TYPE                                         1   353
D713V11, multiclass
                                           clus
vv                                          GBP3 MUTATED GBP3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V12, binary
                cls
clus               0   1
  GBP3 MUTATED     0   4
  GBP3 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP3 MUTATED      0    4
  GBP3 WILD-TYPE   10  394
                        clus
vv                       GBP3 MUTATED GBP3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(714) Variable = FAM186B MUTATION ANALYSIS
D714V1, survival
                   sevent
clus2                 0   1
  FAM186B MUTATED     6   6
  FAM186B WILD-TYPE 332 210
  FAM186B MUTATED FAM186B WILD-TYPE 
               12               542 
  FAM186B MUTATED FAM186B WILD-TYPE 
                6               210 
$`FAM186B MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-8487 
       19.56         9.44         6.97        30.90         9.67         1.12 
TCGA-CD-A4MG TCGA-CG-4462 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4GT 
        6.58         0.00        11.44        14.47        22.32         6.51 

$`FAM186B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       19.73        26.70        11.70        11.01         9.47         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM186B MUTATED FAM186B WILD-TYPE 
              0.0               0.1 
  FAM186B MUTATED FAM186B WILD-TYPE 
             30.9             122.3 
  FAM186B MUTATED FAM186B WILD-TYPE 
            9.555            13.730 
[1] "0.0 - 30.9 (9.6)"   "0.1 - 122.3 (13.7)"
[1] "hr=" "2"  
D714V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM186B MUTATED         0        0        1        0         3         2
  FAM186B WILD-TYPE      10       20       45       31        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM186B MUTATED           0          1          1          1        1
  FAM186B WILD-TYPE        29         83         61         38       42
                   vv
clus                STAGE IVA
  FAM186B MUTATED           0
  FAM186B WILD-TYPE         4
D714V3, multiclass
            clus
vv           FAM186B MUTATED FAM186B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM186B MUTATED       0   2   7   3
  FAM186B WILD-TYPE    54 133 254  99
D714V4, multiclass
       clus
vv      FAM186B MUTATED FAM186B WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  7               254
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM186B MUTATED     5   1   0   3
  FAM186B WILD-TYPE 190 172  89  82
D714V5, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  N0               5               190
  N1               1               172
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V6, binary
                   cls
clus                  0   1
  FAM186B MUTATED    10   1
  FAM186B WILD-TYPE 472  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED     10    1
  FAM186B WILD-TYPE  472   37
   clus
vv  FAM186B MUTATED FAM186B WILD-TYPE
  0              10               472
  1               1                37
[1] 2 2
[1] FALSE
D714V7, binary
                   cls
clus                  0   1
  FAM186B MUTATED     8   5
  FAM186B WILD-TYPE 164 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      8    5
  FAM186B WILD-TYPE  164  401
        clus
vv       FAM186B MUTATED FAM186B WILD-TYPE
  FEMALE               8               164
  MALE                 5               401
[1] 2 2
[1] FALSE
D714V8, binary
                   cls
clus                  0   1
  FAM186B MUTATED    11   0
  FAM186B WILD-TYPE 405 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED     11    0
  FAM186B WILD-TYPE  405  102
     clus
vv    FAM186B MUTATED FAM186B WILD-TYPE
  NO               11               405
  YES               0               102
[1] 2 2
[1] FALSE
D714V9, continuous
D714V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM186B MUTATED       3                         0
  FAM186B WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM186B MUTATED                                           0     9
  FAM186B WILD-TYPE                                         1   348
D714V11, multiclass
                                           clus
vv                                          FAM186B MUTATED FAM186B WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V12, binary
                   cls
clus                  0   1
  FAM186B MUTATED     0  12
  FAM186B WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      0   12
  FAM186B WILD-TYPE   10  386
                        clus
vv                       FAM186B MUTATED FAM186B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(715) Variable = DOCK9 MUTATION ANALYSIS
D715V1, survival
                 sevent
clus2               0   1
  DOCK9 MUTATED    14   4
  DOCK9 WILD-TYPE 324 212
  DOCK9 MUTATED DOCK9 WILD-TYPE 
             18             536 
  DOCK9 MUTATED DOCK9 WILD-TYPE 
              4             212 
$`DOCK9 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3Y9 TCGA-IG-A97H TCGA-Z6-A8JE TCGA-BR-4280 TCGA-BR-6452 
       19.99         0.85        14.50         2.10         6.61        34.68 
TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
        9.17        30.90        35.84        27.12        28.14        31.96 
TCGA-CG-5728 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-HF-7132 TCGA-HU-A4GN TCGA-HU-A4GU 
       65.10         5.92        13.78        77.29        29.98         6.58 

$`DOCK9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DOCK9 MUTATED DOCK9 WILD-TYPE 
           0.85            0.00 
  DOCK9 MUTATED DOCK9 WILD-TYPE 
          77.29          122.30 
  DOCK9 MUTATED DOCK9 WILD-TYPE 
         23.555          13.495 
[1] "0.8 - 77.3 (23.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D715V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOCK9 MUTATED         1        0        3        1         3         3
  DOCK9 WILD-TYPE       9       20       43       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK9 MUTATED           1          3          2          2        1         0
  DOCK9 WILD-TYPE        28         81         60         37       42         4
D715V3, multiclass
            clus
vv           DOCK9 MUTATED DOCK9 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DOCK9 MUTATED       2   6   9   5
  DOCK9 WILD-TYPE    52 129 252  97
D715V4, multiclass
       clus
vv      DOCK9 MUTATED DOCK9 WILD-TYPE
  T0+T1             2              52
  T2                6             129
  T3                9             252
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DOCK9 MUTATED     6   8   2   3
  DOCK9 WILD-TYPE 189 165  87  82
D715V5, multiclass
    clus
vv   DOCK9 MUTATED DOCK9 WILD-TYPE
  N0             6             189
  N1             8             165
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V6, binary
                 cls
clus                0   1
  DOCK9 MUTATED    18   1
  DOCK9 WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK9 MUTATED     18    1
  DOCK9 WILD-TYPE  464   37
   clus
vv  DOCK9 MUTATED DOCK9 WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D715V7, binary
                 cls
clus                0   1
  DOCK9 MUTATED     7  15
  DOCK9 WILD-TYPE 165 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK9 MUTATED      7   15
  DOCK9 WILD-TYPE  165  391
        clus
vv       DOCK9 MUTATED DOCK9 WILD-TYPE
  FEMALE             7             165
  MALE              15             391
[1] 2 2
[1] FALSE
D715V8, binary
                 cls
clus                0   1
  DOCK9 MUTATED    15   2
  DOCK9 WILD-TYPE 401 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK9 MUTATED     15    2
  DOCK9 WILD-TYPE  401  100
     clus
vv    DOCK9 MUTATED DOCK9 WILD-TYPE
  NO             15             401
  YES             2             100
[1] 2 2
[1] FALSE
D715V9, continuous
[1] "Remove cluster labels:" "DOCK9 MUTATED"         
clus
  DOCK9 MUTATED DOCK9 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD 
"DOCK9 WILD-TYPE" "DOCK9 WILD-TYPE" 
D715V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DOCK9 MUTATED       4                         1
  DOCK9 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOCK9 MUTATED                                           0    14
  DOCK9 WILD-TYPE                                         1   343
D715V11, multiclass
                                           clus
vv                                          DOCK9 MUTATED DOCK9 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V12, binary
                 cls
clus                0   1
  DOCK9 MUTATED     0  18
  DOCK9 WILD-TYPE  10 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK9 MUTATED      0   18
  DOCK9 WILD-TYPE   10  380
                        clus
vv                       DOCK9 MUTATED DOCK9 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(716) Variable = TMPRSS5 MUTATION ANALYSIS
D716V1, survival
                   sevent
clus2                 0   1
  TMPRSS5 MUTATED     1   3
  TMPRSS5 WILD-TYPE 337 213
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                4               550 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                3               213 
$`TMPRSS5 MUTATED`
TCGA-L5-A43J TCGA-IG-A4QS TCGA-JY-A93D TCGA-VQ-A8P2 
        4.31         3.88        31.56        38.14 

$`TMPRSS5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
             3.88              0.00 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
            38.14            122.30 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
           17.935            13.565 
[1] "3.9 - 38.1 (17.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D716V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMPRSS5 MUTATED         0        0        0        0         0         1
  TMPRSS5 WILD-TYPE      10       20       46       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS5 MUTATED           0          1          1          1        0
  TMPRSS5 WILD-TYPE        29         83         61         38       43
                   vv
clus                STAGE IVA
  TMPRSS5 MUTATED           0
  TMPRSS5 WILD-TYPE         4
D716V3, multiclass
            clus
vv           TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMPRSS5 MUTATED       0   1   2   1
  TMPRSS5 WILD-TYPE    54 134 259 101
D716V4, multiclass
       clus
vv      TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMPRSS5 MUTATED     1   1   1   1
  TMPRSS5 WILD-TYPE 194 172  88  84
D716V5, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  N0               1               194
  N1               1               172
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V6, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     3   0
  TMPRSS5 WILD-TYPE 479  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      3    0
  TMPRSS5 WILD-TYPE  479   38
   clus
vv  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  0               3               479
  1               0                38
[1] 2 2
[1] FALSE
D716V7, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     0   4
  TMPRSS5 WILD-TYPE 172 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      0    4
  TMPRSS5 WILD-TYPE  172  402
        clus
vv       TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  FEMALE               0               172
  MALE                 4               402
[1] 2 2
[1] FALSE
D716V8, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     1   2
  TMPRSS5 WILD-TYPE 415 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      1    2
  TMPRSS5 WILD-TYPE  415  100
     clus
vv    TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  NO                1               415
  YES               2               100
[1] 2 2
[1] FALSE
D716V9, continuous
D716V10, continuous
[1] "Remove cluster labels:" "TMPRSS5 MUTATED"       
clus
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" "TMPRSS5 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TMPRSS5 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMPRSS5 MUTATED       0                         0
  TMPRSS5 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMPRSS5 MUTATED                                           0     4
  TMPRSS5 WILD-TYPE                                         1   353
D716V11, multiclass
                                           clus
vv                                          TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V12, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     0   1
  TMPRSS5 WILD-TYPE  10 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      0    1
  TMPRSS5 WILD-TYPE   10  397
                        clus
vv                       TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               1               397
[1] 2 2
[1] FALSE

Clustering(717) Variable = FAM104A MUTATION ANALYSIS
D717V1, survival
                   sevent
clus2                 0   1
  FAM104A MUTATED     3   2
  FAM104A WILD-TYPE 335 214
  FAM104A MUTATED FAM104A WILD-TYPE 
                5               549 
  FAM104A MUTATED FAM104A WILD-TYPE 
                2               214 
$`FAM104A MUTATED`
TCGA-IG-A8O2 TCGA-L5-A8NK TCGA-D7-8579 TCGA-HJ-7597 TCGA-VQ-A8P2 
        4.67        13.55        20.91        26.47        38.14 

$`FAM104A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FAM104A MUTATED FAM104A WILD-TYPE 
             4.67              0.00 
  FAM104A MUTATED FAM104A WILD-TYPE 
            38.14            122.30 
  FAM104A MUTATED FAM104A WILD-TYPE 
            20.91             13.51 
[1] "4.7 - 38.1 (20.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D717V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM104A MUTATED         0        0        1        0         1         1
  FAM104A WILD-TYPE      10       20       45       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM104A MUTATED           0          1          1          0        0
  FAM104A WILD-TYPE        29         83         61         39       43
                   vv
clus                STAGE IVA
  FAM104A MUTATED           0
  FAM104A WILD-TYPE         4
D717V3, multiclass
            clus
vv           FAM104A MUTATED FAM104A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM104A MUTATED       0   2   2   1
  FAM104A WILD-TYPE    54 133 259 101
D717V4, multiclass
       clus
vv      FAM104A MUTATED FAM104A WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM104A MUTATED     2   1   2   0
  FAM104A WILD-TYPE 193 172  87  85
D717V5, multiclass
    clus
vv   FAM104A MUTATED FAM104A WILD-TYPE
  N0               2               193
  N1               1               172
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V6, binary
                   cls
clus                  0   1
  FAM104A MUTATED     4   0
  FAM104A WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104A MUTATED      4    0
  FAM104A WILD-TYPE  478   38
   clus
vv  FAM104A MUTATED FAM104A WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D717V7, binary
                   cls
clus                  0   1
  FAM104A MUTATED     3   2
  FAM104A WILD-TYPE 169 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104A MUTATED      3    2
  FAM104A WILD-TYPE  169  404
        clus
vv       FAM104A MUTATED FAM104A WILD-TYPE
  FEMALE               3               169
  MALE                 2               404
[1] 2 2
[1] FALSE
D717V8, binary
                   cls
clus                  0   1
  FAM104A MUTATED     1   2
  FAM104A WILD-TYPE 415 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104A MUTATED      1    2
  FAM104A WILD-TYPE  415  100
     clus
vv    FAM104A MUTATED FAM104A WILD-TYPE
  NO                1               415
  YES               2               100
[1] 2 2
[1] FALSE
D717V9, continuous
D717V10, continuous
[1] "Remove cluster labels:" "FAM104A MUTATED"       
clus
  FAM104A MUTATED FAM104A WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" "FAM104A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM104A MUTATED       1                         0
  FAM104A WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM104A MUTATED                                           0     4
  FAM104A WILD-TYPE                                         1   353
D717V11, multiclass
                                           clus
vv                                          FAM104A MUTATED FAM104A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V12, binary
                   cls
clus                  0   1
  FAM104A MUTATED     0   3
  FAM104A WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM104A MUTATED      0    3
  FAM104A WILD-TYPE   10  395
                        clus
vv                       FAM104A MUTATED FAM104A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(718) Variable = EFHD1 MUTATION ANALYSIS
D718V1, survival
                 sevent
clus2               0   1
  EFHD1 MUTATED     6   1
  EFHD1 WILD-TYPE 332 215
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              7             547 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              1             215 
$`EFHD1 MUTATED`
TCGA-V5-AASX TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-5721 TCGA-HU-A4GU TCGA-HU-A4H3 
        8.98        34.68        16.14         6.02         6.58        29.00 
TCGA-VQ-A8P2 
       38.14 

$`EFHD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  EFHD1 MUTATED EFHD1 WILD-TYPE 
           6.02            0.00 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
          38.14          122.30 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
          16.14           13.55 
[1] "6.0 - 38.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3"  
D718V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHD1 MUTATED         0        0        0        0         1         1
  EFHD1 WILD-TYPE      10       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHD1 MUTATED           0          1          1          1        1         0
  EFHD1 WILD-TYPE        29         83         61         38       42         4
D718V3, multiclass
            clus
vv           EFHD1 MUTATED EFHD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFHD1 MUTATED       0   0   3   3
  EFHD1 WILD-TYPE    54 135 258  99
D718V4, multiclass
       clus
vv      EFHD1 MUTATED EFHD1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFHD1 MUTATED     1   3   0   2
  EFHD1 WILD-TYPE 194 170  89  83
D718V5, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  N0             1             194
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V6, binary
                 cls
clus                0   1
  EFHD1 MUTATED     6   0
  EFHD1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      6    0
  EFHD1 WILD-TYPE  476   38
   clus
vv  EFHD1 MUTATED EFHD1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D718V7, binary
                 cls
clus                0   1
  EFHD1 MUTATED     3   4
  EFHD1 WILD-TYPE 169 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      3    4
  EFHD1 WILD-TYPE  169  402
        clus
vv       EFHD1 MUTATED EFHD1 WILD-TYPE
  FEMALE             3             169
  MALE               4             402
[1] 2 2
[1] FALSE
D718V8, binary
                 cls
clus                0   1
  EFHD1 MUTATED     4   1
  EFHD1 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      4    1
  EFHD1 WILD-TYPE  412  101
     clus
vv    EFHD1 MUTATED EFHD1 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D718V9, continuous
[1] "Remove cluster labels:" "EFHD1 MUTATED"         
clus
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" "EFHD1 WILD-TYPE" 
D718V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHD1 MUTATED       2                         0
  EFHD1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHD1 MUTATED                                           0     4
  EFHD1 WILD-TYPE                                         1   353
D718V11, multiclass
                                           clus
vv                                          EFHD1 MUTATED EFHD1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V12, binary
                 cls
clus                0   1
  EFHD1 MUTATED     0   5
  EFHD1 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      0    5
  EFHD1 WILD-TYPE   10  393
                        clus
vv                       EFHD1 MUTATED EFHD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(719) Variable = CD4 MUTATION ANALYSIS
D719V1, survival
               sevent
clus2             0   1
  CD4 MUTATED     9   2
  CD4 WILD-TYPE 329 214
  CD4 MUTATED CD4 WILD-TYPE 
           11           543 
  CD4 MUTATED CD4 WILD-TYPE 
            2           214 
$`CD4 MUTATED`
TCGA-BR-6802 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4449 
       30.90         4.31        31.27        31.96        11.77        19.07 
TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H3 
        5.92        21.27        22.68         6.51        29.00 

$`CD4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CD4 MUTATED CD4 WILD-TYPE 
         4.31          0.00 
  CD4 MUTATED CD4 WILD-TYPE 
        31.96        122.30 
  CD4 MUTATED CD4 WILD-TYPE 
        21.27         13.51 
[1] "4.3 - 32.0 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D719V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD4 MUTATED         0        0        1        1         1         2
  CD4 WILD-TYPE      10       20       45       30        83        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD4 MUTATED           0          2          1          2        1         0
  CD4 WILD-TYPE        29         82         61         37       42         4
D719V3, multiclass
            clus
vv           CD4 MUTATED CD4 WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             1            45
  STAGE II             1            30
  STAGE IIA            1            83
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CD4 MUTATED       0   2   6   3
  CD4 WILD-TYPE    54 133 255  99
D719V4, multiclass
       clus
vv      CD4 MUTATED CD4 WILD-TYPE
  T0+T1           0            54
  T2              2           133
  T3              6           255
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CD4 MUTATED     2   4   2   3
  CD4 WILD-TYPE 193 169  87  82
D719V5, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  N0           2           193
  N1           4           169
  N2           2            87
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V6, binary
               cls
clus              0   1
  CD4 MUTATED    10   1
  CD4 WILD-TYPE 472  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED     10    1
  CD4 WILD-TYPE  472   37
   clus
vv  CD4 MUTATED CD4 WILD-TYPE
  0          10           472
  1           1            37
[1] 2 2
[1] FALSE
D719V7, binary
               cls
clus              0   1
  CD4 MUTATED     5   6
  CD4 WILD-TYPE 167 400
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      5    6
  CD4 WILD-TYPE  167  400
        clus
vv       CD4 MUTATED CD4 WILD-TYPE
  FEMALE           5           167
  MALE             6           400
[1] 2 2
[1] FALSE
D719V8, binary
               cls
clus              0   1
  CD4 MUTATED     9   1
  CD4 WILD-TYPE 407 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      9    1
  CD4 WILD-TYPE  407  101
     clus
vv    CD4 MUTATED CD4 WILD-TYPE
  NO            9           407
  YES           1           101
[1] 2 2
[1] FALSE
D719V9, continuous
D719V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CD4 MUTATED       5                         0
  CD4 WILD-TYPE   128                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD4 MUTATED                                           0     5
  CD4 WILD-TYPE                                         1   352
D719V11, multiclass
                                           clus
vv                                          CD4 MUTATED CD4 WILD-TYPE
  ASIAN                                               5           128
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V12, binary
               cls
clus              0   1
  CD4 MUTATED     1   9
  CD4 WILD-TYPE   9 389
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      1    9
  CD4 WILD-TYPE    9  389
                        clus
vv                       CD4 MUTATED CD4 WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO           9           389
[1] 2 2
[1] FALSE

Clustering(720) Variable = OR6C65 MUTATION ANALYSIS
D720V1, survival
                  sevent
clus2                0   1
  OR6C65 MUTATED     4   0
  OR6C65 WILD-TYPE 334 216
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               4              550 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               0              216 
$`OR6C65 MUTATED`
TCGA-JY-A6F8 TCGA-LN-A49Y TCGA-CD-8536 TCGA-VQ-AA6F 
      122.10        12.46        12.43        54.12 

$`OR6C65 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        32.94        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OR6C65 MUTATED OR6C65 WILD-TYPE 
           12.43             0.00 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
           122.1            122.3 
  OR6C65 MUTATED OR6C65 WILD-TYPE 
          33.290           13.565 
[1] "12.4 - 122.1 (33.3)" "0.0 - 122.3 (13.6)" 
[1] "hr="     "9400000"
D720V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR6C65 MUTATED         1        0        0        1         1         1
  OR6C65 WILD-TYPE       9       20       46       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR6C65 MUTATED           0          0          0          0        1
  OR6C65 WILD-TYPE        29         84         62         39       42
                  vv
clus               STAGE IVA
  OR6C65 MUTATED           0
  OR6C65 WILD-TYPE         4
D720V3, multiclass
            clus
vv           OR6C65 MUTATED OR6C65 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OR6C65 MUTATED       1   0   3   1
  OR6C65 WILD-TYPE    53 135 258 101
D720V4, multiclass
       clus
vv      OR6C65 MUTATED OR6C65 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR6C65 MUTATED     3   1   1   0
  OR6C65 WILD-TYPE 192 172  88  85
D720V5, multiclass
    clus
vv   OR6C65 MUTATED OR6C65 WILD-TYPE
  N0              3              192
  N1              1              172
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V6, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     5   0
  OR6C65 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      5    0
  OR6C65 WILD-TYPE  477   38
   clus
vv  OR6C65 MUTATED OR6C65 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D720V7, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     1   4
  OR6C65 WILD-TYPE 171 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      1    4
  OR6C65 WILD-TYPE  171  402
        clus
vv       OR6C65 MUTATED OR6C65 WILD-TYPE
  FEMALE              1              171
  MALE                4              402
[1] 2 2
[1] FALSE
D720V8, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     3   1
  OR6C65 WILD-TYPE 413 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      3    1
  OR6C65 WILD-TYPE  413  101
     clus
vv    OR6C65 MUTATED OR6C65 WILD-TYPE
  NO               3              413
  YES              1              101
[1] 2 2
[1] FALSE
D720V9, continuous
[1] "Remove cluster labels:" "OR6C65 MUTATED"        
clus
  OR6C65 MUTATED OR6C65 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A4A1       TCGA-LN-A4A2 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" "OR6C65 WILD-TYPE" 
D720V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OR6C65 MUTATED       2                         0
  OR6C65 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR6C65 MUTATED                                           0     3
  OR6C65 WILD-TYPE                                         1   354
D720V11, multiclass
                                           clus
vv                                          OR6C65 MUTATED OR6C65 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V12, binary
                  cls
clus                 0   1
  OR6C65 MUTATED     0   3
  OR6C65 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C65 MUTATED      0    3
  OR6C65 WILD-TYPE   10  395
                        clus
vv                       OR6C65 MUTATED OR6C65 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(721) Variable = SPATA2L MUTATION ANALYSIS
D721V1, survival
                   sevent
clus2                 0   1
  SPATA2L MUTATED     5   2
  SPATA2L WILD-TYPE 333 214
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                7               547 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                2               214 
$`SPATA2L MUTATED`
TCGA-L5-A43J TCGA-X8-AAAR TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-5721 
        4.31        18.21        34.68         6.18         6.58         6.02 
TCGA-MX-A5UJ 
       19.73 

$`SPATA2L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SPATA2L MUTATED SPATA2L WILD-TYPE 
             4.31              0.00 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
            34.68            122.30 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
             6.58             13.58 
[1] "4.3 - 34.7 (6.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D721V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA2L MUTATED         0        0        0        0         3         1
  SPATA2L WILD-TYPE      10       20       46       31        81        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA2L MUTATED           0          1          0          0        2
  SPATA2L WILD-TYPE        29         83         62         39       41
                   vv
clus                STAGE IVA
  SPATA2L MUTATED           0
  SPATA2L WILD-TYPE         4
D721V3, multiclass
            clus
vv           SPATA2L MUTATED SPATA2L WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SPATA2L MUTATED       1   0   5   2
  SPATA2L WILD-TYPE    53 135 256 100
D721V4, multiclass
       clus
vv      SPATA2L MUTATED SPATA2L WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  5               256
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SPATA2L MUTATED     4   2   2   0
  SPATA2L WILD-TYPE 191 171  87  85
D721V5, multiclass
    clus
vv   SPATA2L MUTATED SPATA2L WILD-TYPE
  N0               4               191
  N1               2               171
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V6, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     6   0
  SPATA2L WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      6    0
  SPATA2L WILD-TYPE  476   38
   clus
vv  SPATA2L MUTATED SPATA2L WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D721V7, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     3   5
  SPATA2L WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      3    5
  SPATA2L WILD-TYPE  169  401
        clus
vv       SPATA2L MUTATED SPATA2L WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D721V8, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     6   0
  SPATA2L WILD-TYPE 410 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      6    0
  SPATA2L WILD-TYPE  410  102
     clus
vv    SPATA2L MUTATED SPATA2L WILD-TYPE
  NO                6               410
  YES               0               102
[1] 2 2
[1] FALSE
D721V9, continuous
D721V10, continuous
[1] "Remove cluster labels:" "SPATA2L MUTATED"       
clus
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" "SPATA2L WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPATA2L MUTATED       1                         0
  SPATA2L WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA2L MUTATED                                           0     6
  SPATA2L WILD-TYPE                                         1   351
D721V11, multiclass
                                           clus
vv                                          SPATA2L MUTATED SPATA2L WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V12, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     0   6
  SPATA2L WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      0    6
  SPATA2L WILD-TYPE   10  392
                        clus
vv                       SPATA2L MUTATED SPATA2L WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(722) Variable = GPR115 MUTATION ANALYSIS
D722V1, survival
                  sevent
clus2                0   1
  GPR115 MUTATED     3   0
  GPR115 WILD-TYPE 335 216
  GPR115 MUTATED GPR115 WILD-TYPE 
               3              551 
  GPR115 MUTATED GPR115 WILD-TYPE 
               0              216 
$`GPR115 MUTATED`
TCGA-L5-A4OI TCGA-HF-7132 TCGA-SW-A7EA 
       19.99        77.29        19.04 

$`GPR115 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GPR115 MUTATED GPR115 WILD-TYPE 
           19.04             0.00 
  GPR115 MUTATED GPR115 WILD-TYPE 
           77.29           122.30 
  GPR115 MUTATED GPR115 WILD-TYPE 
           19.99            13.51 
[1] "19.0 - 77.3 (20.0)" "0.0 - 122.3 (13.5)"
[1] "hr="     "3400000"
D722V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR115 MUTATED         1        0        2        1         0         0
  GPR115 WILD-TYPE       9       20       44       30        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR115 MUTATED           0          1          0          1        0
  GPR115 WILD-TYPE        29         83         62         38       43
                  vv
clus               STAGE IVA
  GPR115 MUTATED           0
  GPR115 WILD-TYPE         4
D722V3, multiclass
            clus
vv           GPR115 MUTATED GPR115 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR115 MUTATED       1   3   1   1
  GPR115 WILD-TYPE    53 132 260 101
D722V4, multiclass
       clus
vv      GPR115 MUTATED GPR115 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 1              260
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR115 MUTATED     3   2   0   1
  GPR115 WILD-TYPE 192 171  89  84
D722V5, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V6, binary
                  cls
clus                 0   1
  GPR115 MUTATED     4   0
  GPR115 WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      4    0
  GPR115 WILD-TYPE  478   38
   clus
vv  GPR115 MUTATED GPR115 WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D722V7, binary
                  cls
clus                 0   1
  GPR115 MUTATED     2   4
  GPR115 WILD-TYPE 170 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      2    4
  GPR115 WILD-TYPE  170  402
        clus
vv       GPR115 MUTATED GPR115 WILD-TYPE
  FEMALE              2              170
  MALE                4              402
[1] 2 2
[1] FALSE
D722V8, binary
                  cls
clus                 0   1
  GPR115 MUTATED     3   1
  GPR115 WILD-TYPE 413 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      3    1
  GPR115 WILD-TYPE  413  101
     clus
vv    GPR115 MUTATED GPR115 WILD-TYPE
  NO               3              413
  YES              1              101
[1] 2 2
[1] FALSE
D722V9, continuous
D722V10, continuous
[1] "Remove cluster labels:" "GPR115 MUTATED"        
clus
  GPR115 MUTATED GPR115 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" "GPR115 WILD-TYPE" 
      TCGA-Z6-AAPN 
"GPR115 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR115 MUTATED       0                         1
  GPR115 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR115 MUTATED                                           0     3
  GPR115 WILD-TYPE                                         1   354
D722V11, multiclass
                                           clus
vv                                          GPR115 MUTATED GPR115 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V12, binary
                  cls
clus                 0   1
  GPR115 MUTATED     0   3
  GPR115 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      0    3
  GPR115 WILD-TYPE   10  395
                        clus
vv                       GPR115 MUTATED GPR115 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(723) Variable = TRPM6 MUTATION ANALYSIS
D723V1, survival
                 sevent
clus2               0   1
  TRPM6 MUTATED    19   9
  TRPM6 WILD-TYPE 319 207
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             28             526 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
              9             207 
$`TRPM6 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FG TCGA-L5-A4ON TCGA-L7-A6VZ TCGA-LN-A49S TCGA-LN-A9FP 
       19.99        41.52        18.35        10.36        13.15        12.03 
TCGA-VR-A8EO TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7716 
       25.81        34.68        32.78        44.94         9.21        39.78 
TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A452 TCGA-BR-A4QL 
       14.43        31.10        31.27        31.96         7.53        16.14 
TCGA-CD-5813 TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-8576 TCGA-HU-8602 
       12.39        12.82        11.77         6.02        14.66        22.32 
TCGA-HU-A4H2 TCGA-IN-7808 TCGA-VQ-A8P2 TCGA-VQ-AA68 
       12.95         3.45        38.14        43.66 

$`TRPM6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TRPM6 MUTATED TRPM6 WILD-TYPE 
           3.45            0.00 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
          44.94          122.30 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
         17.245          13.495 
[1] "3.5 - 44.9 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D723V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRPM6 MUTATED         0        0        0        2         6         3
  TRPM6 WILD-TYPE      10       20       46       29        78        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPM6 MUTATED           2          4          3          5        2         0
  TRPM6 WILD-TYPE        27         80         59         34       41         4
D723V3, multiclass
            clus
vv           TRPM6 MUTATED TRPM6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               2              29
  STAGE IIA              6              78
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             3              59
  STAGE IIIC             5              34
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TRPM6 MUTATED       1   1  17   9
  TRPM6 WILD-TYPE    53 134 244  93
D723V4, multiclass
       clus
vv      TRPM6 MUTATED TRPM6 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3               17             244
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TRPM6 MUTATED     9   9   2   8
  TRPM6 WILD-TYPE 186 164  87  77
D723V5, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  N0             9             186
  N1             9             164
  N2             2              87
  N3             8              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V6, binary
                 cls
clus                0   1
  TRPM6 MUTATED    24   2
  TRPM6 WILD-TYPE 458  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     24    2
  TRPM6 WILD-TYPE  458   36
   clus
vv  TRPM6 MUTATED TRPM6 WILD-TYPE
  0            24             458
  1             2              36
[1] 2 2
[1] FALSE
D723V7, binary
                 cls
clus                0   1
  TRPM6 MUTATED    12  17
  TRPM6 WILD-TYPE 160 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     12   17
  TRPM6 WILD-TYPE  160  389
        clus
vv       TRPM6 MUTATED TRPM6 WILD-TYPE
  FEMALE            12             160
  MALE              17             389
[1] 2 2
[1] FALSE
D723V8, binary
                 cls
clus                0   1
  TRPM6 MUTATED    21   6
  TRPM6 WILD-TYPE 395  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     21    6
  TRPM6 WILD-TYPE  395   96
     clus
vv    TRPM6 MUTATED TRPM6 WILD-TYPE
  NO             21             395
  YES             6              96
[1] 2 2
[1] FALSE
D723V9, continuous
[1] "Remove cluster labels:" "TRPM6 MUTATED"         
clus
  TRPM6 MUTATED TRPM6 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TRPM6 WILD-TYPE" "TRPM6 WILD-TYPE" 
D723V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRPM6 MUTATED       9                         0
  TRPM6 WILD-TYPE   124                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRPM6 MUTATED                                           0    19
  TRPM6 WILD-TYPE                                         1   338
D723V11, multiclass
                                           clus
vv                                          TRPM6 MUTATED TRPM6 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V12, binary
                 cls
clus                0   1
  TRPM6 MUTATED     0  22
  TRPM6 WILD-TYPE  10 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED      0   22
  TRPM6 WILD-TYPE   10  376
                        clus
vv                       TRPM6 MUTATED TRPM6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(724) Variable = MKL1 MUTATION ANALYSIS
D724V1, survival
                sevent
clus2              0   1
  MKL1 MUTATED    12   2
  MKL1 WILD-TYPE 326 214
  MKL1 MUTATED MKL1 WILD-TYPE 
            14            540 
  MKL1 MUTATED MKL1 WILD-TYPE 
             2            214 
$`MKL1 MUTATED`
TCGA-L5-A4OI TCGA-VR-AA4G TCGA-B7-A5TI TCGA-BR-8680 TCGA-CD-8525 TCGA-CG-5723 
       19.99        18.05        19.56        31.96        12.59       105.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GC 
       65.10        21.07        30.51        22.32        22.68         3.25 
TCGA-HU-A4GQ TCGA-HU-A4H8 
        0.10        14.07 

$`MKL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        28.96         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        24.26        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MKL1 MUTATED MKL1 WILD-TYPE 
           0.1            0.0 
  MKL1 MUTATED MKL1 WILD-TYPE 
        105.07         122.30 
  MKL1 MUTATED MKL1 WILD-TYPE 
        20.530         13.445 
[1] "0.1 - 105.1 (20.5)" "0.0 - 122.3 (13.4)"
[1] "hr=" "3.9"
D724V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MKL1 MUTATED         0        0        2        1         0         2
  MKL1 WILD-TYPE      10       20       44       30        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKL1 MUTATED           0          4          1          4        1         0
  MKL1 WILD-TYPE        29         80         61         35       42         4
D724V3, multiclass
            clus
vv           MKL1 MUTATED MKL1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            4             35
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MKL1 MUTATED       1   4   3   7
  MKL1 WILD-TYPE    53 131 258  95
D724V4, multiclass
       clus
vv      MKL1 MUTATED MKL1 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               3            258
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MKL1 MUTATED     3   5   5   3
  MKL1 WILD-TYPE 192 168  84  82
D724V5, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  N0            3            192
  N1            5            168
  N2            5             84
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V6, binary
                cls
clus               0   1
  MKL1 MUTATED    15   1
  MKL1 WILD-TYPE 467  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED     15    1
  MKL1 WILD-TYPE  467   37
   clus
vv  MKL1 MUTATED MKL1 WILD-TYPE
  0           15            467
  1            1             37
[1] 2 2
[1] FALSE
D724V7, binary
                cls
clus               0   1
  MKL1 MUTATED     9   8
  MKL1 WILD-TYPE 163 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      9    8
  MKL1 WILD-TYPE  163  398
        clus
vv       MKL1 MUTATED MKL1 WILD-TYPE
  FEMALE            9            163
  MALE              8            398
[1] 2 2
[1] FALSE
D724V8, binary
                cls
clus               0   1
  MKL1 MUTATED    11   2
  MKL1 WILD-TYPE 405 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED     11    2
  MKL1 WILD-TYPE  405  100
     clus
vv    MKL1 MUTATED MKL1 WILD-TYPE
  NO            11            405
  YES            2            100
[1] 2 2
[1] FALSE
D724V9, continuous
[1] "Remove cluster labels:" "MKL1 MUTATED"          
clus
  MKL1 MUTATED MKL1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA7B 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
D724V10, continuous
[1] "Remove cluster labels:" "MKL1 MUTATED"          
clus
  MKL1 MUTATED MKL1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" "MKL1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MKL1 MUTATED       7                         0
  MKL1 WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKL1 MUTATED                                           0     6
  MKL1 WILD-TYPE                                         1   351
D724V11, multiclass
                                           clus
vv                                          MKL1 MUTATED MKL1 WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V12, binary
                cls
clus               0   1
  MKL1 MUTATED     0  11
  MKL1 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      0   11
  MKL1 WILD-TYPE   10  387
                        clus
vv                       MKL1 MUTATED MKL1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(725) Variable = ZNF185 MUTATION ANALYSIS
D725V1, survival
                  sevent
clus2                0   1
  ZNF185 MUTATED     8   7
  ZNF185 WILD-TYPE 330 209
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              15              539 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               7              209 
$`ZNF185 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GK TCGA-L5-A43H TCGA-L5-A4OQ TCGA-L5-A8NK TCGA-V5-A7RB 
       21.99         7.63         0.30         1.38        13.55         5.29 
TCGA-VR-A8EZ TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-CG-5723 
       18.18        19.56        34.68        36.16        31.10       105.07 
TCGA-CG-5733 TCGA-D7-A4YU TCGA-R5-A7O7 
       21.07        16.44        45.67 

$`ZNF185 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
             0.3              0.0 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
          105.07           122.30 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           19.56            13.48 
[1] "0.3 - 105.1 (19.6)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D725V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF185 MUTATED         0        1        0        1         2         0
  ZNF185 WILD-TYPE      10       19       46       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF185 MUTATED           2          2          1          3        2
  ZNF185 WILD-TYPE        27         82         61         36       41
                  vv
clus               STAGE IVA
  ZNF185 MUTATED           0
  ZNF185 WILD-TYPE         4
D725V3, multiclass
            clus
vv           ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF185 MUTATED       2   3   7   3
  ZNF185 WILD-TYPE    52 132 254  99
D725V4, multiclass
       clus
vv      ZNF185 MUTATED ZNF185 WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 7              254
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF185 MUTATED     3   6   3   3
  ZNF185 WILD-TYPE 192 167  86  82
D725V5, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  N0              3              192
  N1              6              167
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V6, binary
                  cls
clus                 0   1
  ZNF185 MUTATED    11   2
  ZNF185 WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED     11    2
  ZNF185 WILD-TYPE  471   36
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D725V7, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     5  10
  ZNF185 WILD-TYPE 167 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      5   10
  ZNF185 WILD-TYPE  167  396
        clus
vv       ZNF185 MUTATED ZNF185 WILD-TYPE
  FEMALE              5              167
  MALE               10              396
[1] 2 2
[1] FALSE
D725V8, binary
                  cls
clus                 0   1
  ZNF185 MUTATED    14   0
  ZNF185 WILD-TYPE 402 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED     14    0
  ZNF185 WILD-TYPE  402  102
     clus
vv    ZNF185 MUTATED ZNF185 WILD-TYPE
  NO              14              402
  YES              0              102
[1] 2 2
[1] FALSE
D725V9, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8Q7 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
D725V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF185 MUTATED       0                         0
  ZNF185 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF185 MUTATED                                           0    10
  ZNF185 WILD-TYPE                                         1   347
D725V11, multiclass
                                           clus
vv                                          ZNF185 MUTATED ZNF185 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V12, binary
                  cls
clus                 0   1
  ZNF185 MUTATED     2   5
  ZNF185 WILD-TYPE   8 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      2    5
  ZNF185 WILD-TYPE    8  393
                        clus
vv                       ZNF185 MUTATED ZNF185 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(726) Variable = SOAT1 MUTATION ANALYSIS
D726V1, survival
                 sevent
clus2               0   1
  SOAT1 MUTATED     8   3
  SOAT1 WILD-TYPE 330 213
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             11             543 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              3             213 
$`SOAT1 MUTATED`
TCGA-L5-A43M TCGA-CG-4460 TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QL 
        8.94        21.99        36.16        27.12        28.14        16.14 
TCGA-CG-4465 TCGA-HF-7132 TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
        9.01        77.29        74.53        19.04        38.14 

$`SOAT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SOAT1 MUTATED SOAT1 WILD-TYPE 
           8.94            0.00 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
          77.29          122.30 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
          27.12           13.48 
[1] "8.9 - 77.3 (27.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D726V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOAT1 MUTATED         0        1        1        1         0         0
  SOAT1 WILD-TYPE      10       19       45       30        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOAT1 MUTATED           0          1          2          1        3         0
  SOAT1 WILD-TYPE        29         83         60         38       40         4
D726V3, multiclass
            clus
vv           SOAT1 MUTATED SOAT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SOAT1 MUTATED       1   2   2   6
  SOAT1 WILD-TYPE    53 133 259  96
D726V4, multiclass
       clus
vv      SOAT1 MUTATED SOAT1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SOAT1 MUTATED     2   5   1   3
  SOAT1 WILD-TYPE 193 168  88  82
D726V5, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  N0             2             193
  N1             5             168
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V6, binary
                 cls
clus                0   1
  SOAT1 MUTATED     7   3
  SOAT1 WILD-TYPE 475  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      7    3
  SOAT1 WILD-TYPE  475   35
   clus
vv  SOAT1 MUTATED SOAT1 WILD-TYPE
  0             7             475
  1             3              35
[1] 2 2
[1] FALSE
D726V7, binary
                 cls
clus                0   1
  SOAT1 MUTATED     6   5
  SOAT1 WILD-TYPE 166 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      6    5
  SOAT1 WILD-TYPE  166  401
        clus
vv       SOAT1 MUTATED SOAT1 WILD-TYPE
  FEMALE             6             166
  MALE               5             401
[1] 2 2
[1] FALSE
D726V8, binary
                 cls
clus                0   1
  SOAT1 MUTATED     8   2
  SOAT1 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      8    2
  SOAT1 WILD-TYPE  408  100
     clus
vv    SOAT1 MUTATED SOAT1 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D726V9, continuous
D726V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SOAT1 MUTATED       0                         0
  SOAT1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOAT1 MUTATED                                           0     7
  SOAT1 WILD-TYPE                                         1   350
D726V11, multiclass
                                           clus
vv                                          SOAT1 MUTATED SOAT1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V12, binary
                 cls
clus                0   1
  SOAT1 MUTATED     1   5
  SOAT1 WILD-TYPE   9 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      1    5
  SOAT1 WILD-TYPE    9  393
                        clus
vv                       SOAT1 MUTATED SOAT1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(727) Variable = TNKS1BP1 MUTATION ANALYSIS
D727V1, survival
                    sevent
clus2                  0   1
  TNKS1BP1 MUTATED    15  13
  TNKS1BP1 WILD-TYPE 323 203
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                28                526 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                13                203 
$`TNKS1BP1 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-S8-A6BW TCGA-VR-A8EZ TCGA-BR-4184 TCGA-BR-4201 
        4.31        21.99        20.38        18.18         6.97        30.90 
TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-A452 
       34.68         8.05         3.32        31.27        25.05         7.53 
TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG 
       16.14        12.53        12.30        11.64        12.43         6.58 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-8573 TCGA-FP-A4BE 
        1.02         8.05         6.02       105.07        19.50        11.08 
TCGA-HU-A4G8 TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-A91Q 
       22.68        74.53        38.14        20.81 

$`TNKS1BP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        29.59         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        4.31        14.04        11.80        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.59         7.17        12.33        12.39        12.59 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
              1.02               0.00 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
            105.07             122.30 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
            14.335             13.565 
[1] "1.0 - 105.1 (14.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D727V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNKS1BP1 MUTATED         0        0        1        4         4         3
  TNKS1BP1 WILD-TYPE      10       20       45       27        80        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNKS1BP1 MUTATED           0          5          2          4        6
  TNKS1BP1 WILD-TYPE        29         79         60         35       37
                    vv
clus                 STAGE IVA
  TNKS1BP1 MUTATED           0
  TNKS1BP1 WILD-TYPE         4
D727V3, multiclass
            clus
vv           TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  4                 27
  STAGE IIA                 4                 80
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                5                 79
  STAGE IIIB                2                 60
  STAGE IIIC                4                 35
  STAGE IV                  6                 37
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TNKS1BP1 MUTATED       0   4  15  11
  TNKS1BP1 WILD-TYPE    54 131 246  91
D727V4, multiclass
       clus
vv      TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  T0+T1                0                 54
  T2                   4                131
  T3                  15                246
  T4                  11                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TNKS1BP1 MUTATED    11  10   1   7
  TNKS1BP1 WILD-TYPE 184 163  88  78
D727V5, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  N0               11                184
  N1               10                163
  N2                1                 88
  N3                7                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V6, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    23   4
  TNKS1BP1 WILD-TYPE 459  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     23    4
  TNKS1BP1 WILD-TYPE  459   34
   clus
vv  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  0               23                459
  1                4                 34
[1] 2 2
[1] FALSE
D727V7, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    10  20
  TNKS1BP1 WILD-TYPE 162 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     10   20
  TNKS1BP1 WILD-TYPE  162  386
        clus
vv       TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  FEMALE               10                162
  MALE                 20                386
[1] 2 2
[1] FALSE
D727V8, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    23   4
  TNKS1BP1 WILD-TYPE 393  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     23    4
  TNKS1BP1 WILD-TYPE  393   98
     clus
vv    TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  NO                23                393
  YES                4                 98
[1] 2 2
[1] FALSE
D727V9, continuous
[1] "Remove cluster labels:" "TNKS1BP1 MUTATED"      
clus
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8Q7 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"TNKS1BP1 WILD-TYPE" 
D727V10, continuous
[1] "Remove cluster labels:" "TNKS1BP1 MUTATED"      
clus
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A4OE 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" "TNKS1BP1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TNKS1BP1 MUTATED       7                         1
  TNKS1BP1 WILD-TYPE   126                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNKS1BP1 MUTATED                                           0    16
  TNKS1BP1 WILD-TYPE                                         1   341
D727V11, multiclass
                                           clus
vv                                          TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  ASIAN                                                    7                126
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V12, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED     1  20
  TNKS1BP1 WILD-TYPE   9 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED      1   20
  TNKS1BP1 WILD-TYPE    9  378
                        clus
vv                       TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               20                378
[1] 2 2
[1] FALSE

Clustering(728) Variable = NOB1 MUTATION ANALYSIS
D728V1, survival
                sevent
clus2              0   1
  NOB1 MUTATED     6   1
  NOB1 WILD-TYPE 332 215
  NOB1 MUTATED NOB1 WILD-TYPE 
             7            547 
  NOB1 MUTATED NOB1 WILD-TYPE 
             1            215 
$`NOB1 MUTATED`
TCGA-LN-A9FP TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-4306 
       12.03        26.70        35.84         1.12        15.95         1.02 
TCGA-HU-A4H6 
       21.17 

$`NOB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02         3.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NOB1 MUTATED NOB1 WILD-TYPE 
          1.02           0.00 
  NOB1 MUTATED NOB1 WILD-TYPE 
         35.84         122.30 
  NOB1 MUTATED NOB1 WILD-TYPE 
         15.95          13.55 
[1] "1.0 - 35.8 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.6"
D728V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOB1 MUTATED         0        0        1        1         2         1
  NOB1 WILD-TYPE      10       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOB1 MUTATED           0          1          0          0        1         0
  NOB1 WILD-TYPE        29         83         62         39       42         4
D728V3, multiclass
            clus
vv           NOB1 MUTATED NOB1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NOB1 MUTATED       0   3   3   1
  NOB1 WILD-TYPE    54 132 258 101
D728V4, multiclass
       clus
vv      NOB1 MUTATED NOB1 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NOB1 MUTATED     4   1   2   0
  NOB1 WILD-TYPE 191 172  87  85
D728V5, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  N0            4            191
  N1            1            172
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V6, binary
                cls
clus               0   1
  NOB1 MUTATED     7   1
  NOB1 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      7    1
  NOB1 WILD-TYPE  475   37
   clus
vv  NOB1 MUTATED NOB1 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D728V7, binary
                cls
clus               0   1
  NOB1 MUTATED     6   2
  NOB1 WILD-TYPE 166 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      6    2
  NOB1 WILD-TYPE  166  404
        clus
vv       NOB1 MUTATED NOB1 WILD-TYPE
  FEMALE            6            166
  MALE              2            404
[1] 2 2
[1] FALSE
D728V8, binary
                cls
clus               0   1
  NOB1 MUTATED     5   1
  NOB1 WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      5    1
  NOB1 WILD-TYPE  411  101
     clus
vv    NOB1 MUTATED NOB1 WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D728V9, continuous
D728V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOB1 MUTATED       2                         0
  NOB1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOB1 MUTATED                                           0     4
  NOB1 WILD-TYPE                                         1   353
D728V11, multiclass
                                           clus
vv                                          NOB1 MUTATED NOB1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V12, binary
                cls
clus               0   1
  NOB1 MUTATED     0   6
  NOB1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      0    6
  NOB1 WILD-TYPE   10  392
                        clus
vv                       NOB1 MUTATED NOB1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(729) Variable = DENND4C MUTATION ANALYSIS
D729V1, survival
                   sevent
clus2                 0   1
  DENND4C MUTATED    11   8
  DENND4C WILD-TYPE 327 208
  DENND4C MUTATED DENND4C WILD-TYPE 
               19               535 
  DENND4C MUTATED DENND4C WILD-TYPE 
                8               208 
$`DENND4C MUTATED`
TCGA-CG-4460 TCGA-L5-A891 TCGA-R6-A6KZ TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-BR-4184 
       21.99         3.75         5.06        22.82        19.73         6.97 
TCGA-BR-6452 TCGA-BR-8485 TCGA-BR-8680 TCGA-CG-5724 TCGA-CG-5728 TCGA-D7-6818 
       34.68         9.21        31.96        12.03        65.10        12.36 
TCGA-D7-A4YY TCGA-FP-A4BF TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4H3 TCGA-IN-AB1X 
       13.78         5.52        22.68        24.20        29.00        13.51 
TCGA-MX-A5UJ 
       19.73 

$`DENND4C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        6.02         0.99       105.07        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.26         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DENND4C MUTATED DENND4C WILD-TYPE 
             3.75              0.00 
  DENND4C MUTATED DENND4C WILD-TYPE 
             65.1             122.3 
  DENND4C MUTATED DENND4C WILD-TYPE 
            19.73             13.51 
[1] "3.8 - 65.1 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D729V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DENND4C MUTATED         0        1        1        0         2         1
  DENND4C WILD-TYPE      10       19       45       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND4C MUTATED           1          5          1          3        3
  DENND4C WILD-TYPE        28         79         61         36       40
                   vv
clus                STAGE IVA
  DENND4C MUTATED           0
  DENND4C WILD-TYPE         4
D729V3, multiclass
            clus
vv           DENND4C MUTATED DENND4C WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               5                79
  STAGE IIIB               1                61
  STAGE IIIC               3                36
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  DENND4C MUTATED       1   2  11   5
  DENND4C WILD-TYPE    53 133 250  97
D729V4, multiclass
       clus
vv      DENND4C MUTATED DENND4C WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                 11               250
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  DENND4C MUTATED     5   5   3   6
  DENND4C WILD-TYPE 190 168  86  79
D729V5, multiclass
    clus
vv   DENND4C MUTATED DENND4C WILD-TYPE
  N0               5               190
  N1               5               168
  N2               3                86
  N3               6                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V6, binary
                   cls
clus                  0   1
  DENND4C MUTATED    14   3
  DENND4C WILD-TYPE 468  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     14    3
  DENND4C WILD-TYPE  468   35
   clus
vv  DENND4C MUTATED DENND4C WILD-TYPE
  0              14               468
  1               3                35
[1] 2 2
[1] FALSE
D729V7, binary
                   cls
clus                  0   1
  DENND4C MUTATED    10  10
  DENND4C WILD-TYPE 162 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     10   10
  DENND4C WILD-TYPE  162  396
        clus
vv       DENND4C MUTATED DENND4C WILD-TYPE
  FEMALE              10               162
  MALE                10               396
[1] 2 2
[1] FALSE
D729V8, binary
                   cls
clus                  0   1
  DENND4C MUTATED    13   3
  DENND4C WILD-TYPE 403  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     13    3
  DENND4C WILD-TYPE  403   99
     clus
vv    DENND4C MUTATED DENND4C WILD-TYPE
  NO               13               403
  YES               3                99
[1] 2 2
[1] FALSE
D729V9, continuous
[1] "Remove cluster labels:" "DENND4C MUTATED"       
clus
  DENND4C MUTATED DENND4C WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"DENND4C WILD-TYPE" "DENND4C WILD-TYPE" "DENND4C WILD-TYPE" 
D729V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DENND4C MUTATED       4                         0
  DENND4C WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DENND4C MUTATED                                           0    13
  DENND4C WILD-TYPE                                         1   344
D729V11, multiclass
                                           clus
vv                                          DENND4C MUTATED DENND4C WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V12, binary
                   cls
clus                  0   1
  DENND4C MUTATED     0  15
  DENND4C WILD-TYPE  10 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED      0   15
  DENND4C WILD-TYPE   10  383
                        clus
vv                       DENND4C MUTATED DENND4C WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              15               383
[1] 2 2
[1] FALSE

Clustering(730) Variable = EFNA4 MUTATION ANALYSIS
D730V1, survival
                 sevent
clus2               0   1
  EFNA4 MUTATED     4   2
  EFNA4 WILD-TYPE 334 214
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              6             548 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              2             214 
$`EFNA4 MUTATED`
TCGA-L5-A8NQ TCGA-BR-6452 TCGA-BR-A4QL TCGA-HU-8602 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       21.37        34.68        16.14        22.32        19.73        38.14 

$`EFNA4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EFNA4 MUTATED EFNA4 WILD-TYPE 
          16.14            0.00 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
          38.14          122.30 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
         21.845          13.495 
[1] "16.1 - 38.1 (21.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D730V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFNA4 MUTATED         0        0        0        0         2         1
  EFNA4 WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFNA4 MUTATED           0          2          1          0        0         0
  EFNA4 WILD-TYPE        29         82         61         39       43         4
D730V3, multiclass
            clus
vv           EFNA4 MUTATED EFNA4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFNA4 MUTATED       0   1   3   2
  EFNA4 WILD-TYPE    54 134 258 100
D730V4, multiclass
       clus
vv      EFNA4 MUTATED EFNA4 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFNA4 MUTATED     3   1   1   1
  EFNA4 WILD-TYPE 192 172  88  84
D730V5, multiclass
    clus
vv   EFNA4 MUTATED EFNA4 WILD-TYPE
  N0             3             192
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V6, binary
                 cls
clus                0   1
  EFNA4 MUTATED     6   0
  EFNA4 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      6    0
  EFNA4 WILD-TYPE  476   38
   clus
vv  EFNA4 MUTATED EFNA4 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D730V7, binary
                 cls
clus                0   1
  EFNA4 MUTATED     4   2
  EFNA4 WILD-TYPE 168 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      4    2
  EFNA4 WILD-TYPE  168  404
        clus
vv       EFNA4 MUTATED EFNA4 WILD-TYPE
  FEMALE             4             168
  MALE               2             404
[1] 2 2
[1] FALSE
D730V8, binary
                 cls
clus                0   1
  EFNA4 MUTATED     5   1
  EFNA4 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      5    1
  EFNA4 WILD-TYPE  411  101
     clus
vv    EFNA4 MUTATED EFNA4 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D730V9, continuous
D730V10, continuous
[1] "Remove cluster labels:" "EFNA4 MUTATED"         
clus
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" "EFNA4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EFNA4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFNA4 MUTATED       1                         0
  EFNA4 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFNA4 MUTATED                                           0     5
  EFNA4 WILD-TYPE                                         1   352
D730V11, multiclass
                                           clus
vv                                          EFNA4 MUTATED EFNA4 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V12, binary
                 cls
clus                0   1
  EFNA4 MUTATED     0   4
  EFNA4 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      0    4
  EFNA4 WILD-TYPE   10  394
                        clus
vv                       EFNA4 MUTATED EFNA4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(731) Variable = TAF7L MUTATION ANALYSIS
D731V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     8   3
  TAF7L WILD-TYPE 330 213
  TAF7L MUTATED TAF7L WILD-TYPE 
             11             543 
  TAF7L MUTATED TAF7L WILD-TYPE 
              3             213 
$`TAF7L MUTATED`
TCGA-IG-A97I TCGA-Z6-A9VB TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8589 
       12.16         1.32        44.94         0.26        25.05        27.12 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6524 TCGA-HU-A4H4 
       12.62         6.02        21.07        17.85        23.84 

$`TAF7L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TAF7L MUTATED TAF7L WILD-TYPE 
           0.26            0.00 
  TAF7L MUTATED TAF7L WILD-TYPE 
          44.94          122.30 
  TAF7L MUTATED TAF7L WILD-TYPE 
          17.85           13.55 
[1] "0.3 - 44.9 (17.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D731V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF7L MUTATED         0        0        2        1         2         1
  TAF7L WILD-TYPE      10       20       44       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF7L MUTATED           0          2          1          1        1         0
  TAF7L WILD-TYPE        29         82         61         38       42         4
D731V3, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TAF7L MUTATED       0   6   2   3
  TAF7L WILD-TYPE    54 129 259  99
D731V4, multiclass
       clus
vv      TAF7L MUTATED TAF7L WILD-TYPE
  T0+T1             0              54
  T2                6             129
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TAF7L MUTATED     4   4   2   1
  TAF7L WILD-TYPE 191 169  87  84
D731V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V6, binary
                 cls
clus                0   1
  TAF7L MUTATED    11   0
  TAF7L WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     11    0
  TAF7L WILD-TYPE  471   38
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D731V7, binary
                 cls
clus                0   1
  TAF7L MUTATED     5   6
  TAF7L WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      5    6
  TAF7L WILD-TYPE  167  400
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D731V8, binary
                 cls
clus                0   1
  TAF7L MUTATED    10   1
  TAF7L WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     10    1
  TAF7L WILD-TYPE  406  101
     clus
vv    TAF7L MUTATED TAF7L WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D731V9, continuous
D731V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF7L MUTATED       2                         0
  TAF7L WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF7L MUTATED                                           0     7
  TAF7L WILD-TYPE                                         1   350
D731V11, multiclass
                                           clus
vv                                          TAF7L MUTATED TAF7L WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V12, binary
                 cls
clus                0   1
  TAF7L MUTATED     0   9
  TAF7L WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      0    9
  TAF7L WILD-TYPE   10  389
                        clus
vv                       TAF7L MUTATED TAF7L WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(732) Variable = SLC25A17 MUTATION ANALYSIS
D732V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     0   3
  SLC25A17 WILD-TYPE 338 213
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                551 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                213 
$`SLC25A17 MUTATED`
TCGA-BR-4257 TCGA-CD-A4MG TCGA-CG-4306 
        9.67         6.58         1.02 

$`SLC25A17 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              1.02               0.00 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              9.67             122.30 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              6.58              13.68 
[1] "1.0 - 9.7 (6.6)"    "0.0 - 122.3 (13.7)"
[1] "hr=" "8.6"
D732V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC25A17 MUTATED         0        0        0        0         1         1
  SLC25A17 WILD-TYPE      10       20       46       31        83        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        1
  SLC25A17 WILD-TYPE        29         84         62         39       42
                    vv
clus                 STAGE IVA
  SLC25A17 MUTATED           0
  SLC25A17 WILD-TYPE         4
D732V3, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SLC25A17 MUTATED       0   0   2   1
  SLC25A17 WILD-TYPE    54 135 259 101
D732V4, multiclass
       clus
vv      SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T0+T1                0                 54
  T2                   0                135
  T3                   2                259
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SLC25A17 MUTATED     2   0   1   0
  SLC25A17 WILD-TYPE 193 173  88  85
D732V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                2                193
  N1                0                173
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V6, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     3   1
  SLC25A17 WILD-TYPE 479  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      3    1
  SLC25A17 WILD-TYPE  479   37
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                3                479
  1                1                 37
[1] 2 2
[1] FALSE
D732V7, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     1   3
  SLC25A17 WILD-TYPE 171 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      1    3
  SLC25A17 WILD-TYPE  171  403
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  FEMALE                1                171
  MALE                  3                403
[1] 2 2
[1] FALSE
D732V8, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     3   0
  SLC25A17 WILD-TYPE 413 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      3    0
  SLC25A17 WILD-TYPE  413  102
     clus
vv    SLC25A17 MUTATED SLC25A17 WILD-TYPE
  NO                 3                413
  YES                0                102
[1] 2 2
[1] FALSE
D732V9, continuous
D732V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC25A17 MUTATED       1                         0
  SLC25A17 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC25A17 MUTATED                                           0     2
  SLC25A17 WILD-TYPE                                         1   355
D732V11, multiclass
                                           clus
vv                                          SLC25A17 MUTATED SLC25A17 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V12, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     0   3
  SLC25A17 WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      0    3
  SLC25A17 WILD-TYPE   10  395
                        clus
vv                       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(733) Variable = C9ORF41 MUTATION ANALYSIS
D733V1, survival
                   sevent
clus2                 0   1
  C9ORF41 MUTATED     5   1
  C9ORF41 WILD-TYPE 333 215
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                6               548 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                1               215 
$`C9ORF41 MUTATED`
TCGA-IC-A6RE TCGA-JY-A939 TCGA-BR-8078 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-A5NB 
        7.69        21.70        29.59        11.44        21.27        30.51 

$`C9ORF41 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
             7.69              0.00 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
            30.51            122.30 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
           21.485            13.530 
[1] "7.7 - 30.5 (21.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.8"
D733V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF41 MUTATED         0        0        0        0         0         3
  C9ORF41 WILD-TYPE      10       20       46       31        84        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF41 MUTATED           0          0          2          1        0
  C9ORF41 WILD-TYPE        29         84         60         38       43
                   vv
clus                STAGE IVA
  C9ORF41 MUTATED           0
  C9ORF41 WILD-TYPE         4
D733V3, multiclass
            clus
vv           C9ORF41 MUTATED C9ORF41 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C9ORF41 MUTATED       3   0   2   2
  C9ORF41 WILD-TYPE    51 135 259 100
D733V4, multiclass
       clus
vv      C9ORF41 MUTATED C9ORF41 WILD-TYPE
  T0+T1               3                51
  T2                  0               135
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C9ORF41 MUTATED     1   2   0   3
  C9ORF41 WILD-TYPE 194 171  89  82
D733V5, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  N0               1               194
  N1               2               171
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V6, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     7   0
  C9ORF41 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      7    0
  C9ORF41 WILD-TYPE  475   38
   clus
vv  C9ORF41 MUTATED C9ORF41 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D733V7, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     4   3
  C9ORF41 WILD-TYPE 168 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      4    3
  C9ORF41 WILD-TYPE  168  403
        clus
vv       C9ORF41 MUTATED C9ORF41 WILD-TYPE
  FEMALE               4               168
  MALE                 3               403
[1] 2 2
[1] FALSE
D733V8, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     4   2
  C9ORF41 WILD-TYPE 412 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      4    2
  C9ORF41 WILD-TYPE  412  100
     clus
vv    C9ORF41 MUTATED C9ORF41 WILD-TYPE
  NO                4               412
  YES               2               100
[1] 2 2
[1] FALSE
D733V9, continuous
D733V10, continuous
[1] "Remove cluster labels:" "C9ORF41 MUTATED"       
clus
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IG-A3QL 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" "C9ORF41 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C9ORF41 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF41 MUTATED       0                         0
  C9ORF41 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF41 MUTATED                                           0     6
  C9ORF41 WILD-TYPE                                         1   351
D733V11, multiclass
                                           clus
vv                                          C9ORF41 MUTATED C9ORF41 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V12, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     1   4
  C9ORF41 WILD-TYPE   9 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      1    4
  C9ORF41 WILD-TYPE    9  394
                        clus
vv                       C9ORF41 MUTATED C9ORF41 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(734) Variable = EPB41 MUTATION ANALYSIS
D734V1, survival
                 sevent
clus2               0   1
  EPB41 MUTATED     6   6
  EPB41 WILD-TYPE 332 210
  EPB41 MUTATED EPB41 WILD-TYPE 
             12             542 
  EPB41 MUTATED EPB41 WILD-TYPE 
              6             210 
$`EPB41 MUTATED`
TCGA-JY-A6FG TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-7707 TCGA-BR-8363 
       41.52         6.97        34.68        25.61        35.84         0.26 
TCGA-BR-8382 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HU-A4GU TCGA-HU-A4GX TCGA-VQ-A8P2 
       25.05         1.12        11.44         6.58        20.25        38.14 

$`EPB41 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EPB41 MUTATED EPB41 WILD-TYPE 
           0.26            0.00 
  EPB41 MUTATED EPB41 WILD-TYPE 
          41.52          122.30 
  EPB41 MUTATED EPB41 WILD-TYPE 
          22.65           13.53 
[1] "0.3 - 41.5 (22.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D734V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB41 MUTATED         0        0        2        0         2         1
  EPB41 WILD-TYPE      10       20       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPB41 MUTATED           1          3          2          2        1         0
  EPB41 WILD-TYPE        28         81         60         37       42         4
D734V3, multiclass
            clus
vv           EPB41 MUTATED EPB41 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPB41 MUTATED       0   2   7   5
  EPB41 WILD-TYPE    54 133 254  97
D734V4, multiclass
       clus
vv      EPB41 MUTATED EPB41 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPB41 MUTATED     5   4   2   3
  EPB41 WILD-TYPE 190 169  87  82
D734V5, multiclass
    clus
vv   EPB41 MUTATED EPB41 WILD-TYPE
  N0             5             190
  N1             4             169
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V6, binary
                 cls
clus                0   1
  EPB41 MUTATED    13   0
  EPB41 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     13    0
  EPB41 WILD-TYPE  469   38
   clus
vv  EPB41 MUTATED EPB41 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D734V7, binary
                 cls
clus                0   1
  EPB41 MUTATED    10   4
  EPB41 WILD-TYPE 162 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     10    4
  EPB41 WILD-TYPE  162  402
        clus
vv       EPB41 MUTATED EPB41 WILD-TYPE
  FEMALE            10             162
  MALE               4             402
[1] 2 2
[1] FALSE
D734V8, binary
                 cls
clus                0   1
  EPB41 MUTATED    11   1
  EPB41 WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     11    1
  EPB41 WILD-TYPE  405  101
     clus
vv    EPB41 MUTATED EPB41 WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D734V9, continuous
D734V10, continuous
[1] "Remove cluster labels:" "EPB41 MUTATED"         
clus
  EPB41 MUTATED EPB41 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" "EPB41 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EPB41 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPB41 MUTATED       2                         0
  EPB41 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB41 MUTATED                                           0    12
  EPB41 WILD-TYPE                                         1   345
D734V11, multiclass
                                           clus
vv                                          EPB41 MUTATED EPB41 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V12, binary
                 cls
clus                0   1
  EPB41 MUTATED     0  12
  EPB41 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED      0   12
  EPB41 WILD-TYPE   10  386
                        clus
vv                       EPB41 MUTATED EPB41 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(735) Variable = DENND2A MUTATION ANALYSIS
D735V1, survival
                   sevent
clus2                 0   1
  DENND2A MUTATED    16   4
  DENND2A WILD-TYPE 322 212
  DENND2A MUTATED DENND2A WILD-TYPE 
               20               534 
  DENND2A MUTATED DENND2A WILD-TYPE 
                4               212 
$`DENND2A MUTATED`
TCGA-L5-A8NT TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A8NJ TCGA-LN-A49M TCGA-LN-A9FQ 
       27.12         3.16        30.25        16.47        12.66        12.85 
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
       11.70        34.68         3.32        25.05         1.12        28.14 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-8604 
        6.58         1.02         9.01        14.47        22.32        22.82 
TCGA-HU-A4GT TCGA-VQ-A8P3 
        6.51        37.22 

$`DENND2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        28.96        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        38.14        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DENND2A MUTATED DENND2A WILD-TYPE 
             1.02              0.00 
  DENND2A MUTATED DENND2A WILD-TYPE 
            37.22            122.30 
  DENND2A MUTATED DENND2A WILD-TYPE 
           13.660            13.565 
[1] "1.0 - 37.2 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D735V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DENND2A MUTATED         1        0        2        0         7         2
  DENND2A WILD-TYPE       9       20       44       31        77        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND2A MUTATED           1          1          1          2        2
  DENND2A WILD-TYPE        28         83         61         37       41
                   vv
clus                STAGE IVA
  DENND2A MUTATED           0
  DENND2A WILD-TYPE         4
D735V3, multiclass
            clus
vv           DENND2A MUTATED DENND2A WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                7                77
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  DENND2A MUTATED       1   3  10   5
  DENND2A WILD-TYPE    53 132 251  97
D735V4, multiclass
       clus
vv      DENND2A MUTATED DENND2A WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                 10               251
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  DENND2A MUTATED    12   3   1   4
  DENND2A WILD-TYPE 183 170  88  81
D735V5, multiclass
    clus
vv   DENND2A MUTATED DENND2A WILD-TYPE
  N0              12               183
  N1               3               170
  N2               1                88
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V6, binary
                   cls
clus                  0   1
  DENND2A MUTATED    18   2
  DENND2A WILD-TYPE 464  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2A MUTATED     18    2
  DENND2A WILD-TYPE  464   36
   clus
vv  DENND2A MUTATED DENND2A WILD-TYPE
  0              18               464
  1               2                36
[1] 2 2
[1] FALSE
D735V7, binary
                   cls
clus                  0   1
  DENND2A MUTATED     8  13
  DENND2A WILD-TYPE 164 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2A MUTATED      8   13
  DENND2A WILD-TYPE  164  393
        clus
vv       DENND2A MUTATED DENND2A WILD-TYPE
  FEMALE               8               164
  MALE                13               393
[1] 2 2
[1] FALSE
D735V8, binary
                   cls
clus                  0   1
  DENND2A MUTATED    15   3
  DENND2A WILD-TYPE 401  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2A MUTATED     15    3
  DENND2A WILD-TYPE  401   99
     clus
vv    DENND2A MUTATED DENND2A WILD-TYPE
  NO               15               401
  YES               3                99
[1] 2 2
[1] FALSE
D735V9, continuous
[1] "Remove cluster labels:" "DENND2A MUTATED"       
clus
  DENND2A MUTATED DENND2A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"DENND2A WILD-TYPE" "DENND2A WILD-TYPE" "DENND2A WILD-TYPE" 
D735V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DENND2A MUTATED       6                         0
  DENND2A WILD-TYPE   127                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DENND2A MUTATED                                           0    13
  DENND2A WILD-TYPE                                         1   344
D735V11, multiclass
                                           clus
vv                                          DENND2A MUTATED DENND2A WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V12, binary
                   cls
clus                  0   1
  DENND2A MUTATED     0  14
  DENND2A WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND2A MUTATED      0   14
  DENND2A WILD-TYPE   10  384
                        clus
vv                       DENND2A MUTATED DENND2A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(736) Variable = SLC45A4 MUTATION ANALYSIS
D736V1, survival
                   sevent
clus2                 0   1
  SLC45A4 MUTATED    17   4
  SLC45A4 WILD-TYPE 321 212
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               21               533 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                4               212 
$`SLC45A4 MUTATED`
TCGA-L5-A4OI TCGA-IC-A6RE TCGA-JY-A6FH TCGA-L5-A893 TCGA-RE-A7BO TCGA-BR-6452 
       19.99         7.69        47.38         3.02         7.00        34.68 
TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8382 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4449 
        8.05        31.27        25.05        12.43        12.62        19.07 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-8602 
        6.02       105.07        65.10        21.27        11.08        22.32 
TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-RD-A7BW 
       24.20         6.58         5.13 

$`SLC45A4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
             3.02              0.00 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
           105.07            122.30 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
            19.07             13.55 
[1] "3.0 - 105.1 (19.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.5"
D736V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC45A4 MUTATED         2        1        3        3         2         5
  SLC45A4 WILD-TYPE       8       19       43       28        82        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A4 MUTATED           0          1          1          4        1
  SLC45A4 WILD-TYPE        29         83         61         35       42
                   vv
clus                STAGE IVA
  SLC45A4 MUTATED           0
  SLC45A4 WILD-TYPE         4
D736V3, multiclass
            clus
vv           SLC45A4 MUTATED SLC45A4 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 3                28
  STAGE IIA                2                82
  STAGE IIB                5                78
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC45A4 MUTATED       5   6   6   6
  SLC45A4 WILD-TYPE    49 129 255  96
D736V4, multiclass
       clus
vv      SLC45A4 MUTATED SLC45A4 WILD-TYPE
  T0+T1               5                49
  T2                  6               129
  T3                  6               255
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC45A4 MUTATED    10   8   0   5
  SLC45A4 WILD-TYPE 185 165  89  80
D736V5, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  N0              10               185
  N1               8               165
  N2               0                89
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V6, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    22   0
  SLC45A4 WILD-TYPE 460  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     22    0
  SLC45A4 WILD-TYPE  460   38
   clus
vv  SLC45A4 MUTATED SLC45A4 WILD-TYPE
  0              22               460
  1               0                38
[1] 2 2
[1] FALSE
D736V7, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    11  13
  SLC45A4 WILD-TYPE 161 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     11   13
  SLC45A4 WILD-TYPE  161  393
        clus
vv       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  FEMALE              11               161
  MALE                13               393
[1] 2 2
[1] FALSE
D736V8, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    18   3
  SLC45A4 WILD-TYPE 398  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     18    3
  SLC45A4 WILD-TYPE  398   99
     clus
vv    SLC45A4 MUTATED SLC45A4 WILD-TYPE
  NO               18               398
  YES               3                99
[1] 2 2
[1] FALSE
D736V9, continuous
D736V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC45A4 MUTATED       5                         2
  SLC45A4 WILD-TYPE   128                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC45A4 MUTATED                                           0    13
  SLC45A4 WILD-TYPE                                         1   344
D736V11, multiclass
                                           clus
vv                                          SLC45A4 MUTATED SLC45A4 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V12, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED     1  16
  SLC45A4 WILD-TYPE   9 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      1   16
  SLC45A4 WILD-TYPE    9  382
                        clus
vv                       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              16               382
[1] 2 2
[1] FALSE

Clustering(737) Variable = ALDH3A1 MUTATION ANALYSIS
D737V1, survival
                   sevent
clus2                 0   1
  ALDH3A1 MUTATED     5   6
  ALDH3A1 WILD-TYPE 333 210
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               11               543 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
                6               210 
$`ALDH3A1 MUTATED`
TCGA-IG-A4QS TCGA-L5-A8NV TCGA-BR-4257 TCGA-BR-8361 TCGA-BR-8372 TCGA-CD-A4MG 
        3.88        52.57         9.67        31.10        31.27         6.58 
TCGA-CG-4306 TCGA-CG-5723 TCGA-F1-A448 TCGA-HJ-7597 TCGA-VQ-A8P2 
        1.02       105.07        21.27        26.47        38.14 

$`ALDH3A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
             1.02              0.00 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
           105.07            122.30 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
            26.47             13.51 
[1] "1.0 - 105.1 (26.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D737V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH3A1 MUTATED         0        0        1        1         2         1
  ALDH3A1 WILD-TYPE      10       20       45       30        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH3A1 MUTATED           0          1          2          2        1
  ALDH3A1 WILD-TYPE        29         83         60         37       42
                   vv
clus                STAGE IVA
  ALDH3A1 MUTATED           0
  ALDH3A1 WILD-TYPE         4
D737V3, multiclass
            clus
vv           ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ALDH3A1 MUTATED       0   2   5   4
  ALDH3A1 WILD-TYPE    54 133 256  98
D737V4, multiclass
       clus
vv      ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  5               256
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ALDH3A1 MUTATED     4   3   3   2
  ALDH3A1 WILD-TYPE 191 170  86  83
D737V5, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V6, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED    12   1
  ALDH3A1 WILD-TYPE 470  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED     12    1
  ALDH3A1 WILD-TYPE  470   37
   clus
vv  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  0              12               470
  1               1                37
[1] 2 2
[1] FALSE
D737V7, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     5   9
  ALDH3A1 WILD-TYPE 167 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      5    9
  ALDH3A1 WILD-TYPE  167  397
        clus
vv       ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  FEMALE               5               167
  MALE                 9               397
[1] 2 2
[1] FALSE
D737V8, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     9   2
  ALDH3A1 WILD-TYPE 407 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      9    2
  ALDH3A1 WILD-TYPE  407  100
     clus
vv    ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  NO                9               407
  YES               2               100
[1] 2 2
[1] FALSE
D737V9, continuous
D737V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ALDH3A1 MUTATED       1                         0
  ALDH3A1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALDH3A1 MUTATED                                           0    11
  ALDH3A1 WILD-TYPE                                         1   346
D737V11, multiclass
                                           clus
vv                                          ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V12, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     1   9
  ALDH3A1 WILD-TYPE   9 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      1    9
  ALDH3A1 WILD-TYPE    9  389
                        clus
vv                       ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(738) Variable = PAXIP1 MUTATION ANALYSIS
D738V1, survival
                  sevent
clus2                0   1
  PAXIP1 MUTATED    10   6
  PAXIP1 WILD-TYPE 328 210
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              16              538 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               6              210 
$`PAXIP1 MUTATED`
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-LN-A49U 
       14.50        68.02        41.52        16.47         8.71        15.35 
TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-VR-A8EO TCGA-VR-A8EU TCGA-BR-4257 TCGA-BR-6452 
        6.35        15.78        25.81        18.31         9.67        34.68 
TCGA-BR-8487 TCGA-CG-5721 TCGA-CG-5726 TCGA-VQ-A8P2 
        1.12         6.02        28.96        38.14 

$`PAXIP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
      122.10        44.75         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       16.31         7.04        38.40        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            1.12             0.00 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
           68.02           122.30 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          16.125           13.495 
[1] "1.1 - 68.0 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D738V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAXIP1 MUTATED         0        1        0        0         6         0
  PAXIP1 WILD-TYPE      10       19       46       31        78        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAXIP1 MUTATED           3          2          0          0        2
  PAXIP1 WILD-TYPE        26         82         62         39       41
                  vv
clus               STAGE IVA
  PAXIP1 MUTATED           1
  PAXIP1 WILD-TYPE         3
D738V3, multiclass
            clus
vv           PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               6               78
  STAGE IIB               0               83
  STAGE III               3               26
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PAXIP1 MUTATED       2   0  10   3
  PAXIP1 WILD-TYPE    52 135 251  99
D738V4, multiclass
       clus
vv      PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T0+T1              2               52
  T2                 0              135
  T3                10              251
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PAXIP1 MUTATED     7   7   0   0
  PAXIP1 WILD-TYPE 188 166  89  85
D738V5, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  N0              7              188
  N1              7              166
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V6, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    14   2
  PAXIP1 WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     14    2
  PAXIP1 WILD-TYPE  468   36
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D738V7, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     6  11
  PAXIP1 WILD-TYPE 166 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      6   11
  PAXIP1 WILD-TYPE  166  395
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  FEMALE              6              166
  MALE               11              395
[1] 2 2
[1] FALSE
D738V8, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    10   4
  PAXIP1 WILD-TYPE 406  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     10    4
  PAXIP1 WILD-TYPE  406   98
     clus
vv    PAXIP1 MUTATED PAXIP1 WILD-TYPE
  NO              10              406
  YES              4               98
[1] 2 2
[1] FALSE
D738V9, continuous
D738V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PAXIP1 MUTATED       3                         0
  PAXIP1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAXIP1 MUTATED                                           0    11
  PAXIP1 WILD-TYPE                                         1   346
D738V11, multiclass
                                           clus
vv                                          PAXIP1 MUTATED PAXIP1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V12, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     0   8
  PAXIP1 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      0    8
  PAXIP1 WILD-TYPE   10  390
                        clus
vv                       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(739) Variable = PCCA MUTATION ANALYSIS
D739V1, survival
                sevent
clus2              0   1
  PCCA MUTATED     8   6
  PCCA WILD-TYPE 330 210
  PCCA MUTATED PCCA WILD-TYPE 
            14            540 
  PCCA MUTATED PCCA WILD-TYPE 
             6            210 
$`PCCA MUTATED`
TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-L5-A8NQ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6452 
        4.67        47.93        21.37         9.44         6.97        34.68 
TCGA-BR-8078 TCGA-BR-8368 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-A4H4 
       29.59         4.31         6.02        28.96        21.07        23.84 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`PCCA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.47         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PCCA MUTATED PCCA WILD-TYPE 
          4.31           0.00 
  PCCA MUTATED PCCA WILD-TYPE 
         47.93         122.30 
  PCCA MUTATED PCCA WILD-TYPE 
         21.22          13.51 
[1] "4.3 - 47.9 (21.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D739V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCCA MUTATED         0        2        2        0         2         3
  PCCA WILD-TYPE      10       18       44       31        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCCA MUTATED           0          4          1          0        1         0
  PCCA WILD-TYPE        29         80         61         39       42         4
D739V3, multiclass
            clus
vv           PCCA MUTATED PCCA WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PCCA MUTATED       2   5   3   5
  PCCA WILD-TYPE    52 130 258  97
D739V4, multiclass
       clus
vv      PCCA MUTATED PCCA WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3               3            258
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PCCA MUTATED     8   3   3   0
  PCCA WILD-TYPE 187 170  86  85
D739V5, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  N0            8            187
  N1            3            170
  N2            3             86
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V6, binary
                cls
clus               0   1
  PCCA MUTATED    13   0
  PCCA WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED     13    0
  PCCA WILD-TYPE  469   38
   clus
vv  PCCA MUTATED PCCA WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D739V7, binary
                cls
clus               0   1
  PCCA MUTATED     8   7
  PCCA WILD-TYPE 164 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      8    7
  PCCA WILD-TYPE  164  399
        clus
vv       PCCA MUTATED PCCA WILD-TYPE
  FEMALE            8            164
  MALE              7            399
[1] 2 2
[1] FALSE
D739V8, binary
                cls
clus               0   1
  PCCA MUTATED    11   1
  PCCA WILD-TYPE 405 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED     11    1
  PCCA WILD-TYPE  405  101
     clus
vv    PCCA MUTATED PCCA WILD-TYPE
  NO            11            405
  YES            1            101
[1] 2 2
[1] FALSE
D739V9, continuous
D739V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PCCA MUTATED       2                         0
  PCCA WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCCA MUTATED                                           0    10
  PCCA WILD-TYPE                                         1   347
D739V11, multiclass
                                           clus
vv                                          PCCA MUTATED PCCA WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V12, binary
                cls
clus               0   1
  PCCA MUTATED     0   9
  PCCA WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      0    9
  PCCA WILD-TYPE   10  389
                        clus
vv                       PCCA MUTATED PCCA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(740) Variable = WDR11 MUTATION ANALYSIS
D740V1, survival
                 sevent
clus2               0   1
  WDR11 MUTATED     9   2
  WDR11 WILD-TYPE 329 214
  WDR11 MUTATED WDR11 WILD-TYPE 
             11             543 
  WDR11 MUTATED WDR11 WILD-TYPE 
              2             214 
$`WDR11 MUTATED`
TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-L5-A4OU TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8078 
        7.69       122.10        29.00        32.78        30.90        29.59 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-HJ-7597 TCGA-HU-A4H4 TCGA-SW-A7EB 
       28.14        16.14        26.47        23.84         5.79 

$`WDR11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61        19.04         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  WDR11 MUTATED WDR11 WILD-TYPE 
           5.79            0.00 
  WDR11 MUTATED WDR11 WILD-TYPE 
          122.1           122.3 
  WDR11 MUTATED WDR11 WILD-TYPE 
          28.14           13.48 
[1] "5.8 - 122.1 (28.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.5"
D740V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR11 MUTATED         1        0        1        0         2         4
  WDR11 WILD-TYPE       9       20       45       31        82        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR11 MUTATED           0          2          1          1        0         0
  WDR11 WILD-TYPE        29         82         61         38       43         4
D740V3, multiclass
            clus
vv           WDR11 MUTATED WDR11 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  WDR11 MUTATED       2   2   5   3
  WDR11 WILD-TYPE    52 133 256  99
D740V4, multiclass
       clus
vv      WDR11 MUTATED WDR11 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  WDR11 MUTATED     6   1   3   2
  WDR11 WILD-TYPE 189 172  86  83
D740V5, multiclass
    clus
vv   WDR11 MUTATED WDR11 WILD-TYPE
  N0             6             189
  N1             1             172
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V6, binary
                 cls
clus                0   1
  WDR11 MUTATED    11   0
  WDR11 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR11 MUTATED     11    0
  WDR11 WILD-TYPE  471   38
   clus
vv  WDR11 MUTATED WDR11 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D740V7, binary
                 cls
clus                0   1
  WDR11 MUTATED     5   7
  WDR11 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR11 MUTATED      5    7
  WDR11 WILD-TYPE  167  399
        clus
vv       WDR11 MUTATED WDR11 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D740V8, binary
                 cls
clus                0   1
  WDR11 MUTATED    12   0
  WDR11 WILD-TYPE 404 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR11 MUTATED     12    0
  WDR11 WILD-TYPE  404  102
     clus
vv    WDR11 MUTATED WDR11 WILD-TYPE
  NO             12             404
  YES             0             102
[1] 2 2
[1] FALSE
D740V9, continuous
D740V10, continuous
[1] "Remove cluster labels:" "WDR11 MUTATED"         
clus
  WDR11 MUTATED WDR11 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" "WDR11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WDR11 MUTATED       1                         0
  WDR11 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR11 MUTATED                                           0    11
  WDR11 WILD-TYPE                                         1   346
D740V11, multiclass
                                           clus
vv                                          WDR11 MUTATED WDR11 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V12, binary
                 cls
clus                0   1
  WDR11 MUTATED     0  10
  WDR11 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR11 MUTATED      0   10
  WDR11 WILD-TYPE   10  388
                        clus
vv                       WDR11 MUTATED WDR11 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(741) Variable = PSMC3 MUTATION ANALYSIS
D741V1, survival
                 sevent
clus2               0   1
  PSMC3 MUTATED     5   3
  PSMC3 WILD-TYPE 333 213
  PSMC3 MUTATED PSMC3 WILD-TYPE 
              8             546 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
              3             213 
$`PSMC3 MUTATED`
TCGA-L5-A88W TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-CD-8533 TCGA-CG-4437 
       25.12         9.34        34.68        32.25        15.39         8.05 
TCGA-CG-5726 TCGA-HU-A4H8 
       28.96        14.07 

$`PSMC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PSMC3 MUTATED PSMC3 WILD-TYPE 
           8.05            0.00 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
          34.68          122.30 
  PSMC3 MUTATED PSMC3 WILD-TYPE 
         20.255          13.510 
[1] "8.1 - 34.7 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D741V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSMC3 MUTATED         0        1        1        2         2         1
  PSMC3 WILD-TYPE      10       19       45       29        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMC3 MUTATED           0          0          0          0        0         0
  PSMC3 WILD-TYPE        29         84         62         39       43         4
D741V3, multiclass
            clus
vv           PSMC3 MUTATED PSMC3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PSMC3 MUTATED       2   1   4   1
  PSMC3 WILD-TYPE    52 134 257 101
D741V4, multiclass
       clus
vv      PSMC3 MUTATED PSMC3 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PSMC3 MUTATED     5   4   0   0
  PSMC3 WILD-TYPE 190 169  89  85
D741V5, multiclass
    clus
vv   PSMC3 MUTATED PSMC3 WILD-TYPE
  N0             5             190
  N1             4             169
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V6, binary
                 cls
clus                0   1
  PSMC3 MUTATED     8   0
  PSMC3 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      8    0
  PSMC3 WILD-TYPE  474   38
   clus
vv  PSMC3 MUTATED PSMC3 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D741V7, binary
                 cls
clus                0   1
  PSMC3 MUTATED     4   6
  PSMC3 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      4    6
  PSMC3 WILD-TYPE  168  400
        clus
vv       PSMC3 MUTATED PSMC3 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D741V8, binary
                 cls
clus                0   1
  PSMC3 MUTATED     6   1
  PSMC3 WILD-TYPE 410 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      6    1
  PSMC3 WILD-TYPE  410  101
     clus
vv    PSMC3 MUTATED PSMC3 WILD-TYPE
  NO              6             410
  YES             1             101
[1] 2 2
[1] FALSE
D741V9, continuous
D741V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PSMC3 MUTATED       2                         0
  PSMC3 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSMC3 MUTATED                                           0     6
  PSMC3 WILD-TYPE                                         1   351
D741V11, multiclass
                                           clus
vv                                          PSMC3 MUTATED PSMC3 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V12, binary
                 cls
clus                0   1
  PSMC3 MUTATED     0   7
  PSMC3 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC3 MUTATED      0    7
  PSMC3 WILD-TYPE   10  391
                        clus
vv                       PSMC3 MUTATED PSMC3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(742) Variable = STEAP2 MUTATION ANALYSIS
D742V1, survival
                  sevent
clus2                0   1
  STEAP2 MUTATED     5   1
  STEAP2 WILD-TYPE 333 215
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               6              548 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               1              215 
$`STEAP2 MUTATED`
TCGA-2H-A9GR TCGA-BR-6452 TCGA-F1-6874 TCGA-FP-7829 TCGA-HU-8602 TCGA-HU-A4GU 
       32.45        34.68        14.47        19.53        22.32         6.58 

$`STEAP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  STEAP2 MUTATED STEAP2 WILD-TYPE 
            6.58             0.00 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
           34.68           122.30 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
          20.925           13.510 
[1] "6.6 - 34.7 (20.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3"  
D742V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STEAP2 MUTATED         0        0        1        0         2         3
  STEAP2 WILD-TYPE      10       20       45       31        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STEAP2 MUTATED           0          0          0          0        0
  STEAP2 WILD-TYPE        29         84         62         39       43
                  vv
clus               STAGE IVA
  STEAP2 MUTATED           0
  STEAP2 WILD-TYPE         4
D742V3, multiclass
            clus
vv           STEAP2 MUTATED STEAP2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  STEAP2 MUTATED       0   1   4   1
  STEAP2 WILD-TYPE    54 134 257 101
D742V4, multiclass
       clus
vv      STEAP2 MUTATED STEAP2 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 4              257
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  STEAP2 MUTATED     4   3   0   0
  STEAP2 WILD-TYPE 191 170  89  85
D742V5, multiclass
    clus
vv   STEAP2 MUTATED STEAP2 WILD-TYPE
  N0              4              191
  N1              3              170
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V6, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     7   0
  STEAP2 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      7    0
  STEAP2 WILD-TYPE  475   38
   clus
vv  STEAP2 MUTATED STEAP2 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D742V7, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     3   4
  STEAP2 WILD-TYPE 169 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      3    4
  STEAP2 WILD-TYPE  169  402
        clus
vv       STEAP2 MUTATED STEAP2 WILD-TYPE
  FEMALE              3              169
  MALE                4              402
[1] 2 2
[1] FALSE
D742V8, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     5   1
  STEAP2 WILD-TYPE 411 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      5    1
  STEAP2 WILD-TYPE  411  101
     clus
vv    STEAP2 MUTATED STEAP2 WILD-TYPE
  NO               5              411
  YES              1              101
[1] 2 2
[1] FALSE
D742V9, continuous
D742V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  STEAP2 MUTATED       2                         0
  STEAP2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STEAP2 MUTATED                                           0     4
  STEAP2 WILD-TYPE                                         1   353
D742V11, multiclass
                                           clus
vv                                          STEAP2 MUTATED STEAP2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V12, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     0   6
  STEAP2 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      0    6
  STEAP2 WILD-TYPE   10  392
                        clus
vv                       STEAP2 MUTATED STEAP2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(743) Variable = CUL1 MUTATION ANALYSIS
D743V1, survival
                sevent
clus2              0   1
  CUL1 MUTATED    17   5
  CUL1 WILD-TYPE 321 211
  CUL1 MUTATED CUL1 WILD-TYPE 
            22            532 
  CUL1 MUTATED CUL1 WILD-TYPE 
             5            211 
$`CUL1 MUTATED`
TCGA-JY-A6F8 TCGA-L5-A8NL TCGA-L5-A8NM TCGA-VR-AA7B TCGA-B7-5816 TCGA-BR-4184 
      122.10        13.22         7.76        11.24        26.70         6.97 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 
        9.67        34.68        35.84         4.31        25.05         1.12 
TCGA-BR-A4PD TCGA-CD-5804 TCGA-CG-5733 TCGA-F1-6874 TCGA-FP-8211 TCGA-HF-7132 
       20.65        12.10        21.07        14.47        13.58        77.29 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ 
       11.77        29.98        20.25        19.73 

$`CUL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
        2.66        12.92        13.48        16.47        13.55         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52        13.51        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       21.37         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CUL1 MUTATED CUL1 WILD-TYPE 
          1.12           0.00 
  CUL1 MUTATED CUL1 WILD-TYPE 
         122.1          122.3 
  CUL1 MUTATED CUL1 WILD-TYPE 
         17.10          13.51 
[1] "1.1 - 122.1 (17.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D743V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUL1 MUTATED         1        1        4        1         3         5
  CUL1 WILD-TYPE       9       19       42       30        81        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUL1 MUTATED           1          3          0          2        1         0
  CUL1 WILD-TYPE        28         81         62         37       42         4
D743V3, multiclass
            clus
vv           CUL1 MUTATED CUL1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             5             78
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CUL1 MUTATED       2   8   8   5
  CUL1 WILD-TYPE    52 127 253  97
D743V4, multiclass
       clus
vv      CUL1 MUTATED CUL1 WILD-TYPE
  T0+T1            2             52
  T2               8            127
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUL1 MUTATED    11   7   3   2
  CUL1 WILD-TYPE 184 166  86  83
D743V5, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  N0           11            184
  N1            7            166
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V6, binary
                cls
clus               0   1
  CUL1 MUTATED    21   1
  CUL1 WILD-TYPE 461  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     21    1
  CUL1 WILD-TYPE  461   37
   clus
vv  CUL1 MUTATED CUL1 WILD-TYPE
  0           21            461
  1            1             37
[1] 2 2
[1] FALSE
D743V7, binary
                cls
clus               0   1
  CUL1 MUTATED    13  11
  CUL1 WILD-TYPE 159 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     13   11
  CUL1 WILD-TYPE  159  395
        clus
vv       CUL1 MUTATED CUL1 WILD-TYPE
  FEMALE           13            159
  MALE             11            395
[1] 2 2
[1] FALSE
D743V8, binary
                cls
clus               0   1
  CUL1 MUTATED    20   2
  CUL1 WILD-TYPE 396 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     20    2
  CUL1 WILD-TYPE  396  100
     clus
vv    CUL1 MUTATED CUL1 WILD-TYPE
  NO            20            396
  YES            2            100
[1] 2 2
[1] FALSE
D743V9, continuous
[1] "Remove cluster labels:" "CUL1 MUTATED"          
clus
  CUL1 MUTATED CUL1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CUL1 WILD-TYPE" "CUL1 WILD-TYPE" "CUL1 WILD-TYPE" 
D743V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUL1 MUTATED       4                         0
  CUL1 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUL1 MUTATED                                           0    17
  CUL1 WILD-TYPE                                         1   340
D743V11, multiclass
                                           clus
vv                                          CUL1 MUTATED CUL1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V12, binary
                cls
clus               0   1
  CUL1 MUTATED     0  17
  CUL1 WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      0   17
  CUL1 WILD-TYPE   10  381
                        clus
vv                       CUL1 MUTATED CUL1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(744) Variable = TH1L MUTATION ANALYSIS
D744V1, survival
                sevent
clus2              0   1
  TH1L MUTATED     9   5
  TH1L WILD-TYPE 329 211
  TH1L MUTATED TH1L WILD-TYPE 
            14            540 
  TH1L MUTATED TH1L WILD-TYPE 
             5            211 
$`TH1L MUTATED`
TCGA-FP-A8CX TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-L5-A8NW TCGA-BR-4184 TCGA-BR-4201 
        0.23        58.55         8.94        46.09         6.97        30.90 
TCGA-BR-8680 TCGA-CD-8531 TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-8610 TCGA-HU-A4GN 
       31.96        12.59         6.02       105.07         0.76        29.98 
TCGA-HU-A4H0 TCGA-VQ-A8P2 
        2.10        38.14 

$`TH1L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       31.27        14.30         7.63         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       24.39        28.96        22.32        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TH1L MUTATED TH1L WILD-TYPE 
          0.23           0.00 
  TH1L MUTATED TH1L WILD-TYPE 
        105.07         122.30 
  TH1L MUTATED TH1L WILD-TYPE 
        21.285         13.565 
[1] "0.2 - 105.1 (21.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D744V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TH1L MUTATED         1        1        1        1         1         0
  TH1L WILD-TYPE       9       19       45       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TH1L MUTATED           1          3          0          2        2         0
  TH1L WILD-TYPE        28         81         62         37       41         4
D744V3, multiclass
            clus
vv           TH1L MUTATED TH1L WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TH1L MUTATED       2   4   3   5
  TH1L WILD-TYPE    52 131 258  97
D744V4, multiclass
       clus
vv      TH1L MUTATED TH1L WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3               3            258
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TH1L MUTATED     2   8   1   2
  TH1L WILD-TYPE 193 165  88  83
D744V5, multiclass
    clus
vv   TH1L MUTATED TH1L WILD-TYPE
  N0            2            193
  N1            8            165
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V6, binary
                cls
clus               0   1
  TH1L MUTATED    11   1
  TH1L WILD-TYPE 471  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED     11    1
  TH1L WILD-TYPE  471   37
   clus
vv  TH1L MUTATED TH1L WILD-TYPE
  0           11            471
  1            1             37
[1] 2 2
[1] FALSE
D744V7, binary
                cls
clus               0   1
  TH1L MUTATED     2  12
  TH1L WILD-TYPE 170 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      2   12
  TH1L WILD-TYPE  170  394
        clus
vv       TH1L MUTATED TH1L WILD-TYPE
  FEMALE            2            170
  MALE             12            394
[1] 2 2
[1] FALSE
D744V8, binary
                cls
clus               0   1
  TH1L MUTATED    11   2
  TH1L WILD-TYPE 405 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED     11    2
  TH1L WILD-TYPE  405  100
     clus
vv    TH1L MUTATED TH1L WILD-TYPE
  NO            11            405
  YES            2            100
[1] 2 2
[1] FALSE
D744V9, continuous
D744V10, continuous
[1] "Remove cluster labels:" "TH1L MUTATED"          
clus
  TH1L MUTATED TH1L WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-LN-A49O 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" "TH1L WILD-TYPE" 
    TCGA-Z6-AAPN 
"TH1L WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TH1L MUTATED       5                         0
  TH1L WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TH1L MUTATED                                           0     5
  TH1L WILD-TYPE                                         1   352
D744V11, multiclass
                                           clus
vv                                          TH1L MUTATED TH1L WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V12, binary
                cls
clus               0   1
  TH1L MUTATED     0   8
  TH1L WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      0    8
  TH1L WILD-TYPE   10  390
                        clus
vv                       TH1L MUTATED TH1L WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(745) Variable = FARSA MUTATION ANALYSIS
D745V1, survival
                 sevent
clus2               0   1
  FARSA MUTATED     5   3
  FARSA WILD-TYPE 333 213
  FARSA MUTATED FARSA WILD-TYPE 
              8             546 
  FARSA MUTATED FARSA WILD-TYPE 
              3             213 
$`FARSA MUTATED`
TCGA-IG-A50L TCGA-L5-A8NL TCGA-BR-4201 TCGA-BR-8078 TCGA-CD-5801 TCGA-D7-A4YV 
        0.53        13.22        30.90        29.59        13.18         5.92 
TCGA-F1-6874 TCGA-HU-A4GN 
       14.47        29.98 

$`FARSA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FARSA MUTATED FARSA WILD-TYPE 
           0.53            0.00 
  FARSA MUTATED FARSA WILD-TYPE 
           30.9           122.3 
  FARSA MUTATED FARSA WILD-TYPE 
         13.845          13.565 
[1] "0.5 - 30.9 (13.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D745V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FARSA MUTATED         0        0        1        0         1         2
  FARSA WILD-TYPE      10       20       45       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FARSA MUTATED           1          2          0          0        0         0
  FARSA WILD-TYPE        28         82         62         39       43         4
D745V3, multiclass
            clus
vv           FARSA MUTATED FARSA WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FARSA MUTATED       0   3   4   1
  FARSA WILD-TYPE    54 132 257 101
D745V4, multiclass
       clus
vv      FARSA MUTATED FARSA WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FARSA MUTATED     2   5   0   0
  FARSA WILD-TYPE 193 168  89  85
D745V5, multiclass
    clus
vv   FARSA MUTATED FARSA WILD-TYPE
  N0             2             193
  N1             5             168
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V6, binary
                 cls
clus                0   1
  FARSA MUTATED     8   0
  FARSA WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FARSA MUTATED      8    0
  FARSA WILD-TYPE  474   38
   clus
vv  FARSA MUTATED FARSA WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D745V7, binary
                 cls
clus                0   1
  FARSA MUTATED     3   5
  FARSA WILD-TYPE 169 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FARSA MUTATED      3    5
  FARSA WILD-TYPE  169  401
        clus
vv       FARSA MUTATED FARSA WILD-TYPE
  FEMALE             3             169
  MALE               5             401
[1] 2 2
[1] FALSE
D745V8, binary
                 cls
clus                0   1
  FARSA MUTATED     6   0
  FARSA WILD-TYPE 410 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FARSA MUTATED      6    0
  FARSA WILD-TYPE  410  102
     clus
vv    FARSA MUTATED FARSA WILD-TYPE
  NO              6             410
  YES             0             102
[1] 2 2
[1] FALSE
D745V9, continuous
D745V10, continuous
[1] "Remove cluster labels:" "FARSA MUTATED"         
clus
  FARSA MUTATED FARSA WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A5B8      TCGA-IG-A6QS 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" "FARSA WILD-TYPE" 
     TCGA-Z6-AAPN 
"FARSA WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FARSA MUTATED       3                         0
  FARSA WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FARSA MUTATED                                           0     5
  FARSA WILD-TYPE                                         1   352
D745V11, multiclass
                                           clus
vv                                          FARSA MUTATED FARSA WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V12, binary
                 cls
clus                0   1
  FARSA MUTATED     0   7
  FARSA WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FARSA MUTATED      0    7
  FARSA WILD-TYPE   10  391
                        clus
vv                       FARSA MUTATED FARSA WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(746) Variable = EDNRB MUTATION ANALYSIS
D746V1, survival
                 sevent
clus2               0   1
  EDNRB MUTATED    16  12
  EDNRB WILD-TYPE 322 204
  EDNRB MUTATED EDNRB WILD-TYPE 
             28             526 
  EDNRB MUTATED EDNRB WILD-TYPE 
             12             204 
$`EDNRB MUTATED`
TCGA-CG-4460 TCGA-L5-A43E TCGA-L5-A8NH TCGA-L7-A6VZ TCGA-B7-A5TJ TCGA-BR-4184 
       21.99        30.25        12.92        10.36        11.01         6.97 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8372 
       18.35         4.08         6.61        34.68        32.78        31.27 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4466 
       16.14        13.15        12.76        12.43         6.58        18.97 
TCGA-CG-5721 TCGA-CG-5724 TCGA-D7-6527 TCGA-D7-A4Z0 TCGA-HF-7134 TCGA-HU-A4GQ 
        6.02        12.03        10.26        14.76        52.21         0.10 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-VQ-A8PK 
        6.58        23.84        14.07        17.85 

$`EDNRB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.61         4.64         7.43        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.39        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
       36.00         1.02         0.99         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        37.22        22.19         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EDNRB MUTATED EDNRB WILD-TYPE 
            0.1             0.0 
  EDNRB MUTATED EDNRB WILD-TYPE 
          52.21          122.30 
  EDNRB MUTATED EDNRB WILD-TYPE 
         13.035          13.630 
[1] "0.1 - 52.2 (13.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D746V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EDNRB MUTATED         1        1        3        4         3         4
  EDNRB WILD-TYPE       9       19       43       27        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EDNRB MUTATED           1          3          2          3        4         0
  EDNRB WILD-TYPE        28         81         60         36       39         4
D746V3, multiclass
            clus
vv           EDNRB MUTATED EDNRB WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               4              27
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EDNRB MUTATED       5   6  13   6
  EDNRB WILD-TYPE    49 129 248  96
D746V4, multiclass
       clus
vv      EDNRB MUTATED EDNRB WILD-TYPE
  T0+T1             5              49
  T2                6             129
  T3               13             248
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EDNRB MUTATED    12   9   3   5
  EDNRB WILD-TYPE 183 164  86  80
D746V5, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  N0            12             183
  N1             9             164
  N2             3              86
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V6, binary
                 cls
clus                0   1
  EDNRB MUTATED    26   3
  EDNRB WILD-TYPE 456  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     26    3
  EDNRB WILD-TYPE  456   35
   clus
vv  EDNRB MUTATED EDNRB WILD-TYPE
  0            26             456
  1             3              35
[1] 2 2
[1] FALSE
D746V7, binary
                 cls
clus                0   1
  EDNRB MUTATED    13  18
  EDNRB WILD-TYPE 159 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     13   18
  EDNRB WILD-TYPE  159  388
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  FEMALE            13             159
  MALE              18             388
[1] 2 2
[1] FALSE
D746V8, binary
                 cls
clus                0   1
  EDNRB MUTATED    24   3
  EDNRB WILD-TYPE 392  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     24    3
  EDNRB WILD-TYPE  392   99
     clus
vv    EDNRB MUTATED EDNRB WILD-TYPE
  NO             24             392
  YES             3              99
[1] 2 2
[1] FALSE
D746V9, continuous
D746V10, continuous
[1] "Remove cluster labels:" "EDNRB MUTATED"         
clus
  EDNRB MUTATED EDNRB WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" "EDNRB WILD-TYPE" 
     TCGA-Z6-AAPN 
"EDNRB WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EDNRB MUTATED       8                         0
  EDNRB WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EDNRB MUTATED                                           0    17
  EDNRB WILD-TYPE                                         1   340
D746V11, multiclass
                                           clus
vv                                          EDNRB MUTATED EDNRB WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V12, binary
                 cls
clus                0   1
  EDNRB MUTATED     0  22
  EDNRB WILD-TYPE  10 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED      0   22
  EDNRB WILD-TYPE   10  376
                        clus
vv                       EDNRB MUTATED EDNRB WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(747) Variable = SMAD7 MUTATION ANALYSIS
D747V1, survival
                 sevent
clus2               0   1
  SMAD7 MUTATED     3   1
  SMAD7 WILD-TYPE 335 215
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              4             550 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              1             215 
$`SMAD7 MUTATED`
TCGA-BR-7703 TCGA-CD-A4MG TCGA-HU-A4H5 TCGA-HU-A4H8 
       36.16         6.58        23.80        14.07 

$`SMAD7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SMAD7 MUTATED SMAD7 WILD-TYPE 
           6.58            0.00 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
          36.16          122.30 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
         18.935          13.530 
[1] "6.6 - 36.2 (18.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D747V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD7 MUTATED         0        1        2        0         1         1
  SMAD7 WILD-TYPE      10       19       44       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD7 MUTATED           0          0          0          0        1         0
  SMAD7 WILD-TYPE        29         84         62         39       42         4
D747V3, multiclass
            clus
vv           SMAD7 MUTATED SMAD7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SMAD7 MUTATED       2   1   1   2
  SMAD7 WILD-TYPE    52 134 260 100
D747V4, multiclass
       clus
vv      SMAD7 MUTATED SMAD7 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SMAD7 MUTATED     4   1   1   0
  SMAD7 WILD-TYPE 191 172  88  85
D747V5, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  N0             4             191
  N1             1             172
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V6, binary
                 cls
clus                0   1
  SMAD7 MUTATED     7   0
  SMAD7 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      7    0
  SMAD7 WILD-TYPE  475   38
   clus
vv  SMAD7 MUTATED SMAD7 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D747V7, binary
                 cls
clus                0   1
  SMAD7 MUTATED     2   5
  SMAD7 WILD-TYPE 170 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      2    5
  SMAD7 WILD-TYPE  170  401
        clus
vv       SMAD7 MUTATED SMAD7 WILD-TYPE
  FEMALE             2             170
  MALE               5             401
[1] 2 2
[1] FALSE
D747V8, binary
                 cls
clus                0   1
  SMAD7 MUTATED     5   0
  SMAD7 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      5    0
  SMAD7 WILD-TYPE  411  102
     clus
vv    SMAD7 MUTATED SMAD7 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D747V9, continuous
D747V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD7 MUTATED       3                         0
  SMAD7 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD7 MUTATED                                           0     4
  SMAD7 WILD-TYPE                                         1   353
D747V11, multiclass
                                           clus
vv                                          SMAD7 MUTATED SMAD7 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V12, binary
                 cls
clus                0   1
  SMAD7 MUTATED     0   7
  SMAD7 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      0    7
  SMAD7 WILD-TYPE   10  391
                        clus
vv                       SMAD7 MUTATED SMAD7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(748) Variable = PABPC4 MUTATION ANALYSIS
D748V1, survival
                  sevent
clus2                0   1
  PABPC4 MUTATED     7   4
  PABPC4 WILD-TYPE 331 212
  PABPC4 MUTATED PABPC4 WILD-TYPE 
              11              543 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               4              212 
$`PABPC4 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OX TCGA-LN-A49M TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8487 
       21.99         7.43        12.66         6.97         0.26         1.12 
TCGA-BR-8589 TCGA-CD-8536 TCGA-CG-5721 TCGA-HF-7134 TCGA-HU-A4H4 
       27.12        12.43         6.02        52.21        23.84 

$`PABPC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PABPC4 MUTATED PABPC4 WILD-TYPE 
            0.26             0.00 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
           52.21           122.30 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
           12.43            13.68 
[1] "0.3 - 52.2 (12.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D748V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PABPC4 MUTATED         0        1        1        1         2         2
  PABPC4 WILD-TYPE      10       19       45       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PABPC4 MUTATED           0          1          1          0        2
  PABPC4 WILD-TYPE        29         83         61         39       41
                  vv
clus               STAGE IVA
  PABPC4 MUTATED           0
  PABPC4 WILD-TYPE         4
D748V3, multiclass
            clus
vv           PABPC4 MUTATED PABPC4 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PABPC4 MUTATED       1   4   3   3
  PABPC4 WILD-TYPE    53 131 258  99
D748V4, multiclass
       clus
vv      PABPC4 MUTATED PABPC4 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 3              258
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PABPC4 MUTATED     5   5   1   0
  PABPC4 WILD-TYPE 190 168  88  85
D748V5, multiclass
    clus
vv   PABPC4 MUTATED PABPC4 WILD-TYPE
  N0              5              190
  N1              5              168
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V6, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     9   1
  PABPC4 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      9    1
  PABPC4 WILD-TYPE  473   37
   clus
vv  PABPC4 MUTATED PABPC4 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D748V7, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     4   7
  PABPC4 WILD-TYPE 168 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      4    7
  PABPC4 WILD-TYPE  168  399
        clus
vv       PABPC4 MUTATED PABPC4 WILD-TYPE
  FEMALE              4              168
  MALE                7              399
[1] 2 2
[1] FALSE
D748V8, binary
                  cls
clus                 0   1
  PABPC4 MUTATED    10   1
  PABPC4 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED     10    1
  PABPC4 WILD-TYPE  406  101
     clus
vv    PABPC4 MUTATED PABPC4 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D748V9, continuous
[1] "Remove cluster labels:" "PABPC4 MUTATED"        
clus
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
D748V10, continuous
[1] "Remove cluster labels:" "PABPC4 MUTATED"        
clus
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" "PABPC4 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PABPC4 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PABPC4 MUTATED       3                         0
  PABPC4 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PABPC4 MUTATED                                           0     5
  PABPC4 WILD-TYPE                                         1   352
D748V11, multiclass
                                           clus
vv                                          PABPC4 MUTATED PABPC4 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V12, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     0   7
  PABPC4 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      0    7
  PABPC4 WILD-TYPE   10  391
                        clus
vv                       PABPC4 MUTATED PABPC4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(749) Variable = SLC16A1 MUTATION ANALYSIS
D749V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     7   3
  SLC16A1 WILD-TYPE 331 213
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               544 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               213 
$`SLC16A1 MUTATED`
TCGA-Q9-A6FU TCGA-LN-A7HY TCGA-V5-A7RE TCGA-VR-AA4D TCGA-BR-7707 TCGA-CG-4306 
        5.16        12.03        16.44        46.19        35.84         1.02 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4H5 TCGA-VQ-A8P2 
        6.02        11.08        23.80        38.14 

$`SLC16A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             1.02              0.00 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
            46.19            122.30 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           14.235            13.565 
[1] "1.0 - 46.2 (14.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D749V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC16A1 MUTATED         0        0        3        0         1         1
  SLC16A1 WILD-TYPE      10       20       43       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A1 MUTATED           1          1          1          0        2
  SLC16A1 WILD-TYPE        28         83         61         39       41
                   vv
clus                STAGE IVA
  SLC16A1 MUTATED           0
  SLC16A1 WILD-TYPE         4
D749V3, multiclass
            clus
vv           SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC16A1 MUTATED       2   2   4   2
  SLC16A1 WILD-TYPE    52 133 257 100
D749V4, multiclass
       clus
vv      SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC16A1 MUTATED     4   4   2   0
  SLC16A1 WILD-TYPE 191 169  87  85
D749V5, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  N0               4               191
  N1               4               169
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V6, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     9   1
  SLC16A1 WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      9    1
  SLC16A1 WILD-TYPE  473   37
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D749V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     2   8
  SLC16A1 WILD-TYPE 170 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      2    8
  SLC16A1 WILD-TYPE  170  398
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               2               170
  MALE                 8               398
[1] 2 2
[1] FALSE
D749V8, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     5   4
  SLC16A1 WILD-TYPE 411  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      5    4
  SLC16A1 WILD-TYPE  411   98
     clus
vv    SLC16A1 MUTATED SLC16A1 WILD-TYPE
  NO                5               411
  YES               4                98
[1] 2 2
[1] FALSE
D749V9, continuous
D749V10, continuous
[1] "Remove cluster labels:" "SLC16A1 MUTATED"       
clus
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-IC-A6RE        TCGA-IG-A3QL 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"SLC16A1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC16A1 MUTATED       2                         1
  SLC16A1 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC16A1 MUTATED                                           0     5
  SLC16A1 WILD-TYPE                                         1   352
D749V11, multiclass
                                           clus
vv                                          SLC16A1 MUTATED SLC16A1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V12, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     0   6
  SLC16A1 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      0    6
  SLC16A1 WILD-TYPE   10  392
                        clus
vv                       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(750) Variable = KIAA1539 MUTATION ANALYSIS
D750V1, survival
                    sevent
clus2                  0   1
  KIAA1539 MUTATED     8   6
  KIAA1539 WILD-TYPE 330 210
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                14                540 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 6                210 
$`KIAA1539 MUTATED`
TCGA-2H-A9GL TCGA-L5-A8NM TCGA-LN-A4A3 TCGA-VR-AA4G TCGA-B7-5818 TCGA-BR-4257 
        5.92         7.76        12.76        18.05        11.70         9.67 
TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG 
       34.68         9.07         1.12        28.14        16.14         6.58 
TCGA-HU-8602 TCGA-HU-A4GX 
       22.32        20.25 

$`KIAA1539 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
              1.12               0.00 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
             34.68             122.30 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
             12.23              13.63 
[1] "1.1 - 34.7 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D750V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1539 MUTATED         0        0        1        0         3         2
  KIAA1539 WILD-TYPE      10       20       45       31        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1539 MUTATED           2          1          1          2        1
  KIAA1539 WILD-TYPE        27         83         61         37       42
                    vv
clus                 STAGE IVA
  KIAA1539 MUTATED           0
  KIAA1539 WILD-TYPE         4
D750V3, multiclass
            clus
vv           KIAA1539 MUTATED KIAA1539 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 2                 81
  STAGE III                 2                 27
  STAGE IIIA                1                 83
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1539 MUTATED       0   3   7   3
  KIAA1539 WILD-TYPE    54 132 254  99
D750V4, multiclass
       clus
vv      KIAA1539 MUTATED KIAA1539 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   7                254
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1539 MUTATED     5   3   2   3
  KIAA1539 WILD-TYPE 190 170  87  82
D750V5, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  N0                5                190
  N1                3                170
  N2                2                 87
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V6, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED    13   1
  KIAA1539 WILD-TYPE 469  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED     13    1
  KIAA1539 WILD-TYPE  469   37
   clus
vv  KIAA1539 MUTATED KIAA1539 WILD-TYPE
  0               13                469
  1                1                 37
[1] 2 2
[1] FALSE
D750V7, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     9   5
  KIAA1539 WILD-TYPE 163 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      9    5
  KIAA1539 WILD-TYPE  163  401
        clus
vv       KIAA1539 MUTATED KIAA1539 WILD-TYPE
  FEMALE                9                163
  MALE                  5                401
[1] 2 2
[1] FALSE
D750V8, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED    13   1
  KIAA1539 WILD-TYPE 403 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED     13    1
  KIAA1539 WILD-TYPE  403  101
     clus
vv    KIAA1539 MUTATED KIAA1539 WILD-TYPE
  NO                13                403
  YES                1                101
[1] 2 2
[1] FALSE
D750V9, continuous
[1] "Remove cluster labels:" "KIAA1539 MUTATED"      
clus
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA7B         TCGA-VR-AA7D 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
D750V10, continuous
[1] "Remove cluster labels:" "KIAA1539 MUTATED"      
clus
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A6 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA7D 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" "KIAA1539 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1539 MUTATED       4                         0
  KIAA1539 WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1539 MUTATED                                           0     9
  KIAA1539 WILD-TYPE                                         1   348
D750V11, multiclass
                                           clus
vv                                          KIAA1539 MUTATED KIAA1539 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V12, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     0  11
  KIAA1539 WILD-TYPE  10 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      0   11
  KIAA1539 WILD-TYPE   10  387
                        clus
vv                       KIAA1539 MUTATED KIAA1539 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                387
[1] 2 2
[1] FALSE

Clustering(751) Variable = DNAJB13 MUTATION ANALYSIS
D751V1, survival
                   sevent
clus2                 0   1
  DNAJB13 MUTATED     2   2
  DNAJB13 WILD-TYPE 336 214
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                4               550 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                2               214 
$`DNAJB13 MUTATED`
TCGA-BR-8360 TCGA-CD-8527 TCGA-D7-A4YV TCGA-VQ-A8P2 
        6.18         7.17         5.92        38.14 

$`DNAJB13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
             5.92              0.00 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
            38.14            122.30 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
            6.675            13.630 
[1] "5.9 - 38.1 (6.7)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D751V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJB13 MUTATED         0        0        0        1         1         2
  DNAJB13 WILD-TYPE      10       20       46       30        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJB13 MUTATED           0          1          0          0        0
  DNAJB13 WILD-TYPE        29         83         62         39       43
                   vv
clus                STAGE IVA
  DNAJB13 MUTATED           0
  DNAJB13 WILD-TYPE         4
D751V3, multiclass
            clus
vv           DNAJB13 MUTATED DNAJB13 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  DNAJB13 MUTATED       0   1   2   2
  DNAJB13 WILD-TYPE    54 134 259 100
D751V4, multiclass
       clus
vv      DNAJB13 MUTATED DNAJB13 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  DNAJB13 MUTATED     2   4   0   0
  DNAJB13 WILD-TYPE 193 169  89  85
D751V5, multiclass
    clus
vv   DNAJB13 MUTATED DNAJB13 WILD-TYPE
  N0               2               193
  N1               4               169
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V6, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     6   0
  DNAJB13 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      6    0
  DNAJB13 WILD-TYPE  476   38
   clus
vv  DNAJB13 MUTATED DNAJB13 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D751V7, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     3   3
  DNAJB13 WILD-TYPE 169 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      3    3
  DNAJB13 WILD-TYPE  169  403
        clus
vv       DNAJB13 MUTATED DNAJB13 WILD-TYPE
  FEMALE               3               169
  MALE                 3               403
[1] 2 2
[1] FALSE
D751V8, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     4   1
  DNAJB13 WILD-TYPE 412 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      4    1
  DNAJB13 WILD-TYPE  412  101
     clus
vv    DNAJB13 MUTATED DNAJB13 WILD-TYPE
  NO                4               412
  YES               1               101
[1] 2 2
[1] FALSE
D751V9, continuous
D751V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DNAJB13 MUTATED       1                         0
  DNAJB13 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJB13 MUTATED                                           0     5
  DNAJB13 WILD-TYPE                                         1   352
D751V11, multiclass
                                           clus
vv                                          DNAJB13 MUTATED DNAJB13 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V12, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     0   5
  DNAJB13 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      0    5
  DNAJB13 WILD-TYPE   10  393
                        clus
vv                       DNAJB13 MUTATED DNAJB13 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(752) Variable = ZCCHC11 MUTATION ANALYSIS
D752V1, survival
                   sevent
clus2                 0   1
  ZCCHC11 MUTATED    16   5
  ZCCHC11 WILD-TYPE 322 211
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               21               533 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                5               211 
$`ZCCHC11 MUTATED`
TCGA-JY-A6FD TCGA-KH-A6WC TCGA-L5-A8NM TCGA-L5-A8NS TCGA-LN-A9FP TCGA-LN-A9FQ 
       68.02         6.28         7.76        13.41        12.03        12.85 
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8382 
       19.56         6.97         9.34        35.84        31.27        25.05 
TCGA-BR-8680 TCGA-CD-8530 TCGA-CG-4305 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4G8 
       31.96        12.39        15.95        11.44        30.51        22.68 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-SW-A7EA 
       29.98         6.51        19.04 

$`ZCCHC11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
             6.28              0.00 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            68.02            122.30 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            15.95             13.55 
[1] "6.3 - 68.0 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D752V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC11 MUTATED         0        1        2        2         5         4
  ZCCHC11 WILD-TYPE      10       19       44       29        79        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC11 MUTATED           0          1          1          4        2
  ZCCHC11 WILD-TYPE        29         83         61         35       41
                   vv
clus                STAGE IVA
  ZCCHC11 MUTATED           0
  ZCCHC11 WILD-TYPE         4
D752V3, multiclass
            clus
vv           ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 2                29
  STAGE IIA                5                79
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZCCHC11 MUTATED       1   6   8   7
  ZCCHC11 WILD-TYPE    53 129 253  95
D752V4, multiclass
       clus
vv      ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  T0+T1               1                53
  T2                  6               129
  T3                  8               253
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZCCHC11 MUTATED    10   7   2   5
  ZCCHC11 WILD-TYPE 185 166  87  80
D752V5, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  N0              10               185
  N1               7               166
  N2               2                87
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V6, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED    22   1
  ZCCHC11 WILD-TYPE 460  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED     22    1
  ZCCHC11 WILD-TYPE  460   37
   clus
vv  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  0              22               460
  1               1                37
[1] 2 2
[1] FALSE
D752V7, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED    12  12
  ZCCHC11 WILD-TYPE 160 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED     12   12
  ZCCHC11 WILD-TYPE  160  394
        clus
vv       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  FEMALE              12               160
  MALE                12               394
[1] 2 2
[1] FALSE
D752V8, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED    17   5
  ZCCHC11 WILD-TYPE 399  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED     17    5
  ZCCHC11 WILD-TYPE  399   97
     clus
vv    ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  NO               17               399
  YES               5                97
[1] 2 2
[1] FALSE
D752V9, continuous
[1] "Remove cluster labels:" "ZCCHC11 MUTATED"       
clus
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
D752V10, continuous
[1] "Remove cluster labels:" "ZCCHC11 MUTATED"       
clus
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-L5-A43C 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" "ZCCHC11 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC11 MUTATED       8                         0
  ZCCHC11 WILD-TYPE   125                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC11 MUTATED                                           0    14
  ZCCHC11 WILD-TYPE                                         1   343
D752V11, multiclass
                                           clus
vv                                          ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  ASIAN                                                   8               125
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V12, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     0  19
  ZCCHC11 WILD-TYPE  10 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      0   19
  ZCCHC11 WILD-TYPE   10  379
                        clus
vv                       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              19               379
[1] 2 2
[1] FALSE

Clustering(753) Variable = DDX60 MUTATION ANALYSIS
D753V1, survival
                 sevent
clus2               0   1
  DDX60 MUTATED    14   8
  DDX60 WILD-TYPE 324 208
  DDX60 MUTATED DDX60 WILD-TYPE 
             22             532 
  DDX60 MUTATED DDX60 WILD-TYPE 
              8             208 
$`DDX60 MUTATED`
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-LN-A49N TCGA-R6-A6XG 
        7.43        25.12        16.47         7.76        12.43        38.40 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8591 
       22.82        46.19        26.70        30.90        34.68        28.14 
TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5728 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G9 
       31.96         6.02        65.10        30.51        26.47        24.20 
TCGA-HU-A4GN TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       29.98        13.02        38.14        37.22 

$`DDX60 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.66        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        52.21         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DDX60 MUTATED DDX60 WILD-TYPE 
           6.02            0.00 
  DDX60 MUTATED DDX60 WILD-TYPE 
           65.1           122.3 
  DDX60 MUTATED DDX60 WILD-TYPE 
          27.42           13.41 
[1] "6.0 - 65.1 (27.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D753V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX60 MUTATED         0        1        2        0         3         5
  DDX60 WILD-TYPE      10       19       44       31        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX60 MUTATED           2          2          0          2        3         0
  DDX60 WILD-TYPE        27         82         62         37       40         4
D753V3, multiclass
            clus
vv           DDX60 MUTATED DDX60 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DDX60 MUTATED       2   7   4   8
  DDX60 WILD-TYPE    52 128 257  94
D753V4, multiclass
       clus
vv      DDX60 MUTATED DDX60 WILD-TYPE
  T0+T1             2              52
  T2                7             128
  T3                4             257
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDX60 MUTATED     6  10   1   3
  DDX60 WILD-TYPE 189 163  88  82
D753V5, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  N0             6             189
  N1            10             163
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V6, binary
                 cls
clus                0   1
  DDX60 MUTATED    18   2
  DDX60 WILD-TYPE 464  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED     18    2
  DDX60 WILD-TYPE  464   36
   clus
vv  DDX60 MUTATED DDX60 WILD-TYPE
  0            18             464
  1             2              36
[1] 2 2
[1] FALSE
D753V7, binary
                 cls
clus                0   1
  DDX60 MUTATED     9  14
  DDX60 WILD-TYPE 163 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      9   14
  DDX60 WILD-TYPE  163  392
        clus
vv       DDX60 MUTATED DDX60 WILD-TYPE
  FEMALE             9             163
  MALE              14             392
[1] 2 2
[1] FALSE
D753V8, binary
                 cls
clus                0   1
  DDX60 MUTATED    15   6
  DDX60 WILD-TYPE 401  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED     15    6
  DDX60 WILD-TYPE  401   96
     clus
vv    DDX60 MUTATED DDX60 WILD-TYPE
  NO             15             401
  YES             6              96
[1] 2 2
[1] FALSE
D753V9, continuous
D753V10, continuous
[1] "Remove cluster labels:" "DDX60 MUTATED"         
clus
  DDX60 MUTATED DDX60 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" "DDX60 WILD-TYPE" 
     TCGA-Z6-AAPN 
"DDX60 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX60 MUTATED       4                         1
  DDX60 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX60 MUTATED                                           0    15
  DDX60 WILD-TYPE                                         1   342
D753V11, multiclass
                                           clus
vv                                          DDX60 MUTATED DDX60 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V12, binary
                 cls
clus                0   1
  DDX60 MUTATED     0  11
  DDX60 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      0   11
  DDX60 WILD-TYPE   10  387
                        clus
vv                       DDX60 MUTATED DDX60 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(754) Variable = SCN10A MUTATION ANALYSIS
D754V1, survival
                  sevent
clus2                0   1
  SCN10A MUTATED    31  13
  SCN10A WILD-TYPE 307 203
  SCN10A MUTATED SCN10A WILD-TYPE 
              44              510 
  SCN10A MUTATED SCN10A WILD-TYPE 
              13              203 
$`SCN10A MUTATED`
TCGA-2H-A9GI TCGA-L5-A43E TCGA-L5-A8NS TCGA-LN-A7HX TCGA-Q9-A6FW TCGA-R6-A6Y0 
       14.30        30.25        13.41        12.23         7.82        53.95 
TCGA-RE-A7BO TCGA-VR-AA4G TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-6852 
        7.00        18.05        34.68        32.78        40.21        44.94 
TCGA-BR-8078 TCGA-BR-8285 TCGA-BR-8363 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8589 
       29.59         0.56         0.26        26.33         4.31        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8678 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4306 
        9.34        28.14        24.79        12.43         6.58         1.02 
TCGA-CG-4440 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4Z0 TCGA-D7-A6EV 
        4.01         6.02       105.07        65.10        14.76        11.24 
TCGA-FP-8631 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-IN-8663 
        0.56        29.98         0.10        20.25        23.84         3.39 
TCGA-IN-A6RR TCGA-IN-AB1X TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        6.74        13.51        48.79        43.36        38.14        37.22 
TCGA-VQ-AA64 TCGA-VQ-AA68 
       18.41        43.66 

$`SCN10A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26        33.11         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
        8.98        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 
       31.10        22.19        17.52         0.95        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        13.78        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03        13.58        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37         8.98         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 
        5.79         0.92         5.46        13.25        13.02        37.41 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.64        66.81        11.24        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SCN10A MUTATED SCN10A WILD-TYPE 
             0.1              0.0 
  SCN10A MUTATED SCN10A WILD-TYPE 
          105.07           122.30 
  SCN10A MUTATED SCN10A WILD-TYPE 
          18.230           13.445 
[1] "0.1 - 105.1 (18.2)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D754V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCN10A MUTATED         1        0        4        1         9         7
  SCN10A WILD-TYPE       9       20       42       30        75        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCN10A MUTATED           1          6          6          7        4
  SCN10A WILD-TYPE        28         78         56         32       39
                  vv
clus               STAGE IVA
  SCN10A MUTATED           0
  SCN10A WILD-TYPE         4
D754V3, multiclass
            clus
vv           SCN10A MUTATED SCN10A WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               9               75
  STAGE IIB               7               76
  STAGE III               1               28
  STAGE IIIA              6               78
  STAGE IIIB              6               56
  STAGE IIIC              7               32
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SCN10A MUTATED       2  12  18  14
  SCN10A WILD-TYPE    52 123 243  88
D754V4, multiclass
       clus
vv      SCN10A MUTATED SCN10A WILD-TYPE
  T0+T1              2               52
  T2                12              123
  T3                18              243
  T4                14               88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SCN10A MUTATED    16   9  14   7
  SCN10A WILD-TYPE 179 164  75  78
D754V5, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  N0             16              179
  N1              9              164
  N2             14               75
  N3              7               78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V6, binary
                  cls
clus                 0   1
  SCN10A MUTATED    43   2
  SCN10A WILD-TYPE 439  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     43    2
  SCN10A WILD-TYPE  439   36
   clus
vv  SCN10A MUTATED SCN10A WILD-TYPE
  0             43              439
  1              2               36
[1] 2 2
[1] FALSE
D754V7, binary
                  cls
clus                 0   1
  SCN10A MUTATED    20  27
  SCN10A WILD-TYPE 152 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     20   27
  SCN10A WILD-TYPE  152  379
        clus
vv       SCN10A MUTATED SCN10A WILD-TYPE
  FEMALE             20              152
  MALE               27              379
[1] 2 2
[1] FALSE
D754V8, binary
                  cls
clus                 0   1
  SCN10A MUTATED    31  10
  SCN10A WILD-TYPE 385  92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     31   10
  SCN10A WILD-TYPE  385   92
     clus
vv    SCN10A MUTATED SCN10A WILD-TYPE
  NO              31              385
  YES             10               92
[1] 2 2
[1] FALSE
D754V9, continuous
[1] "Remove cluster labels:" "SCN10A MUTATED"        
clus
  SCN10A MUTATED SCN10A WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA7B       TCGA-VR-AA7D 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SCN10A WILD-TYPE" "SCN10A WILD-TYPE" 
D754V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SCN10A MUTATED       8                         0
  SCN10A WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCN10A MUTATED                                           0    32
  SCN10A WILD-TYPE                                         1   325
D754V11, multiclass
                                           clus
vv                                          SCN10A MUTATED SCN10A WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 32              325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V12, binary
                  cls
clus                 0   1
  SCN10A MUTATED     0  32
  SCN10A WILD-TYPE  10 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED      0   32
  SCN10A WILD-TYPE   10  366
                        clus
vv                       SCN10A MUTATED SCN10A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             32              366
[1] 2 2
[1] FALSE

Clustering(755) Variable = BRDT MUTATION ANALYSIS
D755V1, survival
                sevent
clus2              0   1
  BRDT MUTATED     8   4
  BRDT WILD-TYPE 330 212
  BRDT MUTATED BRDT WILD-TYPE 
            12            542 
  BRDT MUTATED BRDT WILD-TYPE 
             4            212 
$`BRDT MUTATED`
TCGA-MX-A663 TCGA-IC-A6RE TCGA-L5-A8NS TCGA-LN-A4A1 TCGA-XP-A8T6 TCGA-BR-6452 
        9.86         7.69        13.41        12.59        25.08        34.68 
TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-5801 TCGA-MX-A5UJ TCGA-R5-A805 TCGA-VQ-A8P2 
       29.59        31.96        13.18        19.73         9.24        38.14 

$`BRDT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BRDT MUTATED BRDT WILD-TYPE 
          7.69           0.00 
  BRDT MUTATED BRDT WILD-TYPE 
         38.14         122.30 
  BRDT MUTATED BRDT WILD-TYPE 
        16.570         13.565 
[1] "7.7 - 38.1 (16.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D755V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRDT MUTATED         0        0        0        0         3         4
  BRDT WILD-TYPE      10       20       46       31        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRDT MUTATED           0          3          1          1        1         0
  BRDT WILD-TYPE        29         81         61         38       42         4
D755V3, multiclass
            clus
vv           BRDT MUTATED BRDT WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BRDT MUTATED       1   1   8   4
  BRDT WILD-TYPE    53 134 253  98
D755V4, multiclass
       clus
vv      BRDT MUTATED BRDT WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               8            253
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BRDT MUTATED     5   4   3   1
  BRDT WILD-TYPE 190 169  86  84
D755V5, multiclass
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  N0            5            190
  N1            4            169
  N2            3             86
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V6, binary
                cls
clus               0   1
  BRDT MUTATED    12   1
  BRDT WILD-TYPE 470  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED     12    1
  BRDT WILD-TYPE  470   37
   clus
vv  BRDT MUTATED BRDT WILD-TYPE
  0           12            470
  1            1             37
[1] 2 2
[1] FALSE
D755V7, binary
                cls
clus               0   1
  BRDT MUTATED     4  10
  BRDT WILD-TYPE 168 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      4   10
  BRDT WILD-TYPE  168  396
        clus
vv       BRDT MUTATED BRDT WILD-TYPE
  FEMALE            4            168
  MALE             10            396
[1] 2 2
[1] FALSE
D755V8, binary
                cls
clus               0   1
  BRDT MUTATED    10   2
  BRDT WILD-TYPE 406 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED     10    2
  BRDT WILD-TYPE  406  100
     clus
vv    BRDT MUTATED BRDT WILD-TYPE
  NO            10            406
  YES            2            100
[1] 2 2
[1] FALSE
D755V9, continuous
[1] "Remove cluster labels:" "BRDT MUTATED"          
clus
  BRDT MUTATED BRDT WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A2 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" 
D755V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRDT MUTATED       3                         1
  BRDT WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRDT MUTATED                                           0    10
  BRDT WILD-TYPE                                         1   347
D755V11, multiclass
                                           clus
vv                                          BRDT MUTATED BRDT WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V12, binary
                cls
clus               0   1
  BRDT MUTATED     1  11
  BRDT WILD-TYPE   9 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      1   11
  BRDT WILD-TYPE    9  387
                        clus
vv                       BRDT MUTATED BRDT WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(756) Variable = CCAR1 MUTATION ANALYSIS
D756V1, survival
                 sevent
clus2               0   1
  CCAR1 MUTATED    14   6
  CCAR1 WILD-TYPE 324 210
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             20             534 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              6             210 
$`CCAR1 MUTATED`
TCGA-L5-A8NT TCGA-L5-A8NH TCGA-R6-A6Y0 TCGA-BR-6452 TCGA-BR-8077 TCGA-BR-8366 
       27.12        12.92        53.95        34.68         0.69         0.95 
TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-CD-8529 TCGA-CD-8530 
       25.05        31.96         9.86        13.87        12.30        12.39 
TCGA-CD-8531 TCGA-CG-5721 TCGA-D7-8576 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4GT 
       12.59         6.02        14.66        11.44        77.29         6.51 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`CCAR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43        11.44        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
        7.17        12.33        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CCAR1 MUTATED CCAR1 WILD-TYPE 
           0.69            0.00 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          77.29          122.30 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
         13.395          13.565 
[1] "0.7 - 77.3 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D756V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCAR1 MUTATED         0        1        1        2         3         1
  CCAR1 WILD-TYPE      10       19       45       29        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCAR1 MUTATED           0          2          5          1        5         0
  CCAR1 WILD-TYPE        29         82         57         38       38         4
D756V3, multiclass
            clus
vv           CCAR1 MUTATED CCAR1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             5              57
  STAGE IIIC             1              38
  STAGE IV               5              38
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CCAR1 MUTATED       2   2   9   8
  CCAR1 WILD-TYPE    52 133 252  94
D756V4, multiclass
       clus
vv      CCAR1 MUTATED CCAR1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                9             252
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CCAR1 MUTATED     9   6   2   4
  CCAR1 WILD-TYPE 186 167  87  81
D756V5, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  N0             9             186
  N1             6             167
  N2             2              87
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V6, binary
                 cls
clus                0   1
  CCAR1 MUTATED    17   4
  CCAR1 WILD-TYPE 465  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     17    4
  CCAR1 WILD-TYPE  465   34
   clus
vv  CCAR1 MUTATED CCAR1 WILD-TYPE
  0            17             465
  1             4              34
[1] 2 2
[1] FALSE
D756V7, binary
                 cls
clus                0   1
  CCAR1 MUTATED     9  13
  CCAR1 WILD-TYPE 163 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      9   13
  CCAR1 WILD-TYPE  163  393
        clus
vv       CCAR1 MUTATED CCAR1 WILD-TYPE
  FEMALE             9             163
  MALE              13             393
[1] 2 2
[1] FALSE
D756V8, binary
                 cls
clus                0   1
  CCAR1 MUTATED    12   7
  CCAR1 WILD-TYPE 404  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     12    7
  CCAR1 WILD-TYPE  404   95
     clus
vv    CCAR1 MUTATED CCAR1 WILD-TYPE
  NO             12             404
  YES             7              95
[1] 2 2
[1] FALSE
D756V9, continuous
D756V10, continuous
[1] "Remove cluster labels:" "CCAR1 MUTATED"         
clus
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" "CCAR1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CCAR1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CCAR1 MUTATED       7                         0
  CCAR1 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCAR1 MUTATED                                           0    12
  CCAR1 WILD-TYPE                                         1   345
D756V11, multiclass
                                           clus
vv                                          CCAR1 MUTATED CCAR1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V12, binary
                 cls
clus                0   1
  CCAR1 MUTATED     1  15
  CCAR1 WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      1   15
  CCAR1 WILD-TYPE    9  383
                        clus
vv                       CCAR1 MUTATED CCAR1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(757) Variable = MCCC2 MUTATION ANALYSIS
D757V1, survival
                 sevent
clus2               0   1
  MCCC2 MUTATED     8   1
  MCCC2 WILD-TYPE 330 215
  MCCC2 MUTATED MCCC2 WILD-TYPE 
              9             545 
  MCCC2 MUTATED MCCC2 WILD-TYPE 
              1             215 
$`MCCC2 MUTATED`
TCGA-L5-A88Z TCGA-L5-A891 TCGA-R6-A6Y2 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-8680 
        7.40         3.75         9.30        35.84        28.14        31.96 
TCGA-CD-8536 TCGA-CG-5723 TCGA-VQ-A8P2 
       12.43       105.07        38.14 

$`MCCC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         2.60        25.12         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MCCC2 MUTATED MCCC2 WILD-TYPE 
           3.75            0.00 
  MCCC2 MUTATED MCCC2 WILD-TYPE 
         105.07          122.30 
  MCCC2 MUTATED MCCC2 WILD-TYPE 
          28.14           13.55 
[1] "3.8 - 105.1 (28.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "5.2"
D757V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MCCC2 MUTATED         0        0        1        2         1         0
  MCCC2 WILD-TYPE      10       20       45       29        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCCC2 MUTATED           0          1          0          1        1         0
  MCCC2 WILD-TYPE        29         83         62         38       42         4
D757V3, multiclass
            clus
vv           MCCC2 MUTATED MCCC2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MCCC2 MUTATED       1   2   2   3
  MCCC2 WILD-TYPE    53 133 259  99
D757V4, multiclass
       clus
vv      MCCC2 MUTATED MCCC2 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MCCC2 MUTATED     2   4   1   1
  MCCC2 WILD-TYPE 193 169  88  84
D757V5, multiclass
    clus
vv   MCCC2 MUTATED MCCC2 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V6, binary
                 cls
clus                0   1
  MCCC2 MUTATED     7   1
  MCCC2 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC2 MUTATED      7    1
  MCCC2 WILD-TYPE  475   37
   clus
vv  MCCC2 MUTATED MCCC2 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D757V7, binary
                 cls
clus                0   1
  MCCC2 MUTATED     2   7
  MCCC2 WILD-TYPE 170 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC2 MUTATED      2    7
  MCCC2 WILD-TYPE  170  399
        clus
vv       MCCC2 MUTATED MCCC2 WILD-TYPE
  FEMALE             2             170
  MALE               7             399
[1] 2 2
[1] FALSE
D757V8, binary
                 cls
clus                0   1
  MCCC2 MUTATED     7   1
  MCCC2 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC2 MUTATED      7    1
  MCCC2 WILD-TYPE  409  101
     clus
vv    MCCC2 MUTATED MCCC2 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D757V9, continuous
D757V10, continuous
[1] "Remove cluster labels:" "MCCC2 MUTATED"         
clus
  MCCC2 MUTATED MCCC2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A8W5 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" "MCCC2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"MCCC2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MCCC2 MUTATED       2                         0
  MCCC2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCCC2 MUTATED                                           0     6
  MCCC2 WILD-TYPE                                         1   351
D757V11, multiclass
                                           clus
vv                                          MCCC2 MUTATED MCCC2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V12, binary
                 cls
clus                0   1
  MCCC2 MUTATED     1   4
  MCCC2 WILD-TYPE   9 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC2 MUTATED      1    4
  MCCC2 WILD-TYPE    9  394
                        clus
vv                       MCCC2 MUTATED MCCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(758) Variable = AKAP13 MUTATION ANALYSIS
D758V1, survival
                  sevent
clus2                0   1
  AKAP13 MUTATED    20  19
  AKAP13 WILD-TYPE 318 197
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              39              515 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              19              197 
$`AKAP13 MUTATED`
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A6QS 
       27.12         5.16        58.55        13.94        35.21         9.96 
TCGA-IG-A8O2 TCGA-L5-A8NM TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6Y2 TCGA-V5-A7RB 
        4.67         7.76        11.54         7.82         9.30         5.29 
TCGA-B7-A5TJ TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 
       11.01        34.68        30.90        36.16        39.78        18.15 
TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CD-8527 TCGA-CD-8536 
        6.18         1.12        31.96         1.48         7.17        12.43 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4477 
        6.58         1.02        54.08        14.01         7.07        30.97 
TCGA-CG-5721 TCGA-D7-A6EZ TCGA-HF-7132 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD 
        6.02        20.32        77.29         6.58        23.84        33.40 
TCGA-R5-A7ZE TCGA-VQ-A8DL TCGA-VQ-A8P2 
       18.21         0.92        38.14 

$`AKAP13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         7.63         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41        12.82        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.76        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN 
        0.13        12.03        12.85        12.26        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 
       21.90         9.21        35.24        35.84        33.63        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 
       27.02        15.95         7.99         8.05         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5717 
       19.07        12.03         0.00         9.01        18.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  AKAP13 MUTATED AKAP13 WILD-TYPE 
            0.92             0.00 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           77.29           122.30 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           12.43            13.58 
[1] "0.9 - 77.3 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D758V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP13 MUTATED         2        1        1        3         7         8
  AKAP13 WILD-TYPE       8       19       45       28        77        75
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP13 MUTATED           0          6          3          1        7
  AKAP13 WILD-TYPE        29         78         59         38       36
                  vv
clus               STAGE IVA
  AKAP13 MUTATED           0
  AKAP13 WILD-TYPE         4
D758V3, multiclass
            clus
vv           AKAP13 MUTATED AKAP13 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                3               28
  STAGE IIA               7               77
  STAGE IIB               8               75
  STAGE III               0               29
  STAGE IIIA              6               78
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                7               36
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  AKAP13 MUTATED       6   9  18   8
  AKAP13 WILD-TYPE    48 126 243  94
D758V4, multiclass
       clus
vv      AKAP13 MUTATED AKAP13 WILD-TYPE
  T0+T1              6               48
  T2                 9              126
  T3                18              243
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  AKAP13 MUTATED    12  13  13   2
  AKAP13 WILD-TYPE 183 160  76  83
D758V5, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  N0             12              183
  N1             13              160
  N2             13               76
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D758V6, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    39   2
  AKAP13 WILD-TYPE 443  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     39    2
  AKAP13 WILD-TYPE  443   36
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0             39              443
  1              2               36
[1] 2 2
[1] FALSE
D758V7, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    14  30
  AKAP13 WILD-TYPE 158 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     14   30
  AKAP13 WILD-TYPE  158  376
        clus
vv       AKAP13 MUTATED AKAP13 WILD-TYPE
  FEMALE             14              158
  MALE               30              376
[1] 2 2
[1] FALSE
D758V8, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    31   4
  AKAP13 WILD-TYPE 385  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     31    4
  AKAP13 WILD-TYPE  385   98
     clus
vv    AKAP13 MUTATED AKAP13 WILD-TYPE
  NO              31              385
  YES              4               98
[1] 2 2
[1] FALSE
D758V9, continuous
D758V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AKAP13 MUTATED       9                         1
  AKAP13 WILD-TYPE   124                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AKAP13 MUTATED                                           0    24
  AKAP13 WILD-TYPE                                         1   333
D758V11, multiclass
                                           clus
vv                                          AKAP13 MUTATED AKAP13 WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 24              333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D758V12, binary
                  cls
clus                 0   1
  AKAP13 MUTATED     2  29
  AKAP13 WILD-TYPE   8 369
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      2   29
  AKAP13 WILD-TYPE    8  369
                        clus
vv                       AKAP13 MUTATED AKAP13 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             29              369
[1] 2 2
[1] FALSE

Clustering(759) Variable = CEP250 MUTATION ANALYSIS
D759V1, survival
                  sevent
clus2                0   1
  CEP250 MUTATED    17   8
  CEP250 WILD-TYPE 321 208
  CEP250 MUTATED CEP250 WILD-TYPE 
              25              529 
  CEP250 MUTATED CEP250 WILD-TYPE 
               8              208 
$`CEP250 MUTATED`
TCGA-EQ-A4SO TCGA-2H-A9GQ TCGA-L5-A8NJ TCGA-LN-A49M TCGA-LN-A8I1 TCGA-LN-A9FO 
       16.24         4.21        16.47        12.66        13.18         0.13 
TCGA-LN-A9FP TCGA-R6-A6XQ TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 
       12.03         6.35        19.56         6.97        36.16        35.84 
TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 
       31.27        28.14        31.96        16.14         6.58         9.01 
TCGA-CG-4469 TCGA-D7-8572 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 
        7.07        16.80         0.10         6.58        20.25        23.84 
TCGA-VQ-A8P2 
       38.14 

$`CEP250 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.03        13.18        12.33        13.38        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       12.03         0.00        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       29.98         8.98         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CEP250 MUTATED CEP250 WILD-TYPE 
             0.1              0.0 
  CEP250 MUTATED CEP250 WILD-TYPE 
           38.14           122.30 
  CEP250 MUTATED CEP250 WILD-TYPE 
           16.14            13.55 
[1] "0.1 - 38.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D759V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP250 MUTATED         0        1        1        0         5         3
  CEP250 WILD-TYPE      10       19       45       31        79        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP250 MUTATED           2          3          2          5        3
  CEP250 WILD-TYPE        27         81         60         34       40
                  vv
clus               STAGE IVA
  CEP250 MUTATED           0
  CEP250 WILD-TYPE         4
D759V3, multiclass
            clus
vv           CEP250 MUTATED CEP250 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               3               80
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              5               34
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CEP250 MUTATED       2   7   7  10
  CEP250 WILD-TYPE    52 128 254  92
D759V4, multiclass
       clus
vv      CEP250 MUTATED CEP250 WILD-TYPE
  T0+T1              2               52
  T2                 7              128
  T3                 7              254
  T4                10               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CEP250 MUTATED     8   7   5   6
  CEP250 WILD-TYPE 187 166  84  79
D759V5, multiclass
    clus
vv   CEP250 MUTATED CEP250 WILD-TYPE
  N0              8              187
  N1              7              166
  N2              5               84
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V6, binary
                  cls
clus                 0   1
  CEP250 MUTATED    23   2
  CEP250 WILD-TYPE 459  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED     23    2
  CEP250 WILD-TYPE  459   36
   clus
vv  CEP250 MUTATED CEP250 WILD-TYPE
  0             23              459
  1              2               36
[1] 2 2
[1] FALSE
D759V7, binary
                  cls
clus                 0   1
  CEP250 MUTATED    10  18
  CEP250 WILD-TYPE 162 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED     10   18
  CEP250 WILD-TYPE  162  388
        clus
vv       CEP250 MUTATED CEP250 WILD-TYPE
  FEMALE             10              162
  MALE               18              388
[1] 2 2
[1] FALSE
D759V8, binary
                  cls
clus                 0   1
  CEP250 MUTATED    18   5
  CEP250 WILD-TYPE 398  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED     18    5
  CEP250 WILD-TYPE  398   97
     clus
vv    CEP250 MUTATED CEP250 WILD-TYPE
  NO              18              398
  YES              5               97
[1] 2 2
[1] FALSE
D759V9, continuous
[1] "Remove cluster labels:" "CEP250 MUTATED"        
clus
  CEP250 MUTATED CEP250 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
D759V10, continuous
[1] "Remove cluster labels:" "CEP250 MUTATED"        
clus
  CEP250 MUTATED CEP250 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" "CEP250 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CEP250 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP250 MUTATED      10                         0
  CEP250 WILD-TYPE   123                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP250 MUTATED                                           0    15
  CEP250 WILD-TYPE                                         1   342
D759V11, multiclass
                                           clus
vv                                          CEP250 MUTATED CEP250 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V12, binary
                  cls
clus                 0   1
  CEP250 MUTATED     0  23
  CEP250 WILD-TYPE  10 375
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED      0   23
  CEP250 WILD-TYPE   10  375
                        clus
vv                       CEP250 MUTATED CEP250 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             23              375
[1] 2 2
[1] FALSE

Clustering(760) Variable = AGAP5 MUTATION ANALYSIS
D760V1, survival
                 sevent
clus2               0   1
  AGAP5 MUTATED     6   2
  AGAP5 WILD-TYPE 332 214
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             546 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              2             214 
$`AGAP5 MUTATED`
TCGA-BR-4257 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-D7-A6EY TCGA-FP-A4BE 
        9.67        31.27         1.12        31.96        11.44        11.08 
TCGA-HU-A4H8 TCGA-RD-A8MV 
       14.07       122.30 

$`AGAP5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  AGAP5 MUTATED AGAP5 WILD-TYPE 
           1.12            0.00 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
          122.3           122.1 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
         12.755          13.565 
[1] "1.1 - 122.3 (12.8)" "0.0 - 122.1 (13.6)"
[1] "hr=" "2"  
D760V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AGAP5 MUTATED         0        0        1        0         2         0
  AGAP5 WILD-TYPE      10       20       45       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGAP5 MUTATED           0          0          2          1        1         0
  AGAP5 WILD-TYPE        29         84         60         38       42         4
D760V3, multiclass
            clus
vv           AGAP5 MUTATED AGAP5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AGAP5 MUTATED       1   0   4   2
  AGAP5 WILD-TYPE    53 135 257 100
D760V4, multiclass
       clus
vv      AGAP5 MUTATED AGAP5 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AGAP5 MUTATED     2   1   2   2
  AGAP5 WILD-TYPE 193 172  87  83
D760V5, multiclass
    clus
vv   AGAP5 MUTATED AGAP5 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V6, binary
                 cls
clus                0   1
  AGAP5 MUTATED     7   1
  AGAP5 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      7    1
  AGAP5 WILD-TYPE  475   37
   clus
vv  AGAP5 MUTATED AGAP5 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D760V7, binary
                 cls
clus                0   1
  AGAP5 MUTATED     3   5
  AGAP5 WILD-TYPE 169 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      3    5
  AGAP5 WILD-TYPE  169  401
        clus
vv       AGAP5 MUTATED AGAP5 WILD-TYPE
  FEMALE             3             169
  MALE               5             401
[1] 2 2
[1] FALSE
D760V8, binary
                 cls
clus                0   1
  AGAP5 MUTATED     6   2
  AGAP5 WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      6    2
  AGAP5 WILD-TYPE  410  100
     clus
vv    AGAP5 MUTATED AGAP5 WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D760V9, continuous
D760V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AGAP5 MUTATED       2                         1
  AGAP5 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGAP5 MUTATED                                           0     5
  AGAP5 WILD-TYPE                                         1   352
D760V11, multiclass
                                           clus
vv                                          AGAP5 MUTATED AGAP5 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V12, binary
                 cls
clus                0   1
  AGAP5 MUTATED     0   8
  AGAP5 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      0    8
  AGAP5 WILD-TYPE   10  390
                        clus
vv                       AGAP5 MUTATED AGAP5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(761) Variable = SCLY MUTATION ANALYSIS
D761V1, survival
                sevent
clus2              0   1
  SCLY MUTATED     5   1
  SCLY WILD-TYPE 333 215
  SCLY MUTATED SCLY WILD-TYPE 
             6            548 
  SCLY MUTATED SCLY WILD-TYPE 
             1            215 
$`SCLY MUTATED`
TCGA-L5-A4OH TCGA-L5-A8NM TCGA-BR-6452 TCGA-HF-A5NB TCGA-HU-A4GN TCGA-VQ-A92D 
       32.61         7.76        34.68        30.51        29.98        66.81 

$`SCLY WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SCLY MUTATED SCLY WILD-TYPE 
          7.76           0.00 
  SCLY MUTATED SCLY WILD-TYPE 
         66.81         122.30 
  SCLY MUTATED SCLY WILD-TYPE 
         31.56          13.51 
[1] "7.8 - 66.8 (31.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.2"
D761V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCLY MUTATED         1        0        1        0         2         1
  SCLY WILD-TYPE       9       20       45       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCLY MUTATED           0          0          0          1        0         0
  SCLY WILD-TYPE        29         84         62         38       43         4
D761V3, multiclass
            clus
vv           SCLY MUTATED SCLY WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SCLY MUTATED       1   3   1   1
  SCLY WILD-TYPE    53 132 260 101
D761V4, multiclass
       clus
vv      SCLY MUTATED SCLY WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               1            260
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SCLY MUTATED     3   2   0   1
  SCLY WILD-TYPE 192 171  89  84
D761V5, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  N0            3            192
  N1            2            171
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V6, binary
                cls
clus               0   1
  SCLY MUTATED     6   0
  SCLY WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      6    0
  SCLY WILD-TYPE  476   38
   clus
vv  SCLY MUTATED SCLY WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D761V7, binary
                cls
clus               0   1
  SCLY MUTATED     3   3
  SCLY WILD-TYPE 169 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      3    3
  SCLY WILD-TYPE  169  403
        clus
vv       SCLY MUTATED SCLY WILD-TYPE
  FEMALE            3            169
  MALE              3            403
[1] 2 2
[1] FALSE
D761V8, binary
                cls
clus               0   1
  SCLY MUTATED     5   1
  SCLY WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      5    1
  SCLY WILD-TYPE  411  101
     clus
vv    SCLY MUTATED SCLY WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D761V9, continuous
D761V10, continuous
[1] "Remove cluster labels:" "SCLY MUTATED"          
clus
  SCLY MUTATED SCLY WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OM 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" "SCLY WILD-TYPE" 
    TCGA-Z6-AAPN 
"SCLY WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SCLY MUTATED       1                         0
  SCLY WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCLY MUTATED                                           0     4
  SCLY WILD-TYPE                                         1   353
D761V11, multiclass
                                           clus
vv                                          SCLY MUTATED SCLY WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V12, binary
                cls
clus               0   1
  SCLY MUTATED     0   2
  SCLY WILD-TYPE  10 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      0    2
  SCLY WILD-TYPE   10  396
                        clus
vv                       SCLY MUTATED SCLY WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            2            396
[1] 2 2
[1] FALSE

Clustering(762) Variable = KRT23 MUTATION ANALYSIS
D762V1, survival
                 sevent
clus2               0   1
  KRT23 MUTATED     9   8
  KRT23 WILD-TYPE 329 208
  KRT23 MUTATED KRT23 WILD-TYPE 
             17             537 
  KRT23 MUTATED KRT23 WILD-TYPE 
              8             208 
$`KRT23 MUTATED`
TCGA-2H-A9GQ TCGA-JY-A6F8 TCGA-L5-A4OS TCGA-L5-A8NM TCGA-R6-A6DQ TCGA-R6-A6L4 
        4.21       122.10        58.59         7.76         7.59        16.31 
TCGA-VR-A8EQ TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-A4MJ 
       22.82        35.84        31.27        25.05         1.12        12.62 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4H3 TCGA-IP-7968 
        5.92        11.08        26.47        29.00         2.53 

$`KRT23 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KRT23 MUTATED KRT23 WILD-TYPE 
           1.12            0.00 
  KRT23 MUTATED KRT23 WILD-TYPE 
          122.1           122.3 
  KRT23 MUTATED KRT23 WILD-TYPE 
          16.31           13.55 
[1] "1.1 - 122.1 (16.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D762V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT23 MUTATED         1        0        3        0         2         3
  KRT23 WILD-TYPE       9       20       43       31        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT23 MUTATED           2          0          1          3        0         0
  KRT23 WILD-TYPE        27         84         61         36       43         4
D762V3, multiclass
            clus
vv           KRT23 MUTATED KRT23 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KRT23 MUTATED       1   5   6   3
  KRT23 WILD-TYPE    53 130 255  99
D762V4, multiclass
       clus
vv      KRT23 MUTATED KRT23 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                6             255
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KRT23 MUTATED     6   5   1   3
  KRT23 WILD-TYPE 189 168  88  82
D762V5, multiclass
    clus
vv   KRT23 MUTATED KRT23 WILD-TYPE
  N0             6             189
  N1             5             168
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V6, binary
                 cls
clus                0   1
  KRT23 MUTATED    13   0
  KRT23 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT23 MUTATED     13    0
  KRT23 WILD-TYPE  469   38
   clus
vv  KRT23 MUTATED KRT23 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D762V7, binary
                 cls
clus                0   1
  KRT23 MUTATED     9   8
  KRT23 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT23 MUTATED      9    8
  KRT23 WILD-TYPE  163  398
        clus
vv       KRT23 MUTATED KRT23 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D762V8, binary
                 cls
clus                0   1
  KRT23 MUTATED    12   2
  KRT23 WILD-TYPE 404 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT23 MUTATED     12    2
  KRT23 WILD-TYPE  404  100
     clus
vv    KRT23 MUTATED KRT23 WILD-TYPE
  NO             12             404
  YES             2             100
[1] 2 2
[1] FALSE
D762V9, continuous
[1] "Remove cluster labels:" "KRT23 MUTATED"         
clus
  KRT23 MUTATED KRT23 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
D762V10, continuous
[1] "Remove cluster labels:" "KRT23 MUTATED"         
clus
  KRT23 MUTATED KRT23 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" "KRT23 WILD-TYPE" 
     TCGA-Z6-AAPN 
"KRT23 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KRT23 MUTATED       2                         1
  KRT23 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRT23 MUTATED                                           0    13
  KRT23 WILD-TYPE                                         1   344
D762V11, multiclass
                                           clus
vv                                          KRT23 MUTATED KRT23 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V12, binary
                 cls
clus                0   1
  KRT23 MUTATED     0  12
  KRT23 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT23 MUTATED      0   12
  KRT23 WILD-TYPE   10  386
                        clus
vv                       KRT23 MUTATED KRT23 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(763) Variable = KIRREL2 MUTATION ANALYSIS
D763V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED    12   4
  KIRREL2 WILD-TYPE 326 212
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               16               538 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                4               212 
$`KIRREL2 MUTATED`
TCGA-V5-AASW TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8487 TCGA-BR-8686 TCGA-BR-A4QL 
        9.27        34.68        32.78         1.12        20.88        16.14 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-F1-6874 TCGA-FP-7735 TCGA-HF-7132 TCGA-HF-7134 
        6.58         6.02        14.47         3.48        77.29        52.21 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-MX-A5UJ TCGA-VQ-A8P2 
       29.98         6.51        19.73        38.14 

$`KIRREL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       26.73        24.79        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             1.12              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            77.29            122.30 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
           17.935            13.510 
[1] "1.1 - 77.3 (17.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D763V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIRREL2 MUTATED         0        1        3        1         6         0
  KIRREL2 WILD-TYPE      10       19       43       30        78        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          2          2          0        1
  KIRREL2 WILD-TYPE        29         82         60         39       42
                   vv
clus                STAGE IVA
  KIRREL2 MUTATED           0
  KIRREL2 WILD-TYPE         4
D763V3, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                6                78
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  KIRREL2 MUTATED       1   5   7   3
  KIRREL2 WILD-TYPE    53 130 254  99
D763V4, multiclass
       clus
vv      KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T0+T1               1                53
  T2                  5               130
  T3                  7               254
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  KIRREL2 MUTATED     9   5   1   1
  KIRREL2 WILD-TYPE 186 168  88  84
D763V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0               9               186
  N1               5               168
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V6, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    15   0
  KIRREL2 WILD-TYPE 467  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     15    0
  KIRREL2 WILD-TYPE  467   38
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              15               467
  1               0                38
[1] 2 2
[1] FALSE
D763V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     6  11
  KIRREL2 WILD-TYPE 166 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      6   11
  KIRREL2 WILD-TYPE  166  395
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               6               166
  MALE                11               395
[1] 2 2
[1] FALSE
D763V8, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    13   3
  KIRREL2 WILD-TYPE 403  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     13    3
  KIRREL2 WILD-TYPE  403   99
     clus
vv    KIRREL2 MUTATED KIRREL2 WILD-TYPE
  NO               13               403
  YES               3                99
[1] 2 2
[1] FALSE
D763V9, continuous
[1] "Remove cluster labels:" "KIRREL2 MUTATED"       
clus
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" "KIRREL2 WILD-TYPE" 
D763V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  KIRREL2 MUTATED       4                         1
  KIRREL2 WILD-TYPE   129                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIRREL2 MUTATED                                           0     8
  KIRREL2 WILD-TYPE                                         1   349
D763V11, multiclass
                                           clus
vv                                          KIRREL2 MUTATED KIRREL2 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V12, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     0  12
  KIRREL2 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      0   12
  KIRREL2 WILD-TYPE   10  386
                        clus
vv                       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(764) Variable = GTF3C3 MUTATION ANALYSIS
D764V1, survival
                  sevent
clus2                0   1
  GTF3C3 MUTATED    11   8
  GTF3C3 WILD-TYPE 327 208
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              19              535 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               8              208 
$`GTF3C3 MUTATED`
TCGA-L5-A43J TCGA-L5-A88V TCGA-L5-A8NW TCGA-R6-A6XQ TCGA-VR-A8EQ TCGA-B7-A5TI 
        4.31         2.60        46.09         6.35        22.82        19.56 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-A4QL TCGA-CG-5721 
       34.68        35.84        32.25         2.66        16.14         6.02 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-HF-A5NB TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        5.92        14.47        30.51        45.67        74.53        38.14 
TCGA-VQ-AA6I 
       16.14 

$`GTF3C3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        26.04        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
             2.6              0.0 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           74.53           122.30 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           19.56            13.48 
[1] "2.6 - 74.5 (19.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D764V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C3 MUTATED         0        0        3        0         1         3
  GTF3C3 WILD-TYPE      10       20       43       31        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C3 MUTATED           2          1          2          2        4
  GTF3C3 WILD-TYPE        27         83         60         37       39
                  vv
clus               STAGE IVA
  GTF3C3 MUTATED           0
  GTF3C3 WILD-TYPE         4
D764V3, multiclass
            clus
vv           GTF3C3 MUTATED GTF3C3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GTF3C3 MUTATED       0   3   8   7
  GTF3C3 WILD-TYPE    54 132 253  95
D764V4, multiclass
       clus
vv      GTF3C3 MUTATED GTF3C3 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 8              253
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GTF3C3 MUTATED     5   8   0   5
  GTF3C3 WILD-TYPE 190 165  89  80
D764V5, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  N0              5              190
  N1              8              165
  N2              0               89
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V6, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    14   3
  GTF3C3 WILD-TYPE 468  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     14    3
  GTF3C3 WILD-TYPE  468   35
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0             14              468
  1              3               35
[1] 2 2
[1] FALSE
D764V7, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED     7  13
  GTF3C3 WILD-TYPE 165 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      7   13
  GTF3C3 WILD-TYPE  165  393
        clus
vv       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  FEMALE              7              165
  MALE               13              393
[1] 2 2
[1] FALSE
D764V8, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    15   3
  GTF3C3 WILD-TYPE 401  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     15    3
  GTF3C3 WILD-TYPE  401   99
     clus
vv    GTF3C3 MUTATED GTF3C3 WILD-TYPE
  NO              15              401
  YES              3               99
[1] 2 2
[1] FALSE
D764V9, continuous
[1] "Remove cluster labels:" "GTF3C3 MUTATED"        
clus
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
D764V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GTF3C3 MUTATED       0                         0
  GTF3C3 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF3C3 MUTATED                                           0    18
  GTF3C3 WILD-TYPE                                         1   339
D764V11, multiclass
                                           clus
vv                                          GTF3C3 MUTATED GTF3C3 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V12, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED     2  10
  GTF3C3 WILD-TYPE   8 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      2   10
  GTF3C3 WILD-TYPE    8  388
                        clus
vv                       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(765) Variable = CCDC27 MUTATION ANALYSIS
D765V1, survival
                  sevent
clus2                0   1
  CCDC27 MUTATED     7   4
  CCDC27 WILD-TYPE 331 212
  CCDC27 MUTATED CCDC27 WILD-TYPE 
              11              543 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               4              212 
$`CCDC27 MUTATED`
TCGA-LN-A4A4 TCGA-LN-A7HY TCGA-VR-A8EU TCGA-XP-A8T8 TCGA-BR-4201 TCGA-BR-6452 
       12.59        12.03        18.31        14.37        30.90        34.68 
TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-8590 TCGA-CG-5721 TCGA-CG-5728 
       18.15        32.25         9.34         6.02        65.10 

$`CCDC27 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79        27.12        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CCDC27 MUTATED CCDC27 WILD-TYPE 
            6.02             0.00 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
            65.1            122.3 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
           18.15            13.51 
[1] "6.0 - 65.1 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D765V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC27 MUTATED         1        0        1        0         1         2
  CCDC27 WILD-TYPE       9       20       45       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC27 MUTATED           2          0          0          1        3
  CCDC27 WILD-TYPE        27         84         62         38       40
                  vv
clus               STAGE IVA
  CCDC27 MUTATED           0
  CCDC27 WILD-TYPE         4
D765V3, multiclass
            clus
vv           CCDC27 MUTATED CCDC27 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CCDC27 MUTATED       3   2   3   4
  CCDC27 WILD-TYPE    51 133 258  98
D765V4, multiclass
       clus
vv      CCDC27 MUTATED CCDC27 WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CCDC27 MUTATED     3   7   1   0
  CCDC27 WILD-TYPE 192 166  88  85
D765V5, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  N0              3              192
  N1              7              166
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V6, binary
                  cls
clus                 0   1
  CCDC27 MUTATED    10   1
  CCDC27 WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED     10    1
  CCDC27 WILD-TYPE  472   37
   clus
vv  CCDC27 MUTATED CCDC27 WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D765V7, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     4   8
  CCDC27 WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      4    8
  CCDC27 WILD-TYPE  168  398
        clus
vv       CCDC27 MUTATED CCDC27 WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D765V8, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     8   3
  CCDC27 WILD-TYPE 408  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      8    3
  CCDC27 WILD-TYPE  408   99
     clus
vv    CCDC27 MUTATED CCDC27 WILD-TYPE
  NO               8              408
  YES              3               99
[1] 2 2
[1] FALSE
D765V9, continuous
D765V10, continuous
[1] "Remove cluster labels:" "CCDC27 MUTATED"        
clus
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-Z6-AAPN 
"CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" "CCDC27 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC27 MUTATED       2                         2
  CCDC27 WILD-TYPE   131                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC27 MUTATED                                           0     6
  CCDC27 WILD-TYPE                                         1   351
D765V11, multiclass
                                           clus
vv                                          CCDC27 MUTATED CCDC27 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V12, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     1   8
  CCDC27 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      1    8
  CCDC27 WILD-TYPE    9  390
                        clus
vv                       CCDC27 MUTATED CCDC27 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(766) Variable = SH3BP2 MUTATION ANALYSIS
D766V1, survival
                  sevent
clus2                0   1
  SH3BP2 MUTATED     5   1
  SH3BP2 WILD-TYPE 333 215
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               6              548 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               1              215 
$`SH3BP2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8372 TCGA-HU-A4GT 
       30.90        34.68        44.94        29.59        31.27         6.51 

$`SH3BP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
            6.51             0.00 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
           44.94           122.30 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
          31.085           13.510 
[1] "6.5 - 44.9 (31.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.8"
D766V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH3BP2 MUTATED         0        0        0        0         3         1
  SH3BP2 WILD-TYPE      10       20       46       31        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3BP2 MUTATED           0          1          0          1        0
  SH3BP2 WILD-TYPE        29         83         62         38       43
                  vv
clus               STAGE IVA
  SH3BP2 MUTATED           0
  SH3BP2 WILD-TYPE         4
D766V3, multiclass
            clus
vv           SH3BP2 MUTATED SH3BP2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SH3BP2 MUTATED       0   1   3   3
  SH3BP2 WILD-TYPE    54 134 258  99
D766V4, multiclass
       clus
vv      SH3BP2 MUTATED SH3BP2 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SH3BP2 MUTATED     5   0   0   1
  SH3BP2 WILD-TYPE 190 173  89  84
D766V5, multiclass
    clus
vv   SH3BP2 MUTATED SH3BP2 WILD-TYPE
  N0              5              190
  N1              0              173
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V6, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     7   0
  SH3BP2 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      7    0
  SH3BP2 WILD-TYPE  475   38
   clus
vv  SH3BP2 MUTATED SH3BP2 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D766V7, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     6   1
  SH3BP2 WILD-TYPE 166 405
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      6    1
  SH3BP2 WILD-TYPE  166  405
        clus
vv       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  FEMALE              6              166
  MALE                1              405
[1] 2 2
[1] FALSE
D766V8, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     6   0
  SH3BP2 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      6    0
  SH3BP2 WILD-TYPE  410  102
     clus
vv    SH3BP2 MUTATED SH3BP2 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D766V9, continuous
D766V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SH3BP2 MUTATED       1                         0
  SH3BP2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3BP2 MUTATED                                           0     6
  SH3BP2 WILD-TYPE                                         1   351
D766V11, multiclass
                                           clus
vv                                          SH3BP2 MUTATED SH3BP2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V12, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     0   7
  SH3BP2 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      0    7
  SH3BP2 WILD-TYPE   10  391
                        clus
vv                       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(767) Variable = TIGD7 MUTATION ANALYSIS
D767V1, survival
                 sevent
clus2               0   1
  TIGD7 MUTATED     5   6
  TIGD7 WILD-TYPE 333 210
  TIGD7 MUTATED TIGD7 WILD-TYPE 
             11             543 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
              6             210 
$`TIGD7 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GN TCGA-IG-A6QS TCGA-L5-A4ON TCGA-L5-A4OR TCGA-BR-6852 
       19.99         8.94         9.96        18.35         3.16        44.94 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A6EY TCGA-KB-A6F7 
        1.12        31.96         6.58        11.44        63.62 

$`TIGD7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TIGD7 MUTATED TIGD7 WILD-TYPE 
           1.12            0.00 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
          63.62          122.30 
  TIGD7 MUTATED TIGD7 WILD-TYPE 
          11.44           13.58 
[1] "1.1 - 63.6 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D767V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIGD7 MUTATED         0        1        1        0         3         3
  TIGD7 WILD-TYPE      10       19       45       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIGD7 MUTATED           1          0          1          1        1         0
  TIGD7 WILD-TYPE        28         84         61         38       42         4
D767V3, multiclass
            clus
vv           TIGD7 MUTATED TIGD7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TIGD7 MUTATED       3   1   6   2
  TIGD7 WILD-TYPE    51 134 255 100
D767V4, multiclass
       clus
vv      TIGD7 MUTATED TIGD7 WILD-TYPE
  T0+T1             3              51
  T2                1             134
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TIGD7 MUTATED     5   4   1   2
  TIGD7 WILD-TYPE 190 169  88  83
D767V5, multiclass
    clus
vv   TIGD7 MUTATED TIGD7 WILD-TYPE
  N0             5             190
  N1             4             169
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V6, binary
                 cls
clus                0   1
  TIGD7 MUTATED     8   1
  TIGD7 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      8    1
  TIGD7 WILD-TYPE  474   37
   clus
vv  TIGD7 MUTATED TIGD7 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D767V7, binary
                 cls
clus                0   1
  TIGD7 MUTATED     4   8
  TIGD7 WILD-TYPE 168 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      4    8
  TIGD7 WILD-TYPE  168  398
        clus
vv       TIGD7 MUTATED TIGD7 WILD-TYPE
  FEMALE             4             168
  MALE               8             398
[1] 2 2
[1] FALSE
D767V8, binary
                 cls
clus                0   1
  TIGD7 MUTATED    10   1
  TIGD7 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED     10    1
  TIGD7 WILD-TYPE  406  101
     clus
vv    TIGD7 MUTATED TIGD7 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D767V9, continuous
D767V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TIGD7 MUTATED       2                         0
  TIGD7 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIGD7 MUTATED                                           0     8
  TIGD7 WILD-TYPE                                         1   349
D767V11, multiclass
                                           clus
vv                                          TIGD7 MUTATED TIGD7 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V12, binary
                 cls
clus                0   1
  TIGD7 MUTATED     0   7
  TIGD7 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD7 MUTATED      0    7
  TIGD7 WILD-TYPE   10  391
                        clus
vv                       TIGD7 MUTATED TIGD7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(768) Variable = B4GALNT4 MUTATION ANALYSIS
D768V1, survival
                    sevent
clus2                  0   1
  B4GALNT4 MUTATED     9   6
  B4GALNT4 WILD-TYPE 329 210
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                15                539 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 6                210 
$`B4GALNT4 MUTATED`
TCGA-L5-A4OI TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8591 
       19.99         9.67         6.18        29.59         4.31        28.14 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-MX-A5UJ 
       31.96        16.14         6.02        11.44        22.68        19.73 
TCGA-R5-A7ZR TCGA-RD-A8N5 TCGA-VQ-A8P2 
        6.08        57.44        38.14 

$`B4GALNT4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         4.08         9.34         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      115.69       116.38        71.38         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
              4.31               0.00 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             57.44             122.30 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             19.73              13.51 
[1] "4.3 - 57.4 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D768V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B4GALNT4 MUTATED         0        0        2        0         0         3
  B4GALNT4 WILD-TYPE      10       20       44       31        84        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALNT4 MUTATED           1          4          2          2        3
  B4GALNT4 WILD-TYPE        28         80         60         37       40
                    vv
clus                 STAGE IVA
  B4GALNT4 MUTATED           0
  B4GALNT4 WILD-TYPE         4
D768V3, multiclass
            clus
vv           B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 3                 80
  STAGE III                 1                 28
  STAGE IIIA                4                 80
  STAGE IIIB                2                 60
  STAGE IIIC                2                 37
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  B4GALNT4 MUTATED       1   2   7   8
  B4GALNT4 WILD-TYPE    53 133 254  94
D768V4, multiclass
       clus
vv      B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  T0+T1                1                 53
  T2                   2                133
  T3                   7                254
  T4                   8                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  B4GALNT4 MUTATED     5   4   3   4
  B4GALNT4 WILD-TYPE 190 169  86  81
D768V5, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  N0                5                190
  N1                4                169
  N2                3                 86
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V6, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    17   1
  B4GALNT4 WILD-TYPE 465  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     17    1
  B4GALNT4 WILD-TYPE  465   37
   clus
vv  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  0               17                465
  1                1                 37
[1] 2 2
[1] FALSE
D768V7, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    11   8
  B4GALNT4 WILD-TYPE 161 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     11    8
  B4GALNT4 WILD-TYPE  161  398
        clus
vv       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  FEMALE               11                161
  MALE                  8                398
[1] 2 2
[1] FALSE
D768V8, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    14   2
  B4GALNT4 WILD-TYPE 402 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     14    2
  B4GALNT4 WILD-TYPE  402  100
     clus
vv    B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  NO                14                402
  YES                2                100
[1] 2 2
[1] FALSE
D768V9, continuous
D768V10, continuous
[1] "Remove cluster labels:" "B4GALNT4 MUTATED"      
clus
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" "B4GALNT4 WILD-TYPE" 
        TCGA-Z6-AAPN 
"B4GALNT4 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  B4GALNT4 MUTATED       2                         1
  B4GALNT4 WILD-TYPE   131                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B4GALNT4 MUTATED                                           0    15
  B4GALNT4 WILD-TYPE                                         1   342
D768V11, multiclass
                                           clus
vv                                          B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V12, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     0  16
  B4GALNT4 WILD-TYPE  10 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      0   16
  B4GALNT4 WILD-TYPE   10  382
                        clus
vv                       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               16                382
[1] 2 2
[1] FALSE

Clustering(769) Variable = ARHGEF11 MUTATION ANALYSIS
D769V1, survival
                    sevent
clus2                  0   1
  ARHGEF11 MUTATED    14   7
  ARHGEF11 WILD-TYPE 324 209
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                21                533 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                 7                209 
$`ARHGEF11 MUTATED`
TCGA-LN-A5U6 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8372 
       12.33        30.90         9.67        34.68        35.84        31.27 
TCGA-BR-8487 TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-6519 TCGA-D7-6527 TCGA-FP-A9TM 
        1.12         9.01         6.02        20.55        10.26         6.21 
TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H8 
       77.29        22.32        22.68         0.10         6.58        14.07 
TCGA-MX-A5UJ TCGA-VQ-A8PM TCGA-VQ-AA6I 
       19.73         1.87        16.14 

$`ARHGEF11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56        11.08         5.52        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
       17.85        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
               0.1                0.0 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
             77.29             122.30 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
             14.07              13.55 
[1] "0.1 - 77.3 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D769V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF11 MUTATED         0        0        2        2         2         4
  ARHGEF11 WILD-TYPE      10       20       44       29        82        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF11 MUTATED           0          2          1          2        3
  ARHGEF11 WILD-TYPE        29         82         61         37       40
                    vv
clus                 STAGE IVA
  ARHGEF11 MUTATED           0
  ARHGEF11 WILD-TYPE         4
D769V3, multiclass
            clus
vv           ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  2                 29
  STAGE IIA                 2                 82
  STAGE IIB                 4                 79
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ARHGEF11 MUTATED       2   6   6   7
  ARHGEF11 WILD-TYPE    52 129 255  95
D769V4, multiclass
       clus
vv      ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  T0+T1                2                 52
  T2                   6                129
  T3                   6                255
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ARHGEF11 MUTATED     5   9   2   4
  ARHGEF11 WILD-TYPE 190 164  87  81
D769V5, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  N0                5                190
  N1                9                164
  N2                2                 87
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V6, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    21   1
  ARHGEF11 WILD-TYPE 461  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     21    1
  ARHGEF11 WILD-TYPE  461   37
   clus
vv  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  0               21                461
  1                1                 37
[1] 2 2
[1] FALSE
D769V7, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    11  11
  ARHGEF11 WILD-TYPE 161 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     11   11
  ARHGEF11 WILD-TYPE  161  395
        clus
vv       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  FEMALE               11                161
  MALE                 11                395
[1] 2 2
[1] FALSE
D769V8, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    15   5
  ARHGEF11 WILD-TYPE 401  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     15    5
  ARHGEF11 WILD-TYPE  401   97
     clus
vv    ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  NO                15                401
  YES                5                 97
[1] 2 2
[1] FALSE
D769V9, continuous
[1] "Remove cluster labels:" "ARHGEF11 MUTATED"      
clus
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U7         TCGA-LN-A7HV 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-Z6-A8JE 
"ARHGEF11 WILD-TYPE" 
D769V10, continuous
[1] "Remove cluster labels:" "ARHGEF11 MUTATED"      
clus
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U7 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" "ARHGEF11 WILD-TYPE" 
        TCGA-Z6-AAPN 
"ARHGEF11 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF11 MUTATED       6                         0
  ARHGEF11 WILD-TYPE   127                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF11 MUTATED                                           0    13
  ARHGEF11 WILD-TYPE                                         1   344
D769V11, multiclass
                                           clus
vv                                          ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  ASIAN                                                    6                127
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V12, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED     0  17
  ARHGEF11 WILD-TYPE  10 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED      0   17
  ARHGEF11 WILD-TYPE   10  381
                        clus
vv                       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               17                381
[1] 2 2
[1] FALSE

Clustering(770) Variable = SHMT2 MUTATION ANALYSIS
D770V1, survival
                 sevent
clus2               0   1
  SHMT2 MUTATED     8   3
  SHMT2 WILD-TYPE 330 213
  SHMT2 MUTATED SHMT2 WILD-TYPE 
             11             543 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
              3             213 
$`SHMT2 MUTATED`
TCGA-L5-A4OE TCGA-CG-4460 TCGA-XP-A8T7 TCGA-BR-4201 TCGA-BR-8372 TCGA-BR-8373 
       24.00        21.99        41.23        30.90        31.27        14.79 
TCGA-CD-5798 TCGA-CD-A4MJ TCGA-CG-5723 TCGA-HU-A4GU TCGA-VQ-A8P2 
       13.41        12.62       105.07         6.58        38.14 

$`SHMT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       20.42         1.15        21.44        16.14         5.13        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SHMT2 MUTATED SHMT2 WILD-TYPE 
           6.58            0.00 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
         105.07          122.30 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
          24.00           13.51 
[1] "6.6 - 105.1 (24.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D770V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SHMT2 MUTATED         0        0        1        2         1         1
  SHMT2 WILD-TYPE      10       20       45       29        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SHMT2 MUTATED           0          2          1          1        1         0
  SHMT2 WILD-TYPE        29         82         61         38       42         4
D770V3, multiclass
            clus
vv           SHMT2 MUTATED SHMT2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SHMT2 MUTATED       1   4   3   4
  SHMT2 WILD-TYPE    53 131 258  98
D770V4, multiclass
       clus
vv      SHMT2 MUTATED SHMT2 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SHMT2 MUTATED     3   5   1   1
  SHMT2 WILD-TYPE 192 168  88  84
D770V5, multiclass
    clus
vv   SHMT2 MUTATED SHMT2 WILD-TYPE
  N0             3             192
  N1             5             168
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V6, binary
                 cls
clus                0   1
  SHMT2 MUTATED    10   1
  SHMT2 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED     10    1
  SHMT2 WILD-TYPE  472   37
   clus
vv  SHMT2 MUTATED SHMT2 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D770V7, binary
                 cls
clus                0   1
  SHMT2 MUTATED     5   7
  SHMT2 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      5    7
  SHMT2 WILD-TYPE  167  399
        clus
vv       SHMT2 MUTATED SHMT2 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D770V8, binary
                 cls
clus                0   1
  SHMT2 MUTATED    10   1
  SHMT2 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED     10    1
  SHMT2 WILD-TYPE  406  101
     clus
vv    SHMT2 MUTATED SHMT2 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D770V9, continuous
[1] "Remove cluster labels:" "SHMT2 MUTATED"         
clus
  SHMT2 MUTATED SHMT2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
D770V10, continuous
[1] "Remove cluster labels:" "SHMT2 MUTATED"         
clus
  SHMT2 MUTATED SHMT2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OG 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" "SHMT2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SHMT2 MUTATED       3                         0
  SHMT2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SHMT2 MUTATED                                           0     7
  SHMT2 WILD-TYPE                                         1   350
D770V11, multiclass
                                           clus
vv                                          SHMT2 MUTATED SHMT2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V12, binary
                 cls
clus                0   1
  SHMT2 MUTATED     1   7
  SHMT2 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      1    7
  SHMT2 WILD-TYPE    9  391
                        clus
vv                       SHMT2 MUTATED SHMT2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(771) Variable = USP30 MUTATION ANALYSIS
D771V1, survival
                 sevent
clus2               0   1
  USP30 MUTATED     8   1
  USP30 WILD-TYPE 330 215
  USP30 MUTATED USP30 WILD-TYPE 
              9             545 
  USP30 MUTATED USP30 WILD-TYPE 
              1             215 
$`USP30 MUTATED`
TCGA-V5-A7RE TCGA-BR-6452 TCGA-BR-8591 TCGA-CG-4440 TCGA-CG-5721 TCGA-FP-A4BE 
       16.44        34.68        28.14         4.01         6.02        11.08 
TCGA-HF-7132 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       77.29        14.07        38.14 

$`USP30 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  USP30 MUTATED USP30 WILD-TYPE 
           4.01            0.00 
  USP30 MUTATED USP30 WILD-TYPE 
          77.29          122.30 
  USP30 MUTATED USP30 WILD-TYPE 
          16.44           13.51 
[1] "4.0 - 77.3 (16.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.7"
D771V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP30 MUTATED         0        0        2        1         2         0
  USP30 WILD-TYPE      10       20       44       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP30 MUTATED           0          1          0          1        2         0
  USP30 WILD-TYPE        29         83         62         38       41         4
D771V3, multiclass
            clus
vv           USP30 MUTATED USP30 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  USP30 MUTATED       3   1   3   3
  USP30 WILD-TYPE    51 134 258  99
D771V4, multiclass
       clus
vv      USP30 MUTATED USP30 WILD-TYPE
  T0+T1             3              51
  T2                1             134
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  USP30 MUTATED     3   4   0   2
  USP30 WILD-TYPE 192 169  89  83
D771V5, multiclass
    clus
vv   USP30 MUTATED USP30 WILD-TYPE
  N0             3             192
  N1             4             169
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V6, binary
                 cls
clus                0   1
  USP30 MUTATED     9   1
  USP30 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      9    1
  USP30 WILD-TYPE  473   37
   clus
vv  USP30 MUTATED USP30 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D771V7, binary
                 cls
clus                0   1
  USP30 MUTATED     3   7
  USP30 WILD-TYPE 169 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      3    7
  USP30 WILD-TYPE  169  399
        clus
vv       USP30 MUTATED USP30 WILD-TYPE
  FEMALE             3             169
  MALE               7             399
[1] 2 2
[1] FALSE
D771V8, binary
                 cls
clus                0   1
  USP30 MUTATED     4   4
  USP30 WILD-TYPE 412  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      4    4
  USP30 WILD-TYPE  412   98
     clus
vv    USP30 MUTATED USP30 WILD-TYPE
  NO              4             412
  YES             4              98
[1] 2 2
[1] FALSE
D771V9, continuous
[1] "Remove cluster labels:" "USP30 MUTATED"         
clus
  USP30 MUTATED USP30 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"USP30 WILD-TYPE" "USP30 WILD-TYPE" "USP30 WILD-TYPE" 
D771V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP30 MUTATED       1                         1
  USP30 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP30 MUTATED                                           0     5
  USP30 WILD-TYPE                                         1   352
D771V11, multiclass
                                           clus
vv                                          USP30 MUTATED USP30 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V12, binary
                 cls
clus                0   1
  USP30 MUTATED     0   6
  USP30 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      0    6
  USP30 WILD-TYPE   10  392
                        clus
vv                       USP30 MUTATED USP30 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(772) Variable = ASPN MUTATION ANALYSIS
D772V1, survival
                sevent
clus2              0   1
  ASPN MUTATED     4   3
  ASPN WILD-TYPE 334 213
  ASPN MUTATED ASPN WILD-TYPE 
             7            547 
  ASPN MUTATED ASPN WILD-TYPE 
             3            213 
$`ASPN MUTATED`
TCGA-VR-A8ER TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8680 
       12.43        36.16        32.25         0.26        31.27        31.96 
TCGA-CG-4306 
        1.02 

$`ASPN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ASPN MUTATED ASPN WILD-TYPE 
          0.26           0.00 
  ASPN MUTATED ASPN WILD-TYPE 
         36.16         122.30 
  ASPN MUTATED ASPN WILD-TYPE 
         31.27          13.55 
[1] "0.3 - 36.2 (31.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D772V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASPN MUTATED         0        1        1        0         0         1
  ASPN WILD-TYPE      10       19       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPN MUTATED           1          0          0          1        2         0
  ASPN WILD-TYPE        28         84         62         38       41         4
D772V3, multiclass
            clus
vv           ASPN MUTATED ASPN WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ASPN MUTATED       1   1   1   4
  ASPN WILD-TYPE    53 134 260  98
D772V4, multiclass
       clus
vv      ASPN MUTATED ASPN WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               1            260
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ASPN MUTATED     3   1   2   1
  ASPN WILD-TYPE 192 172  87  84
D772V5, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  N0            3            192
  N1            1            172
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V6, binary
                cls
clus               0   1
  ASPN MUTATED     5   2
  ASPN WILD-TYPE 477  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      5    2
  ASPN WILD-TYPE  477   36
   clus
vv  ASPN MUTATED ASPN WILD-TYPE
  0            5            477
  1            2             36
[1] 2 2
[1] FALSE
D772V7, binary
                cls
clus               0   1
  ASPN MUTATED     2   5
  ASPN WILD-TYPE 170 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      2    5
  ASPN WILD-TYPE  170  401
        clus
vv       ASPN MUTATED ASPN WILD-TYPE
  FEMALE            2            170
  MALE              5            401
[1] 2 2
[1] FALSE
D772V8, binary
                cls
clus               0   1
  ASPN MUTATED     5   1
  ASPN WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      5    1
  ASPN WILD-TYPE  411  101
     clus
vv    ASPN MUTATED ASPN WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D772V9, continuous
[1] "Remove cluster labels:" "ASPN MUTATED"          
clus
  ASPN MUTATED ASPN WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ET     TCGA-VR-A8EU 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
D772V10, continuous
[1] "Remove cluster labels:" "ASPN MUTATED"          
clus
  ASPN MUTATED ASPN WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" "ASPN WILD-TYPE" 
    TCGA-Z6-AAPN 
"ASPN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ASPN MUTATED       1                         0
  ASPN WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASPN MUTATED                                           0     4
  ASPN WILD-TYPE                                         1   353
D772V11, multiclass
                                           clus
vv                                          ASPN MUTATED ASPN WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V12, binary
                cls
clus               0   1
  ASPN MUTATED     0   5
  ASPN WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      0    5
  ASPN WILD-TYPE   10  393
                        clus
vv                       ASPN MUTATED ASPN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(773) Variable = LZTR1 MUTATION ANALYSIS
D773V1, survival
                 sevent
clus2               0   1
  LZTR1 MUTATED    10  10
  LZTR1 WILD-TYPE 328 206
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             20             534 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             206 
$`LZTR1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-CG-4460 TCGA-IC-A6RE TCGA-IG-A4QS 
       60.39         4.31        19.99        21.99         7.69         3.88 
TCGA-L5-A8NM TCGA-LN-A49K TCGA-LN-A9FQ TCGA-R6-A6XQ TCGA-CG-5721 TCGA-CG-5726 
        7.76         5.92        12.85         6.35         6.02        28.96 
TCGA-D7-5578 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX 
       12.66        11.44        22.32        22.68         0.10        20.25 
TCGA-IN-A6RL TCGA-VQ-A8P2 
       13.35        38.14 

$`LZTR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LZTR1 MUTATED LZTR1 WILD-TYPE 
            0.1             0.0 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
          60.39          122.30 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
         12.755          13.730 
[1] "0.1 - 60.4 (12.8)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.4"
D773V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LZTR1 MUTATED         1        1        1        0         2         5
  LZTR1 WILD-TYPE       9       19       45       31        82        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LZTR1 MUTATED           0          4          2          3        2         0
  LZTR1 WILD-TYPE        29         80         60         36       41         4
D773V3, multiclass
            clus
vv           LZTR1 MUTATED LZTR1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LZTR1 MUTATED       4   3   8   7
  LZTR1 WILD-TYPE    50 132 253  95
D773V4, multiclass
       clus
vv      LZTR1 MUTATED LZTR1 WILD-TYPE
  T0+T1             4              50
  T2                3             132
  T3                8             253
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LZTR1 MUTATED     8   8   4   2
  LZTR1 WILD-TYPE 187 165  85  83
D773V5, multiclass
    clus
vv   LZTR1 MUTATED LZTR1 WILD-TYPE
  N0             8             187
  N1             8             165
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V6, binary
                 cls
clus                0   1
  LZTR1 MUTATED    20   1
  LZTR1 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED     20    1
  LZTR1 WILD-TYPE  462   37
   clus
vv  LZTR1 MUTATED LZTR1 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D773V7, binary
                 cls
clus                0   1
  LZTR1 MUTATED     9  15
  LZTR1 WILD-TYPE 163 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      9   15
  LZTR1 WILD-TYPE  163  391
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  FEMALE             9             163
  MALE              15             391
[1] 2 2
[1] FALSE
D773V8, binary
                 cls
clus                0   1
  LZTR1 MUTATED    17   1
  LZTR1 WILD-TYPE 399 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED     17    1
  LZTR1 WILD-TYPE  399  101
     clus
vv    LZTR1 MUTATED LZTR1 WILD-TYPE
  NO             17             399
  YES             1             101
[1] 2 2
[1] FALSE
D773V9, continuous
[1] "Remove cluster labels:" "LZTR1 MUTATED"         
clus
  LZTR1 MUTATED LZTR1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49L      TCGA-LN-A49M 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" "LZTR1 WILD-TYPE" 
D773V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LZTR1 MUTATED       6                         0
  LZTR1 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LZTR1 MUTATED                                           0    14
  LZTR1 WILD-TYPE                                         1   343
D773V11, multiclass
                                           clus
vv                                          LZTR1 MUTATED LZTR1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V12, binary
                 cls
clus                0   1
  LZTR1 MUTATED     0  15
  LZTR1 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTR1 MUTATED      0   15
  LZTR1 WILD-TYPE   10  383
                        clus
vv                       LZTR1 MUTATED LZTR1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(774) Variable = CNOT6 MUTATION ANALYSIS
D774V1, survival
                 sevent
clus2               0   1
  CNOT6 MUTATED     5   3
  CNOT6 WILD-TYPE 333 213
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              8             546 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              3             213 
$`CNOT6 MUTATED`
TCGA-L5-A4OU TCGA-R6-A8W8 TCGA-B7-5816 TCGA-B7-A5TI TCGA-CG-5721 TCGA-CG-5728 
       29.00         2.89        26.70        19.56         6.02        65.10 
TCGA-HJ-7597 TCGA-HU-A4GQ 
       26.47         0.10 

$`CNOT6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CNOT6 MUTATED CNOT6 WILD-TYPE 
            0.1             0.0 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
           65.1           122.3 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
         23.015          13.530 
[1] "0.1 - 65.1 (23.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D774V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNOT6 MUTATED         0        0        3        0         1         1
  CNOT6 WILD-TYPE      10       20       43       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNOT6 MUTATED           0          0          0          2        1         0
  CNOT6 WILD-TYPE        29         84         62         37       42         4
D774V3, multiclass
            clus
vv           CNOT6 MUTATED CNOT6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CNOT6 MUTATED       1   3   1   4
  CNOT6 WILD-TYPE    53 132 260  98
D774V4, multiclass
       clus
vv      CNOT6 MUTATED CNOT6 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                1             260
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CNOT6 MUTATED     5   1   1   1
  CNOT6 WILD-TYPE 190 172  88  84
D774V5, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  N0             5             190
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V6, binary
                 cls
clus                0   1
  CNOT6 MUTATED     8   0
  CNOT6 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      8    0
  CNOT6 WILD-TYPE  474   38
   clus
vv  CNOT6 MUTATED CNOT6 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D774V7, binary
                 cls
clus                0   1
  CNOT6 MUTATED     4   6
  CNOT6 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      4    6
  CNOT6 WILD-TYPE  168  400
        clus
vv       CNOT6 MUTATED CNOT6 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D774V8, binary
                 cls
clus                0   1
  CNOT6 MUTATED     7   0
  CNOT6 WILD-TYPE 409 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      7    0
  CNOT6 WILD-TYPE  409  102
     clus
vv    CNOT6 MUTATED CNOT6 WILD-TYPE
  NO              7             409
  YES             0             102
[1] 2 2
[1] FALSE
D774V9, continuous
D774V10, continuous
[1] "Remove cluster labels:" "CNOT6 MUTATED"         
clus
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" "CNOT6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNOT6 MUTATED       1                         0
  CNOT6 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNOT6 MUTATED                                           0     6
  CNOT6 WILD-TYPE                                         1   351
D774V11, multiclass
                                           clus
vv                                          CNOT6 MUTATED CNOT6 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V12, binary
                 cls
clus                0   1
  CNOT6 MUTATED     0   6
  CNOT6 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      0    6
  CNOT6 WILD-TYPE   10  392
                        clus
vv                       CNOT6 MUTATED CNOT6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(775) Variable = KIFAP3 MUTATION ANALYSIS
D775V1, survival
                  sevent
clus2                0   1
  KIFAP3 MUTATED    11   4
  KIFAP3 WILD-TYPE 327 212
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              15              539 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               4              212 
$`KIFAP3 MUTATED`
TCGA-CG-4460 TCGA-LN-A49S TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7715 
       21.99        13.15        30.90         9.34        34.68        33.63 
TCGA-BR-8360 TCGA-BR-8369 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-D7-8572 TCGA-HU-A4G8 
        6.18        14.04         6.58        12.62        16.80        22.68 
TCGA-HU-A4H8 TCGA-KB-A6F7 TCGA-VQ-A8P2 
       14.07        63.62        38.14 

$`KIFAP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J 
       11.70        15.75        13.51         2.53         5.56        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
            6.18             0.00 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
           63.62           122.30 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
           16.80            13.51 
[1] "6.2 - 63.6 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D775V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIFAP3 MUTATED         0        0        3        0         5         2
  KIFAP3 WILD-TYPE      10       20       43       31        79        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIFAP3 MUTATED           0          1          1          0        1
  KIFAP3 WILD-TYPE        29         83         61         39       42
                  vv
clus               STAGE IVA
  KIFAP3 MUTATED           0
  KIFAP3 WILD-TYPE         4
D775V3, multiclass
            clus
vv           KIFAP3 MUTATED KIFAP3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KIFAP3 MUTATED       2   3   7   2
  KIFAP3 WILD-TYPE    52 132 254 100
D775V4, multiclass
       clus
vv      KIFAP3 MUTATED KIFAP3 WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 7              254
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KIFAP3 MUTATED     6   6   1   1
  KIFAP3 WILD-TYPE 189 167  88  84
D775V5, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  N0              6              189
  N1              6              167
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V6, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED    14   1
  KIFAP3 WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED     14    1
  KIFAP3 WILD-TYPE  468   37
   clus
vv  KIFAP3 MUTATED KIFAP3 WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D775V7, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     6   9
  KIFAP3 WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      6    9
  KIFAP3 WILD-TYPE  166  397
        clus
vv       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D775V8, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED    12   3
  KIFAP3 WILD-TYPE 404  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED     12    3
  KIFAP3 WILD-TYPE  404   99
     clus
vv    KIFAP3 MUTATED KIFAP3 WILD-TYPE
  NO              12              404
  YES              3               99
[1] 2 2
[1] FALSE
D775V9, continuous
[1] "Remove cluster labels:" "KIFAP3 MUTATED"        
clus
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
D775V10, continuous
[1] "Remove cluster labels:" "KIFAP3 MUTATED"        
clus
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49U 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" "KIFAP3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"KIFAP3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIFAP3 MUTATED       5                         0
  KIFAP3 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIFAP3 MUTATED                                           0     8
  KIFAP3 WILD-TYPE                                         1   349
D775V11, multiclass
                                           clus
vv                                          KIFAP3 MUTATED KIFAP3 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V12, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     0  12
  KIFAP3 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      0   12
  KIFAP3 WILD-TYPE   10  386
                        clus
vv                       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(776) Variable = MFN1 MUTATION ANALYSIS
D776V1, survival
                sevent
clus2              0   1
  MFN1 MUTATED     9   3
  MFN1 WILD-TYPE 329 213
  MFN1 MUTATED MFN1 WILD-TYPE 
            12            542 
  MFN1 MUTATED MFN1 WILD-TYPE 
             3            213 
$`MFN1 MUTATED`
TCGA-L5-A4OS TCGA-LN-A49O TCGA-R6-A6Y0 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 
       58.59        13.41        53.95        26.70         6.97        34.68 
TCGA-CG-4305 TCGA-CG-5726 TCGA-HF-7132 TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-VQ-A8DV 
       15.95        28.96        77.29        23.84        74.53        13.25 

$`MFN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MFN1 MUTATED MFN1 WILD-TYPE 
          6.97           0.00 
  MFN1 MUTATED MFN1 WILD-TYPE 
         77.29         122.30 
  MFN1 MUTATED MFN1 WILD-TYPE 
        27.830         13.495 
[1] "7.0 - 77.3 (27.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.9"
D776V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFN1 MUTATED         0        1        1        2         2         3
  MFN1 WILD-TYPE      10       19       45       29        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFN1 MUTATED           0          1          0          0        1         0
  MFN1 WILD-TYPE        29         83         62         39       42         4
D776V3, multiclass
            clus
vv           MFN1 MUTATED MFN1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MFN1 MUTATED       1   5   3   2
  MFN1 WILD-TYPE    53 130 258 100
D776V4, multiclass
       clus
vv      MFN1 MUTATED MFN1 WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MFN1 MUTATED     5   5   1   0
  MFN1 WILD-TYPE 190 168  88  85
D776V5, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  N0            5            190
  N1            5            168
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V6, binary
                cls
clus               0   1
  MFN1 MUTATED     9   1
  MFN1 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      9    1
  MFN1 WILD-TYPE  473   37
   clus
vv  MFN1 MUTATED MFN1 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D776V7, binary
                cls
clus               0   1
  MFN1 MUTATED     5   7
  MFN1 WILD-TYPE 167 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      5    7
  MFN1 WILD-TYPE  167  399
        clus
vv       MFN1 MUTATED MFN1 WILD-TYPE
  FEMALE            5            167
  MALE              7            399
[1] 2 2
[1] FALSE
D776V8, binary
                cls
clus               0   1
  MFN1 MUTATED     9   2
  MFN1 WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      9    2
  MFN1 WILD-TYPE  407  100
     clus
vv    MFN1 MUTATED MFN1 WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D776V9, continuous
[1] "Remove cluster labels:" "MFN1 MUTATED"          
clus
  MFN1 MUTATED MFN1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49P     TCGA-LN-A49R 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
D776V10, continuous
[1] "Remove cluster labels:" "MFN1 MUTATED"          
clus
  MFN1 MUTATED MFN1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" "MFN1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"MFN1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MFN1 MUTATED       2                         0
  MFN1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFN1 MUTATED                                           0     7
  MFN1 WILD-TYPE                                         1   350
D776V11, multiclass
                                           clus
vv                                          MFN1 MUTATED MFN1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V12, binary
                cls
clus               0   1
  MFN1 MUTATED     1   6
  MFN1 WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      1    6
  MFN1 WILD-TYPE    9  392
                        clus
vv                       MFN1 MUTATED MFN1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(777) Variable = MZF1 MUTATION ANALYSIS
D777V1, survival
                sevent
clus2              0   1
  MZF1 MUTATED     8   6
  MZF1 WILD-TYPE 330 210
  MZF1 MUTATED MZF1 WILD-TYPE 
            14            540 
  MZF1 MUTATED MZF1 WILD-TYPE 
             6            210 
$`MZF1 MUTATED`
TCGA-2H-A9GK TCGA-IG-A3I8 TCGA-BR-7722 TCGA-BR-8078 TCGA-CG-5721 TCGA-CG-5726 
        7.63        33.27        15.32        29.59         6.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-8572 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6EY 
       65.10        21.07        16.80         5.92        13.78        11.44 
TCGA-HF-A5NB TCGA-HU-A4GN 
       30.51        29.98 

$`MZF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
      105.07        12.03        15.02         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27        16.44        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MZF1 MUTATED MZF1 WILD-TYPE 
          5.92           0.00 
  MZF1 MUTATED MZF1 WILD-TYPE 
          65.1          122.3 
  MZF1 MUTATED MZF1 WILD-TYPE 
        18.935         13.495 
[1] "5.9 - 65.1 (18.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D777V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MZF1 MUTATED         1        1        1        0         2         4
  MZF1 WILD-TYPE       9       19       45       31        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MZF1 MUTATED           1          1          2          1        1         0
  MZF1 WILD-TYPE        28         83         60         38       42         4
D777V3, multiclass
            clus
vv           MZF1 MUTATED MZF1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MZF1 MUTATED       2   4   6   3
  MZF1 WILD-TYPE    52 131 255  99
D777V4, multiclass
       clus
vv      MZF1 MUTATED MZF1 WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3               6            255
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MZF1 MUTATED     4   6   2   3
  MZF1 WILD-TYPE 191 167  87  82
D777V5, multiclass
    clus
vv   MZF1 MUTATED MZF1 WILD-TYPE
  N0            4            191
  N1            6            167
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V6, binary
                cls
clus               0   1
  MZF1 MUTATED    14   0
  MZF1 WILD-TYPE 468  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED     14    0
  MZF1 WILD-TYPE  468   38
   clus
vv  MZF1 MUTATED MZF1 WILD-TYPE
  0           14            468
  1            0             38
[1] 2 2
[1] FALSE
D777V7, binary
                cls
clus               0   1
  MZF1 MUTATED     7   8
  MZF1 WILD-TYPE 165 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED      7    8
  MZF1 WILD-TYPE  165  398
        clus
vv       MZF1 MUTATED MZF1 WILD-TYPE
  FEMALE            7            165
  MALE              8            398
[1] 2 2
[1] FALSE
D777V8, binary
                cls
clus               0   1
  MZF1 MUTATED    11   2
  MZF1 WILD-TYPE 405 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED     11    2
  MZF1 WILD-TYPE  405  100
     clus
vv    MZF1 MUTATED MZF1 WILD-TYPE
  NO            11            405
  YES            2            100
[1] 2 2
[1] FALSE
D777V9, continuous
[1] "Remove cluster labels:" "MZF1 MUTATED"          
clus
  MZF1 MUTATED MZF1 WILD-TYPE 
             1             67 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YB 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3     TCGA-IG-A7DP 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MZF1 WILD-TYPE" "MZF1 WILD-TYPE" "MZF1 WILD-TYPE" 
D777V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MZF1 MUTATED       1                         1
  MZF1 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MZF1 MUTATED                                           0     7
  MZF1 WILD-TYPE                                         1   350
D777V11, multiclass
                                           clus
vv                                          MZF1 MUTATED MZF1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V12, binary
                cls
clus               0   1
  MZF1 MUTATED     0   9
  MZF1 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  MZF1 MUTATED      0    9
  MZF1 WILD-TYPE   10  389
                        clus
vv                       MZF1 MUTATED MZF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(778) Variable = SCAMP2 MUTATION ANALYSIS
D778V1, survival
                  sevent
clus2                0   1
  SCAMP2 MUTATED     4   2
  SCAMP2 WILD-TYPE 334 214
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               6              548 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               2              214 
$`SCAMP2 MUTATED`
TCGA-IG-A4P3 TCGA-BR-8382 TCGA-CD-8534 TCGA-CG-4305 TCGA-HU-A4GT TCGA-R5-A7ZI 
       18.64        25.05        12.07        15.95         6.51        74.53 

$`SCAMP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
            6.51             0.00 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
           74.53           122.30 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
          17.295           13.530 
[1] "6.5 - 74.5 (17.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D778V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCAMP2 MUTATED         0        0        0        2         1         2
  SCAMP2 WILD-TYPE      10       20       46       29        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCAMP2 MUTATED           0          0          0          1        1
  SCAMP2 WILD-TYPE        29         84         62         38       42
                  vv
clus               STAGE IVA
  SCAMP2 MUTATED           0
  SCAMP2 WILD-TYPE         4
D778V3, multiclass
            clus
vv           SCAMP2 MUTATED SCAMP2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                2               29
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SCAMP2 MUTATED       0   2   2   3
  SCAMP2 WILD-TYPE    54 133 259  99
D778V4, multiclass
       clus
vv      SCAMP2 MUTATED SCAMP2 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 2              259
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SCAMP2 MUTATED     3   4   0   1
  SCAMP2 WILD-TYPE 192 169  89  84
D778V5, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V6, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     7   1
  SCAMP2 WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      7    1
  SCAMP2 WILD-TYPE  475   37
   clus
vv  SCAMP2 MUTATED SCAMP2 WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D778V7, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     4   4
  SCAMP2 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      4    4
  SCAMP2 WILD-TYPE  168  402
        clus
vv       SCAMP2 MUTATED SCAMP2 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D778V8, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     6   1
  SCAMP2 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      6    1
  SCAMP2 WILD-TYPE  410  101
     clus
vv    SCAMP2 MUTATED SCAMP2 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D778V9, continuous
D778V10, continuous
[1] "Remove cluster labels:" "SCAMP2 MUTATED"        
clus
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" "SCAMP2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"SCAMP2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SCAMP2 MUTATED       2                         0
  SCAMP2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCAMP2 MUTATED                                           0     5
  SCAMP2 WILD-TYPE                                         1   352
D778V11, multiclass
                                           clus
vv                                          SCAMP2 MUTATED SCAMP2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V12, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     1   6
  SCAMP2 WILD-TYPE   9 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      1    6
  SCAMP2 WILD-TYPE    9  392
                        clus
vv                       SCAMP2 MUTATED SCAMP2 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(779) Variable = LCE1A MUTATION ANALYSIS
D779V1, survival
                 sevent
clus2               0   1
  LCE1A MUTATED     2   2
  LCE1A WILD-TYPE 336 214
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             550 
  LCE1A MUTATED LCE1A WILD-TYPE 
              2             214 
$`LCE1A MUTATED`
TCGA-BR-8059 TCGA-BR-8297 TCGA-BR-A452 TCGA-BR-A4PD 
       14.43         7.40         7.53        20.65 

$`LCE1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  LCE1A MUTATED LCE1A WILD-TYPE 
            7.4             0.0 
  LCE1A MUTATED LCE1A WILD-TYPE 
          20.65          122.30 
  LCE1A MUTATED LCE1A WILD-TYPE 
         10.980          13.565 
[1] "7.4 - 20.6 (11.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D779V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LCE1A MUTATED         0        0        0        0         0         1
  LCE1A WILD-TYPE      10       20       46       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LCE1A MUTATED           1          1          0          1        0         0
  LCE1A WILD-TYPE        28         83         62         38       43         4
D779V3, multiclass
            clus
vv           LCE1A MUTATED LCE1A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LCE1A MUTATED       0   0   0   4
  LCE1A WILD-TYPE    54 135 261  98
D779V4, multiclass
       clus
vv      LCE1A MUTATED LCE1A WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                0             261
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LCE1A MUTATED     1   2   0   1
  LCE1A WILD-TYPE 194 171  89  84
D779V5, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  N0             1             194
  N1             2             171
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V6, binary
                 cls
clus                0   1
  LCE1A MUTATED     4   0
  LCE1A WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      4    0
  LCE1A WILD-TYPE  478   38
   clus
vv  LCE1A MUTATED LCE1A WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D779V7, binary
                 cls
clus                0   1
  LCE1A MUTATED     1   3
  LCE1A WILD-TYPE 171 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      1    3
  LCE1A WILD-TYPE  171  403
        clus
vv       LCE1A MUTATED LCE1A WILD-TYPE
  FEMALE             1             171
  MALE               3             403
[1] 2 2
[1] FALSE
D779V8, binary
                 cls
clus                0   1
  LCE1A MUTATED     4   0
  LCE1A WILD-TYPE 412 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      4    0
  LCE1A WILD-TYPE  412  102
     clus
vv    LCE1A MUTATED LCE1A WILD-TYPE
  NO              4             412
  YES             0             102
[1] 2 2
[1] FALSE
D779V9, continuous
D779V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LCE1A MUTATED       1                         0
  LCE1A WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LCE1A MUTATED                                           0     3
  LCE1A WILD-TYPE                                         1   354
D779V11, multiclass
                                           clus
vv                                          LCE1A MUTATED LCE1A WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V12, binary
                 cls
clus                0   1
  LCE1A MUTATED     0   4
  LCE1A WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      0    4
  LCE1A WILD-TYPE   10  394
                        clus
vv                       LCE1A MUTATED LCE1A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(780) Variable = TMEM55A MUTATION ANALYSIS
D780V1, survival
                   sevent
clus2                 0   1
  TMEM55A MUTATED     3   1
  TMEM55A WILD-TYPE 335 215
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                4               550 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                1               215 
$`TMEM55A MUTATED`
TCGA-L5-A4OI TCGA-XP-A8T7 TCGA-BR-8361 TCGA-CD-A4MI 
       19.99        41.23        31.10        11.77 

$`TMEM55A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TMEM55A MUTATED TMEM55A WILD-TYPE 
            11.77              0.00 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
            41.23            122.30 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
           25.545            13.530 
[1] "11.8 - 41.2 (25.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D780V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM55A MUTATED         0        0        0        0         1         0
  TMEM55A WILD-TYPE      10       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM55A MUTATED           0          1          0          2        0
  TMEM55A WILD-TYPE        29         83         62         37       43
                   vv
clus                STAGE IVA
  TMEM55A MUTATED           0
  TMEM55A WILD-TYPE         4
D780V3, multiclass
            clus
vv           TMEM55A MUTATED TMEM55A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM55A MUTATED       0   1   2   1
  TMEM55A WILD-TYPE    54 134 259 101
D780V4, multiclass
       clus
vv      TMEM55A MUTATED TMEM55A WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM55A MUTATED     1   2   1   1
  TMEM55A WILD-TYPE 194 171  88  84
D780V5, multiclass
    clus
vv   TMEM55A MUTATED TMEM55A WILD-TYPE
  N0               1               194
  N1               2               171
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V6, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     4   0
  TMEM55A WILD-TYPE 478  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      4    0
  TMEM55A WILD-TYPE  478   38
   clus
vv  TMEM55A MUTATED TMEM55A WILD-TYPE
  0               4               478
  1               0                38
[1] 2 2
[1] FALSE
D780V7, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     3   2
  TMEM55A WILD-TYPE 169 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      3    2
  TMEM55A WILD-TYPE  169  404
        clus
vv       TMEM55A MUTATED TMEM55A WILD-TYPE
  FEMALE               3               169
  MALE                 2               404
[1] 2 2
[1] FALSE
D780V8, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     4   0
  TMEM55A WILD-TYPE 412 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      4    0
  TMEM55A WILD-TYPE  412  102
     clus
vv    TMEM55A MUTATED TMEM55A WILD-TYPE
  NO                4               412
  YES               0               102
[1] 2 2
[1] FALSE
D780V9, continuous
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
D780V10, continuous
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM55A MUTATED       1                         0
  TMEM55A WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM55A MUTATED                                           0     4
  TMEM55A WILD-TYPE                                         1   353
D780V11, multiclass
                                           clus
vv                                          TMEM55A MUTATED TMEM55A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V12, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     1   3
  TMEM55A WILD-TYPE   9 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      1    3
  TMEM55A WILD-TYPE    9  395
                        clus
vv                       TMEM55A MUTATED TMEM55A WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(781) Variable = PNPLA7 MUTATION ANALYSIS
D781V1, survival
                  sevent
clus2                0   1
  PNPLA7 MUTATED    17   6
  PNPLA7 WILD-TYPE 321 210
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              23              531 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               6              210 
$`PNPLA7 MUTATED`
TCGA-L5-A4OI TCGA-VR-A8EQ TCGA-Z6-A9VB TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7901 
       19.99        22.82         1.32        30.90        44.94         3.45 
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 
       29.59        31.10         0.26        31.27         1.12        27.12 
TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5732 TCGA-HF-7132 TCGA-HU-A4GN TCGA-HU-A4GP 
       15.95       105.07        69.04        77.29        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-A6RP TCGA-VQ-A8P2 
        0.10        23.84        14.07         6.44        38.14 

$`PNPLA7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        25.81        11.77        21.37         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
             0.1              0.0 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
          105.07           122.30 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
           23.84            13.41 
[1] "0.1 - 105.1 (23.8)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2.1"
D781V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PNPLA7 MUTATED         0        0        2        3         4         4
  PNPLA7 WILD-TYPE      10       20       44       28        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA7 MUTATED           1          3          1          5        1
  PNPLA7 WILD-TYPE        28         81         61         34       42
                  vv
clus               STAGE IVA
  PNPLA7 MUTATED           0
  PNPLA7 WILD-TYPE         4
D781V3, multiclass
            clus
vv           PNPLA7 MUTATED PNPLA7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                3               28
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              5               34
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PNPLA7 MUTATED       3   9   6   8
  PNPLA7 WILD-TYPE    51 126 255  94
D781V4, multiclass
       clus
vv      PNPLA7 MUTATED PNPLA7 WILD-TYPE
  T0+T1              3               51
  T2                 9              126
  T3                 6              255
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PNPLA7 MUTATED     6  11   3   4
  PNPLA7 WILD-TYPE 189 162  86  81
D781V5, multiclass
    clus
vv   PNPLA7 MUTATED PNPLA7 WILD-TYPE
  N0              6              189
  N1             11              162
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V6, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    25   0
  PNPLA7 WILD-TYPE 457  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     25    0
  PNPLA7 WILD-TYPE  457   38
   clus
vv  PNPLA7 MUTATED PNPLA7 WILD-TYPE
  0             25              457
  1              0               38
[1] 2 2
[1] FALSE
D781V7, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    10  16
  PNPLA7 WILD-TYPE 162 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     10   16
  PNPLA7 WILD-TYPE  162  390
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  FEMALE             10              162
  MALE               16              390
[1] 2 2
[1] FALSE
D781V8, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    20   4
  PNPLA7 WILD-TYPE 396  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     20    4
  PNPLA7 WILD-TYPE  396   98
     clus
vv    PNPLA7 MUTATED PNPLA7 WILD-TYPE
  NO              20              396
  YES              4               98
[1] 2 2
[1] FALSE
D781V9, continuous
[1] "Remove cluster labels:" "PNPLA7 MUTATED"        
clus
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
D781V10, continuous
[1] "Remove cluster labels:" "PNPLA7 MUTATED"        
clus
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PNPLA7 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PNPLA7 MUTATED       5                         0
  PNPLA7 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PNPLA7 MUTATED                                           0    17
  PNPLA7 WILD-TYPE                                         1   340
D781V11, multiclass
                                           clus
vv                                          PNPLA7 MUTATED PNPLA7 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V12, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED     0  19
  PNPLA7 WILD-TYPE  10 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED      0   19
  PNPLA7 WILD-TYPE   10  379
                        clus
vv                       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             19              379
[1] 2 2
[1] FALSE

Clustering(782) Variable = STAT6 MUTATION ANALYSIS
D782V1, survival
                 sevent
clus2               0   1
  STAT6 MUTATED     3   5
  STAT6 WILD-TYPE 335 211
  STAT6 MUTATED STAT6 WILD-TYPE 
              8             546 
  STAT6 MUTATED STAT6 WILD-TYPE 
              5             211 
$`STAT6 MUTATED`
TCGA-L5-A4OE TCGA-LN-A7HW TCGA-VR-A8EO TCGA-BR-4184 TCGA-BR-A4QL TCGA-CD-8536 
       24.00        12.00        25.81         6.97        16.14        12.43 
TCGA-CD-A4MI TCGA-D7-A6EY 
       11.77        11.44 

$`STAT6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  STAT6 MUTATED STAT6 WILD-TYPE 
           6.97            0.00 
  STAT6 MUTATED STAT6 WILD-TYPE 
          25.81          122.30 
  STAT6 MUTATED STAT6 WILD-TYPE 
         12.215          13.630 
[1] "7.0 - 25.8 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D782V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAT6 MUTATED         0        0        0        1         2         0
  STAT6 WILD-TYPE      10       20       46       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAT6 MUTATED           0          2          3          0        0         0
  STAT6 WILD-TYPE        29         82         59         39       43         4
D782V3, multiclass
            clus
vv           STAT6 MUTATED STAT6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  STAT6 MUTATED       0   1   7   0
  STAT6 WILD-TYPE    54 134 254 102
D782V4, multiclass
       clus
vv      STAT6 MUTATED STAT6 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                7             254
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STAT6 MUTATED     3   3   1   2
  STAT6 WILD-TYPE 192 170  88  83
D782V5, multiclass
    clus
vv   STAT6 MUTATED STAT6 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V6, binary
                 cls
clus                0   1
  STAT6 MUTATED     7   0
  STAT6 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      7    0
  STAT6 WILD-TYPE  475   38
   clus
vv  STAT6 MUTATED STAT6 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D782V7, binary
                 cls
clus                0   1
  STAT6 MUTATED     3   6
  STAT6 WILD-TYPE 169 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      3    6
  STAT6 WILD-TYPE  169  400
        clus
vv       STAT6 MUTATED STAT6 WILD-TYPE
  FEMALE             3             169
  MALE               6             400
[1] 2 2
[1] FALSE
D782V8, binary
                 cls
clus                0   1
  STAT6 MUTATED     7   1
  STAT6 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      7    1
  STAT6 WILD-TYPE  409  101
     clus
vv    STAT6 MUTATED STAT6 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D782V9, continuous
[1] "Remove cluster labels:" "STAT6 MUTATED"         
clus
  STAT6 MUTATED STAT6 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
D782V10, continuous
[1] "Remove cluster labels:" "STAT6 MUTATED"         
clus
  STAT6 MUTATED STAT6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OG 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" "STAT6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STAT6 MUTATED       3                         0
  STAT6 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STAT6 MUTATED                                           0     6
  STAT6 WILD-TYPE                                         1   351
D782V11, multiclass
                                           clus
vv                                          STAT6 MUTATED STAT6 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V12, binary
                 cls
clus                0   1
  STAT6 MUTATED     0   7
  STAT6 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      0    7
  STAT6 WILD-TYPE   10  391
                        clus
vv                       STAT6 MUTATED STAT6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(783) Variable = STK33 MUTATION ANALYSIS
D783V1, survival
                 sevent
clus2               0   1
  STK33 MUTATED    10   2
  STK33 WILD-TYPE 328 214
  STK33 MUTATED STK33 WILD-TYPE 
             12             542 
  STK33 MUTATED STK33 WILD-TYPE 
              2             214 
$`STK33 MUTATED`
TCGA-IC-A6RE TCGA-L5-A88V TCGA-R6-A6XG TCGA-V5-AASX TCGA-BR-8680 TCGA-CG-5723 
        7.69         2.60        38.40         8.98        31.96       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-KB-A93J 
       28.96        65.10        77.29        30.51         0.10        36.95 

$`STK33 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        15.02         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  STK33 MUTATED STK33 WILD-TYPE 
            0.1             0.0 
  STK33 MUTATED STK33 WILD-TYPE 
         105.07          122.30 
  STK33 MUTATED STK33 WILD-TYPE 
         31.235          13.510 
[1] "0.1 - 105.1 (31.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4.1"
D783V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK33 MUTATED         0        1        1        3         0         1
  STK33 WILD-TYPE      10       19       45       28        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK33 MUTATED           1          1          0          2        1         0
  STK33 WILD-TYPE        28         83         62         37       42         4
D783V3, multiclass
            clus
vv           STK33 MUTATED STK33 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  STK33 MUTATED       2   4   1   4
  STK33 WILD-TYPE    52 131 260  98
D783V4, multiclass
       clus
vv      STK33 MUTATED STK33 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                1             260
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STK33 MUTATED     3   5   2   1
  STK33 WILD-TYPE 192 168  87  84
D783V5, multiclass
    clus
vv   STK33 MUTATED STK33 WILD-TYPE
  N0             3             192
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V6, binary
                 cls
clus                0   1
  STK33 MUTATED     9   1
  STK33 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED      9    1
  STK33 WILD-TYPE  473   37
   clus
vv  STK33 MUTATED STK33 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D783V7, binary
                 cls
clus                0   1
  STK33 MUTATED     3  10
  STK33 WILD-TYPE 169 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED      3   10
  STK33 WILD-TYPE  169  396
        clus
vv       STK33 MUTATED STK33 WILD-TYPE
  FEMALE             3             169
  MALE              10             396
[1] 2 2
[1] FALSE
D783V8, binary
                 cls
clus                0   1
  STK33 MUTATED     6   3
  STK33 WILD-TYPE 410  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED      6    3
  STK33 WILD-TYPE  410   99
     clus
vv    STK33 MUTATED STK33 WILD-TYPE
  NO              6             410
  YES             3              99
[1] 2 2
[1] FALSE
D783V9, continuous
[1] "Remove cluster labels:" "STK33 MUTATED"         
clus
  STK33 MUTATED STK33 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
D783V10, continuous
[1] "Remove cluster labels:" "STK33 MUTATED"         
clus
  STK33 MUTATED STK33 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" "STK33 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STK33 MUTATED       2                         0
  STK33 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STK33 MUTATED                                           0     6
  STK33 WILD-TYPE                                         1   351
D783V11, multiclass
                                           clus
vv                                          STK33 MUTATED STK33 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V12, binary
                 cls
clus                0   1
  STK33 MUTATED     0   6
  STK33 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED      0    6
  STK33 WILD-TYPE   10  392
                        clus
vv                       STK33 MUTATED STK33 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(784) Variable = DNAJA1 MUTATION ANALYSIS
D784V1, survival
                  sevent
clus2                0   1
  DNAJA1 MUTATED     7   3
  DNAJA1 WILD-TYPE 331 213
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
              10              544 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               3              213 
$`DNAJA1 MUTATED`
TCGA-L5-A4OI TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-BR-8591 TCGA-CG-4306 TCGA-CG-5721 
       19.99        16.44        22.82        28.14         1.02         6.02 
TCGA-CG-5726 TCGA-HF-A5NB TCGA-HU-A4H8 TCGA-VQ-A8P2 
       28.96        30.51        14.07        38.14 

$`DNAJA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
            1.02             0.00 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
           38.14           122.30 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
          21.405           13.495 
[1] "1.0 - 38.1 (21.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D784V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJA1 MUTATED         1        1        2        0         0         0
  DNAJA1 WILD-TYPE       9       19       44       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJA1 MUTATED           1          2          0          3        2
  DNAJA1 WILD-TYPE        28         82         62         36       41
                  vv
clus               STAGE IVA
  DNAJA1 MUTATED           0
  DNAJA1 WILD-TYPE         4
D784V3, multiclass
            clus
vv           DNAJA1 MUTATED DNAJA1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DNAJA1 MUTATED       4   0   3   5
  DNAJA1 WILD-TYPE    50 135 258  97
D784V4, multiclass
       clus
vv      DNAJA1 MUTATED DNAJA1 WILD-TYPE
  T0+T1              4               50
  T2                 0              135
  T3                 3              258
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DNAJA1 MUTATED     3   5   1   3
  DNAJA1 WILD-TYPE 192 168  88  82
D784V5, multiclass
    clus
vv   DNAJA1 MUTATED DNAJA1 WILD-TYPE
  N0              3              192
  N1              5              168
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V6, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     9   1
  DNAJA1 WILD-TYPE 473  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      9    1
  DNAJA1 WILD-TYPE  473   37
   clus
vv  DNAJA1 MUTATED DNAJA1 WILD-TYPE
  0              9              473
  1              1               37
[1] 2 2
[1] FALSE
D784V7, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     2  10
  DNAJA1 WILD-TYPE 170 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      2   10
  DNAJA1 WILD-TYPE  170  396
        clus
vv       DNAJA1 MUTATED DNAJA1 WILD-TYPE
  FEMALE              2              170
  MALE               10              396
[1] 2 2
[1] FALSE
D784V8, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     5   4
  DNAJA1 WILD-TYPE 411  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      5    4
  DNAJA1 WILD-TYPE  411   98
     clus
vv    DNAJA1 MUTATED DNAJA1 WILD-TYPE
  NO               5              411
  YES              4               98
[1] 2 2
[1] FALSE
D784V9, continuous
[1] "Remove cluster labels:" "DNAJA1 MUTATED"        
clus
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
D784V10, continuous
[1] "Remove cluster labels:" "DNAJA1 MUTATED"        
clus
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" "DNAJA1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"DNAJA1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DNAJA1 MUTATED       1                         1
  DNAJA1 WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJA1 MUTATED                                           0     6
  DNAJA1 WILD-TYPE                                         1   351
D784V11, multiclass
                                           clus
vv                                          DNAJA1 MUTATED DNAJA1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V12, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     0   5
  DNAJA1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      0    5
  DNAJA1 WILD-TYPE   10  393
                        clus
vv                       DNAJA1 MUTATED DNAJA1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(785) Variable = IFITM1 MUTATION ANALYSIS
D785V1, survival
                  sevent
clus2                0   1
  IFITM1 MUTATED     3   2
  IFITM1 WILD-TYPE 335 214
  IFITM1 MUTATED IFITM1 WILD-TYPE 
               5              549 
  IFITM1 MUTATED IFITM1 WILD-TYPE 
               2              214 
$`IFITM1 MUTATED`
TCGA-LN-A49M TCGA-B7-A5TI TCGA-BR-6452 TCGA-CD-A4MI TCGA-D7-A6EY 
       12.66        19.56        34.68        11.77        11.44 

$`IFITM1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IFITM1 MUTATED IFITM1 WILD-TYPE 
           11.44             0.00 
  IFITM1 MUTATED IFITM1 WILD-TYPE 
           34.68           122.30 
  IFITM1 MUTATED IFITM1 WILD-TYPE 
           12.66            13.58 
[1] "11.4 - 34.7 (12.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D785V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFITM1 MUTATED         0        0        0        0         2         0
  IFITM1 WILD-TYPE      10       20       46       31        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM1 MUTATED           0          1          1          1        0
  IFITM1 WILD-TYPE        29         83         61         38       43
                  vv
clus               STAGE IVA
  IFITM1 MUTATED           0
  IFITM1 WILD-TYPE         4
D785V3, multiclass
            clus
vv           IFITM1 MUTATED IFITM1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  IFITM1 MUTATED       0   1   3   1
  IFITM1 WILD-TYPE    54 134 258 101
D785V4, multiclass
       clus
vv      IFITM1 MUTATED IFITM1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  IFITM1 MUTATED     2   1   0   2
  IFITM1 WILD-TYPE 193 172  89  83
D785V5, multiclass
    clus
vv   IFITM1 MUTATED IFITM1 WILD-TYPE
  N0              2              193
  N1              1              172
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V6, binary
                  cls
clus                 0   1
  IFITM1 MUTATED     5   0
  IFITM1 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM1 MUTATED      5    0
  IFITM1 WILD-TYPE  477   38
   clus
vv  IFITM1 MUTATED IFITM1 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D785V7, binary
                  cls
clus                 0   1
  IFITM1 MUTATED     2   3
  IFITM1 WILD-TYPE 170 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM1 MUTATED      2    3
  IFITM1 WILD-TYPE  170  403
        clus
vv       IFITM1 MUTATED IFITM1 WILD-TYPE
  FEMALE              2              170
  MALE                3              403
[1] 2 2
[1] FALSE
D785V8, binary
                  cls
clus                 0   1
  IFITM1 MUTATED     4   1
  IFITM1 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM1 MUTATED      4    1
  IFITM1 WILD-TYPE  412  101
     clus
vv    IFITM1 MUTATED IFITM1 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D785V9, continuous
[1] "Remove cluster labels:" "IFITM1 MUTATED"        
clus
  IFITM1 MUTATED IFITM1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" "IFITM1 WILD-TYPE" 
D785V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IFITM1 MUTATED       2                         0
  IFITM1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFITM1 MUTATED                                           0     3
  IFITM1 WILD-TYPE                                         1   354
D785V11, multiclass
                                           clus
vv                                          IFITM1 MUTATED IFITM1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V12, binary
                  cls
clus                 0   1
  IFITM1 MUTATED     0   5
  IFITM1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM1 MUTATED      0    5
  IFITM1 WILD-TYPE   10  393
                        clus
vv                       IFITM1 MUTATED IFITM1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(786) Variable = FAM151A MUTATION ANALYSIS
D786V1, survival
                   sevent
clus2                 0   1
  FAM151A MUTATED     5   1
  FAM151A WILD-TYPE 333 215
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               548 
  FAM151A MUTATED FAM151A WILD-TYPE 
                1               215 
$`FAM151A MUTATED`
TCGA-L5-A4OI TCGA-VR-A8Q7 TCGA-Z6-A8JE TCGA-BR-8487 TCGA-CG-4306 TCGA-HU-A4H3 
       19.99        52.27         2.10         1.12         1.02        29.00 

$`FAM151A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM151A MUTATED FAM151A WILD-TYPE 
             1.02              0.00 
  FAM151A MUTATED FAM151A WILD-TYPE 
            52.27            122.30 
  FAM151A MUTATED FAM151A WILD-TYPE 
           11.045            13.565 
[1] "1.0 - 52.3 (11.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D786V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM151A MUTATED         1        0        0        0         1         0
  FAM151A WILD-TYPE       9       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM151A MUTATED           0          2          0          2        1
  FAM151A WILD-TYPE        29         82         62         37       42
                   vv
clus                STAGE IVA
  FAM151A MUTATED           0
  FAM151A WILD-TYPE         4
D786V3, multiclass
            clus
vv           FAM151A MUTATED FAM151A WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM151A MUTATED       1   0   5   1
  FAM151A WILD-TYPE    53 135 256 101
D786V4, multiclass
       clus
vv      FAM151A MUTATED FAM151A WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  5               256
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM151A MUTATED     1   4   1   2
  FAM151A WILD-TYPE 194 169  88  83
D786V5, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  N0               1               194
  N1               4               169
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V6, binary
                   cls
clus                  0   1
  FAM151A MUTATED     5   1
  FAM151A WILD-TYPE 477  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      5    1
  FAM151A WILD-TYPE  477   37
   clus
vv  FAM151A MUTATED FAM151A WILD-TYPE
  0               5               477
  1               1                37
[1] 2 2
[1] FALSE
D786V7, binary
                   cls
clus                  0   1
  FAM151A MUTATED     3   5
  FAM151A WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      3    5
  FAM151A WILD-TYPE  169  401
        clus
vv       FAM151A MUTATED FAM151A WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D786V8, binary
                   cls
clus                  0   1
  FAM151A MUTATED     5   0
  FAM151A WILD-TYPE 411 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      5    0
  FAM151A WILD-TYPE  411  102
     clus
vv    FAM151A MUTATED FAM151A WILD-TYPE
  NO                5               411
  YES               0               102
[1] 2 2
[1] FALSE
D786V9, continuous
[1] "Remove cluster labels:" "FAM151A MUTATED"       
clus
  FAM151A MUTATED FAM151A WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
D786V10, continuous
[1] "Remove cluster labels:" "FAM151A MUTATED"       
clus
  FAM151A MUTATED FAM151A WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" "FAM151A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM151A MUTATED       1                         1
  FAM151A WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM151A MUTATED                                           0     5
  FAM151A WILD-TYPE                                         1   352
D786V11, multiclass
                                           clus
vv                                          FAM151A MUTATED FAM151A WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V12, binary
                   cls
clus                  0   1
  FAM151A MUTATED     0   5
  FAM151A WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      0    5
  FAM151A WILD-TYPE   10  393
                        clus
vv                       FAM151A MUTATED FAM151A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(787) Variable = HMGCLL1 MUTATION ANALYSIS
D787V1, survival
                   sevent
clus2                 0   1
  HMGCLL1 MUTATED     7   3
  HMGCLL1 WILD-TYPE 331 213
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               544 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
                3               213 
$`HMGCLL1 MUTATED`
TCGA-BR-6458 TCGA-BR-8588 TCGA-CD-8529 TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6818 
       19.33        12.79        12.30        15.95         6.02        12.36 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-A6RR 
        6.58        29.00        14.07         6.74 

$`HMGCLL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
             6.02              0.00 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
             29.0             122.3 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
           12.575            13.630 
[1] "6.0 - 29.0 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D787V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HMGCLL1 MUTATED         0        0        1        1         0         3
  HMGCLL1 WILD-TYPE      10       20       45       30        84        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HMGCLL1 MUTATED           0          2          0          1        2
  HMGCLL1 WILD-TYPE        29         82         62         38       41
                   vv
clus                STAGE IVA
  HMGCLL1 MUTATED           0
  HMGCLL1 WILD-TYPE         4
D787V3, multiclass
            clus
vv           HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  HMGCLL1 MUTATED       1   2   3   4
  HMGCLL1 WILD-TYPE    53 133 258  98
D787V4, multiclass
       clus
vv      HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  3               258
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HMGCLL1 MUTATED     2   6   0   2
  HMGCLL1 WILD-TYPE 193 167  89  83
D787V5, multiclass
    clus
vv   HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  N0               2               193
  N1               6               167
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V6, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     9   1
  HMGCLL1 WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      9    1
  HMGCLL1 WILD-TYPE  473   37
   clus
vv  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D787V7, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     3   7
  HMGCLL1 WILD-TYPE 169 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      3    7
  HMGCLL1 WILD-TYPE  169  399
        clus
vv       HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  FEMALE               3               169
  MALE                 7               399
[1] 2 2
[1] FALSE
D787V8, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     7   2
  HMGCLL1 WILD-TYPE 409 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      7    2
  HMGCLL1 WILD-TYPE  409  100
     clus
vv    HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  NO                7               409
  YES               2               100
[1] 2 2
[1] FALSE
D787V9, continuous
D787V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HMGCLL1 MUTATED       4                         0
  HMGCLL1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HMGCLL1 MUTATED                                           0     4
  HMGCLL1 WILD-TYPE                                         1   353
D787V11, multiclass
                                           clus
vv                                          HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V12, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     0   8
  HMGCLL1 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      0    8
  HMGCLL1 WILD-TYPE   10  390
                        clus
vv                       HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(788) Variable = GIPC3 MUTATION ANALYSIS
D788V1, survival
                 sevent
clus2               0   1
  GIPC3 MUTATED     6   3
  GIPC3 WILD-TYPE 332 213
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              9             545 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              3             213 
$`GIPC3 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GM TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-A4MI 
       19.99        13.94        36.16        35.84        29.59        11.77 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-A5NB 
        5.92        11.08        30.51 

$`GIPC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       44.94        21.90         9.21        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  GIPC3 MUTATED GIPC3 WILD-TYPE 
           5.92            0.00 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
          36.16          122.30 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
          19.99           13.51 
[1] "5.9 - 36.2 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D788V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GIPC3 MUTATED         0        1        1        0         1         3
  GIPC3 WILD-TYPE      10       19       45       31        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GIPC3 MUTATED           0          1          0          2        0         0
  GIPC3 WILD-TYPE        29         83         62         37       43         4
D788V3, multiclass
            clus
vv           GIPC3 MUTATED GIPC3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GIPC3 MUTATED       2   1   4   2
  GIPC3 WILD-TYPE    52 134 257 100
D788V4, multiclass
       clus
vv      GIPC3 MUTATED GIPC3 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GIPC3 MUTATED     4   3   0   2
  GIPC3 WILD-TYPE 191 170  89  83
D788V5, multiclass
    clus
vv   GIPC3 MUTATED GIPC3 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V6, binary
                 cls
clus                0   1
  GIPC3 MUTATED     8   0
  GIPC3 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      8    0
  GIPC3 WILD-TYPE  474   38
   clus
vv  GIPC3 MUTATED GIPC3 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D788V7, binary
                 cls
clus                0   1
  GIPC3 MUTATED     4   5
  GIPC3 WILD-TYPE 168 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      4    5
  GIPC3 WILD-TYPE  168  401
        clus
vv       GIPC3 MUTATED GIPC3 WILD-TYPE
  FEMALE             4             168
  MALE               5             401
[1] 2 2
[1] FALSE
D788V8, binary
                 cls
clus                0   1
  GIPC3 MUTATED     7   2
  GIPC3 WILD-TYPE 409 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      7    2
  GIPC3 WILD-TYPE  409  100
     clus
vv    GIPC3 MUTATED GIPC3 WILD-TYPE
  NO              7             409
  YES             2             100
[1] 2 2
[1] FALSE
D788V9, continuous
D788V10, continuous
[1] "Remove cluster labels:" "GIPC3 MUTATED"         
clus
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" "GIPC3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"GIPC3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GIPC3 MUTATED       1                         1
  GIPC3 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GIPC3 MUTATED                                           0     5
  GIPC3 WILD-TYPE                                         1   352
D788V11, multiclass
                                           clus
vv                                          GIPC3 MUTATED GIPC3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V12, binary
                 cls
clus                0   1
  GIPC3 MUTATED     0   6
  GIPC3 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      0    6
  GIPC3 WILD-TYPE   10  392
                        clus
vv                       GIPC3 MUTATED GIPC3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(789) Variable = EFHA2 MUTATION ANALYSIS
D789V1, survival
                 sevent
clus2               0   1
  EFHA2 MUTATED    11   4
  EFHA2 WILD-TYPE 327 212
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             15             539 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
              4             212 
$`EFHA2 MUTATED`
TCGA-L5-A8NM TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8081 
        7.76        19.56        34.68        35.84        14.43        32.25 
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 TCGA-CG-4438 TCGA-CG-5726 TCGA-D7-A6EY 
        1.12        28.14        12.43        54.08        28.96        11.44 
TCGA-HU-A4GN TCGA-HU-A4H8 TCGA-R5-A7ZI 
       29.98        14.07        74.53 

$`EFHA2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  EFHA2 MUTATED EFHA2 WILD-TYPE 
           1.12            0.00 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
          74.53          122.30 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
          28.14           13.48 
[1] "1.1 - 74.5 (28.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D789V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHA2 MUTATED         0        1        2        1         3         2
  EFHA2 WILD-TYPE      10       19       44       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHA2 MUTATED           1          0          1          2        2         0
  EFHA2 WILD-TYPE        28         84         61         37       41         4
D789V3, multiclass
            clus
vv           EFHA2 MUTATED EFHA2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFHA2 MUTATED       2   3   4   6
  EFHA2 WILD-TYPE    52 132 257  96
D789V4, multiclass
       clus
vv      EFHA2 MUTATED EFHA2 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFHA2 MUTATED     6   5   1   3
  EFHA2 WILD-TYPE 189 168  88  82
D789V5, multiclass
    clus
vv   EFHA2 MUTATED EFHA2 WILD-TYPE
  N0             6             189
  N1             5             168
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V6, binary
                 cls
clus                0   1
  EFHA2 MUTATED    14   1
  EFHA2 WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED     14    1
  EFHA2 WILD-TYPE  468   37
   clus
vv  EFHA2 MUTATED EFHA2 WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D789V7, binary
                 cls
clus                0   1
  EFHA2 MUTATED     7   8
  EFHA2 WILD-TYPE 165 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED      7    8
  EFHA2 WILD-TYPE  165  398
        clus
vv       EFHA2 MUTATED EFHA2 WILD-TYPE
  FEMALE             7             165
  MALE               8             398
[1] 2 2
[1] FALSE
D789V8, binary
                 cls
clus                0   1
  EFHA2 MUTATED    13   0
  EFHA2 WILD-TYPE 403 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED     13    0
  EFHA2 WILD-TYPE  403  102
     clus
vv    EFHA2 MUTATED EFHA2 WILD-TYPE
  NO             13             403
  YES             0             102
[1] 2 2
[1] FALSE
D789V9, continuous
D789V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHA2 MUTATED       3                         0
  EFHA2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHA2 MUTATED                                           0    10
  EFHA2 WILD-TYPE                                         1   347
D789V11, multiclass
                                           clus
vv                                          EFHA2 MUTATED EFHA2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V12, binary
                 cls
clus                0   1
  EFHA2 MUTATED     1  11
  EFHA2 WILD-TYPE   9 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED      1   11
  EFHA2 WILD-TYPE    9  387
                        clus
vv                       EFHA2 MUTATED EFHA2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(790) Variable = PSD3 MUTATION ANALYSIS
D790V1, survival
                sevent
clus2              0   1
  PSD3 MUTATED    15   4
  PSD3 WILD-TYPE 323 212
  PSD3 MUTATED PSD3 WILD-TYPE 
            19            535 
  PSD3 MUTATED PSD3 WILD-TYPE 
             4            212 
$`PSD3 MUTATED`
TCGA-L5-A4OI TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8368 
       19.99        20.38         6.97        44.94        29.59         4.31 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG 
        3.72         1.12        28.14        31.96        12.43         6.58 
TCGA-CG-4305 TCGA-D7-6525 TCGA-F1-A448 TCGA-FP-7735 TCGA-HU-A4GN TCGA-HU-A4GU 
       15.95        13.35        21.27         3.48        29.98         6.58 
TCGA-VQ-A8P2 
       38.14 

$`PSD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79         7.36        25.05         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PSD3 MUTATED PSD3 WILD-TYPE 
          1.12           0.00 
  PSD3 MUTATED PSD3 WILD-TYPE 
         44.94         122.30 
  PSD3 MUTATED PSD3 WILD-TYPE 
         15.95          13.55 
[1] "1.1 - 44.9 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D790V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSD3 MUTATED         0        0        4        2         4         2
  PSD3 WILD-TYPE      10       20       42       29        80        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSD3 MUTATED           0          3          1          3        1         0
  PSD3 WILD-TYPE        29         81         61         36       42         4
D790V3, multiclass
            clus
vv           PSD3 MUTATED PSD3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              4             42
  STAGE II              2             29
  STAGE IIA             4             80
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PSD3 MUTATED       0   7   8   5
  PSD3 WILD-TYPE    54 128 253  97
D790V4, multiclass
       clus
vv      PSD3 MUTATED PSD3 WILD-TYPE
  T0+T1            0             54
  T2               7            128
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PSD3 MUTATED     9   5   3   3
  PSD3 WILD-TYPE 186 168  86  82
D790V5, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  N0            9            186
  N1            5            168
  N2            3             86
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V6, binary
                cls
clus               0   1
  PSD3 MUTATED    15   1
  PSD3 WILD-TYPE 467  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED     15    1
  PSD3 WILD-TYPE  467   37
   clus
vv  PSD3 MUTATED PSD3 WILD-TYPE
  0           15            467
  1            1             37
[1] 2 2
[1] FALSE
D790V7, binary
                cls
clus               0   1
  PSD3 MUTATED     4  16
  PSD3 WILD-TYPE 168 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      4   16
  PSD3 WILD-TYPE  168  390
        clus
vv       PSD3 MUTATED PSD3 WILD-TYPE
  FEMALE            4            168
  MALE             16            390
[1] 2 2
[1] FALSE
D790V8, binary
                cls
clus               0   1
  PSD3 MUTATED    17   2
  PSD3 WILD-TYPE 399 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED     17    2
  PSD3 WILD-TYPE  399  100
     clus
vv    PSD3 MUTATED PSD3 WILD-TYPE
  NO            17            399
  YES            2            100
[1] 2 2
[1] FALSE
D790V9, continuous
D790V10, continuous
[1] "Remove cluster labels:" "PSD3 MUTATED"          
clus
  PSD3 MUTATED PSD3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" "PSD3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PSD3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PSD3 MUTATED       5                         1
  PSD3 WILD-TYPE   128                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSD3 MUTATED                                           0    12
  PSD3 WILD-TYPE                                         1   345
D790V11, multiclass
                                           clus
vv                                          PSD3 MUTATED PSD3 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V12, binary
                cls
clus               0   1
  PSD3 MUTATED     1  15
  PSD3 WILD-TYPE   9 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      1   15
  PSD3 WILD-TYPE    9  383
                        clus
vv                       PSD3 MUTATED PSD3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(791) Variable = HSPB8 MUTATION ANALYSIS
D791V1, survival
                 sevent
clus2               0   1
  HSPB8 MUTATED     6   0
  HSPB8 WILD-TYPE 332 216
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             548 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              0             216 
$`HSPB8 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-VQ-A8P2 
       34.68        35.84        29.59        30.51         6.51        38.14 

$`HSPB8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  HSPB8 MUTATED HSPB8 WILD-TYPE 
           6.51            0.00 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
          38.14          122.30 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
         32.595          13.510 
[1] "6.5 - 38.1 (32.6)"  "0.0 - 122.3 (13.5)"
[1] "hr="     "9200000"
D791V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSPB8 MUTATED         0        0        1        0         2         1
  HSPB8 WILD-TYPE      10       20       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HSPB8 MUTATED           0          1          0          1        0         0
  HSPB8 WILD-TYPE        29         83         62         38       43         4
D791V3, multiclass
            clus
vv           HSPB8 MUTATED HSPB8 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HSPB8 MUTATED       0   1   2   3
  HSPB8 WILD-TYPE    54 134 259  99
D791V4, multiclass
       clus
vv      HSPB8 MUTATED HSPB8 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HSPB8 MUTATED     4   1   0   1
  HSPB8 WILD-TYPE 191 172  89  84
D791V5, multiclass
    clus
vv   HSPB8 MUTATED HSPB8 WILD-TYPE
  N0             4             191
  N1             1             172
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V6, binary
                 cls
clus                0   1
  HSPB8 MUTATED     6   0
  HSPB8 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      6    0
  HSPB8 WILD-TYPE  476   38
   clus
vv  HSPB8 MUTATED HSPB8 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D791V7, binary
                 cls
clus                0   1
  HSPB8 MUTATED     5   1
  HSPB8 WILD-TYPE 167 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      5    1
  HSPB8 WILD-TYPE  167  405
        clus
vv       HSPB8 MUTATED HSPB8 WILD-TYPE
  FEMALE             5             167
  MALE               1             405
[1] 2 2
[1] FALSE
D791V8, binary
                 cls
clus                0   1
  HSPB8 MUTATED     4   2
  HSPB8 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      4    2
  HSPB8 WILD-TYPE  412  100
     clus
vv    HSPB8 MUTATED HSPB8 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D791V9, continuous
D791V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HSPB8 MUTATED       1                         0
  HSPB8 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPB8 MUTATED                                           0     4
  HSPB8 WILD-TYPE                                         1   353
D791V11, multiclass
                                           clus
vv                                          HSPB8 MUTATED HSPB8 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V12, binary
                 cls
clus                0   1
  HSPB8 MUTATED     0   4
  HSPB8 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      0    4
  HSPB8 WILD-TYPE   10  394
                        clus
vv                       HSPB8 MUTATED HSPB8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(792) Variable = CASKIN2 MUTATION ANALYSIS
D792V1, survival
                   sevent
clus2                 0   1
  CASKIN2 MUTATED     9   5
  CASKIN2 WILD-TYPE 329 211
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               14               540 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
                5               211 
$`CASKIN2 MUTATED`
TCGA-Z6-A8JD TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8591 TCGA-CG-4441 TCGA-CG-5718 
        3.42        44.94        14.43        28.14        14.01        36.00 
TCGA-CG-5725 TCGA-D7-5578 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-IN-AB1X 
       15.02        12.66        30.51        22.32        22.68        13.51 
TCGA-VQ-A8PM TCGA-VQ-AA6J 
        1.87        27.55 

$`CASKIN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19        17.85        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 

  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
             1.87              0.00 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
            44.94            122.30 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
           18.670            13.445 
[1] "1.9 - 44.9 (18.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D792V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASKIN2 MUTATED         1        0        1        1         2         3
  CASKIN2 WILD-TYPE       9       20       45       30        82        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASKIN2 MUTATED           1          2          1          2        1
  CASKIN2 WILD-TYPE        28         82         61         37       42
                   vv
clus                STAGE IVA
  CASKIN2 MUTATED           0
  CASKIN2 WILD-TYPE         4
D792V3, multiclass
            clus
vv           CASKIN2 MUTATED CASKIN2 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CASKIN2 MUTATED       1   3   6   6
  CASKIN2 WILD-TYPE    53 132 255  96
D792V4, multiclass
       clus
vv      CASKIN2 MUTATED CASKIN2 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  6               255
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CASKIN2 MUTATED     5   4   3   3
  CASKIN2 WILD-TYPE 190 169  86  82
D792V5, multiclass
    clus
vv   CASKIN2 MUTATED CASKIN2 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               3                86
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V6, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED    14   0
  CASKIN2 WILD-TYPE 468  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED     14    0
  CASKIN2 WILD-TYPE  468   38
   clus
vv  CASKIN2 MUTATED CASKIN2 WILD-TYPE
  0              14               468
  1               0                38
[1] 2 2
[1] FALSE
D792V7, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED     7   9
  CASKIN2 WILD-TYPE 165 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED      7    9
  CASKIN2 WILD-TYPE  165  397
        clus
vv       CASKIN2 MUTATED CASKIN2 WILD-TYPE
  FEMALE               7               165
  MALE                 9               397
[1] 2 2
[1] FALSE
D792V8, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED    13   1
  CASKIN2 WILD-TYPE 403 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED     13    1
  CASKIN2 WILD-TYPE  403  101
     clus
vv    CASKIN2 MUTATED CASKIN2 WILD-TYPE
  NO               13               403
  YES               1               101
[1] 2 2
[1] FALSE
D792V9, continuous
[1] "Remove cluster labels:" "CASKIN2 MUTATED"       
clus
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
       TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-A8JE 
"CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" "CASKIN2 WILD-TYPE" 
D792V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CASKIN2 MUTATED       2                         2
  CASKIN2 WILD-TYPE   131                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASKIN2 MUTATED                                           0     8
  CASKIN2 WILD-TYPE                                         1   349
D792V11, multiclass
                                           clus
vv                                          CASKIN2 MUTATED CASKIN2 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V12, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED     0  10
  CASKIN2 WILD-TYPE  10 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED      0   10
  CASKIN2 WILD-TYPE   10  388
                        clus
vv                       CASKIN2 MUTATED CASKIN2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(793) Variable = IFI27L2 MUTATION ANALYSIS
D793V1, survival
                   sevent
clus2                 0   1
  IFI27L2 MUTATED     1   1
  IFI27L2 WILD-TYPE 337 215
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                2               552 
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                1               215 
$`IFI27L2 MUTATED`
TCGA-IG-A3Y9 TCGA-R6-A6XG 
        0.85        38.40 

$`IFI27L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
             0.85              0.00 
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
             38.4             122.3 
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
           19.625            13.565 
[1] "0.8 - 38.4 (19.6)"  "0.0 - 122.3 (13.6)"
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
D793V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFI27L2 MUTATED         0        0        0        0         0         0
  IFI27L2 WILD-TYPE      10       20       46       31        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFI27L2 MUTATED           0          1          0          0        0
  IFI27L2 WILD-TYPE        29         83         62         39       43
                   vv
clus                STAGE IVA
  IFI27L2 MUTATED           0
  IFI27L2 WILD-TYPE         4
D793V3, multiclass
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
clus
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                1               534 
       TCGA-IC-A6RF        TCGA-JY-A6FB        TCGA-JY-A938        TCGA-L5-A43I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43J        TCGA-L5-A4OE        TCGA-L5-A4OG        TCGA-L5-A4OI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A88T        TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-S8-A6BV        TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-F1-6177        TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-MX-A663        TCGA-2H-A9GF        TCGA-2H-A9GG        TCGA-2H-A9GH 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GI        TCGA-2H-A9GJ        TCGA-2H-A9GK        TCGA-2H-A9GL 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GM        TCGA-2H-A9GN        TCGA-2H-A9GO        TCGA-2H-A9GQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GR        TCGA-IC-A6RE        TCGA-IG-A3I8        TCGA-IG-A3QL 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3YA        TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A4P3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A4QS        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A51D 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A5B8        TCGA-IG-A5S3        TCGA-IG-A625        TCGA-IG-A6QS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-IG-A97I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6F8        TCGA-JY-A6FA        TCGA-JY-A6FD        TCGA-JY-A6FE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-JY-A939        TCGA-JY-A93C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A93D        TCGA-JY-A93E        TCGA-JY-A93F        TCGA-KH-A6WC 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OF        TCGA-L5-A4OH 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OJ        TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OR        TCGA-L5-A4OS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A88W        TCGA-L5-A88Z 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NH 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NI        TCGA-L5-A8NJ        TCGA-L5-A8NK        TCGA-L5-A8NL 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NM        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NU        TCGA-L5-A8NV        TCGA-L5-A8NW 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L7-A6VZ        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-LN-A8I1        TCGA-LN-A9FO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A9FP        TCGA-LN-A9FQ        TCGA-LN-A9FR        TCGA-M9-A5M8 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-Q9-A6FW        TCGA-R6-A8W5        TCGA-RE-A7BO        TCGA-S8-A6BW 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-VR-A8EO        TCGA-VR-A8EP 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE        TCGA-Z6-A9VB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-Z6-AAPN        TCGA-ZR-A9CJ        TCGA-B7-5816        TCGA-B7-5818 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-B7-A5TI        TCGA-B7-A5TJ        TCGA-B7-A5TK        TCGA-B7-A5TN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4253        TCGA-BR-4255 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6520 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV        TCGA-D7-A6EX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0        TCGA-D7-A6F2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A        TCGA-D7-A74B 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874        TCGA-F1-6875 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-A4BF        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-7136        TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8243 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RJ        TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RP        TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A7NT        TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IP-7968        TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666        TCGA-R5-A7O7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A7ZR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS        TCGA-RD-A7BT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
                   vv
clus                T0+T1  T2  T3  T4
  IFI27L2 MUTATED       0   0   0   1
  IFI27L2 WILD-TYPE    54 135 261 101
D793V4, multiclass
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
clus
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                1               551 
       TCGA-IC-A6RF        TCGA-JY-A6FB        TCGA-JY-A938        TCGA-L5-A43I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43J        TCGA-L5-A43M        TCGA-L5-A4OE        TCGA-L5-A4OG 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-S8-A6BV        TCGA-CG-4444 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-5716 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663        TCGA-2H-A9GF 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GG        TCGA-2H-A9GH        TCGA-2H-A9GI        TCGA-2H-A9GJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GK        TCGA-2H-A9GL        TCGA-2H-A9GM        TCGA-2H-A9GN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GO        TCGA-2H-A9GQ        TCGA-2H-A9GR        TCGA-IC-A6RE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-IG-A4QT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A50L        TCGA-IG-A51D        TCGA-IG-A5B8        TCGA-IG-A5S3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A625        TCGA-IG-A6QS        TCGA-IG-A7DP        TCGA-IG-A8O2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A97H        TCGA-IG-A97I        TCGA-JY-A6F8        TCGA-JY-A6FA 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6FD        TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A939        TCGA-JY-A93C        TCGA-JY-A93D        TCGA-JY-A93E 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A93F        TCGA-KH-A6WC        TCGA-L5-A43E        TCGA-L5-A43H 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OF        TCGA-L5-A4OH        TCGA-L5-A4OJ        TCGA-L5-A4OM 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OR        TCGA-L5-A4OS        TCGA-L5-A4OT        TCGA-L5-A4OU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A88W        TCGA-L5-A88Z        TCGA-L5-A891        TCGA-L5-A893 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NH        TCGA-L5-A8NI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NJ        TCGA-L5-A8NK        TCGA-L5-A8NL        TCGA-L5-A8NM 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NU        TCGA-L5-A8NV        TCGA-L5-A8NW        TCGA-L7-A6VZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M        TCGA-LN-A49N 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A49X 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2        TCGA-LN-A4A3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6        TCGA-LN-A4A8 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR        TCGA-LN-A5U5 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-LN-A8I1        TCGA-LN-A9FO        TCGA-LN-A9FP 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A9FQ        TCGA-LN-A9FR        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-RE-A7BO        TCGA-S8-A6BW        TCGA-V5-A7RB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-VR-A8EO        TCGA-VR-A8EP 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR        TCGA-XP-A8T6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-Z6-A9VB        TCGA-Z6-AAPN        TCGA-ZR-A9CJ        TCGA-B7-5816 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-B7-5818        TCGA-B7-A5TI        TCGA-B7-A5TJ        TCGA-B7-A5TK 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-B7-A5TN        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4201 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4357 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368        TCGA-BR-4371 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798        TCGA-CD-5799 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A6EV        TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A6F0        TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A74A        TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462        TCGA-IN-8663 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RI        TCGA-IN-A6RJ        TCGA-IN-A6RL        TCGA-IN-A6RN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RO        TCGA-IN-A6RP        TCGA-IN-A6RR        TCGA-IN-A6RS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A7NR        TCGA-IN-A7NT        TCGA-IN-A7NU        TCGA-IN-AB1V 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-AB1X        TCGA-IP-7968        TCGA-KB-A6F5        TCGA-KB-A6F7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-KB-A93J        TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R5-A7O7        TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R5-A7ZR        TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A7BT        TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8MW        TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8N4        TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-SW-A7EA        TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8DU        TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8E7        TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8PK        TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A91U        TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA64        TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6B        TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6J        TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
                   vv
clus                 N0  N1  N2  N3
  IFI27L2 MUTATED     1   1   0   0
  IFI27L2 WILD-TYPE 194 172  89  85
D793V5, multiclass
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
clus
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                2               540 
       TCGA-IC-A6RF        TCGA-JY-A6FB        TCGA-JY-A938        TCGA-L5-A43I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43J        TCGA-L5-A43M        TCGA-L5-A4OE        TCGA-L5-A4OG 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-S8-A6BV        TCGA-CG-4444 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-5716 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663        TCGA-2H-A9GF 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GG        TCGA-2H-A9GH        TCGA-2H-A9GI        TCGA-2H-A9GJ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GK        TCGA-2H-A9GL        TCGA-2H-A9GM        TCGA-2H-A9GN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-2H-A9GO        TCGA-2H-A9GQ        TCGA-2H-A9GR        TCGA-IC-A6RE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QS        TCGA-IG-A4QT 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A50L        TCGA-IG-A51D        TCGA-IG-A5B8        TCGA-IG-A5S3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A625        TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6F8        TCGA-JY-A6FA        TCGA-JY-A6FD        TCGA-JY-A6FE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-JY-A939        TCGA-JY-A93C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A93D        TCGA-JY-A93E        TCGA-JY-A93F        TCGA-KH-A6WC 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OF        TCGA-L5-A4OH 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OJ        TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OR        TCGA-L5-A4OS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A88W        TCGA-L5-A88Z 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A891        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NH        TCGA-L5-A8NI        TCGA-L5-A8NJ        TCGA-L5-A8NK 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NL        TCGA-L5-A8NM        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NU        TCGA-L5-A8NV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NW        TCGA-L7-A6VZ        TCGA-LN-A49K        TCGA-LN-A49L 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-LN-A8I1 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A9FO        TCGA-LN-A9FP        TCGA-LN-A9FQ        TCGA-LN-A9FR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A8W5        TCGA-RE-A7BO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-S8-A6BW        TCGA-V5-A7RB        TCGA-V5-A7RE        TCGA-V5-AASV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE        TCGA-Z6-A9VB        TCGA-Z6-AAPN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-ZR-A9CJ        TCGA-B7-5816        TCGA-B7-5818        TCGA-B7-A5TI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188        TCGA-BR-4191 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4267 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8363 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4PD 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-BR-A4QM        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CD-A4MH        TCGA-CD-A4MI        TCGA-CD-A4MJ        TCGA-CG-4300 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4449 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5717 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM        TCGA-HF-7132 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-HF-A5NB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-7808        TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RJ        TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A6RP        TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IN-A7NT        TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IP-7968        TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-R5-A7O7        TCGA-R5-A7ZE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A804        TCGA-R5-A805 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A7BS        TCGA-RD-A7BT        TCGA-RD-A7BW        TCGA-RD-A7C1 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8MV        TCGA-RD-A8MW        TCGA-RD-A8N0        TCGA-RD-A8N1 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8N2        TCGA-RD-A8N4        TCGA-RD-A8N5        TCGA-RD-A8N6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-RD-A8N9        TCGA-SW-A7EA        TCGA-SW-A7EB        TCGA-VQ-A8DL 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8DT        TCGA-VQ-A8DU        TCGA-VQ-A8DV        TCGA-VQ-A8DZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8E2        TCGA-VQ-A8E7        TCGA-VQ-A8P2        TCGA-VQ-A8P3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A8PE        TCGA-VQ-A8PK        TCGA-VQ-A8PM        TCGA-VQ-A8PQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A91Q        TCGA-VQ-A91U        TCGA-VQ-A91V        TCGA-VQ-A92D 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-A94T        TCGA-VQ-AA64        TCGA-VQ-AA68        TCGA-VQ-AA69 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6A        TCGA-VQ-AA6B        TCGA-VQ-AA6F        TCGA-VQ-AA6G 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VQ-AA6I        TCGA-VQ-AA6J        TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
D793V6, binary
                   cls
clus                  0   1
  IFI27L2 MUTATED     2   0
  IFI27L2 WILD-TYPE 480  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IFI27L2 MUTATED      2    0
  IFI27L2 WILD-TYPE  480   38
   clus
vv  IFI27L2 MUTATED IFI27L2 WILD-TYPE
  0               2               480
  1               0                38
[1] 2 2
[1] FALSE
D793V7, binary
                   cls
clus                  0   1
  IFI27L2 MUTATED     1   2
  IFI27L2 WILD-TYPE 171 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IFI27L2 MUTATED      1    2
  IFI27L2 WILD-TYPE  171  404
        clus
vv       IFI27L2 MUTATED IFI27L2 WILD-TYPE
  FEMALE               1               171
  MALE                 2               404
[1] 2 2
[1] FALSE
D793V8, binary
                   cls
clus                  0   1
  IFI27L2 MUTATED     2   0
  IFI27L2 WILD-TYPE 414 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IFI27L2 MUTATED      2    0
  IFI27L2 WILD-TYPE  414  102
     clus
vv    IFI27L2 MUTATED IFI27L2 WILD-TYPE
  NO                2               414
  YES               0               102
[1] 2 2
[1] FALSE
D793V9, continuous
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
clus
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
D793V10, continuous
[1] "Remove cluster labels:" "IFI27L2 MUTATED"       
clus
  IFI27L2 MUTATED IFI27L2 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" "IFI27L2 WILD-TYPE" 
       TCGA-Z6-AAPN 
"IFI27L2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  IFI27L2 MUTATED       0                         0
  IFI27L2 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFI27L2 MUTATED                                           0     3
  IFI27L2 WILD-TYPE                                         1   354
D793V11, multiclass
                                           clus
vv                                          IFI27L2 MUTATED IFI27L2 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V12, binary
                   cls
clus                  0   1
  IFI27L2 MUTATED     0   3
  IFI27L2 WILD-TYPE  10 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IFI27L2 MUTATED      0    3
  IFI27L2 WILD-TYPE   10  395
                        clus
vv                       IFI27L2 MUTATED IFI27L2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(794) Variable = PKN3 MUTATION ANALYSIS
D794V1, survival
                sevent
clus2              0   1
  PKN3 MUTATED     9   7
  PKN3 WILD-TYPE 329 209
  PKN3 MUTATED PKN3 WILD-TYPE 
            16            538 
  PKN3 MUTATED PKN3 WILD-TYPE 
             7            209 
$`PKN3 MUTATED`
TCGA-L5-A43J TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8363 
        4.31        26.70         6.97        32.78         6.18         0.26 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GQ 
        1.12        16.14         6.02        28.96        22.32         0.10 
TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-VQ-A8P2 
       19.73        18.21        74.53        38.14 

$`PKN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       63.62        36.95         3.72        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PKN3 MUTATED PKN3 WILD-TYPE 
           0.1            0.0 
  PKN3 MUTATED PKN3 WILD-TYPE 
         74.53         122.30 
  PKN3 MUTATED PKN3 WILD-TYPE 
        17.175         13.530 
[1] "0.1 - 74.5 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D794V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKN3 MUTATED         0        1        1        0         3         3
  PKN3 WILD-TYPE      10       19       45       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKN3 MUTATED           0          4          1          1        2         0
  PKN3 WILD-TYPE        29         80         61         38       41         4
D794V3, multiclass
            clus
vv           PKN3 MUTATED PKN3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PKN3 MUTATED       1   1   8   6
  PKN3 WILD-TYPE    53 134 253  96
D794V4, multiclass
       clus
vv      PKN3 MUTATED PKN3 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               8            253
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PKN3 MUTATED     8   5   3   1
  PKN3 WILD-TYPE 187 168  86  84
D794V5, multiclass
    clus
vv   PKN3 MUTATED PKN3 WILD-TYPE
  N0            8            187
  N1            5            168
  N2            3             86
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V6, binary
                cls
clus               0   1
  PKN3 MUTATED    14   1
  PKN3 WILD-TYPE 468  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN3 MUTATED     14    1
  PKN3 WILD-TYPE  468   37
   clus
vv  PKN3 MUTATED PKN3 WILD-TYPE
  0           14            468
  1            1             37
[1] 2 2
[1] FALSE
D794V7, binary
                cls
clus               0   1
  PKN3 MUTATED    10   7
  PKN3 WILD-TYPE 162 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN3 MUTATED     10    7
  PKN3 WILD-TYPE  162  399
        clus
vv       PKN3 MUTATED PKN3 WILD-TYPE
  FEMALE           10            162
  MALE              7            399
[1] 2 2
[1] FALSE
D794V8, binary
                cls
clus               0   1
  PKN3 MUTATED    13   1
  PKN3 WILD-TYPE 403 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN3 MUTATED     13    1
  PKN3 WILD-TYPE  403  101
     clus
vv    PKN3 MUTATED PKN3 WILD-TYPE
  NO            13            403
  YES            1            101
[1] 2 2
[1] FALSE
D794V9, continuous
D794V10, continuous
[1] "Remove cluster labels:" "PKN3 MUTATED"          
clus
  PKN3 MUTATED PKN3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" "PKN3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PKN3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKN3 MUTATED       2                         0
  PKN3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKN3 MUTATED                                           0    13
  PKN3 WILD-TYPE                                         1   344
D794V11, multiclass
                                           clus
vv                                          PKN3 MUTATED PKN3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V12, binary
                cls
clus               0   1
  PKN3 MUTATED     1  12
  PKN3 WILD-TYPE   9 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN3 MUTATED      1   12
  PKN3 WILD-TYPE    9  386
                        clus
vv                       PKN3 MUTATED PKN3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(795) Variable = GPR160 MUTATION ANALYSIS
D795V1, survival
                  sevent
clus2                0   1
  GPR160 MUTATED     4   2
  GPR160 WILD-TYPE 334 214
  GPR160 MUTATED GPR160 WILD-TYPE 
               6              548 
  GPR160 MUTATED GPR160 WILD-TYPE 
               2              214 
$`GPR160 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GX 
        6.97        34.68        11.44        31.96        65.10        20.25 

$`GPR160 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GPR160 MUTATED GPR160 WILD-TYPE 
            6.97             0.00 
  GPR160 MUTATED GPR160 WILD-TYPE 
            65.1            122.3 
  GPR160 MUTATED GPR160 WILD-TYPE 
          26.105           13.530 
[1] "7.0 - 65.1 (26.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D795V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR160 MUTATED         0        0        1        0         1         1
  GPR160 WILD-TYPE      10       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR160 MUTATED           0          1          0          1        1
  GPR160 WILD-TYPE        29         83         62         38       42
                  vv
clus               STAGE IVA
  GPR160 MUTATED           0
  GPR160 WILD-TYPE         4
D795V3, multiclass
            clus
vv           GPR160 MUTATED GPR160 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR160 MUTATED       1   2   2   2
  GPR160 WILD-TYPE    53 133 259 100
D795V4, multiclass
       clus
vv      GPR160 MUTATED GPR160 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 2              259
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR160 MUTATED     2   1   3   0
  GPR160 WILD-TYPE 193 172  86  85
D795V5, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  N0              2              193
  N1              1              172
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V6, binary
                  cls
clus                 0   1
  GPR160 MUTATED     6   1
  GPR160 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      6    1
  GPR160 WILD-TYPE  476   37
   clus
vv  GPR160 MUTATED GPR160 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D795V7, binary
                  cls
clus                 0   1
  GPR160 MUTATED     6   2
  GPR160 WILD-TYPE 166 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      6    2
  GPR160 WILD-TYPE  166  404
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  FEMALE              6              166
  MALE                2              404
[1] 2 2
[1] FALSE
D795V8, binary
                  cls
clus                 0   1
  GPR160 MUTATED     5   0
  GPR160 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      5    0
  GPR160 WILD-TYPE  411  102
     clus
vv    GPR160 MUTATED GPR160 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D795V9, continuous
D795V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR160 MUTATED       2                         0
  GPR160 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR160 MUTATED                                           0     5
  GPR160 WILD-TYPE                                         1   352
D795V11, multiclass
                                           clus
vv                                          GPR160 MUTATED GPR160 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V12, binary
                  cls
clus                 0   1
  GPR160 MUTATED     0   7
  GPR160 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      0    7
  GPR160 WILD-TYPE   10  391
                        clus
vv                       GPR160 MUTATED GPR160 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(796) Variable = OTUD7B MUTATION ANALYSIS
D796V1, survival
                  sevent
clus2                0   1
  OTUD7B MUTATED    11   5
  OTUD7B WILD-TYPE 327 211
  OTUD7B MUTATED OTUD7B WILD-TYPE 
              16              538 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               5              211 
$`OTUD7B MUTATED`
TCGA-IG-A3YA TCGA-JY-A6F8 TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L7-A6VZ 
       20.78       122.10        13.55         7.76         8.71        10.36 
TCGA-V5-A7RC TCGA-BR-4255 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-4306 
        3.42         4.08         6.61        34.68        29.59         1.02 
TCGA-HF-7132 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8P2 
       77.29         6.51        29.00        38.14 

$`OTUD7B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.22         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OTUD7B MUTATED OTUD7B WILD-TYPE 
            1.02             0.00 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
           122.1            122.3 
  OTUD7B MUTATED OTUD7B WILD-TYPE 
          11.955           13.630 
[1] "1.0 - 122.1 (12.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D796V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OTUD7B MUTATED         1        0        0        1         3         2
  OTUD7B WILD-TYPE       9       20       46       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OTUD7B MUTATED           2          3          0          2        2
  OTUD7B WILD-TYPE        27         81         62         37       41
                  vv
clus               STAGE IVA
  OTUD7B MUTATED           0
  OTUD7B WILD-TYPE         4
D796V3, multiclass
            clus
vv           OTUD7B MUTATED OTUD7B WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OTUD7B MUTATED       1   3   7   5
  OTUD7B WILD-TYPE    53 132 254  97
D796V4, multiclass
       clus
vv      OTUD7B MUTATED OTUD7B WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 7              254
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OTUD7B MUTATED     6   6   2   2
  OTUD7B WILD-TYPE 189 167  87  83
D796V5, multiclass
    clus
vv   OTUD7B MUTATED OTUD7B WILD-TYPE
  N0              6              189
  N1              6              167
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V6, binary
                  cls
clus                 0   1
  OTUD7B MUTATED    14   1
  OTUD7B WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED     14    1
  OTUD7B WILD-TYPE  468   37
   clus
vv  OTUD7B MUTATED OTUD7B WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D796V7, binary
                  cls
clus                 0   1
  OTUD7B MUTATED    10   7
  OTUD7B WILD-TYPE 162 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED     10    7
  OTUD7B WILD-TYPE  162  399
        clus
vv       OTUD7B MUTATED OTUD7B WILD-TYPE
  FEMALE             10              162
  MALE                7              399
[1] 2 2
[1] FALSE
D796V8, binary
                  cls
clus                 0   1
  OTUD7B MUTATED     9   4
  OTUD7B WILD-TYPE 407  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      9    4
  OTUD7B WILD-TYPE  407   98
     clus
vv    OTUD7B MUTATED OTUD7B WILD-TYPE
  NO               9              407
  YES              4               98
[1] 2 2
[1] FALSE
D796V9, continuous
[1] "Remove cluster labels:" "OTUD7B MUTATED"        
clus
  OTUD7B MUTATED OTUD7B WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YB 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OTUD7B WILD-TYPE" "OTUD7B WILD-TYPE" 
D796V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OTUD7B MUTATED       2                         1
  OTUD7B WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OTUD7B MUTATED                                           0    11
  OTUD7B WILD-TYPE                                         1   346
D796V11, multiclass
                                           clus
vv                                          OTUD7B MUTATED OTUD7B WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V12, binary
                  cls
clus                 0   1
  OTUD7B MUTATED     0  10
  OTUD7B WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OTUD7B MUTATED      0   10
  OTUD7B WILD-TYPE   10  388
                        clus
vv                       OTUD7B MUTATED OTUD7B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(797) Variable = ICAM4 MUTATION ANALYSIS
D797V1, survival
                 sevent
clus2               0   1
  ICAM4 MUTATED     4   3
  ICAM4 WILD-TYPE 334 213
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              7             547 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              3             213 
$`ICAM4 MUTATED`
TCGA-CG-4306 TCGA-CG-5723 TCGA-EQ-5647 TCGA-HU-A4GF TCGA-HU-A4GQ TCGA-HU-A4H3 
        1.02       105.07         0.62        25.81         0.10        29.00 
TCGA-MX-A5UJ 
       19.73 

$`ICAM4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ICAM4 MUTATED ICAM4 WILD-TYPE 
            0.1             0.0 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
         105.07          122.30 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
          19.73           13.55 
[1] "0.1 - 105.1 (19.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D797V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ICAM4 MUTATED         0        0        1        1         1         0
  ICAM4 WILD-TYPE      10       20       45       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICAM4 MUTATED           0          1          0          2        2         0
  ICAM4 WILD-TYPE        29         83         62         37       41         4
D797V3, multiclass
            clus
vv           ICAM4 MUTATED ICAM4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ICAM4 MUTATED       0   2   3   3
  ICAM4 WILD-TYPE    54 133 258  99
D797V4, multiclass
       clus
vv      ICAM4 MUTATED ICAM4 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ICAM4 MUTATED     2   1   3   2
  ICAM4 WILD-TYPE 193 172  86  83
D797V5, multiclass
    clus
vv   ICAM4 MUTATED ICAM4 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V6, binary
                 cls
clus                0   1
  ICAM4 MUTATED     6   2
  ICAM4 WILD-TYPE 476  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      6    2
  ICAM4 WILD-TYPE  476   36
   clus
vv  ICAM4 MUTATED ICAM4 WILD-TYPE
  0             6             476
  1             2              36
[1] 2 2
[1] FALSE
D797V7, binary
                 cls
clus                0   1
  ICAM4 MUTATED     3   5
  ICAM4 WILD-TYPE 169 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      3    5
  ICAM4 WILD-TYPE  169  401
        clus
vv       ICAM4 MUTATED ICAM4 WILD-TYPE
  FEMALE             3             169
  MALE               5             401
[1] 2 2
[1] FALSE
D797V8, binary
                 cls
clus                0   1
  ICAM4 MUTATED     5   0
  ICAM4 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      5    0
  ICAM4 WILD-TYPE  411  102
     clus
vv    ICAM4 MUTATED ICAM4 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D797V9, continuous
D797V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ICAM4 MUTATED       3                         0
  ICAM4 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ICAM4 MUTATED                                           0     2
  ICAM4 WILD-TYPE                                         1   355
D797V11, multiclass
                                           clus
vv                                          ICAM4 MUTATED ICAM4 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V12, binary
                 cls
clus                0   1
  ICAM4 MUTATED     0   5
  ICAM4 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      0    5
  ICAM4 WILD-TYPE   10  393
                        clus
vv                       ICAM4 MUTATED ICAM4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(798) Variable = ZNF174 MUTATION ANALYSIS
D798V1, survival
                  sevent
clus2                0   1
  ZNF174 MUTATED     7   0
  ZNF174 WILD-TYPE 331 216
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               7              547 
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               0              216 
$`ZNF174 MUTATED`
TCGA-L7-A6VZ TCGA-LN-A49W TCGA-BR-6452 TCGA-HF-7132 TCGA-HU-A4GN TCGA-HU-A4GX 
       10.36        13.25        34.68        77.29        29.98        20.25 
TCGA-MX-A5UJ 
       19.73 

$`ZNF174 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZNF174 MUTATED ZNF174 WILD-TYPE 
           10.36             0.00 
  ZNF174 MUTATED ZNF174 WILD-TYPE 
           77.29           122.30 
  ZNF174 MUTATED ZNF174 WILD-TYPE 
           20.25            13.51 
[1] "10.4 - 77.3 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9200000"
D798V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF174 MUTATED         0        0        0        1         2         0
  ZNF174 WILD-TYPE      10       20       46       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF174 MUTATED           1          1          0          2        1
  ZNF174 WILD-TYPE        28         83         62         37       42
                  vv
clus               STAGE IVA
  ZNF174 MUTATED           0
  ZNF174 WILD-TYPE         4
D798V3, multiclass
            clus
vv           ZNF174 MUTATED ZNF174 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF174 MUTATED       0   2   4   2
  ZNF174 WILD-TYPE    54 133 257 100
D798V4, multiclass
       clus
vv      ZNF174 MUTATED ZNF174 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF174 MUTATED     1   3   3   1
  ZNF174 WILD-TYPE 194 170  86  84
D798V5, multiclass
    clus
vv   ZNF174 MUTATED ZNF174 WILD-TYPE
  N0              1              194
  N1              3              170
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V6, binary
                  cls
clus                 0   1
  ZNF174 MUTATED     7   0
  ZNF174 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF174 MUTATED      7    0
  ZNF174 WILD-TYPE  475   38
   clus
vv  ZNF174 MUTATED ZNF174 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D798V7, binary
                  cls
clus                 0   1
  ZNF174 MUTATED     4   4
  ZNF174 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF174 MUTATED      4    4
  ZNF174 WILD-TYPE  168  402
        clus
vv       ZNF174 MUTATED ZNF174 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D798V8, binary
                  cls
clus                 0   1
  ZNF174 MUTATED     4   3
  ZNF174 WILD-TYPE 412  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF174 MUTATED      4    3
  ZNF174 WILD-TYPE  412   99
     clus
vv    ZNF174 MUTATED ZNF174 WILD-TYPE
  NO               4              412
  YES              3               99
[1] 2 2
[1] FALSE
D798V9, continuous
[1] "Remove cluster labels:" "ZNF174 MUTATED"        
clus
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
D798V10, continuous
[1] "Remove cluster labels:" "ZNF174 MUTATED"        
clus
  ZNF174 MUTATED ZNF174 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" "ZNF174 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZNF174 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF174 MUTATED       3                         0
  ZNF174 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF174 MUTATED                                           0     4
  ZNF174 WILD-TYPE                                         1   353
D798V11, multiclass
                                           clus
vv                                          ZNF174 MUTATED ZNF174 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V12, binary
                  cls
clus                 0   1
  ZNF174 MUTATED     0   6
  ZNF174 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF174 MUTATED      0    6
  ZNF174 WILD-TYPE   10  392
                        clus
vv                       ZNF174 MUTATED ZNF174 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(799) Variable = POMGNT1 MUTATION ANALYSIS
D799V1, survival
                   sevent
clus2                 0   1
  POMGNT1 MUTATED     5   7
  POMGNT1 WILD-TYPE 333 209
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               12               542 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                7               209 
$`POMGNT1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-R6-A6XQ TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-A4PE 
       19.99        21.99         6.35        34.68        44.94        20.42 
TCGA-CD-A4MG TCGA-CG-4441 TCGA-CG-4465 TCGA-D7-A6ET TCGA-FP-A4BF TCGA-VQ-AA6G 
        6.58        14.01         9.01        26.43         5.52        26.04 

$`POMGNT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
        4.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56        11.08         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
             5.52              0.00 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            44.94            122.30 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
           20.205            13.510 
[1] "5.5 - 44.9 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D799V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POMGNT1 MUTATED         0        0        1        0         4         0
  POMGNT1 WILD-TYPE      10       20       45       31        80        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POMGNT1 MUTATED           0          2          1          1        2
  POMGNT1 WILD-TYPE        29         82         61         38       41
                   vv
clus                STAGE IVA
  POMGNT1 MUTATED           0
  POMGNT1 WILD-TYPE         4
D799V3, multiclass
            clus
vv           POMGNT1 MUTATED POMGNT1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                4                80
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  POMGNT1 MUTATED       0   2   7   2
  POMGNT1 WILD-TYPE    54 133 254 100
D799V4, multiclass
       clus
vv      POMGNT1 MUTATED POMGNT1 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  7               254
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  POMGNT1 MUTATED     5   1   2   3
  POMGNT1 WILD-TYPE 190 172  87  82
D799V5, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  N0               5               190
  N1               1               172
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V6, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     8   2
  POMGNT1 WILD-TYPE 474  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      8    2
  POMGNT1 WILD-TYPE  474   36
   clus
vv  POMGNT1 MUTATED POMGNT1 WILD-TYPE
  0               8               474
  1               2                36
[1] 2 2
[1] FALSE
D799V7, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     5   7
  POMGNT1 WILD-TYPE 167 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      5    7
  POMGNT1 WILD-TYPE  167  399
        clus
vv       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  FEMALE               5               167
  MALE                 7               399
[1] 2 2
[1] FALSE
D799V8, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED    10   0
  POMGNT1 WILD-TYPE 406 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED     10    0
  POMGNT1 WILD-TYPE  406  102
     clus
vv    POMGNT1 MUTATED POMGNT1 WILD-TYPE
  NO               10               406
  YES               0               102
[1] 2 2
[1] FALSE
D799V9, continuous
D799V10, continuous
[1] "Remove cluster labels:" "POMGNT1 MUTATED"       
clus
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" "POMGNT1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  POMGNT1 MUTATED       1                         0
  POMGNT1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POMGNT1 MUTATED                                           0     8
  POMGNT1 WILD-TYPE                                         1   349
D799V11, multiclass
                                           clus
vv                                          POMGNT1 MUTATED POMGNT1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V12, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     0   7
  POMGNT1 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      0    7
  POMGNT1 WILD-TYPE   10  391
                        clus
vv                       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(800) Variable = MEN1 MUTATION ANALYSIS
D800V1, survival
                sevent
clus2              0   1
  MEN1 MUTATED     6   2
  MEN1 WILD-TYPE 332 214
  MEN1 MUTATED MEN1 WILD-TYPE 
             8            546 
  MEN1 MUTATED MEN1 WILD-TYPE 
             2            214 
$`MEN1 MUTATED`
TCGA-BR-6852 TCGA-BR-A4QL TCGA-CG-5723 TCGA-F1-A448 TCGA-HU-A4G8 TCGA-HU-A4H8 
       44.94        16.14       105.07        21.27        22.68        14.07 
TCGA-IN-7806 TCGA-VQ-AA6K 
       36.36        12.43 

$`MEN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        27.55        17.26 

  MEN1 MUTATED MEN1 WILD-TYPE 
         12.43           0.00 
  MEN1 MUTATED MEN1 WILD-TYPE 
        105.07         122.30 
  MEN1 MUTATED MEN1 WILD-TYPE 
        21.975         13.495 
[1] "12.4 - 105.1 (22.0)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "2.6"
D800V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MEN1 MUTATED         0        0        1        1         1         2
  MEN1 WILD-TYPE      10       20       45       30        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEN1 MUTATED           0          1          2          1        0         0
  MEN1 WILD-TYPE        29         83         60         38       43         4
D800V3, multiclass
            clus
vv           MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MEN1 MUTATED       2   1   5   2
  MEN1 WILD-TYPE    52 134 256 100
D800V4, multiclass
       clus
vv      MEN1 MUTATED MEN1 WILD-TYPE
  T0+T1            2             52
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MEN1 MUTATED     2   4   0   3
  MEN1 WILD-TYPE 193 169  89  82
D800V5, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  N0            2            193
  N1            4            169
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V6, binary
                cls
clus               0   1
  MEN1 MUTATED    10   0
  MEN1 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     10    0
  MEN1 WILD-TYPE  472   38
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D800V7, binary
                cls
clus               0   1
  MEN1 MUTATED     5   5
  MEN1 WILD-TYPE 167 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      5    5
  MEN1 WILD-TYPE  167  401
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE            5            167
  MALE              5            401
[1] 2 2
[1] FALSE
D800V8, binary
                cls
clus               0   1
  MEN1 MUTATED     6   2
  MEN1 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      6    2
  MEN1 WILD-TYPE  410  100
     clus
vv    MEN1 MUTATED MEN1 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D800V9, continuous
D800V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MEN1 MUTATED       2                         0
  MEN1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MEN1 MUTATED                                           0     7
  MEN1 WILD-TYPE                                         1   350
D800V11, multiclass
                                           clus
vv                                          MEN1 MUTATED MEN1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V12, binary
                cls
clus               0   1
  MEN1 MUTATED     1   7
  MEN1 WILD-TYPE   9 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      1    7
  MEN1 WILD-TYPE    9  391
                        clus
vv                       MEN1 MUTATED MEN1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(801) Variable = MIA3 MUTATION ANALYSIS
D801V1, survival
                sevent
clus2              0   1
  MIA3 MUTATED    18   9
  MIA3 WILD-TYPE 320 207
  MIA3 MUTATED MIA3 WILD-TYPE 
            27            527 
  MIA3 MUTATED MIA3 WILD-TYPE 
             9            207 
$`MIA3 MUTATED`
TCGA-CG-4460 TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-L5-A4OH TCGA-LN-A4A1 
       21.99         7.69         0.85         0.53        32.61        12.59 
TCGA-XP-A8T7 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-7707 TCGA-BR-8360 
       41.23         6.97         9.67        19.33        35.84         6.18 
TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 
       31.27        31.96         1.15        16.14         6.58       105.07 
TCGA-CG-5733 TCGA-D7-A6F0 TCGA-D7-A74A TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GH 
       21.07        22.29        19.96        30.51        26.47        11.77 
TCGA-HU-A4GT TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.51        19.04        38.14 

$`MIA3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        32.52        13.51        20.65        20.42        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        52.21         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MIA3 MUTATED MIA3 WILD-TYPE 
          0.53           0.00 
  MIA3 MUTATED MIA3 WILD-TYPE 
        105.07         122.30 
  MIA3 MUTATED MIA3 WILD-TYPE 
         19.33          13.51 
[1] "0.5 - 105.1 (19.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D801V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MIA3 MUTATED         1        1        4        1         5         2
  MIA3 WILD-TYPE       9       19       42       30        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIA3 MUTATED           0          6          2          2        3         0
  MIA3 WILD-TYPE        29         78         60         37       40         4
D801V3, multiclass
            clus
vv           MIA3 MUTATED MIA3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            6             78
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MIA3 MUTATED       3   7   9   8
  MIA3 WILD-TYPE    51 128 252  94
D801V4, multiclass
       clus
vv      MIA3 MUTATED MIA3 WILD-TYPE
  T0+T1            3             51
  T2               7            128
  T3               9            252
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MIA3 MUTATED    12   7   5   3
  MIA3 WILD-TYPE 183 166  84  82
D801V5, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  N0           12            183
  N1            7            166
  N2            5             84
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V6, binary
                cls
clus               0   1
  MIA3 MUTATED    25   2
  MIA3 WILD-TYPE 457  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     25    2
  MIA3 WILD-TYPE  457   36
   clus
vv  MIA3 MUTATED MIA3 WILD-TYPE
  0           25            457
  1            2             36
[1] 2 2
[1] FALSE
D801V7, binary
                cls
clus               0   1
  MIA3 MUTATED    15  14
  MIA3 WILD-TYPE 157 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     15   14
  MIA3 WILD-TYPE  157  392
        clus
vv       MIA3 MUTATED MIA3 WILD-TYPE
  FEMALE           15            157
  MALE             14            392
[1] 2 2
[1] FALSE
D801V8, binary
                cls
clus               0   1
  MIA3 MUTATED    24   2
  MIA3 WILD-TYPE 392 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     24    2
  MIA3 WILD-TYPE  392  100
     clus
vv    MIA3 MUTATED MIA3 WILD-TYPE
  NO            24            392
  YES            2            100
[1] 2 2
[1] FALSE
D801V9, continuous
D801V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MIA3 MUTATED       6                         0
  MIA3 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MIA3 MUTATED                                           0    19
  MIA3 WILD-TYPE                                         1   338
D801V11, multiclass
                                           clus
vv                                          MIA3 MUTATED MIA3 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V12, binary
                cls
clus               0   1
  MIA3 MUTATED     1  22
  MIA3 WILD-TYPE   9 376
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED      1   22
  MIA3 WILD-TYPE    9  376
                        clus
vv                       MIA3 MUTATED MIA3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           22            376
[1] 2 2
[1] FALSE

Clustering(802) Variable = SRP72 MUTATION ANALYSIS
D802V1, survival
                 sevent
clus2               0   1
  SRP72 MUTATED     7   7
  SRP72 WILD-TYPE 331 209
  SRP72 MUTATED SRP72 WILD-TYPE 
             14             540 
  SRP72 MUTATED SRP72 WILD-TYPE 
              7             209 
$`SRP72 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-IC-A6RE TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8487 
        4.31        21.99         7.69         9.34        35.84         1.12 
TCGA-BR-8677 TCGA-BR-A4IZ TCGA-CD-A4MI TCGA-CG-4465 TCGA-HF-7132 TCGA-MX-A5UJ 
       26.73         8.98        11.77         9.01        77.29        19.73 
TCGA-SW-A7EA TCGA-VQ-A8PQ 
       19.04        15.65 

$`SRP72 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
       17.85         1.87        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SRP72 MUTATED SRP72 WILD-TYPE 
           1.12            0.00 
  SRP72 MUTATED SRP72 WILD-TYPE 
          77.29          122.30 
  SRP72 MUTATED SRP72 WILD-TYPE 
         13.710          13.565 
[1] "1.1 - 77.3 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D802V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRP72 MUTATED         0        0        2        1         1         3
  SRP72 WILD-TYPE      10       20       44       30        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRP72 MUTATED           0          2          2          0        3         0
  SRP72 WILD-TYPE        29         82         60         39       40         4
D802V3, multiclass
            clus
vv           SRP72 MUTATED SRP72 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SRP72 MUTATED       1   3   6   5
  SRP72 WILD-TYPE    53 132 255  97
D802V4, multiclass
       clus
vv      SRP72 MUTATED SRP72 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SRP72 MUTATED     5   6   2   2
  SRP72 WILD-TYPE 190 167  87  83
D802V5, multiclass
    clus
vv   SRP72 MUTATED SRP72 WILD-TYPE
  N0             5             190
  N1             6             167
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V6, binary
                 cls
clus                0   1
  SRP72 MUTATED    11   3
  SRP72 WILD-TYPE 471  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     11    3
  SRP72 WILD-TYPE  471   35
   clus
vv  SRP72 MUTATED SRP72 WILD-TYPE
  0            11             471
  1             3              35
[1] 2 2
[1] FALSE
D802V7, binary
                 cls
clus                0   1
  SRP72 MUTATED    10   6
  SRP72 WILD-TYPE 162 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     10    6
  SRP72 WILD-TYPE  162  400
        clus
vv       SRP72 MUTATED SRP72 WILD-TYPE
  FEMALE            10             162
  MALE               6             400
[1] 2 2
[1] FALSE
D802V8, binary
                 cls
clus                0   1
  SRP72 MUTATED    12   1
  SRP72 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     12    1
  SRP72 WILD-TYPE  404  101
     clus
vv    SRP72 MUTATED SRP72 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D802V9, continuous
D802V10, continuous
[1] "Remove cluster labels:" "SRP72 MUTATED"         
clus
  SRP72 MUTATED SRP72 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OE      TCGA-L5-A4OG 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL      TCGA-IG-A3Y9 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" "SRP72 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SRP72 MUTATED       2                         0
  SRP72 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRP72 MUTATED                                           0    11
  SRP72 WILD-TYPE                                         1   346
D802V11, multiclass
                                           clus
vv                                          SRP72 MUTATED SRP72 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V12, binary
                 cls
clus                0   1
  SRP72 MUTATED     0  11
  SRP72 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED      0   11
  SRP72 WILD-TYPE   10  387
                        clus
vv                       SRP72 MUTATED SRP72 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(803) Variable = UVRAG MUTATION ANALYSIS
D803V1, survival
                 sevent
clus2               0   1
  UVRAG MUTATED     6   3
  UVRAG WILD-TYPE 332 213
  UVRAG MUTATED UVRAG WILD-TYPE 
              9             545 
  UVRAG MUTATED UVRAG WILD-TYPE 
              3             213 
$`UVRAG MUTATED`
TCGA-L5-A4OH TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8591 
       32.61        26.70         6.97         9.67        34.68        28.14 
TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 
       16.14         6.02       105.07 

$`UVRAG WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  UVRAG MUTATED UVRAG WILD-TYPE 
           6.02            0.00 
  UVRAG MUTATED UVRAG WILD-TYPE 
         105.07          122.30 
  UVRAG MUTATED UVRAG WILD-TYPE 
          26.70           13.51 
[1] "6.0 - 105.1 (26.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D803V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UVRAG MUTATED         1        0        0        1         1         2
  UVRAG WILD-TYPE       9       20       46       30        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UVRAG MUTATED           0          1          1          1        1         0
  UVRAG WILD-TYPE        29         83         61         38       42         4
D803V3, multiclass
            clus
vv           UVRAG MUTATED UVRAG WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  UVRAG MUTATED       1   1   4   4
  UVRAG WILD-TYPE    53 134 257  98
D803V4, multiclass
       clus
vv      UVRAG MUTATED UVRAG WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                4             257
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  UVRAG MUTATED     4   4   0   2
  UVRAG WILD-TYPE 191 169  89  83
D803V5, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  N0             4             191
  N1             4             169
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V6, binary
                 cls
clus                0   1
  UVRAG MUTATED    11   0
  UVRAG WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED     11    0
  UVRAG WILD-TYPE  471   38
   clus
vv  UVRAG MUTATED UVRAG WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D803V7, binary
                 cls
clus                0   1
  UVRAG MUTATED     7   6
  UVRAG WILD-TYPE 165 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      7    6
  UVRAG WILD-TYPE  165  400
        clus
vv       UVRAG MUTATED UVRAG WILD-TYPE
  FEMALE             7             165
  MALE               6             400
[1] 2 2
[1] FALSE
D803V8, binary
                 cls
clus                0   1
  UVRAG MUTATED    10   0
  UVRAG WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED     10    0
  UVRAG WILD-TYPE  406  102
     clus
vv    UVRAG MUTATED UVRAG WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D803V9, continuous
D803V10, continuous
[1] "Remove cluster labels:" "UVRAG MUTATED"         
clus
  UVRAG MUTATED UVRAG WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OM 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" "UVRAG WILD-TYPE" 
     TCGA-Z6-AAPN 
"UVRAG WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  UVRAG MUTATED       0                         0
  UVRAG WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UVRAG MUTATED                                           0    11
  UVRAG WILD-TYPE                                         1   346
D803V11, multiclass
                                           clus
vv                                          UVRAG MUTATED UVRAG WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V12, binary
                 cls
clus                0   1
  UVRAG MUTATED     0  10
  UVRAG WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      0   10
  UVRAG WILD-TYPE   10  388
                        clus
vv                       UVRAG MUTATED UVRAG WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(804) Variable = PLXNB2 MUTATION ANALYSIS
D804V1, survival
                  sevent
clus2                0   1
  PLXNB2 MUTATED    20   8
  PLXNB2 WILD-TYPE 318 208
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
              28              526 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
               8              208 
$`PLXNB2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GH TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-LN-A4A2 
       19.99        21.99        31.27         6.28        21.01        12.49 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-R6-A6XQ TCGA-R6-A8WC 
       12.33        10.52        13.38        12.85         6.35         2.30 
TCGA-R6-A8WG TCGA-BR-4184 TCGA-BR-8680 TCGA-CD-5804 TCGA-CD-A4MI TCGA-CG-4305 
       12.69         6.97        31.96        12.10        11.77        15.95 
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB 
        6.02        65.10         5.92        11.44        11.08        30.51 
TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H4 
       22.32         6.51         6.58        23.84 

$`PLXNB2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.03        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04        38.40        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78         2.89         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
             2.3              0.0 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
            65.1            122.3 
  PLXNB2 MUTATED PLXNB2 WILD-TYPE 
           12.41            13.87 
[1] "2.3 - 65.1 (12.4)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.2"
D804V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLXNB2 MUTATED         1        1        1        1         6         7
  PLXNB2 WILD-TYPE       9       19       45       30        78        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNB2 MUTATED           0          2          1          2        3
  PLXNB2 WILD-TYPE        29         82         61         37       40
                  vv
clus               STAGE IVA
  PLXNB2 MUTATED           0
  PLXNB2 WILD-TYPE         4
D804V3, multiclass
            clus
vv           PLXNB2 MUTATED PLXNB2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               7               76
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PLXNB2 MUTATED       4   6  11   6
  PLXNB2 WILD-TYPE    50 129 250  96
D804V4, multiclass
       clus
vv      PLXNB2 MUTATED PLXNB2 WILD-TYPE
  T0+T1              4               50
  T2                 6              129
  T3                11              250
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PLXNB2 MUTATED    11  11   2   3
  PLXNB2 WILD-TYPE 184 162  87  82
D804V5, multiclass
    clus
vv   PLXNB2 MUTATED PLXNB2 WILD-TYPE
  N0             11              184
  N1             11              162
  N2              2               87
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V6, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED    24   2
  PLXNB2 WILD-TYPE 458  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED     24    2
  PLXNB2 WILD-TYPE  458   36
   clus
vv  PLXNB2 MUTATED PLXNB2 WILD-TYPE
  0             24              458
  1              2               36
[1] 2 2
[1] FALSE
D804V7, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED    11  20
  PLXNB2 WILD-TYPE 161 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED     11   20
  PLXNB2 WILD-TYPE  161  386
        clus
vv       PLXNB2 MUTATED PLXNB2 WILD-TYPE
  FEMALE             11              161
  MALE               20              386
[1] 2 2
[1] FALSE
D804V8, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED    21   6
  PLXNB2 WILD-TYPE 395  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED     21    6
  PLXNB2 WILD-TYPE  395   96
     clus
vv    PLXNB2 MUTATED PLXNB2 WILD-TYPE
  NO              21              395
  YES              6               96
[1] 2 2
[1] FALSE
D804V9, continuous
D804V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PLXNB2 MUTATED      12                         1
  PLXNB2 WILD-TYPE   121                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLXNB2 MUTATED                                           0    12
  PLXNB2 WILD-TYPE                                         1   345
D804V11, multiclass
                                           clus
vv                                          PLXNB2 MUTATED PLXNB2 WILD-TYPE
  ASIAN                                                 12              121
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V12, binary
                  cls
clus                 0   1
  PLXNB2 MUTATED     1  22
  PLXNB2 WILD-TYPE   9 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB2 MUTATED      1   22
  PLXNB2 WILD-TYPE    9  376
                        clus
vv                       PLXNB2 MUTATED PLXNB2 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             22              376
[1] 2 2
[1] FALSE

Clustering(805) Variable = KIF2B MUTATION ANALYSIS
D805V1, survival
                 sevent
clus2               0   1
  KIF2B MUTATED    24   9
  KIF2B WILD-TYPE 314 207
  KIF2B MUTATED KIF2B WILD-TYPE 
             33             521 
  KIF2B MUTATED KIF2B WILD-TYPE 
              9             207 
$`KIF2B MUTATED`
TCGA-IC-A6RF TCGA-EQ-A4SO TCGA-2H-A9GI TCGA-LN-A7HX TCGA-B7-5816 TCGA-BR-6453 
       15.68        16.24        14.30        12.23        26.70        15.95 
TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-8297 TCGA-BR-8361 
       39.12        35.84        15.32        28.73         7.40        31.10 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8687 TCGA-CD-A4MG TCGA-CG-4436 
        9.21         1.12        27.12         8.22         6.58         7.99 
TCGA-CG-4438 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4Z0 
       54.08         6.02        65.10        12.79        14.66        14.76 
TCGA-D7-A747 TCGA-FP-7829 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4H5 TCGA-IN-A6RI 
        8.38        19.53        77.29        26.47        23.80        18.38 
TCGA-IN-A6RL TCGA-IN-AB1V TCGA-VQ-AA6J 
       13.35        15.75        27.55 

$`KIF2B WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        18.15         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.18        20.22        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44        20.32        22.29        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81         3.39        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        12.43        17.26 

  KIF2B MUTATED KIF2B WILD-TYPE 
           1.12            0.00 
  KIF2B MUTATED KIF2B WILD-TYPE 
          77.29          122.30 
  KIF2B MUTATED KIF2B WILD-TYPE 
          15.75           13.41 
[1] "1.1 - 77.3 (15.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.7"
D805V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF2B MUTATED         1        2        5        1         5         7
  KIF2B WILD-TYPE       9       18       41       30        79        76
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF2B MUTATED           1          2          5          4        2         0
  KIF2B WILD-TYPE        28         82         57         35       41         4
D805V3, multiclass
            clus
vv           KIF2B MUTATED KIF2B WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               5              41
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              7              76
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             5              57
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KIF2B MUTATED       3  11  10  11
  KIF2B WILD-TYPE    51 124 251  91
D805V4, multiclass
       clus
vv      KIF2B MUTATED KIF2B WILD-TYPE
  T0+T1             3              51
  T2               11             124
  T3               10             251
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KIF2B MUTATED    14  11   5   5
  KIF2B WILD-TYPE 181 162  84  80
D805V5, multiclass
    clus
vv   KIF2B MUTATED KIF2B WILD-TYPE
  N0            14             181
  N1            11             162
  N2             5              84
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V6, binary
                 cls
clus                0   1
  KIF2B MUTATED    33   0
  KIF2B WILD-TYPE 449  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     33    0
  KIF2B WILD-TYPE  449   38
   clus
vv  KIF2B MUTATED KIF2B WILD-TYPE
  0            33             449
  1             0              38
[1] 2 2
[1] FALSE
D805V7, binary
                 cls
clus                0   1
  KIF2B MUTATED    11  24
  KIF2B WILD-TYPE 161 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     11   24
  KIF2B WILD-TYPE  161  382
        clus
vv       KIF2B MUTATED KIF2B WILD-TYPE
  FEMALE            11             161
  MALE              24             382
[1] 2 2
[1] FALSE
D805V8, binary
                 cls
clus                0   1
  KIF2B MUTATED    26   6
  KIF2B WILD-TYPE 390  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     26    6
  KIF2B WILD-TYPE  390   96
     clus
vv    KIF2B MUTATED KIF2B WILD-TYPE
  NO             26             390
  YES             6              96
[1] 2 2
[1] FALSE
D805V9, continuous
[1] "Remove cluster labels:" "KIF2B MUTATED"         
clus
  KIF2B MUTATED KIF2B WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
D805V10, continuous
[1] "Remove cluster labels:" "KIF2B MUTATED"         
clus
  KIF2B MUTATED KIF2B WILD-TYPE 
              2              96 
     TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" "KIF2B WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KIF2B MUTATED       3                         1
  KIF2B WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF2B MUTATED                                           0    25
  KIF2B WILD-TYPE                                         1   332
D805V11, multiclass
                                           clus
vv                                          KIF2B MUTATED KIF2B WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                25             332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V12, binary
                 cls
clus                0   1
  KIF2B MUTATED     0  28
  KIF2B WILD-TYPE  10 370
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED      0   28
  KIF2B WILD-TYPE   10  370
                        clus
vv                       KIF2B MUTATED KIF2B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            28             370
[1] 2 2
[1] FALSE

Clustering(806) Variable = HNF1B MUTATION ANALYSIS
D806V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     2   2
  HNF1B WILD-TYPE 336 214
  HNF1B MUTATED HNF1B WILD-TYPE 
              4             550 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             214 
$`HNF1B MUTATED`
TCGA-B7-5816 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MG 
       26.70        12.89        16.14         6.58 

$`HNF1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HNF1B MUTATED HNF1B WILD-TYPE 
           6.58            0.00 
  HNF1B MUTATED HNF1B WILD-TYPE 
           26.7           122.3 
  HNF1B MUTATED HNF1B WILD-TYPE 
         14.515          13.565 
[1] "6.6 - 26.7 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D806V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HNF1B MUTATED         0        0        0        0         1         2
  HNF1B WILD-TYPE      10       20       46       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNF1B MUTATED           0          0          1          0        0         0
  HNF1B WILD-TYPE        29         84         61         39       43         4
D806V3, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HNF1B MUTATED       0   0   2   2
  HNF1B WILD-TYPE    54 135 259 100
D806V4, multiclass
       clus
vv      HNF1B MUTATED HNF1B WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HNF1B MUTATED     3   1   0   1
  HNF1B WILD-TYPE 192 172  89  84
D806V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             3             192
  N1             1             172
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     5   0
  HNF1B WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      5    0
  HNF1B WILD-TYPE  477   38
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D806V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     3   2
  HNF1B WILD-TYPE 169 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      3    2
  HNF1B WILD-TYPE  169  404
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             3             169
  MALE               2             404
[1] 2 2
[1] FALSE
D806V8, binary
                 cls
clus                0   1
  HNF1B MUTATED     4   0
  HNF1B WILD-TYPE 412 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      4    0
  HNF1B WILD-TYPE  412  102
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              4             412
  YES             0             102
[1] 2 2
[1] FALSE
D806V9, continuous
D806V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HNF1B MUTATED       2                         0
  HNF1B WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HNF1B MUTATED                                           0     3
  HNF1B WILD-TYPE                                         1   354
D806V11, multiclass
                                           clus
vv                                          HNF1B MUTATED HNF1B WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V12, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   5
  HNF1B WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    5
  HNF1B WILD-TYPE   10  393
                        clus
vv                       HNF1B MUTATED HNF1B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(807) Variable = CEP290 MUTATION ANALYSIS
D807V1, survival
                  sevent
clus2                0   1
  CEP290 MUTATED    14   8
  CEP290 WILD-TYPE 324 208
  CEP290 MUTATED CEP290 WILD-TYPE 
              22              532 
  CEP290 MUTATED CEP290 WILD-TYPE 
               8              208 
$`CEP290 MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-JY-A6FE TCGA-L5-A8NS TCGA-LN-A49R TCGA-LN-A49S 
        0.85        18.64         3.68        13.41        13.38        13.15 
TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-VR-AA4D TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7197 
       12.03        13.18        46.19         9.67        34.68         9.21 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4J1 TCGA-CD-A487 TCGA-CD-A4MG 
        6.18        31.10        31.96         0.72        12.30         6.58 
TCGA-D7-A4YV TCGA-HF-7134 TCGA-HU-A4G8 TCGA-HU-A4GT 
        5.92        52.21        22.68         6.51 

$`CEP290 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       33.27        35.21        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       15.39        12.07        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CEP290 MUTATED CEP290 WILD-TYPE 
            0.72             0.00 
  CEP290 MUTATED CEP290 WILD-TYPE 
           52.21           122.30 
  CEP290 MUTATED CEP290 WILD-TYPE 
          12.725           13.870 
[1] "0.7 - 52.2 (12.7)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1"  
D807V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP290 MUTATED         1        1        0        1         6         6
  CEP290 WILD-TYPE       9       19       46       30        78        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP290 MUTATED           3          2          0          1        1
  CEP290 WILD-TYPE        26         82         62         38       42
                  vv
clus               STAGE IVA
  CEP290 MUTATED           0
  CEP290 WILD-TYPE         4
D807V3, multiclass
            clus
vv           CEP290 MUTATED CEP290 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               6               77
  STAGE III               3               26
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CEP290 MUTATED       3   2  13   4
  CEP290 WILD-TYPE    51 133 248  98
D807V4, multiclass
       clus
vv      CEP290 MUTATED CEP290 WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                13              248
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CEP290 MUTATED    10  10   2   0
  CEP290 WILD-TYPE 185 163  87  85
D807V5, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  N0             10              185
  N1             10              163
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V6, binary
                  cls
clus                 0   1
  CEP290 MUTATED    21   1
  CEP290 WILD-TYPE 461  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     21    1
  CEP290 WILD-TYPE  461   37
   clus
vv  CEP290 MUTATED CEP290 WILD-TYPE
  0             21              461
  1              1               37
[1] 2 2
[1] FALSE
D807V7, binary
                  cls
clus                 0   1
  CEP290 MUTATED     7  16
  CEP290 WILD-TYPE 165 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      7   16
  CEP290 WILD-TYPE  165  390
        clus
vv       CEP290 MUTATED CEP290 WILD-TYPE
  FEMALE              7              165
  MALE               16              390
[1] 2 2
[1] FALSE
D807V8, binary
                  cls
clus                 0   1
  CEP290 MUTATED    16   6
  CEP290 WILD-TYPE 400  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     16    6
  CEP290 WILD-TYPE  400   96
     clus
vv    CEP290 MUTATED CEP290 WILD-TYPE
  NO              16              400
  YES              6               96
[1] 2 2
[1] FALSE
D807V9, continuous
D807V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP290 MUTATED      10                         1
  CEP290 WILD-TYPE   123                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP290 MUTATED                                           0    11
  CEP290 WILD-TYPE                                         1   346
D807V11, multiclass
                                           clus
vv                                          CEP290 MUTATED CEP290 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V12, binary
                  cls
clus                 0   1
  CEP290 MUTATED     0  19
  CEP290 WILD-TYPE  10 379
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      0   19
  CEP290 WILD-TYPE   10  379
                        clus
vv                       CEP290 MUTATED CEP290 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             19              379
[1] 2 2
[1] FALSE

Clustering(808) Variable = COL20A1 MUTATION ANALYSIS
D808V1, survival
                   sevent
clus2                 0   1
  COL20A1 MUTATED    16   6
  COL20A1 WILD-TYPE 322 210
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               22               532 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
                6               210 
$`COL20A1 MUTATED`
TCGA-JY-A938 TCGA-LN-A7HZ TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-8078 
       34.85        13.18        34.68        39.12        35.84        29.59 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4QL TCGA-CD-8536 
       31.10         1.12        31.96         9.86        16.14        12.43 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5733 
       12.30         6.58        11.77        15.95         6.02        21.07 
TCGA-D7-6822 TCGA-HU-A4GY TCGA-R5-A7ZE TCGA-VQ-A8P2 
       12.33         0.26        18.21        38.14 

$`COL20A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 
        6.28         7.53        26.73        24.79        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07        12.82         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  COL20A1 MUTATED COL20A1 WILD-TYPE 
             0.26              0.00 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
            39.12            122.30 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
           16.045            13.530 
[1] "0.3 - 39.1 (16.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D808V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL20A1 MUTATED         0        0        2        2         4         4
  COL20A1 WILD-TYPE      10       20       44       29        80        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL20A1 MUTATED           0          5          2          1        2
  COL20A1 WILD-TYPE        29         79         60         38       41
                   vv
clus                STAGE IVA
  COL20A1 MUTATED           0
  COL20A1 WILD-TYPE         4
D808V3, multiclass
            clus
vv           COL20A1 MUTATED COL20A1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 2                29
  STAGE IIA                4                80
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               5                79
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  COL20A1 MUTATED       0   5  10   7
  COL20A1 WILD-TYPE    54 130 251  95
D808V4, multiclass
       clus
vv      COL20A1 MUTATED COL20A1 WILD-TYPE
  T0+T1               0                54
  T2                  5               130
  T3                 10               251
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  COL20A1 MUTATED     9   7   5   1
  COL20A1 WILD-TYPE 186 166  84  84
D808V5, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  N0               9               186
  N1               7               166
  N2               5                84
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V6, binary
                   cls
clus                  0   1
  COL20A1 MUTATED    21   1
  COL20A1 WILD-TYPE 461  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED     21    1
  COL20A1 WILD-TYPE  461   37
   clus
vv  COL20A1 MUTATED COL20A1 WILD-TYPE
  0              21               461
  1               1                37
[1] 2 2
[1] FALSE
D808V7, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     9  13
  COL20A1 WILD-TYPE 163 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      9   13
  COL20A1 WILD-TYPE  163  393
        clus
vv       COL20A1 MUTATED COL20A1 WILD-TYPE
  FEMALE               9               163
  MALE                13               393
[1] 2 2
[1] FALSE
D808V8, binary
                   cls
clus                  0   1
  COL20A1 MUTATED    21   1
  COL20A1 WILD-TYPE 395 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED     21    1
  COL20A1 WILD-TYPE  395  101
     clus
vv    COL20A1 MUTATED COL20A1 WILD-TYPE
  NO               21               395
  YES               1               101
[1] 2 2
[1] FALSE
D808V9, continuous
[1] "Remove cluster labels:" "COL20A1 MUTATED"       
clus
  COL20A1 MUTATED COL20A1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
D808V10, continuous
[1] "Remove cluster labels:" "COL20A1 MUTATED"       
clus
  COL20A1 MUTATED COL20A1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A8HZ 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" "COL20A1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"COL20A1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL20A1 MUTATED       8                         0
  COL20A1 WILD-TYPE   125                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL20A1 MUTATED                                           0    11
  COL20A1 WILD-TYPE                                         1   346
D808V11, multiclass
                                           clus
vv                                          COL20A1 MUTATED COL20A1 WILD-TYPE
  ASIAN                                                   8               125
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V12, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     0  17
  COL20A1 WILD-TYPE  10 381
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      0   17
  COL20A1 WILD-TYPE   10  381
                        clus
vv                       COL20A1 MUTATED COL20A1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              17               381
[1] 2 2
[1] FALSE

Clustering(809) Variable = THSD1 MUTATION ANALYSIS
D809V1, survival
                 sevent
clus2               0   1
  THSD1 MUTATED    21   3
  THSD1 WILD-TYPE 317 213
  THSD1 MUTATED THSD1 WILD-TYPE 
             24             530 
  THSD1 MUTATED THSD1 WILD-TYPE 
              3             213 
$`THSD1 MUTATED`
TCGA-L5-A88T TCGA-IG-A3I8 TCGA-LN-A9FP TCGA-R6-A6Y2 TCGA-B7-5816 TCGA-BR-4184 
       22.82        33.27        12.03         9.30        26.70         6.97 
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-5800 
       34.68        44.94        29.59         0.26         1.12        13.15 
TCGA-CD-8535 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-5728 TCGA-FP-A4BE 
       12.82        15.95         7.99         8.05        65.10        11.08 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-RD-A8MV 
       22.32        22.68        29.98        23.84        74.53       122.30 

$`THSD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       27.02         1.02        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  THSD1 MUTATED THSD1 WILD-TYPE 
           0.26            0.00 
  THSD1 MUTATED THSD1 WILD-TYPE 
          122.3           122.1 
  THSD1 MUTATED THSD1 WILD-TYPE 
          22.50           13.51 
[1] "0.3 - 122.3 (22.5)" "0.0 - 122.1 (13.5)"
[1] "hr=" "4.4"
D809V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THSD1 MUTATED         0        0        3        3         7         6
  THSD1 WILD-TYPE      10       20       43       28        77        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THSD1 MUTATED           0          2          1          0        3         0
  THSD1 WILD-TYPE        29         82         61         39       40         4
D809V3, multiclass
            clus
vv           THSD1 MUTATED THSD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               3              28
  STAGE IIA              7              77
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  THSD1 MUTATED       0   9  10   6
  THSD1 WILD-TYPE    54 126 251  96
D809V4, multiclass
       clus
vv      THSD1 MUTATED THSD1 WILD-TYPE
  T0+T1             0              54
  T2                9             126
  T3               10             251
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  THSD1 MUTATED    13   8   4   0
  THSD1 WILD-TYPE 182 165  85  85
D809V5, multiclass
    clus
vv   THSD1 MUTATED THSD1 WILD-TYPE
  N0            13             182
  N1             8             165
  N2             4              85
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V6, binary
                 cls
clus                0   1
  THSD1 MUTATED    22   2
  THSD1 WILD-TYPE 460  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     22    2
  THSD1 WILD-TYPE  460   36
   clus
vv  THSD1 MUTATED THSD1 WILD-TYPE
  0            22             460
  1             2              36
[1] 2 2
[1] FALSE
D809V7, binary
                 cls
clus                0   1
  THSD1 MUTATED    16  10
  THSD1 WILD-TYPE 156 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     16   10
  THSD1 WILD-TYPE  156  396
        clus
vv       THSD1 MUTATED THSD1 WILD-TYPE
  FEMALE            16             156
  MALE              10             396
[1] 2 2
[1] FALSE
D809V8, binary
                 cls
clus                0   1
  THSD1 MUTATED    20   3
  THSD1 WILD-TYPE 396  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     20    3
  THSD1 WILD-TYPE  396   99
     clus
vv    THSD1 MUTATED THSD1 WILD-TYPE
  NO             20             396
  YES             3              99
[1] 2 2
[1] FALSE
D809V9, continuous
[1] "Remove cluster labels:" "THSD1 MUTATED"         
clus
  THSD1 MUTATED THSD1 WILD-TYPE 
              1              67 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
D809V10, continuous
[1] "Remove cluster labels:" "THSD1 MUTATED"         
clus
  THSD1 MUTATED THSD1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88Y      TCGA-L5-A8NG 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A8W5      TCGA-R6-A8W8 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" "THSD1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  THSD1 MUTATED       7                         1
  THSD1 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THSD1 MUTATED                                           0    13
  THSD1 WILD-TYPE                                         1   344
D809V11, multiclass
                                           clus
vv                                          THSD1 MUTATED THSD1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V12, binary
                 cls
clus                0   1
  THSD1 MUTATED     2  18
  THSD1 WILD-TYPE   8 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED      2   18
  THSD1 WILD-TYPE    8  380
                        clus
vv                       THSD1 MUTATED THSD1 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(810) Variable = TADA2B MUTATION ANALYSIS
D810V1, survival
                  sevent
clus2                0   1
  TADA2B MUTATED    10   3
  TADA2B WILD-TYPE 328 213
  TADA2B MUTATED TADA2B WILD-TYPE 
              13              541 
  TADA2B MUTATED TADA2B WILD-TYPE 
               3              213 
$`TADA2B MUTATED`
TCGA-L5-A43M TCGA-KH-A6WC TCGA-LN-A49U TCGA-R6-A6XG TCGA-Z6-A8JD TCGA-BR-4184 
        8.94         6.28        15.35        38.40         3.42         6.97 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8080 TCGA-F1-6874 TCGA-HU-A4GN TCGA-HU-A4GT 
        6.61        34.68         9.60        14.47        29.98         6.51 
TCGA-VQ-A8P2 
       38.14 

$`TADA2B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        13.15        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TADA2B MUTATED TADA2B WILD-TYPE 
            3.42             0.00 
  TADA2B MUTATED TADA2B WILD-TYPE 
            38.4            122.3 
  TADA2B MUTATED TADA2B WILD-TYPE 
            9.60            13.58 
[1] "3.4 - 38.4 (9.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D810V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TADA2B MUTATED         1        1        1        0         4         1
  TADA2B WILD-TYPE       9       19       45       31        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TADA2B MUTATED           1          2          0          1        0
  TADA2B WILD-TYPE        28         82         62         38       43
                  vv
clus               STAGE IVA
  TADA2B MUTATED           0
  TADA2B WILD-TYPE         4
D810V3, multiclass
            clus
vv           TADA2B MUTATED TADA2B WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TADA2B MUTATED       2   3   7   2
  TADA2B WILD-TYPE    52 132 254 100
D810V4, multiclass
       clus
vv      TADA2B MUTATED TADA2B WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 7              254
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TADA2B MUTATED     6   5   1   1
  TADA2B WILD-TYPE 189 168  88  84
D810V5, multiclass
    clus
vv   TADA2B MUTATED TADA2B WILD-TYPE
  N0              6              189
  N1              5              168
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V6, binary
                  cls
clus                 0   1
  TADA2B MUTATED    10   0
  TADA2B WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TADA2B MUTATED     10    0
  TADA2B WILD-TYPE  472   38
   clus
vv  TADA2B MUTATED TADA2B WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D810V7, binary
                  cls
clus                 0   1
  TADA2B MUTATED     6   9
  TADA2B WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TADA2B MUTATED      6    9
  TADA2B WILD-TYPE  166  397
        clus
vv       TADA2B MUTATED TADA2B WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D810V8, binary
                  cls
clus                 0   1
  TADA2B MUTATED    11   3
  TADA2B WILD-TYPE 405  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TADA2B MUTATED     11    3
  TADA2B WILD-TYPE  405   99
     clus
vv    TADA2B MUTATED TADA2B WILD-TYPE
  NO              11              405
  YES              3               99
[1] 2 2
[1] FALSE
D810V9, continuous
D810V10, continuous
[1] "Remove cluster labels:" "TADA2B MUTATED"        
clus
  TADA2B MUTATED TADA2B WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-L5-A43C 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49V 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" "TADA2B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TADA2B MUTATED       3                         1
  TADA2B WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TADA2B MUTATED                                           0    10
  TADA2B WILD-TYPE                                         1   347
D810V11, multiclass
                                           clus
vv                                          TADA2B MUTATED TADA2B WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V12, binary
                  cls
clus                 0   1
  TADA2B MUTATED     0  13
  TADA2B WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TADA2B MUTATED      0   13
  TADA2B WILD-TYPE   10  385
                        clus
vv                       TADA2B MUTATED TADA2B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(811) Variable = HSP90AA1 MUTATION ANALYSIS
D811V1, survival
                    sevent
clus2                  0   1
  HSP90AA1 MUTATED    10   3
  HSP90AA1 WILD-TYPE 328 213
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                13                541 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 3                213 
$`HSP90AA1 MUTATED`
TCGA-L5-A8NM TCGA-S8-A6BW TCGA-BR-7196 TCGA-BR-7716 TCGA-BR-8078 TCGA-CG-5733 
        7.76        20.38        21.90        39.78        29.59        21.07 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-F1-6874 TCGA-FP-A4BF TCGA-HU-A4H3 TCGA-VQ-A8P2 
       16.44        13.78        14.47         5.52        29.00        38.14 
TCGA-VQ-A8P3 
       37.22 

$`HSP90AA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56        11.08         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE 
        5.46        13.25        13.02        43.36        37.41        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
              5.52               0.00 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             39.78             122.30 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             21.07              13.41 
[1] "5.5 - 39.8 (21.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D811V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSP90AA1 MUTATED         1        0        2        0         0         3
  HSP90AA1 WILD-TYPE       9       20       44       31        84        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90AA1 MUTATED           0          4          2          1        1
  HSP90AA1 WILD-TYPE        29         80         60         38       42
                    vv
clus                 STAGE IVA
  HSP90AA1 MUTATED           0
  HSP90AA1 WILD-TYPE         4
D811V3, multiclass
            clus
vv           HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                4                 80
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  HSP90AA1 MUTATED       1   4   5   4
  HSP90AA1 WILD-TYPE    53 131 256  98
D811V4, multiclass
       clus
vv      HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  T0+T1                1                 53
  T2                   4                131
  T3                   5                256
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  HSP90AA1 MUTATED     3   5   2   4
  HSP90AA1 WILD-TYPE 192 168  87  81
D811V5, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  N0                3                192
  N1                5                168
  N2                2                 87
  N3                4                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V6, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED    11   1
  HSP90AA1 WILD-TYPE 471  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED     11    1
  HSP90AA1 WILD-TYPE  471   37
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0               11                471
  1                1                 37
[1] 2 2
[1] FALSE
D811V7, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     5   9
  HSP90AA1 WILD-TYPE 167 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      5    9
  HSP90AA1 WILD-TYPE  167  397
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  FEMALE                5                167
  MALE                  9                397
[1] 2 2
[1] FALSE
D811V8, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED    10   3
  HSP90AA1 WILD-TYPE 406  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED     10    3
  HSP90AA1 WILD-TYPE  406   99
     clus
vv    HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  NO                10                406
  YES                3                 99
[1] 2 2
[1] FALSE
D811V9, continuous
D811V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HSP90AA1 MUTATED       1                         1
  HSP90AA1 WILD-TYPE   132                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSP90AA1 MUTATED                                           0    11
  HSP90AA1 WILD-TYPE                                         1   346
D811V11, multiclass
                                           clus
vv                                          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V12, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     0  10
  HSP90AA1 WILD-TYPE  10 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      0   10
  HSP90AA1 WILD-TYPE   10  388
                        clus
vv                       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               10                388
[1] 2 2
[1] FALSE

Clustering(812) Variable = CRAT MUTATION ANALYSIS
D812V1, survival
                sevent
clus2              0   1
  CRAT MUTATED     8   4
  CRAT WILD-TYPE 330 212
  CRAT MUTATED CRAT WILD-TYPE 
            12            542 
  CRAT MUTATED CRAT WILD-TYPE 
             4            212 
$`CRAT MUTATED`
TCGA-L5-A43J TCGA-L5-A8NE TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-8363 
        4.31        55.50        26.70        19.56        30.90         0.26 
TCGA-CG-4466 TCGA-CG-5721 TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-A4G8 TCGA-HU-A4GX 
       18.97         6.02        26.47        24.39        22.68        20.25 

$`CRAT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CRAT MUTATED CRAT WILD-TYPE 
          0.26           0.00 
  CRAT MUTATED CRAT WILD-TYPE 
          55.5          122.3 
  CRAT MUTATED CRAT WILD-TYPE 
        21.465         13.495 
[1] "0.3 - 55.5 (21.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D812V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRAT MUTATED         1        1        3        0         0         4
  CRAT WILD-TYPE       9       19       43       31        84        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRAT MUTATED           0          0          0          2        1         0
  CRAT WILD-TYPE        29         84         62         37       42         4
D812V3, multiclass
            clus
vv           CRAT MUTATED CRAT WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CRAT MUTATED       2   5   2   4
  CRAT WILD-TYPE    52 130 259  98
D812V4, multiclass
       clus
vv      CRAT MUTATED CRAT WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CRAT MUTATED     6   5   1   1
  CRAT WILD-TYPE 189 168  88  84
D812V5, multiclass
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  N0            6            189
  N1            5            168
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V6, binary
                cls
clus               0   1
  CRAT MUTATED    11   0
  CRAT WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED     11    0
  CRAT WILD-TYPE  471   38
   clus
vv  CRAT MUTATED CRAT WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D812V7, binary
                cls
clus               0   1
  CRAT MUTATED     9   5
  CRAT WILD-TYPE 163 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      9    5
  CRAT WILD-TYPE  163  401
        clus
vv       CRAT MUTATED CRAT WILD-TYPE
  FEMALE            9            163
  MALE              5            401
[1] 2 2
[1] FALSE
D812V8, binary
                cls
clus               0   1
  CRAT MUTATED    12   0
  CRAT WILD-TYPE 404 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED     12    0
  CRAT WILD-TYPE  404  102
     clus
vv    CRAT MUTATED CRAT WILD-TYPE
  NO            12            404
  YES            0            102
[1] 2 2
[1] FALSE
D812V9, continuous
D812V10, continuous
[1] "Remove cluster labels:" "CRAT MUTATED"          
clus
  CRAT MUTATED CRAT WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NF 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CRAT MUTATED       3                         1
  CRAT WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRAT MUTATED                                           0     8
  CRAT WILD-TYPE                                         1   349
D812V11, multiclass
                                           clus
vv                                          CRAT MUTATED CRAT WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V12, binary
                cls
clus               0   1
  CRAT MUTATED     0  10
  CRAT WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      0   10
  CRAT WILD-TYPE   10  388
                        clus
vv                       CRAT MUTATED CRAT WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(813) Variable = MON2 MUTATION ANALYSIS
D813V1, survival
                sevent
clus2              0   1
  MON2 MUTATED    14   5
  MON2 WILD-TYPE 324 211
  MON2 MUTATED MON2 WILD-TYPE 
            19            535 
  MON2 MUTATED MON2 WILD-TYPE 
             5            211 
$`MON2 MUTATED`
TCGA-JY-A6FB TCGA-JY-A6FA TCGA-LN-A4A3 TCGA-S8-A6BW TCGA-VR-A8ER TCGA-B7-5816 
       60.39        44.75        12.76        20.38        12.43        26.70 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7196 
        6.97         9.34         9.57        34.68        44.94        21.90 
TCGA-BR-8370 TCGA-BR-8680 TCGA-CG-5723 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GT 
        3.32        31.96       105.07        30.51        22.68         6.51 
TCGA-VQ-A8P2 
       38.14 

$`MON2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6453 
        4.08         4.08         9.67         6.18         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 
        8.98        40.21        30.90        31.20         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MON2 MUTATED MON2 WILD-TYPE 
          3.32           0.00 
  MON2 MUTATED MON2 WILD-TYPE 
        105.07         122.30 
  MON2 MUTATED MON2 WILD-TYPE 
         22.68          13.51 
[1] "3.3 - 105.1 (22.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D813V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MON2 MUTATED         1        0        2        2         3         3
  MON2 WILD-TYPE       9       20       44       29        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MON2 MUTATED           2          2          1          1        2         0
  MON2 WILD-TYPE        27         82         61         38       41         4
D813V3, multiclass
            clus
vv           MON2 MUTATED MON2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              2             29
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MON2 MUTATED       2   5   8   5
  MON2 WILD-TYPE    52 130 253  97
D813V4, multiclass
       clus
vv      MON2 MUTATED MON2 WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MON2 MUTATED     7   9   1   3
  MON2 WILD-TYPE 188 164  88  82
D813V5, multiclass
    clus
vv   MON2 MUTATED MON2 WILD-TYPE
  N0            7            188
  N1            9            164
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V6, binary
                cls
clus               0   1
  MON2 MUTATED    17   2
  MON2 WILD-TYPE 465  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED     17    2
  MON2 WILD-TYPE  465   36
   clus
vv  MON2 MUTATED MON2 WILD-TYPE
  0           17            465
  1            2             36
[1] 2 2
[1] FALSE
D813V7, binary
                cls
clus               0   1
  MON2 MUTATED     7  14
  MON2 WILD-TYPE 165 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED      7   14
  MON2 WILD-TYPE  165  392
        clus
vv       MON2 MUTATED MON2 WILD-TYPE
  FEMALE            7            165
  MALE             14            392
[1] 2 2
[1] FALSE
D813V8, binary
                cls
clus               0   1
  MON2 MUTATED    15   4
  MON2 WILD-TYPE 401  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED     15    4
  MON2 WILD-TYPE  401   98
     clus
vv    MON2 MUTATED MON2 WILD-TYPE
  NO            15            401
  YES            4             98
[1] 2 2
[1] FALSE
D813V9, continuous
[1] "Remove cluster labels:" "MON2 MUTATED"          
clus
  MON2 MUTATED MON2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" "MON2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MON2 WILD-TYPE" "MON2 WILD-TYPE" 
D813V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MON2 MUTATED       5                         0
  MON2 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MON2 MUTATED                                           0    12
  MON2 WILD-TYPE                                         1   345
D813V11, multiclass
                                           clus
vv                                          MON2 MUTATED MON2 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V12, binary
                cls
clus               0   1
  MON2 MUTATED     0  14
  MON2 WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED      0   14
  MON2 WILD-TYPE   10  384
                        clus
vv                       MON2 MUTATED MON2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(814) Variable = ZKSCAN1 MUTATION ANALYSIS
D814V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     5   6
  ZKSCAN1 WILD-TYPE 333 210
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
               11               543 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                6               210 
$`ZKSCAN1 MUTATED`
TCGA-KH-A6WC TCGA-L5-A8NH TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8289 TCGA-BR-8297 
        6.28        12.92        26.70        34.68         2.66         7.40 
TCGA-BR-8363 TCGA-BR-8487 TCGA-FP-7916 TCGA-IN-A6RL TCGA-RD-A8MW 
        0.26         1.12        14.07        13.35        37.91 

$`ZKSCAN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             0.26              0.00 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            37.91            122.30 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
            12.92             13.68 
[1] "0.3 - 37.9 (12.9)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.8"
D814V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZKSCAN1 MUTATED         0        1        1        0         2         1
  ZKSCAN1 WILD-TYPE      10       19       45       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN1 MUTATED           0          1          1          2        2
  ZKSCAN1 WILD-TYPE        29         83         61         37       41
                   vv
clus                STAGE IVA
  ZKSCAN1 MUTATED           0
  ZKSCAN1 WILD-TYPE         4
D814V3, multiclass
            clus
vv           ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZKSCAN1 MUTATED       2   2   3   4
  ZKSCAN1 WILD-TYPE    52 133 258  98
D814V4, multiclass
       clus
vv      ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  3               258
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZKSCAN1 MUTATED     6   2   1   3
  ZKSCAN1 WILD-TYPE 189 171  88  82
D814V5, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  N0               6               189
  N1               2               171
  N2               1                88
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V6, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     9   2
  ZKSCAN1 WILD-TYPE 473  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      9    2
  ZKSCAN1 WILD-TYPE  473   36
   clus
vv  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  0               9               473
  1               2                36
[1] 2 2
[1] FALSE
D814V7, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     5   7
  ZKSCAN1 WILD-TYPE 167 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      5    7
  ZKSCAN1 WILD-TYPE  167  399
        clus
vv       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  FEMALE               5               167
  MALE                 7               399
[1] 2 2
[1] FALSE
D814V8, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     8   2
  ZKSCAN1 WILD-TYPE 408 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      8    2
  ZKSCAN1 WILD-TYPE  408  100
     clus
vv    ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  NO                8               408
  YES               2               100
[1] 2 2
[1] FALSE
D814V9, continuous
[1] "Remove cluster labels:" "ZKSCAN1 MUTATED"       
clus
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
D814V10, continuous
[1] "Remove cluster labels:" "ZKSCAN1 MUTATED"       
clus
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-L5-A43C 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"ZKSCAN1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZKSCAN1 MUTATED       1                         0
  ZKSCAN1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZKSCAN1 MUTATED                                           0    11
  ZKSCAN1 WILD-TYPE                                         1   346
D814V11, multiclass
                                           clus
vv                                          ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V12, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     0  11
  ZKSCAN1 WILD-TYPE  10 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      0   11
  ZKSCAN1 WILD-TYPE   10  387
                        clus
vv                       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(815) Variable = HAUS6 MUTATION ANALYSIS
D815V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED     9   4
  HAUS6 WILD-TYPE 329 212
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             13             541 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              4             212 
$`HAUS6 MUTATED`
TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8680 TCGA-BR-A4QL 
       20.38         6.97        34.68        32.78        31.96        16.14 
TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-7132 
       12.43         6.02       105.07        28.96        11.44        77.29 
TCGA-VQ-A8P2 
       38.14 

$`HAUS6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       15.78         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        1.02         0.99         0.99        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
           6.02            0.00 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
         105.07          122.30 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          28.96           13.51 
[1] "6.0 - 105.1 (29.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D815V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAUS6 MUTATED         0        1        1        3         2         0
  HAUS6 WILD-TYPE      10       19       45       28        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS6 MUTATED           0          3          2          0        2         0
  HAUS6 WILD-TYPE        29         81         60         39       41         4
D815V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HAUS6 MUTATED       1   3   7   3
  HAUS6 WILD-TYPE    53 132 254  99
D815V4, multiclass
       clus
vv      HAUS6 MUTATED HAUS6 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HAUS6 MUTATED     5   6   1   2
  HAUS6 WILD-TYPE 190 167  88  83
D815V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             5             190
  N1             6             167
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V6, binary
                 cls
clus                0   1
  HAUS6 MUTATED    11   1
  HAUS6 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     11    1
  HAUS6 WILD-TYPE  471   37
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D815V7, binary
                 cls
clus                0   1
  HAUS6 MUTATED     4  10
  HAUS6 WILD-TYPE 168 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      4   10
  HAUS6 WILD-TYPE  168  396
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE             4             168
  MALE              10             396
[1] 2 2
[1] FALSE
D815V8, binary
                 cls
clus                0   1
  HAUS6 MUTATED    10   3
  HAUS6 WILD-TYPE 406  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     10    3
  HAUS6 WILD-TYPE  406   99
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO             10             406
  YES             3              99
[1] 2 2
[1] FALSE
D815V9, continuous
D815V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HAUS6 MUTATED       2                         0
  HAUS6 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAUS6 MUTATED                                           0     7
  HAUS6 WILD-TYPE                                         1   350
D815V11, multiclass
                                           clus
vv                                          HAUS6 MUTATED HAUS6 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V12, binary
                 cls
clus                0   1
  HAUS6 MUTATED     0   8
  HAUS6 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      0    8
  HAUS6 WILD-TYPE   10  390
                        clus
vv                       HAUS6 MUTATED HAUS6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(816) Variable = CHRNA4 MUTATION ANALYSIS
D816V1, survival
                  sevent
clus2                0   1
  CHRNA4 MUTATED    11   6
  CHRNA4 WILD-TYPE 327 210
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
              17              537 
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
               6              210 
$`CHRNA4 MUTATED`
TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A4OT TCGA-LN-A49X TCGA-R6-A6L6 TCGA-BR-4184 
      122.10        25.22         4.90        12.62         7.04         6.97 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-D7-8572 TCGA-D7-8573 TCGA-F1-6874 TCGA-FP-A4BF 
       31.96        11.77        16.80        19.50        14.47         5.52 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-VQ-A8P2 
       24.30         3.25         0.10        20.25        38.14 

$`CHRNA4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07         0.76         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
             0.1              0.0 
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
           122.1            122.3 
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
           14.47            13.55 
[1] "0.1 - 122.1 (14.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D816V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHRNA4 MUTATED         1        0        1        0         2         2
  CHRNA4 WILD-TYPE       9       20       45       31        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA4 MUTATED           0          5          1          2        2
  CHRNA4 WILD-TYPE        29         79         61         37       41
                  vv
clus               STAGE IVA
  CHRNA4 MUTATED           0
  CHRNA4 WILD-TYPE         4
D816V3, multiclass
            clus
vv           CHRNA4 MUTATED CHRNA4 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              5               79
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CHRNA4 MUTATED       1   2   8   5
  CHRNA4 WILD-TYPE    53 133 253  97
D816V4, multiclass
       clus
vv      CHRNA4 MUTATED CHRNA4 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 8              253
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CHRNA4 MUTATED     4   6   6   0
  CHRNA4 WILD-TYPE 191 167  83  85
D816V5, multiclass
    clus
vv   CHRNA4 MUTATED CHRNA4 WILD-TYPE
  N0              4              191
  N1              6              167
  N2              6               83
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V6, binary
                  cls
clus                 0   1
  CHRNA4 MUTATED    14   2
  CHRNA4 WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA4 MUTATED     14    2
  CHRNA4 WILD-TYPE  468   36
   clus
vv  CHRNA4 MUTATED CHRNA4 WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D816V7, binary
                  cls
clus                 0   1
  CHRNA4 MUTATED     2  16
  CHRNA4 WILD-TYPE 170 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA4 MUTATED      2   16
  CHRNA4 WILD-TYPE  170  390
        clus
vv       CHRNA4 MUTATED CHRNA4 WILD-TYPE
  FEMALE              2              170
  MALE               16              390
[1] 2 2
[1] FALSE
D816V8, binary
                  cls
clus                 0   1
  CHRNA4 MUTATED    15   2
  CHRNA4 WILD-TYPE 401 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA4 MUTATED     15    2
  CHRNA4 WILD-TYPE  401  100
     clus
vv    CHRNA4 MUTATED CHRNA4 WILD-TYPE
  NO              15              401
  YES              2              100
[1] 2 2
[1] FALSE
D816V9, continuous
[1] "Remove cluster labels:" "CHRNA4 MUTATED"        
clus
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
D816V10, continuous
[1] "Remove cluster labels:" "CHRNA4 MUTATED"        
clus
  CHRNA4 MUTATED CHRNA4 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" "CHRNA4 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CHRNA4 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CHRNA4 MUTATED       7                         0
  CHRNA4 WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHRNA4 MUTATED                                           0    11
  CHRNA4 WILD-TYPE                                         1   346
D816V11, multiclass
                                           clus
vv                                          CHRNA4 MUTATED CHRNA4 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V12, binary
                  cls
clus                 0   1
  CHRNA4 MUTATED     0  14
  CHRNA4 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA4 MUTATED      0   14
  CHRNA4 WILD-TYPE   10  384
                        clus
vv                       CHRNA4 MUTATED CHRNA4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(817) Variable = FBXO43 MUTATION ANALYSIS
D817V1, survival
                  sevent
clus2                0   1
  FBXO43 MUTATED     9   5
  FBXO43 WILD-TYPE 329 211
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              14              540 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
               5              211 
$`FBXO43 MUTATED`
TCGA-2H-A9GG TCGA-LN-A5U5 TCGA-VR-AA7B TCGA-Z6-A9VB TCGA-BR-4184 TCGA-BR-6452 
       20.05         4.47        11.24         1.32         6.97        34.68 
TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5721 TCGA-HU-8602 
        4.31        25.18        16.14        15.95         6.02        22.32 
TCGA-HU-A4H8 TCGA-MX-A5UJ 
       14.07        19.73 

$`FBXO43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       14.79         7.36        25.05         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  FBXO43 MUTATED FBXO43 WILD-TYPE 
            1.32             0.00 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
           34.68           122.30 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
           15.01            13.53 
[1] "1.3 - 34.7 (15.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D817V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO43 MUTATED         0        0        2        1         1         1
  FBXO43 WILD-TYPE      10       20       44       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO43 MUTATED           1          4          1          0        3
  FBXO43 WILD-TYPE        28         80         61         39       40
                  vv
clus               STAGE IVA
  FBXO43 MUTATED           0
  FBXO43 WILD-TYPE         4
D817V3, multiclass
            clus
vv           FBXO43 MUTATED FBXO43 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FBXO43 MUTATED       1   2   8   3
  FBXO43 WILD-TYPE    53 133 253  99
D817V4, multiclass
       clus
vv      FBXO43 MUTATED FBXO43 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 8              253
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FBXO43 MUTATED     3   8   1   2
  FBXO43 WILD-TYPE 192 165  88  83
D817V5, multiclass
    clus
vv   FBXO43 MUTATED FBXO43 WILD-TYPE
  N0              3              192
  N1              8              165
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V6, binary
                  cls
clus                 0   1
  FBXO43 MUTATED    11   2
  FBXO43 WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED     11    2
  FBXO43 WILD-TYPE  471   36
   clus
vv  FBXO43 MUTATED FBXO43 WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D817V7, binary
                  cls
clus                 0   1
  FBXO43 MUTATED     6   8
  FBXO43 WILD-TYPE 166 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED      6    8
  FBXO43 WILD-TYPE  166  398
        clus
vv       FBXO43 MUTATED FBXO43 WILD-TYPE
  FEMALE              6              166
  MALE                8              398
[1] 2 2
[1] FALSE
D817V8, binary
                  cls
clus                 0   1
  FBXO43 MUTATED    14   0
  FBXO43 WILD-TYPE 402 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED     14    0
  FBXO43 WILD-TYPE  402  102
     clus
vv    FBXO43 MUTATED FBXO43 WILD-TYPE
  NO              14              402
  YES              0              102
[1] 2 2
[1] FALSE
D817V9, continuous
[1] "Remove cluster labels:" "FBXO43 MUTATED"        
clus
  FBXO43 MUTATED FBXO43 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7D 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FBXO43 WILD-TYPE" "FBXO43 WILD-TYPE" 
D817V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO43 MUTATED       3                         0
  FBXO43 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO43 MUTATED                                           0     8
  FBXO43 WILD-TYPE                                         1   349
D817V11, multiclass
                                           clus
vv                                          FBXO43 MUTATED FBXO43 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V12, binary
                  cls
clus                 0   1
  FBXO43 MUTATED     0  10
  FBXO43 WILD-TYPE  10 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED      0   10
  FBXO43 WILD-TYPE   10  388
                        clus
vv                       FBXO43 MUTATED FBXO43 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(818) Variable = PIK3R1 MUTATION ANALYSIS
D818V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    11   2
  PIK3R1 WILD-TYPE 327 214
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              541 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               2              214 
$`PIK3R1 MUTATED`
TCGA-JY-A93C TCGA-L5-A4OQ TCGA-LN-A8I0 TCGA-V5-AASX TCGA-VR-AA4D TCGA-BR-6452 
       23.18         1.38        13.38         8.98        46.19        34.68 
TCGA-CG-5721 TCGA-D7-6528 TCGA-D7-8572 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-R5-A7ZI 
        6.02        15.22        16.80        29.98         6.58        74.53 
TCGA-VQ-A8P2 
       38.14 

$`PIK3R1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            1.38             0.00 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           74.53           122.30 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           16.80            13.51 
[1] "1.4 - 74.5 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D818V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3R1 MUTATED         1        0        1        0         3         3
  PIK3R1 WILD-TYPE       9       20       45       31        81        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R1 MUTATED           0          3          1          0        2
  PIK3R1 WILD-TYPE        29         81         61         39       41
                  vv
clus               STAGE IVA
  PIK3R1 MUTATED           0
  PIK3R1 WILD-TYPE         4
D818V3, multiclass
            clus
vv           PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PIK3R1 MUTATED       2   5   3   4
  PIK3R1 WILD-TYPE    52 130 258  98
D818V4, multiclass
       clus
vv      PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T0+T1              2               52
  T2                 5              130
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIK3R1 MUTATED     4   7   3   0
  PIK3R1 WILD-TYPE 191 166  86  85
D818V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0              4              191
  N1              7              166
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V6, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    12   1
  PIK3R1 WILD-TYPE 470  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     12    1
  PIK3R1 WILD-TYPE  470   37
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0             12              470
  1              1               37
[1] 2 2
[1] FALSE
D818V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     4  12
  PIK3R1 WILD-TYPE 168 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      4   12
  PIK3R1 WILD-TYPE  168  394
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              4              168
  MALE               12              394
[1] 2 2
[1] FALSE
D818V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    11   2
  PIK3R1 WILD-TYPE 405 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     11    2
  PIK3R1 WILD-TYPE  405  100
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              11              405
  YES              2              100
[1] 2 2
[1] FALSE
D818V9, continuous
[1] "Remove cluster labels:" "PIK3R1 MUTATED"        
clus
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
D818V10, continuous
[1] "Remove cluster labels:" "PIK3R1 MUTATED"        
clus
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3R1 MUTATED       4                         1
  PIK3R1 WILD-TYPE   129                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3R1 MUTATED                                           0    10
  PIK3R1 WILD-TYPE                                         1   347
D818V11, multiclass
                                           clus
vv                                          PIK3R1 MUTATED PIK3R1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V12, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED     1  10
  PIK3R1 WILD-TYPE   9 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      1   10
  PIK3R1 WILD-TYPE    9  388
                        clus
vv                       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(819) Variable = ZMYND19 MUTATION ANALYSIS
D819V1, survival
                   sevent
clus2                 0   1
  ZMYND19 MUTATED     4   4
  ZMYND19 WILD-TYPE 334 212
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                8               546 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                4               212 
$`ZMYND19 MUTATED`
TCGA-L5-A43J TCGA-LN-A4A5 TCGA-BR-6452 TCGA-BR-8590 TCGA-CD-A4MG TCGA-CG-5723 
        4.31        22.39        34.68         9.34         6.58       105.07 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`ZMYND19 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
             4.31              0.00 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
           105.07            122.30 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
            18.23             13.53 
[1] "4.3 - 105.1 (18.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D819V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYND19 MUTATED         0        0        2        1         3         1
  ZMYND19 WILD-TYPE      10       20       44       30        81        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND19 MUTATED           0          0          0          1        1
  ZMYND19 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  ZMYND19 MUTATED           0
  ZMYND19 WILD-TYPE         4
D819V3, multiclass
            clus
vv           ZMYND19 MUTATED ZMYND19 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZMYND19 MUTATED       1   3   3   2
  ZMYND19 WILD-TYPE    53 132 258 100
D819V4, multiclass
       clus
vv      ZMYND19 MUTATED ZMYND19 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZMYND19 MUTATED     5   3   1   0
  ZMYND19 WILD-TYPE 190 170  88  85
D819V5, multiclass
    clus
vv   ZMYND19 MUTATED ZMYND19 WILD-TYPE
  N0               5               190
  N1               3               170
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V6, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     8   1
  ZMYND19 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      8    1
  ZMYND19 WILD-TYPE  474   37
   clus
vv  ZMYND19 MUTATED ZMYND19 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D819V7, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     3   7
  ZMYND19 WILD-TYPE 169 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      3    7
  ZMYND19 WILD-TYPE  169  399
        clus
vv       ZMYND19 MUTATED ZMYND19 WILD-TYPE
  FEMALE               3               169
  MALE                 7               399
[1] 2 2
[1] FALSE
D819V8, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     7   0
  ZMYND19 WILD-TYPE 409 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      7    0
  ZMYND19 WILD-TYPE  409  102
     clus
vv    ZMYND19 MUTATED ZMYND19 WILD-TYPE
  NO                7               409
  YES               0               102
[1] 2 2
[1] FALSE
D819V9, continuous
[1] "Remove cluster labels:" "ZMYND19 MUTATED"       
clus
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A6 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
D819V10, continuous
[1] "Remove cluster labels:" "ZMYND19 MUTATED"       
clus
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" "ZMYND19 WILD-TYPE" 
       TCGA-Z6-AAPN 
"ZMYND19 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZMYND19 MUTATED       3                         0
  ZMYND19 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYND19 MUTATED                                           0     5
  ZMYND19 WILD-TYPE                                         1   352
D819V11, multiclass
                                           clus
vv                                          ZMYND19 MUTATED ZMYND19 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V12, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     1   6
  ZMYND19 WILD-TYPE   9 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      1    6
  ZMYND19 WILD-TYPE    9  392
                        clus
vv                       ZMYND19 MUTATED ZMYND19 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(820) Variable = DYRK1A MUTATION ANALYSIS
D820V1, survival
                  sevent
clus2                0   1
  DYRK1A MUTATED    12   4
  DYRK1A WILD-TYPE 326 212
  DYRK1A MUTATED DYRK1A WILD-TYPE 
              16              538 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               4              212 
$`DYRK1A MUTATED`
TCGA-L5-A4OI TCGA-FP-A8CX TCGA-JY-A6FG TCGA-L5-A4OJ TCGA-L5-A88W TCGA-B7-5816 
       19.99         0.23        41.52        21.01        25.12        26.70 
TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-8487 TCGA-BR-8680 
        6.97        30.90        21.90        35.24         1.12        31.96 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-IN-A6RL 
       11.08        77.29        30.51        13.35 

$`DYRK1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48         2.60         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       44.94         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DYRK1A MUTATED DYRK1A WILD-TYPE 
            0.23             0.00 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
           77.29           122.30 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
          23.510           13.495 
[1] "0.2 - 77.3 (23.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D820V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYRK1A MUTATED         1        0        0        2         4         1
  DYRK1A WILD-TYPE       9       20       46       29        80        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYRK1A MUTATED           1          3          0          3        2
  DYRK1A WILD-TYPE        28         81         62         36       41
                  vv
clus               STAGE IVA
  DYRK1A MUTATED           0
  DYRK1A WILD-TYPE         4
D820V3, multiclass
            clus
vv           DYRK1A MUTATED DYRK1A WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DYRK1A MUTATED       1   2  10   4
  DYRK1A WILD-TYPE    53 133 251  98
D820V4, multiclass
       clus
vv      DYRK1A MUTATED DYRK1A WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                10              251
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DYRK1A MUTATED     7   4   2   4
  DYRK1A WILD-TYPE 188 169  87  81
D820V5, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  N0              7              188
  N1              4              169
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V6, binary
                  cls
clus                 0   1
  DYRK1A MUTATED    11   2
  DYRK1A WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED     11    2
  DYRK1A WILD-TYPE  471   36
   clus
vv  DYRK1A MUTATED DYRK1A WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D820V7, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     5  12
  DYRK1A WILD-TYPE 167 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      5   12
  DYRK1A WILD-TYPE  167  394
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  FEMALE              5              167
  MALE               12              394
[1] 2 2
[1] FALSE
D820V8, binary
                  cls
clus                 0   1
  DYRK1A MUTATED    11   4
  DYRK1A WILD-TYPE 405  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED     11    4
  DYRK1A WILD-TYPE  405   98
     clus
vv    DYRK1A MUTATED DYRK1A WILD-TYPE
  NO              11              405
  YES              4               98
[1] 2 2
[1] FALSE
D820V9, continuous
D820V10, continuous
[1] "Remove cluster labels:" "DYRK1A MUTATED"        
clus
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" "DYRK1A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DYRK1A MUTATED       1                         1
  DYRK1A WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYRK1A MUTATED                                           0    13
  DYRK1A WILD-TYPE                                         1   344
D820V11, multiclass
                                           clus
vv                                          DYRK1A MUTATED DYRK1A WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V12, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     0  11
  DYRK1A WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      0   11
  DYRK1A WILD-TYPE   10  387
                        clus
vv                       DYRK1A MUTATED DYRK1A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(821) Variable = KIF6 MUTATION ANALYSIS
D821V1, survival
                sevent
clus2              0   1
  KIF6 MUTATED    10   7
  KIF6 WILD-TYPE 328 209
  KIF6 MUTATED KIF6 WILD-TYPE 
            17            537 
  KIF6 MUTATED KIF6 WILD-TYPE 
             7            209 
$`KIF6 MUTATED`
TCGA-L5-A4OI TCGA-L5-A88T TCGA-JY-A6FG TCGA-L5-A4OO TCGA-L5-A8NH TCGA-LN-A49P 
       19.99        22.82        41.52         3.32        12.92        12.33 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8683 TCGA-CD-A4MI 
        4.08         9.34        34.68        31.10         9.86        11.77 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-R5-A7O7 TCGA-SW-A7EA TCGA-VQ-A8E2 
       11.44        11.08        45.67        19.04        43.36 

$`KIF6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        5.92        10.45        12.66        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        13.25        13.02        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KIF6 MUTATED KIF6 WILD-TYPE 
          3.32           0.00 
  KIF6 MUTATED KIF6 WILD-TYPE 
         45.67         122.30 
  KIF6 MUTATED KIF6 WILD-TYPE 
         12.92          13.58 
[1] "3.3 - 45.7 (12.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D821V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF6 MUTATED         0        0        1        0         3         1
  KIF6 WILD-TYPE      10       20       45       31        81        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF6 MUTATED           1          2          3          3        2         0
  KIF6 WILD-TYPE        28         82         59         36       41         4
D821V3, multiclass
            clus
vv           KIF6 MUTATED KIF6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            3             59
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  KIF6 MUTATED       1   2  11   2
  KIF6 WILD-TYPE    53 133 250 100
D821V4, multiclass
       clus
vv      KIF6 MUTATED KIF6 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3              11            250
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  KIF6 MUTATED     5   7   3   3
  KIF6 WILD-TYPE 190 166  86  82
D821V5, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  N0            5            190
  N1            7            166
  N2            3             86
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V6, binary
                cls
clus               0   1
  KIF6 MUTATED    15   2
  KIF6 WILD-TYPE 467  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED     15    2
  KIF6 WILD-TYPE  467   36
   clus
vv  KIF6 MUTATED KIF6 WILD-TYPE
  0           15            467
  1            2             36
[1] 2 2
[1] FALSE
D821V7, binary
                cls
clus               0   1
  KIF6 MUTATED     6  12
  KIF6 WILD-TYPE 166 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      6   12
  KIF6 WILD-TYPE  166  394
        clus
vv       KIF6 MUTATED KIF6 WILD-TYPE
  FEMALE            6            166
  MALE             12            394
[1] 2 2
[1] FALSE
D821V8, binary
                cls
clus               0   1
  KIF6 MUTATED    12   3
  KIF6 WILD-TYPE 404  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED     12    3
  KIF6 WILD-TYPE  404   99
     clus
vv    KIF6 MUTATED KIF6 WILD-TYPE
  NO            12            404
  YES            3             99
[1] 2 2
[1] FALSE
D821V9, continuous
[1] "Remove cluster labels:" "KIF6 MUTATED"          
clus
  KIF6 MUTATED KIF6 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49R 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"KIF6 WILD-TYPE" "KIF6 WILD-TYPE" "KIF6 WILD-TYPE" 
D821V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KIF6 MUTATED       4                         1
  KIF6 WILD-TYPE   129                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF6 MUTATED                                           0    13
  KIF6 WILD-TYPE                                         1   344
D821V11, multiclass
                                           clus
vv                                          KIF6 MUTATED KIF6 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V12, binary
                cls
clus               0   1
  KIF6 MUTATED     1  11
  KIF6 WILD-TYPE   9 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      1   11
  KIF6 WILD-TYPE    9  387
                        clus
vv                       KIF6 MUTATED KIF6 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(822) Variable = XPO1 MUTATION ANALYSIS
D822V1, survival
                sevent
clus2              0   1
  XPO1 MUTATED    13   1
  XPO1 WILD-TYPE 325 215
  XPO1 MUTATED XPO1 WILD-TYPE 
            14            540 
  XPO1 MUTATED XPO1 WILD-TYPE 
             1            215 
$`XPO1 MUTATED`
TCGA-JY-A6FD TCGA-L5-A8NL TCGA-LN-A9FQ TCGA-Z6-A8JD TCGA-BR-4280 TCGA-BR-6452 
       68.02        13.22        12.85         3.42         6.61        34.68 
TCGA-BR-8078 TCGA-BR-8680 TCGA-HU-A4G8 TCGA-IN-A7NT TCGA-IN-AB1X TCGA-MX-A5UJ 
       29.59        31.96        22.68        10.62        13.51        19.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       37.41        38.14 

$`XPO1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        6.74        12.59         6.51        11.70        15.75         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.25        13.02        43.36        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  XPO1 MUTATED XPO1 WILD-TYPE 
          3.42           0.00 
  XPO1 MUTATED XPO1 WILD-TYPE 
         68.02         122.30 
  XPO1 MUTATED XPO1 WILD-TYPE 
        21.205         13.530 
[1] "3.4 - 68.0 (21.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "7.3"
D822V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XPO1 MUTATED         0        0        0        0         4         4
  XPO1 WILD-TYPE      10       20       46       31        80        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XPO1 MUTATED           2          2          0          0        2         0
  XPO1 WILD-TYPE        27         82         62         39       41         4
D822V3, multiclass
            clus
vv           XPO1 MUTATED XPO1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             4             79
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  XPO1 MUTATED       0   1  10   3
  XPO1 WILD-TYPE    54 134 251  99
D822V4, multiclass
       clus
vv      XPO1 MUTATED XPO1 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3              10            251
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  XPO1 MUTATED     6   6   2   0
  XPO1 WILD-TYPE 189 167  87  85
D822V5, multiclass
    clus
vv   XPO1 MUTATED XPO1 WILD-TYPE
  N0            6            189
  N1            6            167
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V6, binary
                cls
clus               0   1
  XPO1 MUTATED    12   2
  XPO1 WILD-TYPE 470  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO1 MUTATED     12    2
  XPO1 WILD-TYPE  470   36
   clus
vv  XPO1 MUTATED XPO1 WILD-TYPE
  0           12            470
  1            2             36
[1] 2 2
[1] FALSE
D822V7, binary
                cls
clus               0   1
  XPO1 MUTATED     8   6
  XPO1 WILD-TYPE 164 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO1 MUTATED      8    6
  XPO1 WILD-TYPE  164  400
        clus
vv       XPO1 MUTATED XPO1 WILD-TYPE
  FEMALE            8            164
  MALE              6            400
[1] 2 2
[1] FALSE
D822V8, binary
                cls
clus               0   1
  XPO1 MUTATED    12   1
  XPO1 WILD-TYPE 404 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO1 MUTATED     12    1
  XPO1 WILD-TYPE  404  101
     clus
vv    XPO1 MUTATED XPO1 WILD-TYPE
  NO            12            404
  YES            1            101
[1] 2 2
[1] FALSE
D822V9, continuous
[1] "Remove cluster labels:" "XPO1 MUTATED"          
clus
  XPO1 MUTATED XPO1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JE 
"XPO1 WILD-TYPE" "XPO1 WILD-TYPE" "XPO1 WILD-TYPE" 
D822V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  XPO1 MUTATED       4                         0
  XPO1 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XPO1 MUTATED                                           0    10
  XPO1 WILD-TYPE                                         1   347
D822V11, multiclass
                                           clus
vv                                          XPO1 MUTATED XPO1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V12, binary
                cls
clus               0   1
  XPO1 MUTATED     0  10
  XPO1 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO1 MUTATED      0   10
  XPO1 WILD-TYPE   10  388
                        clus
vv                       XPO1 MUTATED XPO1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(823) Variable = WHSC1L1 MUTATION ANALYSIS
D823V1, survival
                   sevent
clus2                 0   1
  WHSC1L1 MUTATED    15   4
  WHSC1L1 WILD-TYPE 323 212
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               19               535 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                4               212 
$`WHSC1L1 MUTATED`
TCGA-L5-A8NG TCGA-KB-A93G TCGA-2H-A9GI TCGA-2H-A9GO TCGA-LN-A4MR TCGA-VR-A8EW 
       35.97        20.15        14.30        16.24        13.22         8.12 
TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-8536 TCGA-CD-A4MJ 
       26.70         9.34        34.68         4.31        12.43        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-D7-6822 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-RD-A8N1 
       27.02        15.95        12.33        29.98         6.58       115.69 
TCGA-VQ-A8P2 
       38.14 

$`WHSC1L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       12.43        11.61         6.58        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
             4.31              0.00 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
           115.69            122.30 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
            15.95             13.51 
[1] "4.3 - 115.7 (15.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.3"
D823V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WHSC1L1 MUTATED         0        0        6        2         3         2
  WHSC1L1 WILD-TYPE      10       20       40       29        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WHSC1L1 MUTATED           2          2          2          0        0
  WHSC1L1 WILD-TYPE        27         82         60         39       43
                   vv
clus                STAGE IVA
  WHSC1L1 MUTATED           1
  WHSC1L1 WILD-TYPE         3
D823V3, multiclass
            clus
vv           WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 6                40
  STAGE II                 2                29
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                2                27
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  WHSC1L1 MUTATED       0   9   8   3
  WHSC1L1 WILD-TYPE    54 126 253  99
D823V4, multiclass
       clus
vv      WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  T0+T1               0                54
  T2                  9               126
  T3                  8               253
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  WHSC1L1 MUTATED    11   9   2   0
  WHSC1L1 WILD-TYPE 184 164  87  85
D823V5, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  N0              11               184
  N1               9               164
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V6, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED    22   1
  WHSC1L1 WILD-TYPE 460  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED     22    1
  WHSC1L1 WILD-TYPE  460   37
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0              22               460
  1               1                37
[1] 2 2
[1] FALSE
D823V7, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     6  17
  WHSC1L1 WILD-TYPE 166 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      6   17
  WHSC1L1 WILD-TYPE  166  389
        clus
vv       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  FEMALE               6               166
  MALE                17               389
[1] 2 2
[1] FALSE
D823V8, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED    16   2
  WHSC1L1 WILD-TYPE 400 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED     16    2
  WHSC1L1 WILD-TYPE  400  100
     clus
vv    WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  NO               16               400
  YES               2               100
[1] 2 2
[1] FALSE
D823V9, continuous
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
clus
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
D823V10, continuous
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
clus
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  WHSC1L1 MUTATED       6                         0
  WHSC1L1 WILD-TYPE   127                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WHSC1L1 MUTATED                                           0    12
  WHSC1L1 WILD-TYPE                                         1   345
D823V11, multiclass
                                           clus
vv                                          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V12, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     0  14
  WHSC1L1 WILD-TYPE  10 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0   14
  WHSC1L1 WILD-TYPE   10  384
                        clus
vv                       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              14               384
[1] 2 2
[1] FALSE

Clustering(824) Variable = NAA25 MUTATION ANALYSIS
D824V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED    11   7
  NAA25 WILD-TYPE 327 209
  NAA25 MUTATED NAA25 WILD-TYPE 
             18             536 
  NAA25 MUTATED NAA25 WILD-TYPE 
              7             209 
$`NAA25 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A8NK TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-VR-A8EP 
       19.99        21.99        13.55         9.30         7.00        27.09 
TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 TCGA-CD-8534 
       19.33        39.78        32.25         0.26        31.27        12.07 
TCGA-CD-A486 TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-A6EV TCGA-HU-A4GX TCGA-HU-A4H3 
        6.31        11.77        65.10        11.24        20.25        29.00 

$`NAA25 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NAA25 MUTATED NAA25 WILD-TYPE 
           0.26            0.00 
  NAA25 MUTATED NAA25 WILD-TYPE 
           65.1           122.3 
  NAA25 MUTATED NAA25 WILD-TYPE 
          19.66           13.51 
[1] "0.3 - 65.1 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D824V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA25 MUTATED         1        0        2        1         2         6
  NAA25 WILD-TYPE       9       20       44       30        82        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA25 MUTATED           0          1          1          4        1         0
  NAA25 WILD-TYPE        29         83         61         35       42         4
D824V3, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NAA25 MUTATED       2   3   8   6
  NAA25 WILD-TYPE    52 132 253  96
D824V4, multiclass
       clus
vv      NAA25 MUTATED NAA25 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                8             253
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NAA25 MUTATED     7   6   3   3
  NAA25 WILD-TYPE 188 167  86  82
D824V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V6, binary
                 cls
clus                0   1
  NAA25 MUTATED    16   1
  NAA25 WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     16    1
  NAA25 WILD-TYPE  466   37
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D824V7, binary
                 cls
clus                0   1
  NAA25 MUTATED    11   9
  NAA25 WILD-TYPE 161 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     11    9
  NAA25 WILD-TYPE  161  397
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE            11             161
  MALE               9             397
[1] 2 2
[1] FALSE
D824V8, binary
                 cls
clus                0   1
  NAA25 MUTATED    17   0
  NAA25 WILD-TYPE 399 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     17    0
  NAA25 WILD-TYPE  399  102
     clus
vv    NAA25 MUTATED NAA25 WILD-TYPE
  NO             17             399
  YES             0             102
[1] 2 2
[1] FALSE
D824V9, continuous
[1] "Remove cluster labels:" "NAA25 MUTATED"         
clus
  NAA25 MUTATED NAA25 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NAA25 WILD-TYPE" "NAA25 WILD-TYPE" "NAA25 WILD-TYPE" 
D824V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAA25 MUTATED       5                         1
  NAA25 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAA25 MUTATED                                           0    12
  NAA25 WILD-TYPE                                         1   345
D824V11, multiclass
                                           clus
vv                                          NAA25 MUTATED NAA25 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V12, binary
                 cls
clus                0   1
  NAA25 MUTATED     1  14
  NAA25 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      1   14
  NAA25 WILD-TYPE    9  384
                        clus
vv                       NAA25 MUTATED NAA25 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(825) Variable = MANEA MUTATION ANALYSIS
D825V1, survival
                 sevent
clus2               0   1
  MANEA MUTATED    10   4
  MANEA WILD-TYPE 328 212
  MANEA MUTATED MANEA WILD-TYPE 
             14             540 
  MANEA MUTATED MANEA WILD-TYPE 
              4             212 
$`MANEA MUTATED`
TCGA-IG-A5B8 TCGA-L5-A8NL TCGA-V5-AASV TCGA-VR-AA7B TCGA-B7-A5TI TCGA-BR-6852 
        0.79        13.22        15.35        11.24        19.56        44.94 
TCGA-BR-8368 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-HU-A4G9 TCGA-HU-A4GN 
        4.31        12.82         6.58        11.77        24.20        29.98 
TCGA-IN-7808 TCGA-VQ-A8P2 
        3.45        38.14 

$`MANEA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MANEA MUTATED MANEA WILD-TYPE 
           0.79            0.00 
  MANEA MUTATED MANEA WILD-TYPE 
          44.94          122.30 
  MANEA MUTATED MANEA WILD-TYPE 
          13.02           13.63 
[1] "0.8 - 44.9 (13.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D825V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MANEA MUTATED         0        1        2        0         3         1
  MANEA WILD-TYPE      10       19       44       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MANEA MUTATED           1          3          0          1        1         0
  MANEA WILD-TYPE        28         81         62         38       42         4
D825V3, multiclass
            clus
vv           MANEA MUTATED MANEA WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MANEA MUTATED       1   2   9   2
  MANEA WILD-TYPE    53 133 252 100
D825V4, multiclass
       clus
vv      MANEA MUTATED MANEA WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                9             252
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MANEA MUTATED     6   6   0   3
  MANEA WILD-TYPE 189 167  89  82
D825V5, multiclass
    clus
vv   MANEA MUTATED MANEA WILD-TYPE
  N0             6             189
  N1             6             167
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V6, binary
                 cls
clus                0   1
  MANEA MUTATED    12   2
  MANEA WILD-TYPE 470  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANEA MUTATED     12    2
  MANEA WILD-TYPE  470   36
   clus
vv  MANEA MUTATED MANEA WILD-TYPE
  0            12             470
  1             2              36
[1] 2 2
[1] FALSE
D825V7, binary
                 cls
clus                0   1
  MANEA MUTATED     5  10
  MANEA WILD-TYPE 167 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANEA MUTATED      5   10
  MANEA WILD-TYPE  167  396
        clus
vv       MANEA MUTATED MANEA WILD-TYPE
  FEMALE             5             167
  MALE              10             396
[1] 2 2
[1] FALSE
D825V8, binary
                 cls
clus                0   1
  MANEA MUTATED    11   2
  MANEA WILD-TYPE 405 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANEA MUTATED     11    2
  MANEA WILD-TYPE  405  100
     clus
vv    MANEA MUTATED MANEA WILD-TYPE
  NO             11             405
  YES             2             100
[1] 2 2
[1] FALSE
D825V9, continuous
[1] "Remove cluster labels:" "MANEA MUTATED"         
clus
  MANEA MUTATED MANEA WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7D 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" 
D825V10, continuous
[1] "Remove cluster labels:" "MANEA MUTATED"         
clus
  MANEA MUTATED MANEA WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A6QS 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" "MANEA WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MANEA MUTATED       5                         1
  MANEA WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MANEA MUTATED                                           0     9
  MANEA WILD-TYPE                                         1   348
D825V11, multiclass
                                           clus
vv                                          MANEA MUTATED MANEA WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V12, binary
                 cls
clus                0   1
  MANEA MUTATED     0  12
  MANEA WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANEA MUTATED      0   12
  MANEA WILD-TYPE   10  386
                        clus
vv                       MANEA MUTATED MANEA WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(826) Variable = CCR3 MUTATION ANALYSIS
D826V1, survival
                sevent
clus2              0   1
  CCR3 MUTATED     8   5
  CCR3 WILD-TYPE 330 211
  CCR3 MUTATED CCR3 WILD-TYPE 
            13            541 
  CCR3 MUTATED CCR3 WILD-TYPE 
             5            211 
$`CCR3 MUTATED`
TCGA-L5-A43J TCGA-JY-A6FD TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MI 
        4.31        68.02         9.34        34.68         6.18        11.77 
TCGA-CG-4305 TCGA-CG-4441 TCGA-FP-A9TM TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-RD-A7BT 
       15.95        14.01         6.21        29.98        29.00         8.61 
TCGA-VQ-A8P2 
       38.14 

$`CCR3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CCR3 MUTATED CCR3 WILD-TYPE 
          4.31           0.00 
  CCR3 MUTATED CCR3 WILD-TYPE 
         68.02         122.30 
  CCR3 MUTATED CCR3 WILD-TYPE 
         14.01          13.55 
[1] "4.3 - 68.0 (14.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D826V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCR3 MUTATED         0        0        0        1         4         1
  CCR3 WILD-TYPE      10       20       46       30        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCR3 MUTATED           0          3          0          1        1         0
  CCR3 WILD-TYPE        29         81         62         38       42         4
D826V3, multiclass
            clus
vv           CCR3 MUTATED CCR3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CCR3 MUTATED       1   3   6   2
  CCR3 WILD-TYPE    53 132 255 100
D826V4, multiclass
       clus
vv      CCR3 MUTATED CCR3 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               6            255
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CCR3 MUTATED     4   6   1   2
  CCR3 WILD-TYPE 191 167  88  83
D826V5, multiclass
    clus
vv   CCR3 MUTATED CCR3 WILD-TYPE
  N0            4            191
  N1            6            167
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V6, binary
                cls
clus               0   1
  CCR3 MUTATED    12   0
  CCR3 WILD-TYPE 470  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED     12    0
  CCR3 WILD-TYPE  470   38
   clus
vv  CCR3 MUTATED CCR3 WILD-TYPE
  0           12            470
  1            0             38
[1] 2 2
[1] FALSE
D826V7, binary
                cls
clus               0   1
  CCR3 MUTATED     3  10
  CCR3 WILD-TYPE 169 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      3   10
  CCR3 WILD-TYPE  169  396
        clus
vv       CCR3 MUTATED CCR3 WILD-TYPE
  FEMALE            3            169
  MALE             10            396
[1] 2 2
[1] FALSE
D826V8, binary
                cls
clus               0   1
  CCR3 MUTATED     8   2
  CCR3 WILD-TYPE 408 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      8    2
  CCR3 WILD-TYPE  408  100
     clus
vv    CCR3 MUTATED CCR3 WILD-TYPE
  NO             8            408
  YES            2            100
[1] 2 2
[1] FALSE
D826V9, continuous
D826V10, continuous
[1] "Remove cluster labels:" "CCR3 MUTATED"          
clus
  CCR3 MUTATED CCR3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"CCR3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CCR3 MUTATED       4                         0
  CCR3 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCR3 MUTATED                                           1     6
  CCR3 WILD-TYPE                                         0   351
D826V11, multiclass
                                           clus
vv                                          CCR3 MUTATED CCR3 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V12, binary
                cls
clus               0   1
  CCR3 MUTATED     0   8
  CCR3 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      0    8
  CCR3 WILD-TYPE   10  390
                        clus
vv                       CCR3 MUTATED CCR3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(827) Variable = HAX1 MUTATION ANALYSIS
D827V1, survival
                sevent
clus2              0   1
  HAX1 MUTATED     4   3
  HAX1 WILD-TYPE 334 213
  HAX1 MUTATED HAX1 WILD-TYPE 
             7            547 
  HAX1 MUTATED HAX1 WILD-TYPE 
             3            213 
$`HAX1 MUTATED`
TCGA-2H-A9GK TCGA-IG-A5B8 TCGA-BR-8078 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HF-7132 
        7.63         0.79        29.59         6.02        11.44        77.29 
TCGA-VQ-A8P2 
       38.14 

$`HAX1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HAX1 MUTATED HAX1 WILD-TYPE 
          0.79           0.00 
  HAX1 MUTATED HAX1 WILD-TYPE 
         77.29         122.30 
  HAX1 MUTATED HAX1 WILD-TYPE 
         11.44          13.58 
[1] "0.8 - 77.3 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D827V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAX1 MUTATED         0        0        1        1         0         1
  HAX1 WILD-TYPE      10       20       45       30        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAX1 MUTATED           1          1          1          0        1         0
  HAX1 WILD-TYPE        28         83         61         39       42         4
D827V3, multiclass
            clus
vv           HAX1 MUTATED HAX1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HAX1 MUTATED       0   1   3   3
  HAX1 WILD-TYPE    54 134 258  99
D827V4, multiclass
       clus
vv      HAX1 MUTATED HAX1 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HAX1 MUTATED     2   4   0   1
  HAX1 WILD-TYPE 193 169  89  84
D827V5, multiclass
    clus
vv   HAX1 MUTATED HAX1 WILD-TYPE
  N0            2            193
  N1            4            169
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V6, binary
                cls
clus               0   1
  HAX1 MUTATED     7   0
  HAX1 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      7    0
  HAX1 WILD-TYPE  475   38
   clus
vv  HAX1 MUTATED HAX1 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D827V7, binary
                cls
clus               0   1
  HAX1 MUTATED     2   5
  HAX1 WILD-TYPE 170 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      2    5
  HAX1 WILD-TYPE  170  401
        clus
vv       HAX1 MUTATED HAX1 WILD-TYPE
  FEMALE            2            170
  MALE              5            401
[1] 2 2
[1] FALSE
D827V8, binary
                cls
clus               0   1
  HAX1 MUTATED     5   2
  HAX1 WILD-TYPE 411 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      5    2
  HAX1 WILD-TYPE  411  100
     clus
vv    HAX1 MUTATED HAX1 WILD-TYPE
  NO             5            411
  YES            2            100
[1] 2 2
[1] FALSE
D827V9, continuous
D827V10, continuous
[1] "Remove cluster labels:" "HAX1 MUTATED"          
clus
  HAX1 MUTATED HAX1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A6QS 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" "HAX1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"HAX1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HAX1 MUTATED       0                         0
  HAX1 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAX1 MUTATED                                           0     4
  HAX1 WILD-TYPE                                         1   353
D827V11, multiclass
                                           clus
vv                                          HAX1 MUTATED HAX1 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V12, binary
                cls
clus               0   1
  HAX1 MUTATED     0   3
  HAX1 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      0    3
  HAX1 WILD-TYPE   10  395
                        clus
vv                       HAX1 MUTATED HAX1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(828) Variable = TAF1D MUTATION ANALYSIS
D828V1, survival
                 sevent
clus2               0   1
  TAF1D MUTATED     7   1
  TAF1D WILD-TYPE 331 215
  TAF1D MUTATED TAF1D WILD-TYPE 
              8             546 
  TAF1D MUTATED TAF1D WILD-TYPE 
              1             215 
$`TAF1D MUTATED`
TCGA-VR-AA7B TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A4YY TCGA-EQ-5647 TCGA-HF-A5NB 
       11.24         8.05         6.02        13.78         0.62        30.51 
TCGA-HU-A4GN TCGA-HU-A4HD 
       29.98        33.40 

$`TAF1D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       15.65         8.38         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TAF1D MUTATED TAF1D WILD-TYPE 
           0.62            0.00 
  TAF1D MUTATED TAF1D WILD-TYPE 
           33.4           122.3 
  TAF1D MUTATED TAF1D WILD-TYPE 
         12.510          13.565 
[1] "0.6 - 33.4 (12.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3"  
D828V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF1D MUTATED         0        0        0        1         1         0
  TAF1D WILD-TYPE      10       20       46       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1D MUTATED           0          1          1          1        3         0
  TAF1D WILD-TYPE        29         83         61         38       40         4
D828V3, multiclass
            clus
vv           TAF1D MUTATED TAF1D WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TAF1D MUTATED       0   2   3   3
  TAF1D WILD-TYPE    54 133 258  99
D828V4, multiclass
       clus
vv      TAF1D MUTATED TAF1D WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TAF1D MUTATED     0   3   1   4
  TAF1D WILD-TYPE 195 170  88  81
D828V5, multiclass
    clus
vv   TAF1D MUTATED TAF1D WILD-TYPE
  N0             0             195
  N1             3             170
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V6, binary
                 cls
clus                0   1
  TAF1D MUTATED     6   2
  TAF1D WILD-TYPE 476  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      6    2
  TAF1D WILD-TYPE  476   36
   clus
vv  TAF1D MUTATED TAF1D WILD-TYPE
  0             6             476
  1             2              36
[1] 2 2
[1] FALSE
D828V7, binary
                 cls
clus                0   1
  TAF1D MUTATED     3   5
  TAF1D WILD-TYPE 169 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      3    5
  TAF1D WILD-TYPE  169  401
        clus
vv       TAF1D MUTATED TAF1D WILD-TYPE
  FEMALE             3             169
  MALE               5             401
[1] 2 2
[1] FALSE
D828V8, binary
                 cls
clus                0   1
  TAF1D MUTATED     6   2
  TAF1D WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      6    2
  TAF1D WILD-TYPE  410  100
     clus
vv    TAF1D MUTATED TAF1D WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D828V9, continuous
[1] "Remove cluster labels:" "TAF1D MUTATED"         
clus
  TAF1D MUTATED TAF1D WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TAF1D WILD-TYPE" "TAF1D WILD-TYPE" "TAF1D WILD-TYPE" 
D828V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF1D MUTATED       2                         0
  TAF1D WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF1D MUTATED                                           0     3
  TAF1D WILD-TYPE                                         1   354
D828V11, multiclass
                                           clus
vv                                          TAF1D MUTATED TAF1D WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V12, binary
                 cls
clus                0   1
  TAF1D MUTATED     0   4
  TAF1D WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      0    4
  TAF1D WILD-TYPE   10  394
                        clus
vv                       TAF1D MUTATED TAF1D WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(829) Variable = KLRF1 MUTATION ANALYSIS
D829V1, survival
                 sevent
clus2               0   1
  KLRF1 MUTATED     4   2
  KLRF1 WILD-TYPE 334 214
  KLRF1 MUTATED KLRF1 WILD-TYPE 
              6             548 
  KLRF1 MUTATED KLRF1 WILD-TYPE 
              2             214 
$`KLRF1 MUTATED`
TCGA-IG-A8O2 TCGA-L5-A4OH TCGA-L5-A4OW TCGA-LN-A4A8 TCGA-BR-8368 TCGA-D7-6528 
        4.67        32.61         7.13        15.52         4.31        15.22 

$`KLRF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KLRF1 MUTATED KLRF1 WILD-TYPE 
           4.31            0.00 
  KLRF1 MUTATED KLRF1 WILD-TYPE 
          32.61          122.30 
  KLRF1 MUTATED KLRF1 WILD-TYPE 
         11.175          13.565 
[1] "4.3 - 32.6 (11.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D829V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLRF1 MUTATED         1        0        2        0         1         1
  KLRF1 WILD-TYPE       9       20       44       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLRF1 MUTATED           0          0          1          0        0         0
  KLRF1 WILD-TYPE        29         84         61         39       43         4
D829V3, multiclass
            clus
vv           KLRF1 MUTATED KLRF1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KLRF1 MUTATED       1   4   1   0
  KLRF1 WILD-TYPE    53 131 260 102
D829V4, multiclass
       clus
vv      KLRF1 MUTATED KLRF1 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                1             260
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KLRF1 MUTATED     4   1   1   0
  KLRF1 WILD-TYPE 191 172  88  85
D829V5, multiclass
    clus
vv   KLRF1 MUTATED KLRF1 WILD-TYPE
  N0             4             191
  N1             1             172
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V6, binary
                 cls
clus                0   1
  KLRF1 MUTATED     6   0
  KLRF1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRF1 MUTATED      6    0
  KLRF1 WILD-TYPE  476   38
   clus
vv  KLRF1 MUTATED KLRF1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D829V7, binary
                 cls
clus                0   1
  KLRF1 MUTATED     3   3
  KLRF1 WILD-TYPE 169 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRF1 MUTATED      3    3
  KLRF1 WILD-TYPE  169  403
        clus
vv       KLRF1 MUTATED KLRF1 WILD-TYPE
  FEMALE             3             169
  MALE               3             403
[1] 2 2
[1] FALSE
D829V8, binary
                 cls
clus                0   1
  KLRF1 MUTATED     5   0
  KLRF1 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRF1 MUTATED      5    0
  KLRF1 WILD-TYPE  411  102
     clus
vv    KLRF1 MUTATED KLRF1 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D829V9, continuous
[1] "Remove cluster labels:" "KLRF1 MUTATED"         
clus
  KLRF1 MUTATED KLRF1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" "KLRF1 WILD-TYPE" 
D829V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KLRF1 MUTATED       2                         0
  KLRF1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLRF1 MUTATED                                           0     3
  KLRF1 WILD-TYPE                                         1   354
D829V11, multiclass
                                           clus
vv                                          KLRF1 MUTATED KLRF1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V12, binary
                 cls
clus                0   1
  KLRF1 MUTATED     0   4
  KLRF1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRF1 MUTATED      0    4
  KLRF1 WILD-TYPE   10  394
                        clus
vv                       KLRF1 MUTATED KLRF1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(830) Variable = SPOCD1 MUTATION ANALYSIS
D830V1, survival
                  sevent
clus2                0   1
  SPOCD1 MUTATED    11   3
  SPOCD1 WILD-TYPE 327 213
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              14              540 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
               3              213 
$`SPOCD1 MUTATED`
TCGA-2H-A9GJ TCGA-JY-A93E TCGA-VR-A8EY TCGA-VR-AA4G TCGA-BR-4184 TCGA-BR-6453 
       58.55        25.22        33.70        18.05         6.97        15.95 
TCGA-BR-7707 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4GT TCGA-HU-A4GX 
       35.84        11.77         6.02        65.10         6.51        20.25 
TCGA-MX-A5UJ TCGA-R5-A7ZI 
       19.73        74.53 

$`SPOCD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
            6.02             0.00 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
           74.53           122.30 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
          19.990           13.495 
[1] "6.0 - 74.5 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D830V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPOCD1 MUTATED         1        1        2        0         3         0
  SPOCD1 WILD-TYPE       9       19       44       31        81        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPOCD1 MUTATED           0          6          0          1        2
  SPOCD1 WILD-TYPE        29         78         62         38       41
                  vv
clus               STAGE IVA
  SPOCD1 MUTATED           0
  SPOCD1 WILD-TYPE         4
D830V3, multiclass
            clus
vv           SPOCD1 MUTATED SPOCD1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              6               78
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SPOCD1 MUTATED       2   4   6   4
  SPOCD1 WILD-TYPE    52 131 255  98
D830V4, multiclass
       clus
vv      SPOCD1 MUTATED SPOCD1 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 6              255
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SPOCD1 MUTATED     7   6   3   0
  SPOCD1 WILD-TYPE 188 167  86  85
D830V5, multiclass
    clus
vv   SPOCD1 MUTATED SPOCD1 WILD-TYPE
  N0              7              188
  N1              6              167
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V6, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED    15   1
  SPOCD1 WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED     15    1
  SPOCD1 WILD-TYPE  467   37
   clus
vv  SPOCD1 MUTATED SPOCD1 WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D830V7, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED    10   7
  SPOCD1 WILD-TYPE 162 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED     10    7
  SPOCD1 WILD-TYPE  162  399
        clus
vv       SPOCD1 MUTATED SPOCD1 WILD-TYPE
  FEMALE             10              162
  MALE                7              399
[1] 2 2
[1] FALSE
D830V8, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED    13   1
  SPOCD1 WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED     13    1
  SPOCD1 WILD-TYPE  403  101
     clus
vv    SPOCD1 MUTATED SPOCD1 WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D830V9, continuous
[1] "Remove cluster labels:" "SPOCD1 MUTATED"        
clus
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA7B       TCGA-VR-AA7D 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
D830V10, continuous
[1] "Remove cluster labels:" "SPOCD1 MUTATED"        
clus
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA7D       TCGA-VR-AA7I 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" "SPOCD1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"SPOCD1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPOCD1 MUTATED       4                         0
  SPOCD1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPOCD1 MUTATED                                           0    10
  SPOCD1 WILD-TYPE                                         1   347
D830V11, multiclass
                                           clus
vv                                          SPOCD1 MUTATED SPOCD1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V12, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED     1  10
  SPOCD1 WILD-TYPE   9 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED      1   10
  SPOCD1 WILD-TYPE    9  388
                        clus
vv                       SPOCD1 MUTATED SPOCD1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(831) Variable = DAPK1 MUTATION ANALYSIS
D831V1, survival
                 sevent
clus2               0   1
  DAPK1 MUTATED    18   9
  DAPK1 WILD-TYPE 320 207
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             27             527 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
              9             207 
$`DAPK1 MUTATED`
TCGA-KH-A6WC TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49Y 
        6.28         7.76         8.71        83.24        12.66        12.46 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE 
        8.02         5.06        25.05        28.14        31.96        20.42 
TCGA-BR-A4QL TCGA-CD-5802 TCGA-CG-4305 TCGA-D7-A6EY TCGA-FP-7829 TCGA-FP-A4BE 
       16.14        13.35        15.95        11.44        19.53        11.08 
TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 
       24.20         8.98         0.10         6.58        20.25        14.07 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A91U 
       19.73        74.53         1.71 

$`DAPK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        5.49        21.37        13.41        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         7.82         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37        29.98         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        15.65        20.81        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DAPK1 MUTATED DAPK1 WILD-TYPE 
            0.1             0.0 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
          83.24          122.30 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
          13.35           13.58 
[1] "0.1 - 83.2 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D831V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DAPK1 MUTATED         0        2        2        2         5         3
  DAPK1 WILD-TYPE      10       18       44       29        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAPK1 MUTATED           1          3          2          4        2         0
  DAPK1 WILD-TYPE        28         81         60         35       41         4
D831V3, multiclass
            clus
vv           DAPK1 MUTATED DAPK1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             4              35
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DAPK1 MUTATED       4   6  10   7
  DAPK1 WILD-TYPE    50 129 251  95
D831V4, multiclass
       clus
vv      DAPK1 MUTATED DAPK1 WILD-TYPE
  T0+T1             4              50
  T2                6             129
  T3               10             251
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DAPK1 MUTATED     9  10   4   4
  DAPK1 WILD-TYPE 186 163  85  81
D831V5, multiclass
    clus
vv   DAPK1 MUTATED DAPK1 WILD-TYPE
  N0             9             186
  N1            10             163
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V6, binary
                 cls
clus                0   1
  DAPK1 MUTATED    26   2
  DAPK1 WILD-TYPE 456  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     26    2
  DAPK1 WILD-TYPE  456   36
   clus
vv  DAPK1 MUTATED DAPK1 WILD-TYPE
  0            26             456
  1             2              36
[1] 2 2
[1] FALSE
D831V7, binary
                 cls
clus                0   1
  DAPK1 MUTATED    14  16
  DAPK1 WILD-TYPE 158 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     14   16
  DAPK1 WILD-TYPE  158  390
        clus
vv       DAPK1 MUTATED DAPK1 WILD-TYPE
  FEMALE            14             158
  MALE              16             390
[1] 2 2
[1] FALSE
D831V8, binary
                 cls
clus                0   1
  DAPK1 MUTATED    20   5
  DAPK1 WILD-TYPE 396  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     20    5
  DAPK1 WILD-TYPE  396   97
     clus
vv    DAPK1 MUTATED DAPK1 WILD-TYPE
  NO             20             396
  YES             5              97
[1] 2 2
[1] FALSE
D831V9, continuous
D831V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DAPK1 MUTATED      11                         1
  DAPK1 WILD-TYPE   122                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DAPK1 MUTATED                                           0    16
  DAPK1 WILD-TYPE                                         1   341
D831V11, multiclass
                                           clus
vv                                          DAPK1 MUTATED DAPK1 WILD-TYPE
  ASIAN                                                11             122
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V12, binary
                 cls
clus                0   1
  DAPK1 MUTATED     1  24
  DAPK1 WILD-TYPE   9 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED      1   24
  DAPK1 WILD-TYPE    9  374
                        clus
vv                       DAPK1 MUTATED DAPK1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            24             374
[1] 2 2
[1] FALSE

Clustering(832) Variable = SERPING1 MUTATION ANALYSIS
D832V1, survival
                    sevent
clus2                  0   1
  SERPING1 MUTATED     4   5
  SERPING1 WILD-TYPE 334 211
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 9                545 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 5                211 
$`SERPING1 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GH TCGA-LN-A49X TCGA-BR-8059 TCGA-BR-8677 TCGA-CD-8532 
       21.99        31.27        12.62        14.43        26.73        11.64 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-D7-A4YX 
        6.58        12.62        36.43 

$`SERPING1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        12.59        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SERPING1 MUTATED SERPING1 WILD-TYPE 
              6.58               0.00 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
             36.43             122.30 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
             14.43              13.55 
[1] "6.6 - 36.4 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D832V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPING1 MUTATED         0        0        1        1         2         3
  SERPING1 WILD-TYPE      10       20       45       30        82        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPING1 MUTATED           1          0          1          0        1
  SERPING1 WILD-TYPE        28         84         61         39       42
                    vv
clus                 STAGE IVA
  SERPING1 MUTATED           0
  SERPING1 WILD-TYPE         4
D832V3, multiclass
            clus
vv           SERPING1 MUTATED SERPING1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 2                 82
  STAGE IIB                 3                 80
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SERPING1 MUTATED       1   1   5   3
  SERPING1 WILD-TYPE    53 134 256  99
D832V4, multiclass
       clus
vv      SERPING1 MUTATED SERPING1 WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   5                256
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SERPING1 MUTATED     5   4   0   1
  SERPING1 WILD-TYPE 190 169  89  84
D832V5, multiclass
    clus
vv   SERPING1 MUTATED SERPING1 WILD-TYPE
  N0                5                190
  N1                4                169
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V6, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     9   1
  SERPING1 WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      9    1
  SERPING1 WILD-TYPE  473   37
   clus
vv  SERPING1 MUTATED SERPING1 WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D832V7, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     2   8
  SERPING1 WILD-TYPE 170 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      2    8
  SERPING1 WILD-TYPE  170  398
        clus
vv       SERPING1 MUTATED SERPING1 WILD-TYPE
  FEMALE                2                170
  MALE                  8                398
[1] 2 2
[1] FALSE
D832V8, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     9   1
  SERPING1 WILD-TYPE 407 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      9    1
  SERPING1 WILD-TYPE  407  101
     clus
vv    SERPING1 MUTATED SERPING1 WILD-TYPE
  NO                 9                407
  YES                1                101
[1] 2 2
[1] FALSE
D832V9, continuous
[1] "Remove cluster labels:" "SERPING1 MUTATED"      
clus
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" "SERPING1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"SERPING1 WILD-TYPE" 
D832V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPING1 MUTATED       4                         0
  SERPING1 WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPING1 MUTATED                                           0     4
  SERPING1 WILD-TYPE                                         1   353
D832V11, multiclass
                                           clus
vv                                          SERPING1 MUTATED SERPING1 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V12, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     0   8
  SERPING1 WILD-TYPE  10 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      0    8
  SERPING1 WILD-TYPE   10  390
                        clus
vv                       SERPING1 MUTATED SERPING1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                8                390
[1] 2 2
[1] FALSE

Clustering(833) Variable = TMEM165 MUTATION ANALYSIS
D833V1, survival
                   sevent
clus2                 0   1
  TMEM165 MUTATED     4   0
  TMEM165 WILD-TYPE 334 216
  TMEM165 MUTATED TMEM165 WILD-TYPE 
                4               550 
  TMEM165 MUTATED TMEM165 WILD-TYPE 
                0               216 
$`TMEM165 MUTATED`
TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-8572 TCGA-VQ-AA6A 
       15.95        65.10        16.80        38.93 

$`TMEM165 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TMEM165 MUTATED TMEM165 WILD-TYPE 
            15.95              0.00 
  TMEM165 MUTATED TMEM165 WILD-TYPE 
             65.1             122.3 
  TMEM165 MUTATED TMEM165 WILD-TYPE 
           27.865            13.510 
[1] "15.9 - 65.1 (27.9)" "0.0 - 122.3 (13.5)"
[1] "hr="     "9100000"
D833V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM165 MUTATED         0        0        1        1         0         1
  TMEM165 WILD-TYPE      10       20       45       30        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM165 MUTATED           0          0          0          1        1
  TMEM165 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  TMEM165 MUTATED           0
  TMEM165 WILD-TYPE         4
D833V3, multiclass
            clus
vv           TMEM165 MUTATED TMEM165 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM165 MUTATED       0   3   0   2
  TMEM165 WILD-TYPE    54 132 261 100
D833V4, multiclass
       clus
vv      TMEM165 MUTATED TMEM165 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  0               261
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM165 MUTATED     1   1   2   1
  TMEM165 WILD-TYPE 194 172  87  84
D833V5, multiclass
    clus
vv   TMEM165 MUTATED TMEM165 WILD-TYPE
  N0               1               194
  N1               1               172
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V6, binary
                   cls
clus                  0   1
  TMEM165 MUTATED     5   0
  TMEM165 WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM165 MUTATED      5    0
  TMEM165 WILD-TYPE  477   38
   clus
vv  TMEM165 MUTATED TMEM165 WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D833V7, binary
                   cls
clus                  0   1
  TMEM165 MUTATED     2   3
  TMEM165 WILD-TYPE 170 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM165 MUTATED      2    3
  TMEM165 WILD-TYPE  170  403
        clus
vv       TMEM165 MUTATED TMEM165 WILD-TYPE
  FEMALE               2               170
  MALE                 3               403
[1] 2 2
[1] FALSE
D833V8, binary
                   cls
clus                  0   1
  TMEM165 MUTATED     2   1
  TMEM165 WILD-TYPE 414 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM165 MUTATED      2    1
  TMEM165 WILD-TYPE  414  101
     clus
vv    TMEM165 MUTATED TMEM165 WILD-TYPE
  NO                2               414
  YES               1               101
[1] 2 2
[1] FALSE
D833V9, continuous
D833V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM165 MUTATED       0                         0
  TMEM165 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM165 MUTATED                                           0     3
  TMEM165 WILD-TYPE                                         1   354
D833V11, multiclass
                                           clus
vv                                          TMEM165 MUTATED TMEM165 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V12, binary
                   cls
clus                  0   1
  TMEM165 MUTATED     0   2
  TMEM165 WILD-TYPE  10 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM165 MUTATED      0    2
  TMEM165 WILD-TYPE   10  396
                        clus
vv                       TMEM165 MUTATED TMEM165 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               2               396
[1] 2 2
[1] FALSE

Clustering(834) Variable = SDC4 MUTATION ANALYSIS
D834V1, survival
                sevent
clus2              0   1
  SDC4 MUTATED     3   3
  SDC4 WILD-TYPE 335 213
  SDC4 MUTATED SDC4 WILD-TYPE 
             6            548 
  SDC4 MUTATED SDC4 WILD-TYPE 
             3            213 
$`SDC4 MUTATED`
TCGA-L5-A8NS TCGA-CG-4465 TCGA-D7-5578 TCGA-D7-6525 TCGA-D7-A4YV TCGA-VQ-A8P2 
       13.41         9.01        12.66        13.35         5.92        38.14 

$`SDC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SDC4 MUTATED SDC4 WILD-TYPE 
          5.92           0.00 
  SDC4 MUTATED SDC4 WILD-TYPE 
         38.14         122.30 
  SDC4 MUTATED SDC4 WILD-TYPE 
        13.005         13.730 
[1] "5.9 - 38.1 (13.0)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.5"
D834V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SDC4 MUTATED         0        0        0        0         0         2
  SDC4 WILD-TYPE      10       20       46       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SDC4 MUTATED           0          3          0          0        1         0
  SDC4 WILD-TYPE        29         81         62         39       42         4
D834V3, multiclass
            clus
vv           SDC4 MUTATED SDC4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SDC4 MUTATED       0   1   3   2
  SDC4 WILD-TYPE    54 134 258 100
D834V4, multiclass
       clus
vv      SDC4 MUTATED SDC4 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SDC4 MUTATED     1   2   2   1
  SDC4 WILD-TYPE 194 171  87  84
D834V5, multiclass
    clus
vv   SDC4 MUTATED SDC4 WILD-TYPE
  N0            1            194
  N1            2            171
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V6, binary
                cls
clus               0   1
  SDC4 MUTATED     5   1
  SDC4 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  SDC4 MUTATED      5    1
  SDC4 WILD-TYPE  477   37
   clus
vv  SDC4 MUTATED SDC4 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D834V7, binary
                cls
clus               0   1
  SDC4 MUTATED     2   4
  SDC4 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  SDC4 MUTATED      2    4
  SDC4 WILD-TYPE  170  402
        clus
vv       SDC4 MUTATED SDC4 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D834V8, binary
                cls
clus               0   1
  SDC4 MUTATED     3   2
  SDC4 WILD-TYPE 413 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SDC4 MUTATED      3    2
  SDC4 WILD-TYPE  413  100
     clus
vv    SDC4 MUTATED SDC4 WILD-TYPE
  NO             3            413
  YES            2            100
[1] 2 2
[1] FALSE
D834V9, continuous
D834V10, continuous
[1] "Remove cluster labels:" "SDC4 MUTATED"          
clus
  SDC4 MUTATED SDC4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NW     TCGA-LN-A49O 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" "SDC4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"SDC4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SDC4 MUTATED       0                         0
  SDC4 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SDC4 MUTATED                                           0     5
  SDC4 WILD-TYPE                                         1   352
D834V11, multiclass
                                           clus
vv                                          SDC4 MUTATED SDC4 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V12, binary
                cls
clus               0   1
  SDC4 MUTATED     0   3
  SDC4 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  SDC4 MUTATED      0    3
  SDC4 WILD-TYPE   10  395
                        clus
vv                       SDC4 MUTATED SDC4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(835) Variable = TAF1B MUTATION ANALYSIS
D835V1, survival
                 sevent
clus2               0   1
  TAF1B MUTATED    11   4
  TAF1B WILD-TYPE 327 212
  TAF1B MUTATED TAF1B WILD-TYPE 
             15             539 
  TAF1B MUTATED TAF1B WILD-TYPE 
              4             212 
$`TAF1B MUTATED`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-IG-A5B8 TCGA-LN-A9FO TCGA-VR-A8EQ TCGA-BR-4184 
       15.68        34.85         0.79         0.13        22.82         6.97 
TCGA-BR-7197 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5728 TCGA-D7-A4Z0 TCGA-F1-A448 
        9.21        31.96        13.18        65.10        14.76        21.27 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-VQ-A8P2 
       24.20        29.98        38.14 

$`TAF1B WILD-TYPE`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        13.78        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TAF1B MUTATED TAF1B WILD-TYPE 
           0.13            0.00 
  TAF1B MUTATED TAF1B WILD-TYPE 
           65.1           122.3 
  TAF1B MUTATED TAF1B WILD-TYPE 
          21.27           13.51 
[1] "0.1 - 65.1 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D835V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF1B MUTATED         0        2        2        1         2         2
  TAF1B WILD-TYPE      10       18       44       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1B MUTATED           1          3          1          0        1         0
  TAF1B WILD-TYPE        28         81         61         39       42         4
D835V3, multiclass
            clus
vv           TAF1B MUTATED TAF1B WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TAF1B MUTATED       2   4   7   2
  TAF1B WILD-TYPE    52 131 254 100
D835V4, multiclass
       clus
vv      TAF1B MUTATED TAF1B WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                7             254
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TAF1B MUTATED     7   5   2   1
  TAF1B WILD-TYPE 188 168  87  84
D835V5, multiclass
    clus
vv   TAF1B MUTATED TAF1B WILD-TYPE
  N0             7             188
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V6, binary
                 cls
clus                0   1
  TAF1B MUTATED    13   1
  TAF1B WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED     13    1
  TAF1B WILD-TYPE  469   37
   clus
vv  TAF1B MUTATED TAF1B WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D835V7, binary
                 cls
clus                0   1
  TAF1B MUTATED     4  11
  TAF1B WILD-TYPE 168 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      4   11
  TAF1B WILD-TYPE  168  395
        clus
vv       TAF1B MUTATED TAF1B WILD-TYPE
  FEMALE             4             168
  MALE              11             395
[1] 2 2
[1] FALSE
D835V8, binary
                 cls
clus                0   1
  TAF1B MUTATED    10   4
  TAF1B WILD-TYPE 406  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED     10    4
  TAF1B WILD-TYPE  406   98
     clus
vv    TAF1B MUTATED TAF1B WILD-TYPE
  NO             10             406
  YES             4              98
[1] 2 2
[1] FALSE
D835V9, continuous
[1] "Remove cluster labels:" "TAF1B MUTATED"         
clus
  TAF1B MUTATED TAF1B WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
D835V10, continuous
[1] "Remove cluster labels:" "TAF1B MUTATED"         
clus
  TAF1B MUTATED TAF1B WILD-TYPE 
              2              96 
     TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A6QS      TCGA-IG-A8O2 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" "TAF1B WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF1B MUTATED       5                         0
  TAF1B WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF1B MUTATED                                           0     9
  TAF1B WILD-TYPE                                         1   348
D835V11, multiclass
                                           clus
vv                                          TAF1B MUTATED TAF1B WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V12, binary
                 cls
clus                0   1
  TAF1B MUTATED     1  10
  TAF1B WILD-TYPE   9 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      1   10
  TAF1B WILD-TYPE    9  388
                        clus
vv                       TAF1B MUTATED TAF1B WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(836) Variable = ITGAE MUTATION ANALYSIS
D836V1, survival
                 sevent
clus2               0   1
  ITGAE MUTATED    13   5
  ITGAE WILD-TYPE 325 211
  ITGAE MUTATED ITGAE WILD-TYPE 
             18             536 
  ITGAE MUTATED ITGAE WILD-TYPE 
              5             211 
$`ITGAE MUTATED`
TCGA-L5-A43I TCGA-IG-A97I TCGA-V5-AASW TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 
       18.28        12.16         9.27        30.90        34.68        15.95 
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A48A 
       32.25         6.18         0.26         1.12        16.14        12.43 
TCGA-CG-5726 TCGA-FP-8211 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8P2 
       28.96        13.58        29.98        20.25        19.73        38.14 

$`ITGAE WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57         6.61        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54         5.03         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ITGAE MUTATED ITGAE WILD-TYPE 
           0.26            0.00 
  ITGAE MUTATED ITGAE WILD-TYPE 
          38.14          122.30 
  ITGAE MUTATED ITGAE WILD-TYPE 
         17.210          13.495 
[1] "0.3 - 38.1 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D836V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAE MUTATED         0        1        1        0         7         2
  ITGAE WILD-TYPE      10       19       45       31        77        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAE MUTATED           0          3          1          1        0         0
  ITGAE WILD-TYPE        29         81         61         38       43         4
D836V3, multiclass
            clus
vv           ITGAE MUTATED ITGAE WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              7              77
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGAE MUTATED       1   5   8   3
  ITGAE WILD-TYPE    53 130 253  99
D836V4, multiclass
       clus
vv      ITGAE MUTATED ITGAE WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                8             253
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGAE MUTATED     8   5   2   1
  ITGAE WILD-TYPE 187 168  87  84
D836V5, multiclass
    clus
vv   ITGAE MUTATED ITGAE WILD-TYPE
  N0             8             187
  N1             5             168
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V6, binary
                 cls
clus                0   1
  ITGAE MUTATED    15   0
  ITGAE WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED     15    0
  ITGAE WILD-TYPE  467   38
   clus
vv  ITGAE MUTATED ITGAE WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D836V7, binary
                 cls
clus                0   1
  ITGAE MUTATED     8  10
  ITGAE WILD-TYPE 164 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED      8   10
  ITGAE WILD-TYPE  164  396
        clus
vv       ITGAE MUTATED ITGAE WILD-TYPE
  FEMALE             8             164
  MALE              10             396
[1] 2 2
[1] FALSE
D836V8, binary
                 cls
clus                0   1
  ITGAE MUTATED    11   6
  ITGAE WILD-TYPE 405  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED     11    6
  ITGAE WILD-TYPE  405   96
     clus
vv    ITGAE MUTATED ITGAE WILD-TYPE
  NO             11             405
  YES             6              96
[1] 2 2
[1] FALSE
D836V9, continuous
[1] "Remove cluster labels:" "ITGAE MUTATED"         
clus
  ITGAE MUTATED ITGAE WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
D836V10, continuous
[1] "Remove cluster labels:" "ITGAE MUTATED"         
clus
  ITGAE MUTATED ITGAE WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" "ITGAE WILD-TYPE" 
     TCGA-Z6-AAPN 
"ITGAE WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGAE MUTATED       3                         0
  ITGAE WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGAE MUTATED                                           0    14
  ITGAE WILD-TYPE                                         1   343
D836V11, multiclass
                                           clus
vv                                          ITGAE MUTATED ITGAE WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V12, binary
                 cls
clus                0   1
  ITGAE MUTATED     0  15
  ITGAE WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED      0   15
  ITGAE WILD-TYPE   10  383
                        clus
vv                       ITGAE MUTATED ITGAE WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(837) Variable = BIN3 MUTATION ANALYSIS
D837V1, survival
                sevent
clus2              0   1
  BIN3 MUTATED     4   1
  BIN3 WILD-TYPE 334 215
  BIN3 MUTATED BIN3 WILD-TYPE 
             5            549 
  BIN3 MUTATED BIN3 WILD-TYPE 
             1            215 
$`BIN3 MUTATED`
TCGA-LN-A49U TCGA-BR-8487 TCGA-CG-5733 TCGA-HF-A5NB TCGA-MX-A5UJ 
       15.35         1.12        21.07        30.51        19.73 

$`BIN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BIN3 MUTATED BIN3 WILD-TYPE 
          1.12           0.00 
  BIN3 MUTATED BIN3 WILD-TYPE 
         30.51         122.30 
  BIN3 MUTATED BIN3 WILD-TYPE 
         19.73          13.51 
[1] "1.1 - 30.5 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D837V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BIN3 MUTATED         0        0        0        0         2         0
  BIN3 WILD-TYPE      10       20       46       31        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIN3 MUTATED           0          2          0          1        0         0
  BIN3 WILD-TYPE        29         82         62         38       43         4
D837V3, multiclass
            clus
vv           BIN3 MUTATED BIN3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BIN3 MUTATED       0   1   3   1
  BIN3 WILD-TYPE    54 134 258 101
D837V4, multiclass
       clus
vv      BIN3 MUTATED BIN3 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BIN3 MUTATED     2   0   2   1
  BIN3 WILD-TYPE 193 173  87  84
D837V5, multiclass
    clus
vv   BIN3 MUTATED BIN3 WILD-TYPE
  N0            2            193
  N1            0            173
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V6, binary
                cls
clus               0   1
  BIN3 MUTATED     5   0
  BIN3 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      5    0
  BIN3 WILD-TYPE  477   38
   clus
vv  BIN3 MUTATED BIN3 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D837V7, binary
                cls
clus               0   1
  BIN3 MUTATED     4   1
  BIN3 WILD-TYPE 168 405
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      4    1
  BIN3 WILD-TYPE  168  405
        clus
vv       BIN3 MUTATED BIN3 WILD-TYPE
  FEMALE            4            168
  MALE              1            405
[1] 2 2
[1] FALSE
D837V8, binary
                cls
clus               0   1
  BIN3 MUTATED     3   2
  BIN3 WILD-TYPE 413 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      3    2
  BIN3 WILD-TYPE  413  100
     clus
vv    BIN3 MUTATED BIN3 WILD-TYPE
  NO             3            413
  YES            2            100
[1] 2 2
[1] FALSE
D837V9, continuous
[1] "Remove cluster labels:" "BIN3 MUTATED"          
clus
  BIN3 MUTATED BIN3 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49V     TCGA-LN-A49W 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
D837V10, continuous
[1] "Remove cluster labels:" "BIN3 MUTATED"          
clus
  BIN3 MUTATED BIN3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"BIN3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BIN3 MUTATED       1                         0
  BIN3 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BIN3 MUTATED                                           0     2
  BIN3 WILD-TYPE                                         1   355
D837V11, multiclass
                                           clus
vv                                          BIN3 MUTATED BIN3 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V12, binary
                cls
clus               0   1
  BIN3 MUTATED     0   3
  BIN3 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      0    3
  BIN3 WILD-TYPE   10  395
                        clus
vv                       BIN3 MUTATED BIN3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(838) Variable = TRIOBP MUTATION ANALYSIS
D838V1, survival
                  sevent
clus2                0   1
  TRIOBP MUTATED    24  12
  TRIOBP WILD-TYPE 314 204
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              36              518 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              12              204 
$`TRIOBP MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NG TCGA-2H-A9GI TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L7-A6VZ 
       19.99        35.97        14.30         7.76        13.41        10.36 
TCGA-LN-A49M TCGA-XP-A8T6 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 
       12.66        25.08         6.97         9.34        34.68        32.78 
TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL 
       25.61        40.21        29.59         1.12        31.96        16.14 
TCGA-CD-5801 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-8572 
       13.18         6.58         6.02        21.07        15.22        16.80 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-A4G8 
       11.44        14.47        14.07         0.56        11.08        22.68 
TCGA-HU-A4GH TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.77        29.00        14.07        33.40        19.73        38.14 

$`TRIOBP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        8.71        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       21.17        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
            0.56             0.00 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
           40.21           122.30 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
          14.845           13.445 
[1] "0.6 - 40.2 (14.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D838V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIOBP MUTATED         0        1        3        0         7         6
  TRIOBP WILD-TYPE      10       19       43       31        77        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIOBP MUTATED           2          8          3          4        3
  TRIOBP WILD-TYPE        27         76         59         35       40
                  vv
clus               STAGE IVA
  TRIOBP MUTATED           0
  TRIOBP WILD-TYPE         4
D838V3, multiclass
            clus
vv           TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               7               77
  STAGE IIB               6               77
  STAGE III               2               27
  STAGE IIIA              8               76
  STAGE IIIB              3               59
  STAGE IIIC              4               35
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TRIOBP MUTATED       2   7  20   8
  TRIOBP WILD-TYPE    52 128 241  94
D838V4, multiclass
       clus
vv      TRIOBP MUTATED TRIOBP WILD-TYPE
  T0+T1              2               52
  T2                 7              128
  T3                20              241
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TRIOBP MUTATED    13  11   7   7
  TRIOBP WILD-TYPE 182 162  82  78
D838V5, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  N0             13              182
  N1             11              162
  N2              7               82
  N3              7               78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V6, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    31   2
  TRIOBP WILD-TYPE 451  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     31    2
  TRIOBP WILD-TYPE  451   36
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0             31              451
  1              2               36
[1] 2 2
[1] FALSE
D838V7, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    14  24
  TRIOBP WILD-TYPE 158 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     14   24
  TRIOBP WILD-TYPE  158  382
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  FEMALE             14              158
  MALE               24              382
[1] 2 2
[1] FALSE
D838V8, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    29   5
  TRIOBP WILD-TYPE 387  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     29    5
  TRIOBP WILD-TYPE  387   97
     clus
vv    TRIOBP MUTATED TRIOBP WILD-TYPE
  NO              29              387
  YES              5               97
[1] 2 2
[1] FALSE
D838V9, continuous
[1] "Remove cluster labels:" "TRIOBP MUTATED"        
clus
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T7       TCGA-XP-A8T8 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TRIOBP WILD-TYPE" "TRIOBP WILD-TYPE" 
D838V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIOBP MUTATED      10                         2
  TRIOBP WILD-TYPE   123                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIOBP MUTATED                                           0    22
  TRIOBP WILD-TYPE                                         1   335
D838V11, multiclass
                                           clus
vv                                          TRIOBP MUTATED TRIOBP WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V12, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     1  28
  TRIOBP WILD-TYPE   9 370
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      1   28
  TRIOBP WILD-TYPE    9  370
                        clus
vv                       TRIOBP MUTATED TRIOBP WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             28              370
[1] 2 2
[1] FALSE

Clustering(839) Variable = BRD1 MUTATION ANALYSIS
D839V1, survival
                sevent
clus2              0   1
  BRD1 MUTATED    11   9
  BRD1 WILD-TYPE 327 207
  BRD1 MUTATED BRD1 WILD-TYPE 
            20            534 
  BRD1 MUTATED BRD1 WILD-TYPE 
             9            207 
$`BRD1 MUTATED`
TCGA-2H-A9GG TCGA-IG-A3Y9 TCGA-L5-A891 TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-7707 
       20.05         0.85         3.75        26.70        30.90        35.84 
TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4CS TCGA-CD-A4MI TCGA-CG-4306 
       29.59        25.05         1.12         1.48        11.77         1.02 
TCGA-CG-5721 TCGA-D7-A4Z0 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.02        14.76        26.47        29.98         6.58        38.14 
TCGA-VQ-A8PM TCGA-VQ-A91V 
        1.87        42.64 

$`BRD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       22.19        17.85        15.65        20.81         1.71        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  BRD1 MUTATED BRD1 WILD-TYPE 
          0.85           0.00 
  BRD1 MUTATED BRD1 WILD-TYPE 
         42.64         122.30 
  BRD1 MUTATED BRD1 WILD-TYPE 
        17.405         13.530 
[1] "0.8 - 42.6 (17.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D839V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRD1 MUTATED         1        0        2        0         2         4
  BRD1 WILD-TYPE       9       20       44       31        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD1 MUTATED           1          4          0          2        3         0
  BRD1 WILD-TYPE        28         80         62         37       40         4
D839V3, multiclass
            clus
vv           BRD1 MUTATED BRD1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BRD1 MUTATED       1   5   7   8
  BRD1 WILD-TYPE    53 130 254  94
D839V4, multiclass
       clus
vv      BRD1 MUTATED BRD1 WILD-TYPE
  T0+T1            1             53
  T2               5            130
  T3               7            254
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BRD1 MUTATED     6   9   3   3
  BRD1 WILD-TYPE 189 164  86  82
D839V5, multiclass
    clus
vv   BRD1 MUTATED BRD1 WILD-TYPE
  N0            6            189
  N1            9            164
  N2            3             86
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V6, binary
                cls
clus               0   1
  BRD1 MUTATED    19   1
  BRD1 WILD-TYPE 463  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD1 MUTATED     19    1
  BRD1 WILD-TYPE  463   37
   clus
vv  BRD1 MUTATED BRD1 WILD-TYPE
  0           19            463
  1            1             37
[1] 2 2
[1] FALSE
D839V7, binary
                cls
clus               0   1
  BRD1 MUTATED     9  13
  BRD1 WILD-TYPE 163 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD1 MUTATED      9   13
  BRD1 WILD-TYPE  163  393
        clus
vv       BRD1 MUTATED BRD1 WILD-TYPE
  FEMALE            9            163
  MALE             13            393
[1] 2 2
[1] FALSE
D839V8, binary
                cls
clus               0   1
  BRD1 MUTATED    16   3
  BRD1 WILD-TYPE 400  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD1 MUTATED     16    3
  BRD1 WILD-TYPE  400   99
     clus
vv    BRD1 MUTATED BRD1 WILD-TYPE
  NO            16            400
  YES            3             99
[1] 2 2
[1] FALSE
D839V9, continuous
[1] "Remove cluster labels:" "BRD1 MUTATED"          
clus
  BRD1 MUTATED BRD1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3YA     TCGA-IG-A3YB 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3     TCGA-IG-A7DP 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
D839V10, continuous
[1] "Remove cluster labels:" "BRD1 MUTATED"          
clus
  BRD1 MUTATED BRD1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" "BRD1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"BRD1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRD1 MUTATED       3                         1
  BRD1 WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRD1 MUTATED                                           0    14
  BRD1 WILD-TYPE                                         1   343
D839V11, multiclass
                                           clus
vv                                          BRD1 MUTATED BRD1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V12, binary
                cls
clus               0   1
  BRD1 MUTATED     0  15
  BRD1 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD1 MUTATED      0   15
  BRD1 WILD-TYPE   10  383
                        clus
vv                       BRD1 MUTATED BRD1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(840) Variable = ITPR2 MUTATION ANALYSIS
D840V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    21  11
  ITPR2 WILD-TYPE 317 205
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             32             522 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             11             205 
$`ITPR2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A3I8 TCGA-L5-A4OQ 
       19.99        21.99         7.63         8.94        33.27         1.38 
TCGA-L5-A88Z TCGA-LN-A9FP TCGA-XP-A8T8 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
        7.40        12.03        14.37         9.34         9.67        34.68 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5801 
        6.18        31.10         1.12        27.12        31.96        13.18 
TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-5577 TCGA-D7-A4YV TCGA-F1-6874 
       12.43         6.02       105.07        25.71         5.92        14.47 
TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H8 
        0.56        28.96        22.32         8.98         0.10        14.07 
TCGA-MX-A5UJ TCGA-R5-A7ZR 
       19.73         6.08 

$`ITPR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03        13.58        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-8608 
       26.47         1.51         5.92        24.39        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
            0.1             0.0 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         105.07          122.30 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         12.805          13.630 
[1] "0.1 - 105.1 (12.8)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D840V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITPR2 MUTATED         0        0        2        2         7         3
  ITPR2 WILD-TYPE      10       20       44       29        77        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITPR2 MUTATED           3          7          1          3        3         0
  ITPR2 WILD-TYPE        26         77         61         36       40         4
D840V3, multiclass
            clus
vv           ITPR2 MUTATED ITPR2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              7              77
  STAGE IIB              3              80
  STAGE III              3              26
  STAGE IIIA             7              77
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITPR2 MUTATED       4   6  14   8
  ITPR2 WILD-TYPE    50 129 247  94
D840V4, multiclass
       clus
vv      ITPR2 MUTATED ITPR2 WILD-TYPE
  T0+T1             4              50
  T2                6             129
  T3               14             247
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITPR2 MUTATED     9  14   7   2
  ITPR2 WILD-TYPE 186 159  82  83
D840V5, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0             9             186
  N1            14             159
  N2             7              82
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V6, binary
                 cls
clus                0   1
  ITPR2 MUTATED    30   2
  ITPR2 WILD-TYPE 452  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     30    2
  ITPR2 WILD-TYPE  452   36
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0            30             452
  1             2              36
[1] 2 2
[1] FALSE
D840V7, binary
                 cls
clus                0   1
  ITPR2 MUTATED    17  18
  ITPR2 WILD-TYPE 155 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     17   18
  ITPR2 WILD-TYPE  155  388
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE            17             155
  MALE              18             388
[1] 2 2
[1] FALSE
D840V8, binary
                 cls
clus                0   1
  ITPR2 MUTATED    29   2
  ITPR2 WILD-TYPE 387 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     29    2
  ITPR2 WILD-TYPE  387  100
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO             29             387
  YES             2             100
[1] 2 2
[1] FALSE
D840V9, continuous
[1] "Remove cluster labels:" "ITPR2 MUTATED"         
clus
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              2              66 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
D840V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITPR2 MUTATED       9                         2
  ITPR2 WILD-TYPE   124                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITPR2 MUTATED                                           0    19
  ITPR2 WILD-TYPE                                         1   338
D840V11, multiclass
                                           clus
vv                                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V12, binary
                 cls
clus                0   1
  ITPR2 MUTATED     1  26
  ITPR2 WILD-TYPE   9 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      1   26
  ITPR2 WILD-TYPE    9  372
                        clus
vv                       ITPR2 MUTATED ITPR2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            26             372
[1] 2 2
[1] FALSE

Clustering(841) Variable = DDO MUTATION ANALYSIS
D841V1, survival
               sevent
clus2             0   1
  DDO MUTATED     5   1
  DDO WILD-TYPE 333 215
  DDO MUTATED DDO WILD-TYPE 
            6           548 
  DDO MUTATED DDO WILD-TYPE 
            1           215 
$`DDO MUTATED`
TCGA-CG-4444 TCGA-L7-A6VZ TCGA-BR-4201 TCGA-BR-A4J8 TCGA-HU-A4GH TCGA-HU-A4GX 
       47.05        10.36        30.90        13.51        11.77        20.25 

$`DDO WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DDO MUTATED DDO WILD-TYPE 
        10.36          0.00 
  DDO MUTATED DDO WILD-TYPE 
        47.05        122.30 
  DDO MUTATED DDO WILD-TYPE 
       16.880        13.565 
[1] "10.4 - 47.0 (16.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.9"
D841V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDO MUTATED         0        1        0        0         0         1
  DDO WILD-TYPE      10       19       46       31        84        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDO MUTATED           0          1          1          2        0         0
  DDO WILD-TYPE        29         83         61         37       43         4
D841V3, multiclass
            clus
vv           DDO MUTATED DDO WILD-TYPE
  STAGE I              0            10
  STAGE IA             1            19
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            0            84
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  DDO MUTATED       1   2   2   2
  DDO WILD-TYPE    53 133 259 100
D841V4, multiclass
       clus
vv      DDO MUTATED DDO WILD-TYPE
  T0+T1           1            53
  T2              2           133
  T3              2           259
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DDO MUTATED     2   0   2   2
  DDO WILD-TYPE 193 173  87  83
D841V5, multiclass
    clus
vv   DDO MUTATED DDO WILD-TYPE
  N0           2           193
  N1           0           173
  N2           2            87
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V6, binary
               cls
clus              0   1
  DDO MUTATED     6   0
  DDO WILD-TYPE 476  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDO MUTATED      6    0
  DDO WILD-TYPE  476   38
   clus
vv  DDO MUTATED DDO WILD-TYPE
  0           6           476
  1           0            38
[1] 2 2
[1] FALSE
D841V7, binary
               cls
clus              0   1
  DDO MUTATED     3   4
  DDO WILD-TYPE 169 402
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDO MUTATED      3    4
  DDO WILD-TYPE  169  402
        clus
vv       DDO MUTATED DDO WILD-TYPE
  FEMALE           3           169
  MALE             4           402
[1] 2 2
[1] FALSE
D841V8, binary
               cls
clus              0   1
  DDO MUTATED     5   2
  DDO WILD-TYPE 411 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDO MUTATED      5    2
  DDO WILD-TYPE  411  100
     clus
vv    DDO MUTATED DDO WILD-TYPE
  NO            5           411
  YES           2           100
[1] 2 2
[1] FALSE
D841V9, continuous
D841V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DDO MUTATED       2                         0
  DDO WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDO MUTATED                                           0     4
  DDO WILD-TYPE                                         1   353
D841V11, multiclass
                                           clus
vv                                          DDO MUTATED DDO WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V12, binary
               cls
clus              0   1
  DDO MUTATED     0   6
  DDO WILD-TYPE  10 392
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDO MUTATED      0    6
  DDO WILD-TYPE   10  392
                        clus
vv                       DDO MUTATED DDO WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           6           392
[1] 2 2
[1] FALSE

Clustering(842) Variable = ZNF295 MUTATION ANALYSIS
D842V1, survival
                  sevent
clus2                0   1
  ZNF295 MUTATED     8   7
  ZNF295 WILD-TYPE 330 209
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              15              539 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               7              209 
$`ZNF295 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-L5-A8NI TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 
       21.99        79.07        13.48        26.70         9.34        34.68 
TCGA-BR-8363 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5728 TCGA-CG-5733 
        0.26        16.14        12.43        11.77        65.10        21.07 
TCGA-HF-7132 TCGA-HU-A4H6 TCGA-SW-A7EA 
       77.29        21.17        19.04 

$`ZNF295 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO 
       27.12         5.16        20.02        47.05        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZNF295 MUTATED ZNF295 WILD-TYPE 
            0.26             0.00 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           79.07           122.30 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           21.07            13.51 
[1] "0.3 - 79.1 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D842V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF295 MUTATED         1        0        3        3         1         1
  ZNF295 WILD-TYPE       9       20       43       28        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF295 MUTATED           1          4          1          0        1
  ZNF295 WILD-TYPE        28         80         61         39       42
                  vv
clus               STAGE IVA
  ZNF295 MUTATED           0
  ZNF295 WILD-TYPE         4
D842V3, multiclass
            clus
vv           ZNF295 MUTATED ZNF295 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF295 MUTATED       1   5   7   3
  ZNF295 WILD-TYPE    53 130 254  99
D842V4, multiclass
       clus
vv      ZNF295 MUTATED ZNF295 WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 7              254
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF295 MUTATED     8   7   2   1
  ZNF295 WILD-TYPE 187 166  87  84
D842V5, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  N0              8              187
  N1              7              166
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V6, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    17   1
  ZNF295 WILD-TYPE 465  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     17    1
  ZNF295 WILD-TYPE  465   37
   clus
vv  ZNF295 MUTATED ZNF295 WILD-TYPE
  0             17              465
  1              1               37
[1] 2 2
[1] FALSE
D842V7, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    12   7
  ZNF295 WILD-TYPE 160 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     12    7
  ZNF295 WILD-TYPE  160  399
        clus
vv       ZNF295 MUTATED ZNF295 WILD-TYPE
  FEMALE             12              160
  MALE                7              399
[1] 2 2
[1] FALSE
D842V8, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    14   1
  ZNF295 WILD-TYPE 402 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     14    1
  ZNF295 WILD-TYPE  402  101
     clus
vv    ZNF295 MUTATED ZNF295 WILD-TYPE
  NO              14              402
  YES              1              101
[1] 2 2
[1] FALSE
D842V9, continuous
D842V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF295 MUTATED       3                         1
  ZNF295 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF295 MUTATED                                           0    10
  ZNF295 WILD-TYPE                                         1   347
D842V11, multiclass
                                           clus
vv                                          ZNF295 MUTATED ZNF295 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V12, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     0  13
  ZNF295 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      0   13
  ZNF295 WILD-TYPE   10  385
                        clus
vv                       ZNF295 MUTATED ZNF295 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(843) Variable = FOXQ1 MUTATION ANALYSIS
D843V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 336 215
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             551 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1             215 
$`FOXQ1 MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-CG-4306 
       35.84        29.59         1.02 

$`FOXQ1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
           1.02            0.00 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          35.84          122.30 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          29.59           13.55 
[1] "1.0 - 35.8 (29.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D843V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOXQ1 MUTATED         0        0        1        0         0         1
  FOXQ1 WILD-TYPE      10       20       45       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXQ1 MUTATED           0          0          0          0        1         0
  FOXQ1 WILD-TYPE        29         84         62         39       42         4
D843V3, multiclass
            clus
vv           FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FOXQ1 MUTATED       0   1   1   1
  FOXQ1 WILD-TYPE    54 134 260 101
D843V4, multiclass
       clus
vv      FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                1             260
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FOXQ1 MUTATED     2   0   1   0
  FOXQ1 WILD-TYPE 193 173  88  85
D843V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             2             193
  N1             0             173
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 480  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  480   37
   clus
vv  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  0             2             480
  1             1              37
[1] 2 2
[1] FALSE
D843V7, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 170 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  170  405
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             2             170
  MALE               1             405
[1] 2 2
[1] FALSE
D843V8, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   0
  FOXQ1 WILD-TYPE 414 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    0
  FOXQ1 WILD-TYPE  414  102
     clus
vv    FOXQ1 MUTATED FOXQ1 WILD-TYPE
  NO              2             414
  YES             0             102
[1] 2 2
[1] FALSE
D843V9, continuous
D843V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FOXQ1 MUTATED       0                         0
  FOXQ1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FOXQ1 MUTATED                                           0     2
  FOXQ1 WILD-TYPE                                         1   355
D843V11, multiclass
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             503 
     TCGA-IC-A6RF      TCGA-JY-A6FB      TCGA-JY-A938      TCGA-L5-A43I 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG      TCGA-L5-A4OI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-S8-A6BV      TCGA-EQ-A4SO      TCGA-F1-6177 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-KB-A93G      TCGA-MX-A663      TCGA-IC-A6RE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A51D      TCGA-IG-A5B8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IG-A5S3      TCGA-IG-A625      TCGA-IG-A6QS      TCGA-IG-A7DP 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-IG-A97I      TCGA-JY-A6F8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-JY-A6FA      TCGA-JY-A6FD      TCGA-JY-A6FE      TCGA-JY-A6FG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-JY-A939      TCGA-JY-A93C      TCGA-JY-A93D 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-JY-A93E      TCGA-JY-A93F      TCGA-KH-A6WC      TCGA-L5-A43C 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OF      TCGA-L5-A4OH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A4OJ      TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OR      TCGA-L5-A4OS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX      TCGA-L5-A88S 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A88W      TCGA-L5-A88Z      TCGA-L5-A891 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A8NI      TCGA-L5-A8NJ      TCGA-L5-A8NK      TCGA-L5-A8NL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A8NM      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L5-A8NU      TCGA-L5-A8NV      TCGA-L5-A8NW      TCGA-L7-A56G 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-L7-A6VZ      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-LN-A8I1      TCGA-LN-A9FO 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-LN-A9FP      TCGA-LN-A9FQ      TCGA-LN-A9FR      TCGA-Q9-A6FW 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6DQ      TCGA-R6-A6KZ      TCGA-R6-A6L4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R6-A6L6      TCGA-R6-A6XG      TCGA-R6-A6XQ      TCGA-R6-A6Y0 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R6-A8WG      TCGA-RE-A7BO      TCGA-S8-A6BW      TCGA-V5-A7RC 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE      TCGA-Z6-A9VB 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-Z6-AAPN      TCGA-ZR-A9CJ      TCGA-B7-5816      TCGA-B7-5818 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4256      TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4361      TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534      TCGA-CD-8535 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-D7-5577      TCGA-D7-5578 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HJ-7597 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R5-A7O7      TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R5-A7ZR      TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A7BT      TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8MW      TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8N4      TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-SW-A7EA      TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8P2      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA64      TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA6B      TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA6J      TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
D843V12, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0   2
  FOXQ1 WILD-TYPE  10 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0    2
  FOXQ1 WILD-TYPE   10  396
                        clus
vv                       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             2             396
[1] 2 2
[1] FALSE

Clustering(844) Variable = HMMR MUTATION ANALYSIS
D844V1, survival
                sevent
clus2              0   1
  HMMR MUTATED     4   5
  HMMR WILD-TYPE 334 211
  HMMR MUTATED HMMR WILD-TYPE 
             9            545 
  HMMR MUTATED HMMR WILD-TYPE 
             5            211 
$`HMMR MUTATED`
TCGA-2H-A9GF TCGA-JY-A6FG TCGA-L5-A4OH TCGA-LN-A49X TCGA-B7-A5TI TCGA-BR-4184 
       25.78        41.52        32.61        12.62        19.56         6.97 
TCGA-BR-4256 TCGA-BR-8680 TCGA-D7-6525 
        9.34        31.96        13.35 

$`HMMR WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  HMMR MUTATED HMMR WILD-TYPE 
          6.97           0.00 
  HMMR MUTATED HMMR WILD-TYPE 
         41.52         122.30 
  HMMR MUTATED HMMR WILD-TYPE 
         19.56          13.55 
[1] "7.0 - 41.5 (19.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D844V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HMMR MUTATED         1        0        0        0         1         1
  HMMR WILD-TYPE       9       20       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMMR MUTATED           2          2          0          1        2         0
  HMMR WILD-TYPE        27         82         62         38       41         4
D844V3, multiclass
            clus
vv           HMMR MUTATED HMMR WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HMMR MUTATED       1   1   4   4
  HMMR WILD-TYPE    53 134 257  98
D844V4, multiclass
       clus
vv      HMMR MUTATED HMMR WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               4            257
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HMMR MUTATED     3   4   3   1
  HMMR WILD-TYPE 192 169  86  84
D844V5, multiclass
    clus
vv   HMMR MUTATED HMMR WILD-TYPE
  N0            3            192
  N1            4            169
  N2            3             86
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V6, binary
                cls
clus               0   1
  HMMR MUTATED     9   1
  HMMR WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      9    1
  HMMR WILD-TYPE  473   37
   clus
vv  HMMR MUTATED HMMR WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D844V7, binary
                cls
clus               0   1
  HMMR MUTATED     1  10
  HMMR WILD-TYPE 171 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      1   10
  HMMR WILD-TYPE  171  396
        clus
vv       HMMR MUTATED HMMR WILD-TYPE
  FEMALE            1            171
  MALE             10            396
[1] 2 2
[1] FALSE
D844V8, binary
                cls
clus               0   1
  HMMR MUTATED     9   1
  HMMR WILD-TYPE 407 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      9    1
  HMMR WILD-TYPE  407  101
     clus
vv    HMMR MUTATED HMMR WILD-TYPE
  NO             9            407
  YES            1            101
[1] 2 2
[1] FALSE
D844V9, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
D844V10, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OM     TCGA-L5-A4ON 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HMMR MUTATED       2                         0
  HMMR WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HMMR MUTATED                                           0     8
  HMMR WILD-TYPE                                         1   349
D844V11, multiclass
                                           clus
vv                                          HMMR MUTATED HMMR WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V12, binary
                cls
clus               0   1
  HMMR MUTATED     0   8
  HMMR WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      0    8
  HMMR WILD-TYPE   10  390
                        clus
vv                       HMMR MUTATED HMMR WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(845) Variable = KIAA1609 MUTATION ANALYSIS
D845V1, survival
                    sevent
clus2                  0   1
  KIAA1609 MUTATED     7   1
  KIAA1609 WILD-TYPE 331 215
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                546 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 1                215 
$`KIAA1609 MUTATED`
TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 TCGA-CG-5721 TCGA-HF-A5NB 
        9.34        29.59        31.10        31.27         6.02        30.51 
TCGA-HU-A4G9 TCGA-VQ-A8P2 
       24.20        38.14 

$`KIAA1609 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
              6.02               0.00 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
             38.14             122.30 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
             30.05              13.51 
[1] "6.0 - 38.1 (30.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.5"
D845V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1609 MUTATED         0        1        0        0         0         1
  KIAA1609 WILD-TYPE      10       19       46       31        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1609 MUTATED           0          1          0          3        1
  KIAA1609 WILD-TYPE        29         83         62         36       42
                    vv
clus                 STAGE IVA
  KIAA1609 MUTATED           0
  KIAA1609 WILD-TYPE         4
D845V3, multiclass
            clus
vv           KIAA1609 MUTATED KIAA1609 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1609 MUTATED       1   0   0   6
  KIAA1609 WILD-TYPE    53 135 261  96
D845V4, multiclass
       clus
vv      KIAA1609 MUTATED KIAA1609 WILD-TYPE
  T0+T1                1                 53
  T2                   0                135
  T3                   0                261
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1609 MUTATED     2   3   1   2
  KIAA1609 WILD-TYPE 193 170  88  83
D845V5, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  N0                2                193
  N1                3                170
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V6, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     8   0
  KIAA1609 WILD-TYPE 474  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      8    0
  KIAA1609 WILD-TYPE  474   38
   clus
vv  KIAA1609 MUTATED KIAA1609 WILD-TYPE
  0                8                474
  1                0                 38
[1] 2 2
[1] FALSE
D845V7, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     4   4
  KIAA1609 WILD-TYPE 168 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      4    4
  KIAA1609 WILD-TYPE  168  402
        clus
vv       KIAA1609 MUTATED KIAA1609 WILD-TYPE
  FEMALE                4                168
  MALE                  4                402
[1] 2 2
[1] FALSE
D845V8, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     6   2
  KIAA1609 WILD-TYPE 410 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      6    2
  KIAA1609 WILD-TYPE  410  100
     clus
vv    KIAA1609 MUTATED KIAA1609 WILD-TYPE
  NO                 6                410
  YES                2                100
[1] 2 2
[1] FALSE
D845V9, continuous
D845V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1609 MUTATED       1                         0
  KIAA1609 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1609 MUTATED                                           0     5
  KIAA1609 WILD-TYPE                                         1   352
D845V11, multiclass
                                           clus
vv                                          KIAA1609 MUTATED KIAA1609 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V12, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     0   5
  KIAA1609 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      0    5
  KIAA1609 WILD-TYPE   10  393
                        clus
vv                       KIAA1609 MUTATED KIAA1609 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(846) Variable = RAB14 MUTATION ANALYSIS
D846V1, survival
                 sevent
clus2               0   1
  RAB14 MUTATED     2   3
  RAB14 WILD-TYPE 336 213
  RAB14 MUTATED RAB14 WILD-TYPE 
              5             549 
  RAB14 MUTATED RAB14 WILD-TYPE 
              3             213 
$`RAB14 MUTATED`
TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-A4QL TCGA-CD-A4MH TCGA-HU-A4GQ 
        6.97        31.10        16.14        12.20         0.10 

$`RAB14 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RAB14 MUTATED RAB14 WILD-TYPE 
            0.1             0.0 
  RAB14 MUTATED RAB14 WILD-TYPE 
           31.1           122.3 
  RAB14 MUTATED RAB14 WILD-TYPE 
          12.20           13.58 
[1] "0.1 - 31.1 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D846V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAB14 MUTATED         0        0        0        0         1         0
  RAB14 WILD-TYPE      10       20       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB14 MUTATED           0          1          1          2        0         0
  RAB14 WILD-TYPE        29         83         61         37       43         4
D846V3, multiclass
            clus
vv           RAB14 MUTATED RAB14 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RAB14 MUTATED       0   0   3   2
  RAB14 WILD-TYPE    54 135 258 100
D846V4, multiclass
       clus
vv      RAB14 MUTATED RAB14 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RAB14 MUTATED     1   2   2   1
  RAB14 WILD-TYPE 194 171  87  84
D846V5, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  N0             1             194
  N1             2             171
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V6, binary
                 cls
clus                0   1
  RAB14 MUTATED     5   0
  RAB14 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      5    0
  RAB14 WILD-TYPE  477   38
   clus
vv  RAB14 MUTATED RAB14 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D846V7, binary
                 cls
clus                0   1
  RAB14 MUTATED     4   2
  RAB14 WILD-TYPE 168 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      4    2
  RAB14 WILD-TYPE  168  404
        clus
vv       RAB14 MUTATED RAB14 WILD-TYPE
  FEMALE             4             168
  MALE               2             404
[1] 2 2
[1] FALSE
D846V8, binary
                 cls
clus                0   1
  RAB14 MUTATED     4   1
  RAB14 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      4    1
  RAB14 WILD-TYPE  412  101
     clus
vv    RAB14 MUTATED RAB14 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D846V9, continuous
D846V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAB14 MUTATED       2                         0
  RAB14 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB14 MUTATED                                           0     4
  RAB14 WILD-TYPE                                         1   353
D846V11, multiclass
                                           clus
vv                                          RAB14 MUTATED RAB14 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V12, binary
                 cls
clus                0   1
  RAB14 MUTATED     0   6
  RAB14 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      0    6
  RAB14 WILD-TYPE   10  392
                        clus
vv                       RAB14 MUTATED RAB14 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(847) Variable = AP2A2 MUTATION ANALYSIS
D847V1, survival
                 sevent
clus2               0   1
  AP2A2 MUTATED     6   8
  AP2A2 WILD-TYPE 332 208
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             14             540 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              8             208 
$`AP2A2 MUTATED`
TCGA-2H-A9GK TCGA-IG-A97H TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8081 
        7.63        14.50        30.90        34.68        18.15        32.25 
TCGA-BR-A4QL TCGA-CD-A4MI TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4GU 
       16.14        11.77        11.44        26.47         0.10         6.58 
TCGA-MX-A5UJ TCGA-VQ-A8DT 
       19.73        48.79 

$`AP2A2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  AP2A2 MUTATED AP2A2 WILD-TYPE 
            0.1             0.0 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
          48.79          122.30 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
         17.145          13.510 
[1] "0.1 - 48.8 (17.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D847V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AP2A2 MUTATED         0        0        2        0         2         2
  AP2A2 WILD-TYPE      10       20       44       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP2A2 MUTATED           1          2          3          1        1         0
  AP2A2 WILD-TYPE        28         82         59         38       42         4
D847V3, multiclass
            clus
vv           AP2A2 MUTATED AP2A2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AP2A2 MUTATED       0   3   9   3
  AP2A2 WILD-TYPE    54 132 252  99
D847V4, multiclass
       clus
vv      AP2A2 MUTATED AP2A2 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                9             252
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AP2A2 MUTATED     4   4   2   3
  AP2A2 WILD-TYPE 191 169  87  82
D847V5, multiclass
    clus
vv   AP2A2 MUTATED AP2A2 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V6, binary
                 cls
clus                0   1
  AP2A2 MUTATED    15   0
  AP2A2 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED     15    0
  AP2A2 WILD-TYPE  467   38
   clus
vv  AP2A2 MUTATED AP2A2 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D847V7, binary
                 cls
clus                0   1
  AP2A2 MUTATED     8   8
  AP2A2 WILD-TYPE 164 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      8    8
  AP2A2 WILD-TYPE  164  398
        clus
vv       AP2A2 MUTATED AP2A2 WILD-TYPE
  FEMALE             8             164
  MALE               8             398
[1] 2 2
[1] FALSE
D847V8, binary
                 cls
clus                0   1
  AP2A2 MUTATED    12   1
  AP2A2 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED     12    1
  AP2A2 WILD-TYPE  404  101
     clus
vv    AP2A2 MUTATED AP2A2 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D847V9, continuous
D847V10, continuous
[1] "Remove cluster labels:" "AP2A2 MUTATED"         
clus
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-JY-A6FA      TCGA-JY-A6FE 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"AP2A2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AP2A2 MUTATED       4                         0
  AP2A2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AP2A2 MUTATED                                           0     9
  AP2A2 WILD-TYPE                                         1   348
D847V11, multiclass
                                           clus
vv                                          AP2A2 MUTATED AP2A2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V12, binary
                 cls
clus                0   1
  AP2A2 MUTATED     0  13
  AP2A2 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      0   13
  AP2A2 WILD-TYPE   10  385
                        clus
vv                       AP2A2 MUTATED AP2A2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(848) Variable = KIAA0427 MUTATION ANALYSIS
D848V1, survival
                    sevent
clus2                  0   1
  KIAA0427 MUTATED     8   5
  KIAA0427 WILD-TYPE 330 211
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                13                541 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                 5                211 
$`KIAA0427 MUTATED`
TCGA-JY-A6FH TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8372 
       47.38        26.70         6.97         6.61        34.68        31.27 
TCGA-CG-5726 TCGA-CG-5733 TCGA-F1-6874 TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8DU 
       28.96        21.07        14.47        20.25        19.73         5.46 
TCGA-VQ-A8P2 
       38.14 

$`KIAA0427 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
              5.46               0.00 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
             47.38             122.30 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
             21.07              13.48 
[1] "5.5 - 47.4 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D848V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0427 MUTATED         1        1        2        0         1         2
  KIAA0427 WILD-TYPE       9       19       44       31        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0427 MUTATED           1          6          0          2        0
  KIAA0427 WILD-TYPE        28         78         62         37       43
                    vv
clus                 STAGE IVA
  KIAA0427 MUTATED           0
  KIAA0427 WILD-TYPE         4
D848V3, multiclass
            clus
vv           KIAA0427 MUTATED KIAA0427 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  1                 19
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 1                 28
  STAGE IIIA                6                 78
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA0427 MUTATED       2   5   5   5
  KIAA0427 WILD-TYPE    52 130 256  97
D848V4, multiclass
       clus
vv      KIAA0427 MUTATED KIAA0427 WILD-TYPE
  T0+T1                2                 52
  T2                   5                130
  T3                   5                256
  T4                   5                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA0427 MUTATED     6   5   4   1
  KIAA0427 WILD-TYPE 189 168  85  84
D848V5, multiclass
    clus
vv   KIAA0427 MUTATED KIAA0427 WILD-TYPE
  N0                6                189
  N1                5                168
  N2                4                 85
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V6, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED    14   0
  KIAA0427 WILD-TYPE 468  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED     14    0
  KIAA0427 WILD-TYPE  468   38
   clus
vv  KIAA0427 MUTATED KIAA0427 WILD-TYPE
  0               14                468
  1                0                 38
[1] 2 2
[1] FALSE
D848V7, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED     8   9
  KIAA0427 WILD-TYPE 164 397
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED      8    9
  KIAA0427 WILD-TYPE  164  397
        clus
vv       KIAA0427 MUTATED KIAA0427 WILD-TYPE
  FEMALE                8                164
  MALE                  9                397
[1] 2 2
[1] FALSE
D848V8, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED    12   1
  KIAA0427 WILD-TYPE 404 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED     12    1
  KIAA0427 WILD-TYPE  404  101
     clus
vv    KIAA0427 MUTATED KIAA0427 WILD-TYPE
  NO                12                404
  YES                1                101
[1] 2 2
[1] FALSE
D848V9, continuous
D848V10, continuous
[1] "Remove cluster labels:" "KIAA0427 MUTATED"      
clus
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-KH-A6WC 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" "KIAA0427 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KIAA0427 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0427 MUTATED       1                         1
  KIAA0427 WILD-TYPE   132                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0427 MUTATED                                           0    12
  KIAA0427 WILD-TYPE                                         1   345
D848V11, multiclass
                                           clus
vv                                          KIAA0427 MUTATED KIAA0427 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V12, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED     0  11
  KIAA0427 WILD-TYPE  10 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED      0   11
  KIAA0427 WILD-TYPE   10  387
                        clus
vv                       KIAA0427 MUTATED KIAA0427 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                387
[1] 2 2
[1] FALSE

Clustering(849) Variable = CACNA1A MUTATION ANALYSIS
D849V1, survival
                   sevent
clus2                 0   1
  CACNA1A MUTATED    19  15
  CACNA1A WILD-TYPE 319 201
  CACNA1A MUTATED CACNA1A WILD-TYPE 
               34               520 
  CACNA1A MUTATED CACNA1A WILD-TYPE 
               15               201 
$`CACNA1A MUTATED`
TCGA-CG-4460 TCGA-2H-A9GN TCGA-IG-A50L TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OT 
       21.99         8.94         0.53         3.68        30.25         4.90 
TCGA-L5-A4OW TCGA-LN-A8HZ TCGA-LN-A9FP TCGA-V5-A7RB TCGA-VR-A8EZ TCGA-XP-A8T6 
        7.13        12.33        12.03         5.29        18.18        25.08 
TCGA-XP-A8T7 TCGA-ZR-A9CJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6852 
       41.23        19.73         9.44        18.35        34.68        44.94 
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL 
       29.59        31.10         0.26         1.12        31.96        16.14 
TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H5 
        6.58         8.05         6.02        22.32         0.10        23.80 
TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-RD-A8N5 TCGA-VQ-A8P3 
       14.07        19.73        57.44        37.22 

$`CACNA1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        1.38         3.16        58.59        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        23.84        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CACNA1A MUTATED CACNA1A WILD-TYPE 
              0.1               0.0 
  CACNA1A MUTATED CACNA1A WILD-TYPE 
            57.44            122.30 
  CACNA1A MUTATED CACNA1A WILD-TYPE 
            17.16             13.51 
[1] "0.1 - 57.4 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D849V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CACNA1A MUTATED         1        0        4        1         7         5
  CACNA1A WILD-TYPE       9       20       42       30        77        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1A MUTATED           2          4          1          4        5
  CACNA1A WILD-TYPE        27         80         61         35       38
                   vv
clus                STAGE IVA
  CACNA1A MUTATED           0
  CACNA1A WILD-TYPE         4
D849V3, multiclass
            clus
vv           CACNA1A MUTATED CACNA1A WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 1                30
  STAGE IIA                7                77
  STAGE IIB                5                78
  STAGE III                2                27
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 5                38
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CACNA1A MUTATED       3  10  14  10
  CACNA1A WILD-TYPE    51 125 247  92
D849V4, multiclass
       clus
vv      CACNA1A MUTATED CACNA1A WILD-TYPE
  T0+T1               3                51
  T2                 10               125
  T3                 14               247
  T4                 10                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CACNA1A MUTATED    13  14   5   3
  CACNA1A WILD-TYPE 182 159  84  82
D849V5, multiclass
    clus
vv   CACNA1A MUTATED CACNA1A WILD-TYPE
  N0              13               182
  N1              14               159
  N2               5                84
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V6, binary
                   cls
clus                  0   1
  CACNA1A MUTATED    33   3
  CACNA1A WILD-TYPE 449  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1A MUTATED     33    3
  CACNA1A WILD-TYPE  449   35
   clus
vv  CACNA1A MUTATED CACNA1A WILD-TYPE
  0              33               449
  1               3                35
[1] 2 2
[1] FALSE
D849V7, binary
                   cls
clus                  0   1
  CACNA1A MUTATED    16  23
  CACNA1A WILD-TYPE 156 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1A MUTATED     16   23
  CACNA1A WILD-TYPE  156  383
        clus
vv       CACNA1A MUTATED CACNA1A WILD-TYPE
  FEMALE              16               156
  MALE                23               383
[1] 2 2
[1] FALSE
D849V8, binary
                   cls
clus                  0   1
  CACNA1A MUTATED    29   4
  CACNA1A WILD-TYPE 387  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1A MUTATED     29    4
  CACNA1A WILD-TYPE  387   98
     clus
vv    CACNA1A MUTATED CACNA1A WILD-TYPE
  NO               29               387
  YES               4                98
[1] 2 2
[1] FALSE
D849V9, continuous
D849V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CACNA1A MUTATED       9                         1
  CACNA1A WILD-TYPE   124                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CACNA1A MUTATED                                           0    22
  CACNA1A WILD-TYPE                                         1   335
D849V11, multiclass
                                           clus
vv                                          CACNA1A MUTATED CACNA1A WILD-TYPE
  ASIAN                                                   9               124
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  22               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V12, binary
                   cls
clus                  0   1
  CACNA1A MUTATED     3  25
  CACNA1A WILD-TYPE   7 373
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1A MUTATED      3   25
  CACNA1A WILD-TYPE    7  373
                        clus
vv                       CACNA1A MUTATED CACNA1A WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              25               373
[1] 2 2
[1] FALSE

Clustering(850) Variable = DCLRE1A MUTATION ANALYSIS
D850V1, survival
                   sevent
clus2                 0   1
  DCLRE1A MUTATED    11   5
  DCLRE1A WILD-TYPE 327 211
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               16               538 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                5               211 
$`DCLRE1A MUTATED`
TCGA-L5-A4OU TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L7-A6VZ TCGA-LN-A8I0 
       29.00        12.92        13.48         7.76        10.36        13.38 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7901 TCGA-BR-8591 TCGA-BR-A4PE TCGA-CD-8536 
       34.68        30.90         3.45        28.14        20.42        12.43 
TCGA-CG-5730 TCGA-FP-8099 TCGA-VQ-A8PM TCGA-VQ-AA6B 
        4.01        17.06         1.87        32.94 

$`DCLRE1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
             1.87              0.00 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            34.68            122.30 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            13.43             13.63 
[1] "1.9 - 34.7 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D850V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DCLRE1A MUTATED         0        0        1        1         4         2
  DCLRE1A WILD-TYPE      10       20       45       30        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1A MUTATED           1          1          1          2        3
  DCLRE1A WILD-TYPE        28         83         61         37       40
                   vv
clus                STAGE IVA
  DCLRE1A MUTATED           0
  DCLRE1A WILD-TYPE         4
D850V3, multiclass
            clus
vv           DCLRE1A MUTATED DCLRE1A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                4                80
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  DCLRE1A MUTATED       1   4   9   2
  DCLRE1A WILD-TYPE    53 131 252 100
D850V4, multiclass
       clus
vv      DCLRE1A MUTATED DCLRE1A WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  9               252
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  DCLRE1A MUTATED     7   4   2   3
  DCLRE1A WILD-TYPE 188 169  87  82
D850V5, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  N0               7               188
  N1               4               169
  N2               2                87
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V6, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED    12   2
  DCLRE1A WILD-TYPE 470  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED     12    2
  DCLRE1A WILD-TYPE  470   36
   clus
vv  DCLRE1A MUTATED DCLRE1A WILD-TYPE
  0              12               470
  1               2                36
[1] 2 2
[1] FALSE
D850V7, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     4  12
  DCLRE1A WILD-TYPE 168 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      4   12
  DCLRE1A WILD-TYPE  168  394
        clus
vv       DCLRE1A MUTATED DCLRE1A WILD-TYPE
  FEMALE               4               168
  MALE                12               394
[1] 2 2
[1] FALSE
D850V8, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED    12   2
  DCLRE1A WILD-TYPE 404 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED     12    2
  DCLRE1A WILD-TYPE  404  100
     clus
vv    DCLRE1A MUTATED DCLRE1A WILD-TYPE
  NO               12               404
  YES               2               100
[1] 2 2
[1] FALSE
D850V9, continuous
D850V10, continuous
[1] "Remove cluster labels:" "DCLRE1A MUTATED"       
clus
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OW        TCGA-L5-A4OX 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" "DCLRE1A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DCLRE1A MUTATED       2                         0
  DCLRE1A WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DCLRE1A MUTATED                                           0    13
  DCLRE1A WILD-TYPE                                         1   344
D850V11, multiclass
                                           clus
vv                                          DCLRE1A MUTATED DCLRE1A WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V12, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     0   9
  DCLRE1A WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      0    9
  DCLRE1A WILD-TYPE   10  389
                        clus
vv                       DCLRE1A MUTATED DCLRE1A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(851) Variable = ZNF570 MUTATION ANALYSIS
D851V1, survival
                  sevent
clus2                0   1
  ZNF570 MUTATED     9   8
  ZNF570 WILD-TYPE 329 208
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              17              537 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               8              208 
$`ZNF570 MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-L5-A4OR TCGA-L5-A8NJ TCGA-LN-A49L TCGA-LN-A49W 
       25.78         7.63         3.16        16.47        10.45        13.25 
TCGA-VR-A8EZ TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4J5 
       18.18         6.97        29.59         0.26        31.96        28.34 
TCGA-CG-5723 TCGA-HU-A4GP TCGA-HU-A4GU TCGA-IN-A7NT TCGA-VQ-AA6I 
      105.07         8.98         6.58        10.62        16.14 

$`ZNF570 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        12.59        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17         0.53         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZNF570 MUTATED ZNF570 WILD-TYPE 
            0.26             0.00 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
          105.07           122.30 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
           13.25            13.58 
[1] "0.3 - 105.1 (13.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D851V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF570 MUTATED         0        2        1        1         2         3
  ZNF570 WILD-TYPE      10       18       45       30        82        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF570 MUTATED           4          2          1          1        1
  ZNF570 WILD-TYPE        25         82         61         38       42
                  vv
clus               STAGE IVA
  ZNF570 MUTATED           0
  ZNF570 WILD-TYPE         4
D851V3, multiclass
            clus
vv           ZNF570 MUTATED ZNF570 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               3               80
  STAGE III               4               25
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF570 MUTATED       2   4   9   3
  ZNF570 WILD-TYPE    52 131 252  99
D851V4, multiclass
       clus
vv      ZNF570 MUTATED ZNF570 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 9              252
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF570 MUTATED     5  10   1   2
  ZNF570 WILD-TYPE 190 163  88  83
D851V5, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  N0              5              190
  N1             10              163
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V6, binary
                  cls
clus                 0   1
  ZNF570 MUTATED    16   1
  ZNF570 WILD-TYPE 466  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED     16    1
  ZNF570 WILD-TYPE  466   37
   clus
vv  ZNF570 MUTATED ZNF570 WILD-TYPE
  0             16              466
  1              1               37
[1] 2 2
[1] FALSE
D851V7, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     5  14
  ZNF570 WILD-TYPE 167 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      5   14
  ZNF570 WILD-TYPE  167  392
        clus
vv       ZNF570 MUTATED ZNF570 WILD-TYPE
  FEMALE              5              167
  MALE               14              392
[1] 2 2
[1] FALSE
D851V8, binary
                  cls
clus                 0   1
  ZNF570 MUTATED    15   3
  ZNF570 WILD-TYPE 401  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED     15    3
  ZNF570 WILD-TYPE  401   99
     clus
vv    ZNF570 MUTATED ZNF570 WILD-TYPE
  NO              15              401
  YES              3               99
[1] 2 2
[1] FALSE
D851V9, continuous
D851V10, continuous
[1] "Remove cluster labels:" "ZNF570 MUTATED"        
clus
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8Q7 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" "ZNF570 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF570 MUTATED       7                         0
  ZNF570 WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF570 MUTATED                                           0     9
  ZNF570 WILD-TYPE                                         1   348
D851V11, multiclass
                                           clus
vv                                          ZNF570 MUTATED ZNF570 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V12, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     0  11
  ZNF570 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      0   11
  ZNF570 WILD-TYPE   10  387
                        clus
vv                       ZNF570 MUTATED ZNF570 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(852) Variable = HAPLN1 MUTATION ANALYSIS
D852V1, survival
                  sevent
clus2                0   1
  HAPLN1 MUTATED     5   3
  HAPLN1 WILD-TYPE 333 213
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               8              546 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               3              213 
$`HAPLN1 MUTATED`
TCGA-CG-4460 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8361 TCGA-BR-8591 
       21.99        32.78        29.59         9.60        31.10        28.14 
TCGA-CG-4306 TCGA-F1-6874 
        1.02        14.47 

$`HAPLN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.69        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
            1.02             0.00 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
           32.78           122.30 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
          25.065           13.510 
[1] "1.0 - 32.8 (25.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D852V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAPLN1 MUTATED         1        0        1        0         1         1
  HAPLN1 WILD-TYPE       9       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAPLN1 MUTATED           0          0          0          3        2
  HAPLN1 WILD-TYPE        29         84         62         36       41
                  vv
clus               STAGE IVA
  HAPLN1 MUTATED           0
  HAPLN1 WILD-TYPE         4
D852V3, multiclass
            clus
vv           HAPLN1 MUTATED HAPLN1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HAPLN1 MUTATED       1   1   2   5
  HAPLN1 WILD-TYPE    53 134 259  97
D852V4, multiclass
       clus
vv      HAPLN1 MUTATED HAPLN1 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 2              259
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HAPLN1 MUTATED     3   2   2   2
  HAPLN1 WILD-TYPE 192 171  87  83
D852V5, multiclass
    clus
vv   HAPLN1 MUTATED HAPLN1 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V6, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     6   2
  HAPLN1 WILD-TYPE 476  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      6    2
  HAPLN1 WILD-TYPE  476   36
   clus
vv  HAPLN1 MUTATED HAPLN1 WILD-TYPE
  0              6              476
  1              2               36
[1] 2 2
[1] FALSE
D852V7, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     5   4
  HAPLN1 WILD-TYPE 167 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      5    4
  HAPLN1 WILD-TYPE  167  402
        clus
vv       HAPLN1 MUTATED HAPLN1 WILD-TYPE
  FEMALE              5              167
  MALE                4              402
[1] 2 2
[1] FALSE
D852V8, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     8   0
  HAPLN1 WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      8    0
  HAPLN1 WILD-TYPE  408  102
     clus
vv    HAPLN1 MUTATED HAPLN1 WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D852V9, continuous
D852V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HAPLN1 MUTATED       0                         1
  HAPLN1 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAPLN1 MUTATED                                           0     6
  HAPLN1 WILD-TYPE                                         1   351
D852V11, multiclass
                                           clus
vv                                          HAPLN1 MUTATED HAPLN1 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V12, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     0   7
  HAPLN1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      0    7
  HAPLN1 WILD-TYPE   10  391
                        clus
vv                       HAPLN1 MUTATED HAPLN1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(853) Variable = N4BP2 MUTATION ANALYSIS
D853V1, survival
                 sevent
clus2               0   1
  N4BP2 MUTATED    10   7
  N4BP2 WILD-TYPE 328 209
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             17             537 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              7             209 
$`N4BP2 MUTATED`
TCGA-EQ-A4SO TCGA-JY-A6FE TCGA-JY-A6FG TCGA-L5-A8NR TCGA-LN-A4A4 TCGA-VR-A8EZ 
       16.24         3.68        41.52         8.71        12.59        18.18 
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8680 
       26.70         6.97         9.67        34.68        19.33        31.96 
TCGA-CG-4305 TCGA-HU-A4G9 TCGA-RD-A7BT TCGA-VQ-A8P2 TCGA-VQ-A92D 
       15.95        24.20         8.61        38.14        66.81 

$`N4BP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
      122.10        44.75        68.02        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        42.64        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  N4BP2 MUTATED N4BP2 WILD-TYPE 
           3.68            0.00 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          66.81          122.30 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          18.18           13.51 
[1] "3.7 - 66.8 (18.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D853V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  N4BP2 MUTATED         1        1        2        1         1         2
  N4BP2 WILD-TYPE       9       19       44       30        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  N4BP2 MUTATED           4          2          1          1        3         0
  N4BP2 WILD-TYPE        25         82         61         38       40         4
D853V3, multiclass
            clus
vv           N4BP2 MUTATED N4BP2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              4              25
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  N4BP2 MUTATED       2   3   9   5
  N4BP2 WILD-TYPE    52 132 252  97
D853V4, multiclass
       clus
vv      N4BP2 MUTATED N4BP2 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                9             252
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  N4BP2 MUTATED     5  10   2   2
  N4BP2 WILD-TYPE 190 163  87  83
D853V5, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  N0             5             190
  N1            10             163
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V6, binary
                 cls
clus                0   1
  N4BP2 MUTATED    16   1
  N4BP2 WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     16    1
  N4BP2 WILD-TYPE  466   37
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D853V7, binary
                 cls
clus                0   1
  N4BP2 MUTATED     7  13
  N4BP2 WILD-TYPE 165 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      7   13
  N4BP2 WILD-TYPE  165  393
        clus
vv       N4BP2 MUTATED N4BP2 WILD-TYPE
  FEMALE             7             165
  MALE              13             393
[1] 2 2
[1] FALSE
D853V8, binary
                 cls
clus                0   1
  N4BP2 MUTATED    15   3
  N4BP2 WILD-TYPE 401  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     15    3
  N4BP2 WILD-TYPE  401   99
     clus
vv    N4BP2 MUTATED N4BP2 WILD-TYPE
  NO             15             401
  YES             3              99
[1] 2 2
[1] FALSE
D853V9, continuous
[1] "Remove cluster labels:" "N4BP2 MUTATED"         
clus
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A5      TCGA-LN-A4A6 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8Q7 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
D853V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  N4BP2 MUTATED       3                         1
  N4BP2 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  N4BP2 MUTATED                                           1    12
  N4BP2 WILD-TYPE                                         0   345
D853V11, multiclass
                                           clus
vv                                          N4BP2 MUTATED N4BP2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V12, binary
                 cls
clus                0   1
  N4BP2 MUTATED     0  12
  N4BP2 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      0   12
  N4BP2 WILD-TYPE   10  386
                        clus
vv                       N4BP2 MUTATED N4BP2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(854) Variable = IPP MUTATION ANALYSIS
D854V1, survival
               sevent
clus2             0   1
  IPP MUTATED     5   4
  IPP WILD-TYPE 333 212
  IPP MUTATED IPP WILD-TYPE 
            9           545 
  IPP MUTATED IPP WILD-TYPE 
            4           212 
$`IPP MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NN 
       14.30         4.21         0.85         7.40        55.50         5.49 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 
        6.58         6.02       105.07 

$`IPP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  IPP MUTATED IPP WILD-TYPE 
         0.85          0.00 
  IPP MUTATED IPP WILD-TYPE 
       105.07        122.30 
  IPP MUTATED IPP WILD-TYPE 
         6.58         13.68 
[1] "0.8 - 105.1 (6.6)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D854V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPP MUTATED         0        0        0        1         2         1
  IPP WILD-TYPE      10       20       46       30        82        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPP MUTATED           3          1          0          0        1         0
  IPP WILD-TYPE        26         83         62         39       42         4
D854V3, multiclass
            clus
vv           IPP MUTATED IPP WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             1            30
  STAGE IIA            2            82
  STAGE IIB            1            82
  STAGE III            3            26
  STAGE IIIA           1            83
  STAGE IIIB           0            62
  STAGE IIIC           0            39
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  IPP MUTATED       1   2   4   2
  IPP WILD-TYPE    53 133 257 100
D854V4, multiclass
       clus
vv      IPP MUTATED IPP WILD-TYPE
  T0+T1           1            53
  T2              2           133
  T3              4           257
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  IPP MUTATED     2   7   0   0
  IPP WILD-TYPE 193 166  89  85
D854V5, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  N0           2           193
  N1           7           166
  N2           0            89
  N3           0            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V6, binary
               cls
clus              0   1
  IPP MUTATED     9   0
  IPP WILD-TYPE 473  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      9    0
  IPP WILD-TYPE  473   38
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0           9           473
  1           0            38
[1] 2 2
[1] FALSE
D854V7, binary
               cls
clus              0   1
  IPP MUTATED     1   8
  IPP WILD-TYPE 171 398
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      1    8
  IPP WILD-TYPE  171  398
        clus
vv       IPP MUTATED IPP WILD-TYPE
  FEMALE           1           171
  MALE             8           398
[1] 2 2
[1] FALSE
D854V8, binary
               cls
clus              0   1
  IPP MUTATED     9   0
  IPP WILD-TYPE 407 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      9    0
  IPP WILD-TYPE  407  102
     clus
vv    IPP MUTATED IPP WILD-TYPE
  NO            9           407
  YES           0           102
[1] 2 2
[1] FALSE
D854V9, continuous
[1] "Remove cluster labels:" "IPP MUTATED"           
clus
  IPP MUTATED IPP WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3YA    TCGA-IG-A3YB    TCGA-IG-A3YC 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC    TCGA-LN-A49K 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O    TCGA-LN-A49P 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"IPP WILD-TYPE" "IPP WILD-TYPE" 
D854V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  IPP MUTATED       1                         0
  IPP WILD-TYPE   132                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IPP MUTATED                                           0     4
  IPP WILD-TYPE                                         1   353
D854V11, multiclass
                                           clus
vv                                          IPP MUTATED IPP WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V12, binary
               cls
clus              0   1
  IPP MUTATED     0   2
  IPP WILD-TYPE  10 396
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      0    2
  IPP WILD-TYPE   10  396
                        clus
vv                       IPP MUTATED IPP WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           2           396
[1] 2 2
[1] FALSE

Clustering(855) Variable = CD6 MUTATION ANALYSIS
D855V1, survival
               sevent
clus2             0   1
  CD6 MUTATED     6   3
  CD6 WILD-TYPE 332 213
  CD6 MUTATED CD6 WILD-TYPE 
            9           545 
  CD6 MUTATED CD6 WILD-TYPE 
            3           213 
$`CD6 MUTATED`
TCGA-LN-A49Y TCGA-R6-A6L6 TCGA-BR-6452 TCGA-BR-8486 TCGA-BR-A4J2 TCGA-FP-A4BF 
       12.46         7.04        34.68        20.22        14.17         5.52 
TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-AA64 
       20.25        38.14        18.41 

$`CD6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35        12.59        13.25        12.62        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CD6 MUTATED CD6 WILD-TYPE 
         5.52          0.00 
  CD6 MUTATED CD6 WILD-TYPE 
        38.14        122.30 
  CD6 MUTATED CD6 WILD-TYPE 
        18.41         13.51 
[1] "5.5 - 38.1 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D855V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD6 MUTATED         1        1        0        0         2         2
  CD6 WILD-TYPE       9       19       46       31        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD6 MUTATED           0          3          1          1        0         0
  CD6 WILD-TYPE        29         81         61         38       43         4
D855V3, multiclass
            clus
vv           CD6 MUTATED CD6 WILD-TYPE
  STAGE I              1             9
  STAGE IA             1            19
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           3            81
  STAGE IIIB           1            61
  STAGE IIIC           1            38
  STAGE IV             0            43
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CD6 MUTATED       2   0   4   5
  CD6 WILD-TYPE    52 135 257  97
D855V4, multiclass
       clus
vv      CD6 MUTATED CD6 WILD-TYPE
  T0+T1           2            52
  T2              0           135
  T3              4           257
  T4              5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CD6 MUTATED     6   2   3   0
  CD6 WILD-TYPE 189 171  86  85
D855V5, multiclass
    clus
vv   CD6 MUTATED CD6 WILD-TYPE
  N0           6           189
  N1           2           171
  N2           3            86
  N3           0            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V6, binary
               cls
clus              0   1
  CD6 MUTATED    10   0
  CD6 WILD-TYPE 472  38
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED     10    0
  CD6 WILD-TYPE  472   38
   clus
vv  CD6 MUTATED CD6 WILD-TYPE
  0          10           472
  1           0            38
[1] 2 2
[1] FALSE
D855V7, binary
               cls
clus              0   1
  CD6 MUTATED     4   8
  CD6 WILD-TYPE 168 398
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      4    8
  CD6 WILD-TYPE  168  398
        clus
vv       CD6 MUTATED CD6 WILD-TYPE
  FEMALE           4           168
  MALE             8           398
[1] 2 2
[1] FALSE
D855V8, binary
               cls
clus              0   1
  CD6 MUTATED     9   2
  CD6 WILD-TYPE 407 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      9    2
  CD6 WILD-TYPE  407  100
     clus
vv    CD6 MUTATED CD6 WILD-TYPE
  NO            9           407
  YES           2           100
[1] 2 2
[1] FALSE
D855V9, continuous
[1] "Remove cluster labels:" "CD6 MUTATED"           
clus
  CD6 MUTATED CD6 WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A4A1    TCGA-LN-A4A2    TCGA-LN-A4A3 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8    TCGA-LN-A4A9 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" "CD6 WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"CD6 WILD-TYPE" "CD6 WILD-TYPE" 
D855V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CD6 MUTATED       3                         1
  CD6 WILD-TYPE   130                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD6 MUTATED                                           0     8
  CD6 WILD-TYPE                                         1   349
D855V11, multiclass
                                           clus
vv                                          CD6 MUTATED CD6 WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               8           349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V12, binary
               cls
clus              0   1
  CD6 MUTATED     0  10
  CD6 WILD-TYPE  10 388
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      0   10
  CD6 WILD-TYPE   10  388
                        clus
vv                       CD6 MUTATED CD6 WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          10           388
[1] 2 2
[1] FALSE

Clustering(856) Variable = ATP6V1H MUTATION ANALYSIS
D856V1, survival
                   sevent
clus2                 0   1
  ATP6V1H MUTATED     9   7
  ATP6V1H WILD-TYPE 329 209
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               16               538 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
                7               209 
$`ATP6V1H MUTATED`
TCGA-L5-A4OT TCGA-L5-A8NR TCGA-LN-A8HZ TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 
        4.90         8.71        12.33         6.97         9.34        34.68 
TCGA-BR-8081 TCGA-BR-8369 TCGA-BR-A4IZ TCGA-BR-A4PE TCGA-BR-A4QL TCGA-HU-8602 
       32.25        14.04         8.98        20.42        16.14        22.32 
TCGA-HU-A4GT TCGA-VQ-A8P2 TCGA-VQ-A94T TCGA-VQ-AA64 
        6.51        38.14        11.24        18.41 

$`ATP6V1H WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       32.52        13.51        20.65         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
              4.9               0.0 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
            38.14            122.30 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
           13.185            13.565 
[1] "4.9 - 38.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D856V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1H MUTATED         0        0        1        0         3         2
  ATP6V1H WILD-TYPE      10       20       45       31        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1H MUTATED           1          2          5          0        1
  ATP6V1H WILD-TYPE        28         82         57         39       42
                   vv
clus                STAGE IVA
  ATP6V1H MUTATED           0
  ATP6V1H WILD-TYPE         4
D856V3, multiclass
            clus
vv           ATP6V1H MUTATED ATP6V1H WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               5                57
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ATP6V1H MUTATED       0   2   9   4
  ATP6V1H WILD-TYPE    54 133 252  98
D856V4, multiclass
       clus
vv      ATP6V1H MUTATED ATP6V1H WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  9               252
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ATP6V1H MUTATED     6   5   3   2
  ATP6V1H WILD-TYPE 189 168  86  83
D856V5, multiclass
    clus
vv   ATP6V1H MUTATED ATP6V1H WILD-TYPE
  N0               6               189
  N1               5               168
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V6, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED    14   1
  ATP6V1H WILD-TYPE 468  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED     14    1
  ATP6V1H WILD-TYPE  468   37
   clus
vv  ATP6V1H MUTATED ATP6V1H WILD-TYPE
  0              14               468
  1               1                37
[1] 2 2
[1] FALSE
D856V7, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED     9   7
  ATP6V1H WILD-TYPE 163 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED      9    7
  ATP6V1H WILD-TYPE  163  399
        clus
vv       ATP6V1H MUTATED ATP6V1H WILD-TYPE
  FEMALE               9               163
  MALE                 7               399
[1] 2 2
[1] FALSE
D856V8, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED    13   3
  ATP6V1H WILD-TYPE 403  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED     13    3
  ATP6V1H WILD-TYPE  403   99
     clus
vv    ATP6V1H MUTATED ATP6V1H WILD-TYPE
  NO               13               403
  YES               3                99
[1] 2 2
[1] FALSE
D856V9, continuous
D856V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1H MUTATED       4                         0
  ATP6V1H WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1H MUTATED                                           0    10
  ATP6V1H WILD-TYPE                                         1   347
D856V11, multiclass
                                           clus
vv                                          ATP6V1H MUTATED ATP6V1H WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V12, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED     0  11
  ATP6V1H WILD-TYPE  10 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED      0   11
  ATP6V1H WILD-TYPE   10  387
                        clus
vv                       ATP6V1H MUTATED ATP6V1H WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              11               387
[1] 2 2
[1] FALSE

Clustering(857) Variable = PAMR1 MUTATION ANALYSIS
D857V1, survival
                 sevent
clus2               0   1
  PAMR1 MUTATED     7   8
  PAMR1 WILD-TYPE 331 208
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             15             539 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              8             208 
$`PAMR1 MUTATED`
TCGA-L5-A4OP TCGA-L5-A8NI TCGA-V5-A7RC TCGA-VR-A8EZ TCGA-BR-4201 TCGA-BR-4280 
        7.17        13.48         3.42        18.18        30.90         6.61 
TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8372 TCGA-CD-5801 TCGA-CD-A4MI TCGA-CG-4306 
       34.68        35.24        31.27        13.18        11.77         1.02 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-IN-A7NR 
        6.51         6.58         6.51 

$`PAMR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44         6.74        12.59        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PAMR1 MUTATED PAMR1 WILD-TYPE 
           1.02            0.00 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          35.24          122.30 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          11.77           13.78 
[1] "1.0 - 35.2 (11.8)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.7"
D857V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAMR1 MUTATED         0        1        0        1         2         1
  PAMR1 WILD-TYPE      10       19       46       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAMR1 MUTATED           2          2          0          2        2         0
  PAMR1 WILD-TYPE        27         82         62         37       41         4
D857V3, multiclass
            clus
vv           PAMR1 MUTATED PAMR1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PAMR1 MUTATED       2   3  10   1
  PAMR1 WILD-TYPE    52 132 251 101
D857V4, multiclass
       clus
vv      PAMR1 MUTATED PAMR1 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3               10             251
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PAMR1 MUTATED     4   6   1   3
  PAMR1 WILD-TYPE 191 167  88  82
D857V5, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  N0             4             191
  N1             6             167
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V6, binary
                 cls
clus                0   1
  PAMR1 MUTATED    15   2
  PAMR1 WILD-TYPE 467  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     15    2
  PAMR1 WILD-TYPE  467   36
   clus
vv  PAMR1 MUTATED PAMR1 WILD-TYPE
  0            15             467
  1             2              36
[1] 2 2
[1] FALSE
D857V7, binary
                 cls
clus                0   1
  PAMR1 MUTATED    10   9
  PAMR1 WILD-TYPE 162 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     10    9
  PAMR1 WILD-TYPE  162  397
        clus
vv       PAMR1 MUTATED PAMR1 WILD-TYPE
  FEMALE            10             162
  MALE               9             397
[1] 2 2
[1] FALSE
D857V8, binary
                 cls
clus                0   1
  PAMR1 MUTATED    12   1
  PAMR1 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     12    1
  PAMR1 WILD-TYPE  404  101
     clus
vv    PAMR1 MUTATED PAMR1 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D857V9, continuous
[1] "Remove cluster labels:" "PAMR1 MUTATED"         
clus
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RE      TCGA-V5-AASV 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8Q7 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
D857V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PAMR1 MUTATED       4                         1
  PAMR1 WILD-TYPE   129                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAMR1 MUTATED                                           0    13
  PAMR1 WILD-TYPE                                         1   344
D857V11, multiclass
                                           clus
vv                                          PAMR1 MUTATED PAMR1 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V12, binary
                 cls
clus                0   1
  PAMR1 MUTATED     0  15
  PAMR1 WILD-TYPE  10 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      0   15
  PAMR1 WILD-TYPE   10  383
                        clus
vv                       PAMR1 MUTATED PAMR1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(858) Variable = NLRC5 MUTATION ANALYSIS
D858V1, survival
                 sevent
clus2               0   1
  NLRC5 MUTATED    15  10
  NLRC5 WILD-TYPE 323 206
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             25             529 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             10             206 
$`NLRC5 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A88Z TCGA-VR-A8ER 
       21.99         5.92        25.22        24.03         7.40        12.43 
TCGA-VR-AA7I TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8591 
       15.91         6.97         9.67        35.84         0.26        28.14 
TCGA-BR-A4CS TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 
        1.48        12.43         6.58         9.01         6.02       105.07 
TCGA-CG-5728 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-8602 
       65.10        13.78        11.31        21.27        30.51        22.32 
TCGA-R5-A7ZI 
       74.53 

$`NLRC5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 
        7.13         7.43        15.48         2.60        25.12         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        22.82         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         0.00        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NLRC5 MUTATED NLRC5 WILD-TYPE 
           0.26            0.00 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
         105.07          122.30 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
          13.78           13.55 
[1] "0.3 - 105.1 (13.8)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D858V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLRC5 MUTATED         0        0        5        2         2         2
  NLRC5 WILD-TYPE      10       20       41       29        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRC5 MUTATED           3          3          2          3        4         0
  NLRC5 WILD-TYPE        26         81         60         36       39         4
D858V3, multiclass
            clus
vv           NLRC5 MUTATED NLRC5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               5              41
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              3              26
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NLRC5 MUTATED       2   6   8  11
  NLRC5 WILD-TYPE    52 129 253  91
D858V4, multiclass
       clus
vv      NLRC5 MUTATED NLRC5 WILD-TYPE
  T0+T1             2              52
  T2                6             129
  T3                8             253
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NLRC5 MUTATED    10   9   1   6
  NLRC5 WILD-TYPE 185 164  88  79
D858V5, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  N0            10             185
  N1             9             164
  N2             1              88
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V6, binary
                 cls
clus                0   1
  NLRC5 MUTATED    25   3
  NLRC5 WILD-TYPE 457  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     25    3
  NLRC5 WILD-TYPE  457   35
   clus
vv  NLRC5 MUTATED NLRC5 WILD-TYPE
  0            25             457
  1             3              35
[1] 2 2
[1] FALSE
D858V7, binary
                 cls
clus                0   1
  NLRC5 MUTATED    14  15
  NLRC5 WILD-TYPE 158 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     14   15
  NLRC5 WILD-TYPE  158  391
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  FEMALE            14             158
  MALE              15             391
[1] 2 2
[1] FALSE
D858V8, binary
                 cls
clus                0   1
  NLRC5 MUTATED    20   4
  NLRC5 WILD-TYPE 396  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     20    4
  NLRC5 WILD-TYPE  396   98
     clus
vv    NLRC5 MUTATED NLRC5 WILD-TYPE
  NO             20             396
  YES             4              98
[1] 2 2
[1] FALSE
D858V9, continuous
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
D858V10, continuous
[1] "Remove cluster labels:" "NLRC5 MUTATED"         
clus
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-X8-AAAR 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" "NLRC5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NLRC5 MUTATED       3                         0
  NLRC5 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NLRC5 MUTATED                                           0    17
  NLRC5 WILD-TYPE                                         1   340
D858V11, multiclass
                                           clus
vv                                          NLRC5 MUTATED NLRC5 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V12, binary
                 cls
clus                0   1
  NLRC5 MUTATED     2  14
  NLRC5 WILD-TYPE   8 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      2   14
  NLRC5 WILD-TYPE    8  384
                        clus
vv                       NLRC5 MUTATED NLRC5 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(859) Variable = CST1 MUTATION ANALYSIS
D859V1, survival
                sevent
clus2              0   1
  CST1 MUTATED     6   2
  CST1 WILD-TYPE 332 214
  CST1 MUTATED CST1 WILD-TYPE 
             8            546 
  CST1 MUTATED CST1 WILD-TYPE 
             2            214 
$`CST1 MUTATED`
TCGA-CG-4460 TCGA-V5-AASX TCGA-BR-7704 TCGA-CD-8530 TCGA-CG-5721 TCGA-D7-A6EY 
       21.99         8.98        35.24        12.39         6.02        11.44 
TCGA-HU-A4G9 TCGA-HU-A4GX 
       24.20        20.25 

$`CST1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CST1 MUTATED CST1 WILD-TYPE 
          6.02           0.00 
  CST1 MUTATED CST1 WILD-TYPE 
         35.24         122.30 
  CST1 MUTATED CST1 WILD-TYPE 
        16.320         13.565 
[1] "6.0 - 35.2 (16.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D859V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CST1 MUTATED         0        1        0        2         0         0
  CST1 WILD-TYPE      10       19       46       29        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CST1 MUTATED           0          0          1          1        2         0
  CST1 WILD-TYPE        29         84         61         38       41         4
D859V3, multiclass
            clus
vv           CST1 MUTATED CST1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CST1 MUTATED       1   0   3   3
  CST1 WILD-TYPE    53 135 258  99
D859V4, multiclass
       clus
vv      CST1 MUTATED CST1 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CST1 MUTATED     3   2   1   1
  CST1 WILD-TYPE 192 171  88  84
D859V5, multiclass
    clus
vv   CST1 MUTATED CST1 WILD-TYPE
  N0            3            192
  N1            2            171
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V6, binary
                cls
clus               0   1
  CST1 MUTATED     6   1
  CST1 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      6    1
  CST1 WILD-TYPE  476   37
   clus
vv  CST1 MUTATED CST1 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D859V7, binary
                cls
clus               0   1
  CST1 MUTATED     5   3
  CST1 WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      5    3
  CST1 WILD-TYPE  167  403
        clus
vv       CST1 MUTATED CST1 WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D859V8, binary
                cls
clus               0   1
  CST1 MUTATED     6   1
  CST1 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      6    1
  CST1 WILD-TYPE  410  101
     clus
vv    CST1 MUTATED CST1 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D859V9, continuous
[1] "Remove cluster labels:" "CST1 MUTATED"          
clus
  CST1 MUTATED CST1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-VR-A8EO     TCGA-VR-A8EP 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CST1 WILD-TYPE" "CST1 WILD-TYPE" "CST1 WILD-TYPE" 
D859V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CST1 MUTATED       3                         0
  CST1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CST1 MUTATED                                           0     3
  CST1 WILD-TYPE                                         1   354
D859V11, multiclass
                                           clus
vv                                          CST1 MUTATED CST1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V12, binary
                cls
clus               0   1
  CST1 MUTATED     0   6
  CST1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      0    6
  CST1 WILD-TYPE   10  392
                        clus
vv                       CST1 MUTATED CST1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(860) Variable = TMEM132D MUTATION ANALYSIS
D860V1, survival
                    sevent
clus2                  0   1
  TMEM132D MUTATED    24  19
  TMEM132D WILD-TYPE 314 197
  TMEM132D MUTATED TMEM132D WILD-TYPE 
                43                511 
  TMEM132D MUTATED TMEM132D WILD-TYPE 
                19                197 
$`TMEM132D MUTATED`
TCGA-S8-A6BV TCGA-CG-4460 TCGA-2H-A9GH TCGA-L5-A4OW TCGA-L5-A8NM TCGA-LN-A49U 
       20.02        21.99        31.27         7.13         7.76        15.35 
TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-Z6-A8JE TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6566 
       11.54         7.82         2.10        11.70        34.68        32.78 
TCGA-BR-6706 TCGA-BR-6852 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8080 
       18.05        44.94        15.32         3.45        33.21         9.60 
TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8591 TCGA-BR-8686 TCGA-BR-A4QL 
        2.66         0.26         3.32        28.14        20.88        16.14 
TCGA-CD-5798 TCGA-CD-5804 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-4465 
       13.41        12.10        11.77        12.62         8.05         9.01 
TCGA-CG-4469 TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-A4Z0 TCGA-FP-A4BE TCGA-HF-A5NB 
        7.07        21.07        13.35        14.76        11.08        30.51 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H0 TCGA-HU-A4H8 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       22.32         0.10         2.10        14.07        37.41        38.14 
TCGA-VQ-A8P3 
       37.22 

$`TMEM132D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       27.12         5.16        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        3.42         1.32         2.66        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        18.15        28.73         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       37.25        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56        29.42        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       26.73        24.79        31.96        32.58         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 
       20.65        20.42         1.15        21.44         5.13        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       12.03         0.00        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PE 
       48.79         5.46        13.25        13.02        43.36        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TMEM132D MUTATED TMEM132D WILD-TYPE 
               0.1                0.0 
  TMEM132D MUTATED TMEM132D WILD-TYPE 
             44.94             122.30 
  TMEM132D MUTATED TMEM132D WILD-TYPE 
             13.41              13.58 
[1] "0.1 - 44.9 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D860V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM132D MUTATED         0        0        4        2         6         7
  TMEM132D WILD-TYPE      10       20       42       29        78        76
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM132D MUTATED           0          9          4          5        5
  TMEM132D WILD-TYPE        29         75         58         34       38
                    vv
clus                 STAGE IVA
  TMEM132D MUTATED           0
  TMEM132D WILD-TYPE         4
D860V3, multiclass
            clus
vv           TMEM132D MUTATED TMEM132D WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  4                 42
  STAGE II                  2                 29
  STAGE IIA                 6                 78
  STAGE IIB                 7                 76
  STAGE III                 0                 29
  STAGE IIIA                9                 75
  STAGE IIIB                4                 58
  STAGE IIIC                5                 34
  STAGE IV                  5                 38
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TMEM132D MUTATED       3  10  18  13
  TMEM132D WILD-TYPE    51 125 243  89
D860V4, multiclass
       clus
vv      TMEM132D MUTATED TMEM132D WILD-TYPE
  T0+T1                3                 51
  T2                  10                125
  T3                  18                243
  T4                  13                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TMEM132D MUTATED    11  18   5   9
  TMEM132D WILD-TYPE 184 155  84  76
D860V5, multiclass
    clus
vv   TMEM132D MUTATED TMEM132D WILD-TYPE
  N0               11                184
  N1               18                155
  N2                5                 84
  N3                9                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V6, binary
                    cls
clus                   0   1
  TMEM132D MUTATED    39   4
  TMEM132D WILD-TYPE 443  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM132D MUTATED     39    4
  TMEM132D WILD-TYPE  443   34
   clus
vv  TMEM132D MUTATED TMEM132D WILD-TYPE
  0               39                443
  1                4                 34
[1] 2 2
[1] FALSE
D860V7, binary
                    cls
clus                   0   1
  TMEM132D MUTATED    15  29
  TMEM132D WILD-TYPE 157 377
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM132D MUTATED     15   29
  TMEM132D WILD-TYPE  157  377
        clus
vv       TMEM132D MUTATED TMEM132D WILD-TYPE
  FEMALE               15                157
  MALE                 29                377
[1] 2 2
[1] FALSE
D860V8, binary
                    cls
clus                   0   1
  TMEM132D MUTATED    35   6
  TMEM132D WILD-TYPE 381  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM132D MUTATED     35    6
  TMEM132D WILD-TYPE  381   96
     clus
vv    TMEM132D MUTATED TMEM132D WILD-TYPE
  NO                35                381
  YES                6                 96
[1] 2 2
[1] FALSE
D860V9, continuous
D860V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TMEM132D MUTATED      11                         1
  TMEM132D WILD-TYPE   122                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM132D MUTATED                                           0    24
  TMEM132D WILD-TYPE                                         1   333
D860V11, multiclass
                                           clus
vv                                          TMEM132D MUTATED TMEM132D WILD-TYPE
  ASIAN                                                   11                122
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   24                333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V12, binary
                    cls
clus                   0   1
  TMEM132D MUTATED     0  32
  TMEM132D WILD-TYPE  10 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM132D MUTATED      0   32
  TMEM132D WILD-TYPE   10  366
                        clus
vv                       TMEM132D MUTATED TMEM132D WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               32                366
[1] 2 2
[1] FALSE

Clustering(861) Variable = XRN1 MUTATION ANALYSIS
D861V1, survival
                sevent
clus2              0   1
  XRN1 MUTATED    14   9
  XRN1 WILD-TYPE 324 207
  XRN1 MUTATED XRN1 WILD-TYPE 
            23            531 
  XRN1 MUTATED XRN1 WILD-TYPE 
             9            207 
$`XRN1 MUTATED`
TCGA-L5-A4OO TCGA-LN-A49L TCGA-V5-A7RB TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 
        3.32        10.45         5.29         6.97        30.90         9.67 
TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8690 TCGA-CD-8529 
       34.68        18.05        27.12        28.14        10.68        12.30 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-7132 
       15.95         1.02         6.02        28.96        11.44        77.29 
TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-8462 
       30.51        24.20        23.80        14.07        18.81 

$`XRN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  XRN1 MUTATED XRN1 WILD-TYPE 
          1.02           0.00 
  XRN1 MUTATED XRN1 WILD-TYPE 
         77.29         122.30 
  XRN1 MUTATED XRN1 WILD-TYPE 
         15.95          13.51 
[1] "1.0 - 77.3 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D861V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XRN1 MUTATED         1        2        2        2         2         1
  XRN1 WILD-TYPE       9       18       44       29        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRN1 MUTATED           0          3          3          3        3         0
  XRN1 WILD-TYPE        29         81         59         36       40         4
D861V3, multiclass
            clus
vv           XRN1 MUTATED XRN1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              2             44
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            3             59
  STAGE IIIC            3             36
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  XRN1 MUTATED       6   6   8   6
  XRN1 WILD-TYPE    48 129 253  96
D861V4, multiclass
       clus
vv      XRN1 MUTATED XRN1 WILD-TYPE
  T0+T1            6             48
  T2               6            129
  T3               8            253
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  XRN1 MUTATED     7  10   1   5
  XRN1 WILD-TYPE 188 163  88  80
D861V5, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  N0            7            188
  N1           10            163
  N2            1             88
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D861V6, binary
                cls
clus               0   1
  XRN1 MUTATED    21   2
  XRN1 WILD-TYPE 461  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     21    2
  XRN1 WILD-TYPE  461   36
   clus
vv  XRN1 MUTATED XRN1 WILD-TYPE
  0           21            461
  1            2             36
[1] 2 2
[1] FALSE
D861V7, binary
                cls
clus               0   1
  XRN1 MUTATED     9  18
  XRN1 WILD-TYPE 163 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED      9   18
  XRN1 WILD-TYPE  163  388
        clus
vv       XRN1 MUTATED XRN1 WILD-TYPE
  FEMALE            9            163
  MALE             18            388
[1] 2 2
[1] FALSE
D861V8, binary
                cls
clus               0   1
  XRN1 MUTATED    17   4
  XRN1 WILD-TYPE 399  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     17    4
  XRN1 WILD-TYPE  399   98
     clus
vv    XRN1 MUTATED XRN1 WILD-TYPE
  NO            17            399
  YES            4             98
[1] 2 2
[1] FALSE
D861V9, continuous
[1] "Remove cluster labels:" "XRN1 MUTATED"          
clus
  XRN1 MUTATED XRN1 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49M 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
D861V10, continuous
[1] "Remove cluster labels:" "XRN1 MUTATED"          
clus
  XRN1 MUTATED XRN1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RC 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" "XRN1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  XRN1 MUTATED       5                         1
  XRN1 WILD-TYPE   128                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XRN1 MUTATED                                           0    14
  XRN1 WILD-TYPE                                         1   343
D861V11, multiclass
                                           clus
vv                                          XRN1 MUTATED XRN1 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D861V12, binary
                cls
clus               0   1
  XRN1 MUTATED     1  19
  XRN1 WILD-TYPE   9 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED      1   19
  XRN1 WILD-TYPE    9  379
                        clus
vv                       XRN1 MUTATED XRN1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           19            379
[1] 2 2
[1] FALSE

Clustering(862) Variable = OSBPL9 MUTATION ANALYSIS
D862V1, survival
                  sevent
clus2                0   1
  OSBPL9 MUTATED     8   3
  OSBPL9 WILD-TYPE 330 213
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
              11              543 
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
               3              213 
$`OSBPL9 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GF TCGA-L5-A88S TCGA-LN-A49S TCGA-LN-A49W TCGA-BR-8361 
       21.99        25.78        15.48        13.15        13.25        31.10 
TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5721 TCGA-HU-A4G9 
        0.26        28.14        31.96         6.02        24.20 

$`OSBPL9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       13.41        12.33        13.38        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
            0.26             0.00 
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
           31.96           122.30 
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
           21.99            13.51 
[1] "0.3 - 32.0 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D862V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSBPL9 MUTATED         0        1        3        0         1         0
  OSBPL9 WILD-TYPE      10       19       43       31        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL9 MUTATED           2          0          0          2        3
  OSBPL9 WILD-TYPE        27         84         62         37       40
                  vv
clus               STAGE IVA
  OSBPL9 MUTATED           0
  OSBPL9 WILD-TYPE         4
D862V3, multiclass
            clus
vv           OSBPL9 MUTATED OSBPL9 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               2               27
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OSBPL9 MUTATED       1   2   4   5
  OSBPL9 WILD-TYPE    53 133 257  97
D862V4, multiclass
       clus
vv      OSBPL9 MUTATED OSBPL9 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 4              257
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OSBPL9 MUTATED     5   4   2   1
  OSBPL9 WILD-TYPE 190 169  87  84
D862V5, multiclass
    clus
vv   OSBPL9 MUTATED OSBPL9 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V6, binary
                  cls
clus                 0   1
  OSBPL9 MUTATED     9   2
  OSBPL9 WILD-TYPE 473  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL9 MUTATED      9    2
  OSBPL9 WILD-TYPE  473   36
   clus
vv  OSBPL9 MUTATED OSBPL9 WILD-TYPE
  0              9              473
  1              2               36
[1] 2 2
[1] FALSE
D862V7, binary
                  cls
clus                 0   1
  OSBPL9 MUTATED     4   8
  OSBPL9 WILD-TYPE 168 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL9 MUTATED      4    8
  OSBPL9 WILD-TYPE  168  398
        clus
vv       OSBPL9 MUTATED OSBPL9 WILD-TYPE
  FEMALE              4              168
  MALE                8              398
[1] 2 2
[1] FALSE
D862V8, binary
                  cls
clus                 0   1
  OSBPL9 MUTATED     9   2
  OSBPL9 WILD-TYPE 407 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL9 MUTATED      9    2
  OSBPL9 WILD-TYPE  407  100
     clus
vv    OSBPL9 MUTATED OSBPL9 WILD-TYPE
  NO               9              407
  YES              2              100
[1] 2 2
[1] FALSE
D862V9, continuous
[1] "Remove cluster labels:" "OSBPL9 MUTATED"        
clus
  OSBPL9 MUTATED OSBPL9 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49X 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OSBPL9 WILD-TYPE" "OSBPL9 WILD-TYPE" 
D862V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OSBPL9 MUTATED       4                         0
  OSBPL9 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSBPL9 MUTATED                                           0     4
  OSBPL9 WILD-TYPE                                         1   353
D862V11, multiclass
                                           clus
vv                                          OSBPL9 MUTATED OSBPL9 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V12, binary
                  cls
clus                 0   1
  OSBPL9 MUTATED     0   6
  OSBPL9 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL9 MUTATED      0    6
  OSBPL9 WILD-TYPE   10  392
                        clus
vv                       OSBPL9 MUTATED OSBPL9 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(863) Variable = SYT4 MUTATION ANALYSIS
D863V1, survival
                sevent
clus2              0   1
  SYT4 MUTATED     7   9
  SYT4 WILD-TYPE 331 207
  SYT4 MUTATED SYT4 WILD-TYPE 
            16            538 
  SYT4 MUTATED SYT4 WILD-TYPE 
             9            207 
$`SYT4 MUTATED`
TCGA-MX-A663 TCGA-2H-A9GG TCGA-R6-A6L6 TCGA-VR-A8EQ TCGA-VR-AA7B TCGA-BR-4253 
        9.86        20.05         7.04        22.82        11.24         4.08 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-5721 TCGA-D7-A4YU 
       29.59         9.60         0.26        16.14         6.02        16.44 
TCGA-HU-8602 TCGA-HU-A4GX TCGA-IN-A6RR TCGA-IN-A7NU 
       22.32        20.25         6.74        11.70 

$`SYT4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GH 
       79.07        16.24         0.23        20.15        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44         0.69        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44        12.59         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SYT4 MUTATED SYT4 WILD-TYPE 
          0.26           0.00 
  SYT4 MUTATED SYT4 WILD-TYPE 
         29.59         122.30 
  SYT4 MUTATED SYT4 WILD-TYPE 
         11.47          13.63 
[1] "0.3 - 29.6 (11.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D863V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYT4 MUTATED         0        0        1        0         1         2
  SYT4 WILD-TYPE      10       20       45       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT4 MUTATED           2          2          3          2        3         0
  SYT4 WILD-TYPE        27         82         59         37       40         4
D863V3, multiclass
            clus
vv           SYT4 MUTATED SYT4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            2             82
  STAGE IIIB            3             59
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SYT4 MUTATED       0   1   9   6
  SYT4 WILD-TYPE    54 134 252  96
D863V4, multiclass
       clus
vv      SYT4 MUTATED SYT4 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               9            252
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SYT4 MUTATED     4   5   2   5
  SYT4 WILD-TYPE 191 168  87  80
D863V5, multiclass
    clus
vv   SYT4 MUTATED SYT4 WILD-TYPE
  N0            4            191
  N1            5            168
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V6, binary
                cls
clus               0   1
  SYT4 MUTATED    16   1
  SYT4 WILD-TYPE 466  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED     16    1
  SYT4 WILD-TYPE  466   37
   clus
vv  SYT4 MUTATED SYT4 WILD-TYPE
  0           16            466
  1            1             37
[1] 2 2
[1] FALSE
D863V7, binary
                cls
clus               0   1
  SYT4 MUTATED    10   8
  SYT4 WILD-TYPE 162 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED     10    8
  SYT4 WILD-TYPE  162  398
        clus
vv       SYT4 MUTATED SYT4 WILD-TYPE
  FEMALE           10            162
  MALE              8            398
[1] 2 2
[1] FALSE
D863V8, binary
                cls
clus               0   1
  SYT4 MUTATED    15   1
  SYT4 WILD-TYPE 401 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED     15    1
  SYT4 WILD-TYPE  401  101
     clus
vv    SYT4 MUTATED SYT4 WILD-TYPE
  NO            15            401
  YES            1            101
[1] 2 2
[1] FALSE
D863V9, continuous
[1] "Remove cluster labels:" "SYT4 MUTATED"          
clus
  SYT4 MUTATED SYT4 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7D 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"SYT4 WILD-TYPE" "SYT4 WILD-TYPE" 
D863V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SYT4 MUTATED       2                         0
  SYT4 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYT4 MUTATED                                           0    14
  SYT4 WILD-TYPE                                         1   343
D863V11, multiclass
                                           clus
vv                                          SYT4 MUTATED SYT4 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V12, binary
                cls
clus               0   1
  SYT4 MUTATED     0  14
  SYT4 WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED      0   14
  SYT4 WILD-TYPE   10  384
                        clus
vv                       SYT4 MUTATED SYT4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(864) Variable = PHF13 MUTATION ANALYSIS
D864V1, survival
                 sevent
clus2               0   1
  PHF13 MUTATED     4   3
  PHF13 WILD-TYPE 334 213
  PHF13 MUTATED PHF13 WILD-TYPE 
              7             547 
  PHF13 MUTATED PHF13 WILD-TYPE 
              3             213 
$`PHF13 MUTATED`
TCGA-L5-A891 TCGA-L5-A8NM TCGA-S8-A6BW TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8368 
        3.75         7.76        20.38         6.97         0.26         4.31 
TCGA-BR-8680 
       31.96 

$`PHF13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PHF13 MUTATED PHF13 WILD-TYPE 
           0.26            0.00 
  PHF13 MUTATED PHF13 WILD-TYPE 
          31.96          122.30 
  PHF13 MUTATED PHF13 WILD-TYPE 
           6.97           13.68 
[1] "0.3 - 32.0 (7.0)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.9"
D864V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHF13 MUTATED         0        0        3        0         0         1
  PHF13 WILD-TYPE      10       20       43       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF13 MUTATED           0          1          0          0        1         0
  PHF13 WILD-TYPE        29         83         62         39       42         4
D864V3, multiclass
            clus
vv           PHF13 MUTATED PHF13 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PHF13 MUTATED       0   4   2   1
  PHF13 WILD-TYPE    54 131 259 101
D864V4, multiclass
       clus
vv      PHF13 MUTATED PHF13 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PHF13 MUTATED     3   3   1   0
  PHF13 WILD-TYPE 192 170  88  85
D864V5, multiclass
    clus
vv   PHF13 MUTATED PHF13 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V6, binary
                 cls
clus                0   1
  PHF13 MUTATED     4   1
  PHF13 WILD-TYPE 478  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      4    1
  PHF13 WILD-TYPE  478   37
   clus
vv  PHF13 MUTATED PHF13 WILD-TYPE
  0             4             478
  1             1              37
[1] 2 2
[1] FALSE
D864V7, binary
                 cls
clus                0   1
  PHF13 MUTATED     3   4
  PHF13 WILD-TYPE 169 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      3    4
  PHF13 WILD-TYPE  169  402
        clus
vv       PHF13 MUTATED PHF13 WILD-TYPE
  FEMALE             3             169
  MALE               4             402
[1] 2 2
[1] FALSE
D864V8, binary
                 cls
clus                0   1
  PHF13 MUTATED     6   0
  PHF13 WILD-TYPE 410 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      6    0
  PHF13 WILD-TYPE  410  102
     clus
vv    PHF13 MUTATED PHF13 WILD-TYPE
  NO              6             410
  YES             0             102
[1] 2 2
[1] FALSE
D864V9, continuous
D864V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PHF13 MUTATED       1                         0
  PHF13 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHF13 MUTATED                                           0     6
  PHF13 WILD-TYPE                                         1   351
D864V11, multiclass
                                           clus
vv                                          PHF13 MUTATED PHF13 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V12, binary
                 cls
clus                0   1
  PHF13 MUTATED     0   5
  PHF13 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      0    5
  PHF13 WILD-TYPE   10  393
                        clus
vv                       PHF13 MUTATED PHF13 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(865) Variable = SMAP2 MUTATION ANALYSIS
D865V1, survival
                 sevent
clus2               0   1
  SMAP2 MUTATED     3   2
  SMAP2 WILD-TYPE 335 214
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             549 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              2             214 
$`SMAP2 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7703 TCGA-CD-A4MI 
        9.67        34.68        30.90        36.16        11.77 

$`SMAP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SMAP2 MUTATED SMAP2 WILD-TYPE 
           9.67            0.00 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
          36.16          122.30 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
          30.90           13.55 
[1] "9.7 - 36.2 (30.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D865V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAP2 MUTATED         0        1        0        0         1         0
  SMAP2 WILD-TYPE      10       19       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAP2 MUTATED           0          2          0          0        0         0
  SMAP2 WILD-TYPE        29         82         62         39       43         4
D865V3, multiclass
            clus
vv           SMAP2 MUTATED SMAP2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SMAP2 MUTATED       1   0   3   0
  SMAP2 WILD-TYPE    53 135 258 102
D865V4, multiclass
       clus
vv      SMAP2 MUTATED SMAP2 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                3             258
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SMAP2 MUTATED     2   1   1   0
  SMAP2 WILD-TYPE 193 172  88  85
D865V5, multiclass
    clus
vv   SMAP2 MUTATED SMAP2 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V6, binary
                 cls
clus                0   1
  SMAP2 MUTATED     5   0
  SMAP2 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      5    0
  SMAP2 WILD-TYPE  477   38
   clus
vv  SMAP2 MUTATED SMAP2 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D865V7, binary
                 cls
clus                0   1
  SMAP2 MUTATED     2   3
  SMAP2 WILD-TYPE 170 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      2    3
  SMAP2 WILD-TYPE  170  403
        clus
vv       SMAP2 MUTATED SMAP2 WILD-TYPE
  FEMALE             2             170
  MALE               3             403
[1] 2 2
[1] FALSE
D865V8, binary
                 cls
clus                0   1
  SMAP2 MUTATED     5   0
  SMAP2 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      5    0
  SMAP2 WILD-TYPE  411  102
     clus
vv    SMAP2 MUTATED SMAP2 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D865V9, continuous
D865V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAP2 MUTATED       1                         0
  SMAP2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAP2 MUTATED                                           0     4
  SMAP2 WILD-TYPE                                         1   353
D865V11, multiclass
                                           clus
vv                                          SMAP2 MUTATED SMAP2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V12, binary
                 cls
clus                0   1
  SMAP2 MUTATED     0   5
  SMAP2 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      0    5
  SMAP2 WILD-TYPE   10  393
                        clus
vv                       SMAP2 MUTATED SMAP2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(866) Variable = GLYATL2 MUTATION ANALYSIS
D866V1, survival
                   sevent
clus2                 0   1
  GLYATL2 MUTATED     4   6
  GLYATL2 WILD-TYPE 334 210
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
               10               544 
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
                6               210 
$`GLYATL2 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NJ TCGA-R6-A8W5 TCGA-VR-A8EZ TCGA-BR-4201 TCGA-BR-8289 
       21.99        16.47        15.78        18.18        30.90         2.66 
TCGA-BR-8680 TCGA-CG-4455 TCGA-D7-A4YV TCGA-HU-A4H3 
       31.96        12.03         5.92        29.00 

$`GLYATL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
             2.66              0.00 
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
            31.96            122.30 
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
           17.325            13.510 
[1] "2.7 - 32.0 (17.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D866V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLYATL2 MUTATED         0        0        0        1         0         1
  GLYATL2 WILD-TYPE      10       20       46       30        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLYATL2 MUTATED           1          0          0          2        3
  GLYATL2 WILD-TYPE        28         84         62         37       40
                   vv
clus                STAGE IVA
  GLYATL2 MUTATED           1
  GLYATL2 WILD-TYPE         3
D866V3, multiclass
            clus
vv           GLYATL2 MUTATED GLYATL2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 3                40
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GLYATL2 MUTATED       0   2   4   4
  GLYATL2 WILD-TYPE    54 133 257  98
D866V4, multiclass
       clus
vv      GLYATL2 MUTATED GLYATL2 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  4               257
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GLYATL2 MUTATED     0   5   1   3
  GLYATL2 WILD-TYPE 195 168  88  82
D866V5, multiclass
    clus
vv   GLYATL2 MUTATED GLYATL2 WILD-TYPE
  N0               0               195
  N1               5               168
  N2               1                88
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V6, binary
                   cls
clus                  0   1
  GLYATL2 MUTATED     6   4
  GLYATL2 WILD-TYPE 476  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLYATL2 MUTATED      6    4
  GLYATL2 WILD-TYPE  476   34
   clus
vv  GLYATL2 MUTATED GLYATL2 WILD-TYPE
  0               6               476
  1               4                34
[1] 2 2
[1] FALSE
D866V7, binary
                   cls
clus                  0   1
  GLYATL2 MUTATED     4   6
  GLYATL2 WILD-TYPE 168 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLYATL2 MUTATED      4    6
  GLYATL2 WILD-TYPE  168  400
        clus
vv       GLYATL2 MUTATED GLYATL2 WILD-TYPE
  FEMALE               4               168
  MALE                 6               400
[1] 2 2
[1] FALSE
D866V8, binary
                   cls
clus                  0   1
  GLYATL2 MUTATED     9   0
  GLYATL2 WILD-TYPE 407 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLYATL2 MUTATED      9    0
  GLYATL2 WILD-TYPE  407  102
     clus
vv    GLYATL2 MUTATED GLYATL2 WILD-TYPE
  NO                9               407
  YES               0               102
[1] 2 2
[1] FALSE
D866V9, continuous
[1] "Remove cluster labels:" "GLYATL2 MUTATED"       
clus
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
D866V10, continuous
[1] "Remove cluster labels:" "GLYATL2 MUTATED"       
clus
  GLYATL2 MUTATED GLYATL2 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8Q7 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" "GLYATL2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GLYATL2 MUTATED       2                         0
  GLYATL2 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLYATL2 MUTATED                                           0     6
  GLYATL2 WILD-TYPE                                         1   351
D866V11, multiclass
                                           clus
vv                                          GLYATL2 MUTATED GLYATL2 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V12, binary
                   cls
clus                  0   1
  GLYATL2 MUTATED     0   6
  GLYATL2 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLYATL2 MUTATED      0    6
  GLYATL2 WILD-TYPE   10  392
                        clus
vv                       GLYATL2 MUTATED GLYATL2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(867) Variable = C9ORF98 MUTATION ANALYSIS
D867V1, survival
                   sevent
clus2                 0   1
  C9ORF98 MUTATED     7   3
  C9ORF98 WILD-TYPE 331 213
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
               10               544 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
                3               213 
$`C9ORF98 MUTATED`
TCGA-2H-A9GO TCGA-LN-A5U5 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8535 TCGA-CD-8536 
       16.24         4.47         1.12        28.14        12.82        12.43 
TCGA-CG-4306 TCGA-CG-5723 TCGA-HU-A4G9 TCGA-HU-A4H8 
        1.02       105.07        24.20        14.07 

$`C9ORF98 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       15.39        12.07         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
             1.02              0.00 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
           105.07            122.30 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
           13.445            13.565 
[1] "1.0 - 105.1 (13.4)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D867V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF98 MUTATED         0        1        1        2         1         0
  C9ORF98 WILD-TYPE      10       19       45       29        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF98 MUTATED           0          1          0          1        2
  C9ORF98 WILD-TYPE        29         83         62         38       41
                   vv
clus                STAGE IVA
  C9ORF98 MUTATED           1
  C9ORF98 WILD-TYPE         3
D867V3, multiclass
            clus
vv           C9ORF98 MUTATED C9ORF98 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 2                29
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C9ORF98 MUTATED       2   1   7   1
  C9ORF98 WILD-TYPE    52 134 254 101
D867V4, multiclass
       clus
vv      C9ORF98 MUTATED C9ORF98 WILD-TYPE
  T0+T1               2                52
  T2                  1               134
  T3                  7               254
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C9ORF98 MUTATED     3   6   1   1
  C9ORF98 WILD-TYPE 192 167  88  84
D867V5, multiclass
    clus
vv   C9ORF98 MUTATED C9ORF98 WILD-TYPE
  N0               3               192
  N1               6               167
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V6, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     8   3
  C9ORF98 WILD-TYPE 474  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      8    3
  C9ORF98 WILD-TYPE  474   35
   clus
vv  C9ORF98 MUTATED C9ORF98 WILD-TYPE
  0               8               474
  1               3                35
[1] 2 2
[1] FALSE
D867V7, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     4   8
  C9ORF98 WILD-TYPE 168 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      4    8
  C9ORF98 WILD-TYPE  168  398
        clus
vv       C9ORF98 MUTATED C9ORF98 WILD-TYPE
  FEMALE               4               168
  MALE                 8               398
[1] 2 2
[1] FALSE
D867V8, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     9   0
  C9ORF98 WILD-TYPE 407 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      9    0
  C9ORF98 WILD-TYPE  407  102
     clus
vv    C9ORF98 MUTATED C9ORF98 WILD-TYPE
  NO                9               407
  YES               0               102
[1] 2 2
[1] FALSE
D867V9, continuous
[1] "Remove cluster labels:" "C9ORF98 MUTATED"       
clus
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" "C9ORF98 WILD-TYPE" 
D867V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF98 MUTATED       5                         0
  C9ORF98 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF98 MUTATED                                           0     4
  C9ORF98 WILD-TYPE                                         1   353
D867V11, multiclass
                                           clus
vv                                          C9ORF98 MUTATED C9ORF98 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V12, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     0   9
  C9ORF98 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      0    9
  C9ORF98 WILD-TYPE   10  389
                        clus
vv                       C9ORF98 MUTATED C9ORF98 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(868) Variable = ZNF341 MUTATION ANALYSIS
D868V1, survival
                  sevent
clus2                0   1
  ZNF341 MUTATED     9  10
  ZNF341 WILD-TYPE 329 206
  ZNF341 MUTATED ZNF341 WILD-TYPE 
              19              535 
  ZNF341 MUTATED ZNF341 WILD-TYPE 
              10              206 
$`ZNF341 MUTATED`
TCGA-2H-A9GF TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A7HX TCGA-B7-5816 TCGA-BR-4201 
       25.78        12.76        11.54        12.23        26.70        30.90 
TCGA-BR-7707 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5726 
       35.84        11.44         8.05        31.96        11.77        28.96 
TCGA-D7-6815 TCGA-D7-A4YV TCGA-FP-7829 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-RD-A8N1 
       15.98         5.92        19.53        22.32         0.10       115.69 
TCGA-RD-A8N6 
        8.94 

$`ZNF341 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ 
       12.49        12.59        22.39        12.85        15.52        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZNF341 MUTATED ZNF341 WILD-TYPE 
             0.1              0.0 
  ZNF341 MUTATED ZNF341 WILD-TYPE 
          115.69           122.30 
  ZNF341 MUTATED ZNF341 WILD-TYPE 
           15.98            13.55 
[1] "0.1 - 115.7 (16.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D868V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF341 MUTATED         0        1        1        0         2         6
  ZNF341 WILD-TYPE      10       19       45       31        82        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF341 MUTATED           2          2          1          2        2
  ZNF341 WILD-TYPE        27         82         61         37       41
                  vv
clus               STAGE IVA
  ZNF341 MUTATED           0
  ZNF341 WILD-TYPE         4
D868V3, multiclass
            clus
vv           ZNF341 MUTATED ZNF341 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               6               77
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF341 MUTATED       1   7   6   6
  ZNF341 WILD-TYPE    53 128 255  96
D868V4, multiclass
       clus
vv      ZNF341 MUTATED ZNF341 WILD-TYPE
  T0+T1              1               53
  T2                 7              128
  T3                 6              255
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF341 MUTATED     6   5   7   1
  ZNF341 WILD-TYPE 189 168  82  84
D868V5, multiclass
    clus
vv   ZNF341 MUTATED ZNF341 WILD-TYPE
  N0              6              189
  N1              5              168
  N2              7               82
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V6, binary
                  cls
clus                 0   1
  ZNF341 MUTATED    19   1
  ZNF341 WILD-TYPE 463  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF341 MUTATED     19    1
  ZNF341 WILD-TYPE  463   37
   clus
vv  ZNF341 MUTATED ZNF341 WILD-TYPE
  0             19              463
  1              1               37
[1] 2 2
[1] FALSE
D868V7, binary
                  cls
clus                 0   1
  ZNF341 MUTATED    10  10
  ZNF341 WILD-TYPE 162 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF341 MUTATED     10   10
  ZNF341 WILD-TYPE  162  396
        clus
vv       ZNF341 MUTATED ZNF341 WILD-TYPE
  FEMALE             10              162
  MALE               10              396
[1] 2 2
[1] FALSE
D868V8, binary
                  cls
clus                 0   1
  ZNF341 MUTATED    14   4
  ZNF341 WILD-TYPE 402  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF341 MUTATED     14    4
  ZNF341 WILD-TYPE  402   98
     clus
vv    ZNF341 MUTATED ZNF341 WILD-TYPE
  NO              14              402
  YES              4               98
[1] 2 2
[1] FALSE
D868V9, continuous
D868V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF341 MUTATED       7                         0
  ZNF341 WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF341 MUTATED                                           0    11
  ZNF341 WILD-TYPE                                         1   346
D868V11, multiclass
                                           clus
vv                                          ZNF341 MUTATED ZNF341 WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V12, binary
                  cls
clus                 0   1
  ZNF341 MUTATED     0  18
  ZNF341 WILD-TYPE  10 380
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF341 MUTATED      0   18
  ZNF341 WILD-TYPE   10  380
                        clus
vv                       ZNF341 MUTATED ZNF341 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             18              380
[1] 2 2
[1] FALSE

Clustering(869) Variable = MRPL24 MUTATION ANALYSIS
D869V1, survival
                  sevent
clus2                0   1
  MRPL24 MUTATED     5   1
  MRPL24 WILD-TYPE 333 215
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              548 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               1              215 
$`MRPL24 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-CG-4305 TCGA-CG-5726 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       34.68        44.94        15.95        28.96        19.73        38.14 

$`MRPL24 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MRPL24 MUTATED MRPL24 WILD-TYPE 
           15.95             0.00 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
           44.94           122.30 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
          31.820           13.495 
[1] "15.9 - 44.9 (31.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.9"
D869V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRPL24 MUTATED         0        1        0        1         2         0
  MRPL24 WILD-TYPE      10       19       46       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL24 MUTATED           0          2          0          0        0
  MRPL24 WILD-TYPE        29         82         62         39       43
                  vv
clus               STAGE IVA
  MRPL24 MUTATED           0
  MRPL24 WILD-TYPE         4
D869V3, multiclass
            clus
vv           MRPL24 MUTATED MRPL24 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MRPL24 MUTATED       1   1   3   1
  MRPL24 WILD-TYPE    53 134 258 101
D869V4, multiclass
       clus
vv      MRPL24 MUTATED MRPL24 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MRPL24 MUTATED     3   2   1   0
  MRPL24 WILD-TYPE 192 171  88  85
D869V5, multiclass
    clus
vv   MRPL24 MUTATED MRPL24 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V6, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     6   0
  MRPL24 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      6    0
  MRPL24 WILD-TYPE  476   38
   clus
vv  MRPL24 MUTATED MRPL24 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D869V7, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     3   3
  MRPL24 WILD-TYPE 169 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      3    3
  MRPL24 WILD-TYPE  169  403
        clus
vv       MRPL24 MUTATED MRPL24 WILD-TYPE
  FEMALE              3              169
  MALE                3              403
[1] 2 2
[1] FALSE
D869V8, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     4   1
  MRPL24 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      4    1
  MRPL24 WILD-TYPE  412  101
     clus
vv    MRPL24 MUTATED MRPL24 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D869V9, continuous
D869V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MRPL24 MUTATED       0                         0
  MRPL24 WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRPL24 MUTATED                                           0     4
  MRPL24 WILD-TYPE                                         1   353
D869V11, multiclass
                                           clus
vv                                          MRPL24 MUTATED MRPL24 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V12, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     0   3
  MRPL24 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      0    3
  MRPL24 WILD-TYPE   10  395
                        clus
vv                       MRPL24 MUTATED MRPL24 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(870) Variable = NRAS MUTATION ANALYSIS
D870V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     1   4
  NRAS WILD-TYPE 337 212
  NRAS MUTATED NRAS WILD-TYPE 
             5            549 
  NRAS MUTATED NRAS WILD-TYPE 
             4            212 
$`NRAS MUTATED`
TCGA-L5-A4OI TCGA-BR-6455 TCGA-CD-A489 TCGA-HJ-7597 TCGA-RD-A7C1 
       19.99        13.87        11.31        26.47        16.67 

$`NRAS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  NRAS MUTATED NRAS WILD-TYPE 
         11.31           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         26.47         122.30 
  NRAS MUTATED NRAS WILD-TYPE 
         16.67          13.51 
[1] "11.3 - 26.5 (16.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D870V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRAS MUTATED         0        0        2        0         1         1
  NRAS WILD-TYPE      10       20       44       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED           0          0          0          1        0         0
  NRAS WILD-TYPE        29         84         62         38       43         4
D870V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NRAS MUTATED       0   2   3   0
  NRAS WILD-TYPE    54 133 258 102
D870V4, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               3            258
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NRAS MUTATED     3   1   0   1
  NRAS WILD-TYPE 192 172  89  84
D870V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            3            192
  N1            1            172
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V6, binary
                cls
clus               0   1
  NRAS MUTATED     3   0
  NRAS WILD-TYPE 479  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      3    0
  NRAS WILD-TYPE  479   38
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0            3            479
  1            0             38
[1] 2 2
[1] FALSE
D870V7, binary
                cls
clus               0   1
  NRAS MUTATED     1   4
  NRAS WILD-TYPE 171 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    4
  NRAS WILD-TYPE  171  402
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1            171
  MALE              4            402
[1] 2 2
[1] FALSE
D870V8, binary
                cls
clus               0   1
  NRAS MUTATED     5   0
  NRAS WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    0
  NRAS WILD-TYPE  411  102
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D870V9, continuous
D870V10, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-Z6-AAPN 
"NRAS WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NRAS MUTATED       1                         0
  NRAS WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRAS MUTATED                                           0     4
  NRAS WILD-TYPE                                         1   353
D870V11, multiclass
                                           clus
vv                                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V12, binary
                cls
clus               0   1
  NRAS MUTATED     0   4
  NRAS WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    4
  NRAS WILD-TYPE   10  394
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(871) Variable = RSPH4A MUTATION ANALYSIS
D871V1, survival
                  sevent
clus2                0   1
  RSPH4A MUTATED     2   7
  RSPH4A WILD-TYPE 336 209
  RSPH4A MUTATED RSPH4A WILD-TYPE 
               9              545 
  RSPH4A MUTATED RSPH4A WILD-TYPE 
               7              209 
$`RSPH4A MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NF TCGA-XP-A8T6 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8363 
       19.99         2.66        25.08        30.90        29.59         0.26 
TCGA-BR-8687 TCGA-CD-A4MG TCGA-CG-4306 
        8.22         6.58         1.02 

$`RSPH4A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RSPH4A MUTATED RSPH4A WILD-TYPE 
            0.26             0.00 
  RSPH4A MUTATED RSPH4A WILD-TYPE 
            30.9            122.3 
  RSPH4A MUTATED RSPH4A WILD-TYPE 
            8.22            13.58 
[1] "0.3 - 30.9 (8.2)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.6"
D871V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RSPH4A MUTATED         0        0        1        0         1         2
  RSPH4A WILD-TYPE      10       20       45       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RSPH4A MUTATED           0          0          0          2        1
  RSPH4A WILD-TYPE        29         84         62         37       42
                  vv
clus               STAGE IVA
  RSPH4A MUTATED           1
  RSPH4A WILD-TYPE         3
D871V3, multiclass
            clus
vv           RSPH4A MUTATED RSPH4A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RSPH4A MUTATED       1   3   4   2
  RSPH4A WILD-TYPE    53 132 257 100
D871V4, multiclass
       clus
vv      RSPH4A MUTATED RSPH4A WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RSPH4A MUTATED     4   1   2   1
  RSPH4A WILD-TYPE 191 172  87  84
D871V5, multiclass
    clus
vv   RSPH4A MUTATED RSPH4A WILD-TYPE
  N0              4              191
  N1              1              172
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V6, binary
                  cls
clus                 0   1
  RSPH4A MUTATED     6   2
  RSPH4A WILD-TYPE 476  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSPH4A MUTATED      6    2
  RSPH4A WILD-TYPE  476   36
   clus
vv  RSPH4A MUTATED RSPH4A WILD-TYPE
  0              6              476
  1              2               36
[1] 2 2
[1] FALSE
D871V7, binary
                  cls
clus                 0   1
  RSPH4A MUTATED     5   5
  RSPH4A WILD-TYPE 167 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSPH4A MUTATED      5    5
  RSPH4A WILD-TYPE  167  401
        clus
vv       RSPH4A MUTATED RSPH4A WILD-TYPE
  FEMALE              5              167
  MALE                5              401
[1] 2 2
[1] FALSE
D871V8, binary
                  cls
clus                 0   1
  RSPH4A MUTATED     8   0
  RSPH4A WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSPH4A MUTATED      8    0
  RSPH4A WILD-TYPE  408  102
     clus
vv    RSPH4A MUTATED RSPH4A WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D871V9, continuous
[1] "Remove cluster labels:" "RSPH4A MUTATED"        
clus
  RSPH4A MUTATED RSPH4A WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T7 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" "RSPH4A WILD-TYPE" 
D871V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RSPH4A MUTATED       1                         1
  RSPH4A WILD-TYPE   132                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RSPH4A MUTATED                                           0     7
  RSPH4A WILD-TYPE                                         1   350
D871V11, multiclass
                                           clus
vv                                          RSPH4A MUTATED RSPH4A WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V12, binary
                  cls
clus                 0   1
  RSPH4A MUTATED     1   6
  RSPH4A WILD-TYPE   9 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSPH4A MUTATED      1    6
  RSPH4A WILD-TYPE    9  392
                        clus
vv                       RSPH4A MUTATED RSPH4A WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(872) Variable = RING1 MUTATION ANALYSIS
D872V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     6   1
  RING1 WILD-TYPE 332 215
  RING1 MUTATED RING1 WILD-TYPE 
              7             547 
  RING1 MUTATED RING1 WILD-TYPE 
              1             215 
$`RING1 MUTATED`
TCGA-2H-A9GL TCGA-B7-A5TI TCGA-BR-6452 TCGA-CD-5802 TCGA-CG-5721 TCGA-D7-A4YY 
        5.92        19.56        34.68        13.35         6.02        13.78 
TCGA-HU-A4H3 
       29.00 

$`RING1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  RING1 MUTATED RING1 WILD-TYPE 
           5.92            0.00 
  RING1 MUTATED RING1 WILD-TYPE 
          34.68          122.30 
  RING1 MUTATED RING1 WILD-TYPE 
          13.78           13.55 
[1] "5.9 - 34.7 (13.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.7"
D872V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RING1 MUTATED         0        0        0        1         1         0
  RING1 WILD-TYPE      10       20       46       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RING1 MUTATED           1          0          1          2        2         0
  RING1 WILD-TYPE        28         84         61         37       41         4
D872V3, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RING1 MUTATED       0   0   4   4
  RING1 WILD-TYPE    54 135 257  98
D872V4, multiclass
       clus
vv      RING1 MUTATED RING1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                4             257
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RING1 MUTATED     2   2   1   3
  RING1 WILD-TYPE 193 171  88  82
D872V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V6, binary
                 cls
clus                0   1
  RING1 MUTATED     9   0
  RING1 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      9    0
  RING1 WILD-TYPE  473   38
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D872V7, binary
                 cls
clus                0   1
  RING1 MUTATED     4   5
  RING1 WILD-TYPE 168 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      4    5
  RING1 WILD-TYPE  168  401
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  FEMALE             4             168
  MALE               5             401
[1] 2 2
[1] FALSE
D872V8, binary
                 cls
clus                0   1
  RING1 MUTATED     4   2
  RING1 WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      4    2
  RING1 WILD-TYPE  412  100
     clus
vv    RING1 MUTATED RING1 WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D872V9, continuous
D872V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RING1 MUTATED       2                         0
  RING1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RING1 MUTATED                                           0     5
  RING1 WILD-TYPE                                         1   352
D872V11, multiclass
                                           clus
vv                                          RING1 MUTATED RING1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V12, binary
                 cls
clus                0   1
  RING1 MUTATED     0   7
  RING1 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      0    7
  RING1 WILD-TYPE   10  391
                        clus
vv                       RING1 MUTATED RING1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(873) Variable = KCNH4 MUTATION ANALYSIS
D873V1, survival
                 sevent
clus2               0   1
  KCNH4 MUTATED    10   5
  KCNH4 WILD-TYPE 328 211
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             15             539 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              5             211 
$`KCNH4 MUTATED`
TCGA-L5-A43J TCGA-JY-A6FG TCGA-JY-A93C TCGA-LN-A7HX TCGA-BR-6452 TCGA-BR-6566 
        4.31        41.52        23.18        12.23        34.68        32.78 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4437 
       31.10         1.12        12.89        16.14         6.58         8.05 
TCGA-FP-A4BE TCGA-HU-A4GH TCGA-RD-A7BW 
       11.08        11.77         5.13 

$`KCNH4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KCNH4 MUTATED KCNH4 WILD-TYPE 
           1.12            0.00 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          41.52          122.30 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          12.23           13.68 
[1] "1.1 - 41.5 (12.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D873V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH4 MUTATED         0        1        1        1         6         2
  KCNH4 WILD-TYPE      10       19       45       30        78        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNH4 MUTATED           1          0          2          1        0         0
  KCNH4 WILD-TYPE        28         84         60         38       43         4
D873V3, multiclass
            clus
vv           KCNH4 MUTATED KCNH4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              6              78
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNH4 MUTATED       1   3   9   2
  KCNH4 WILD-TYPE    53 132 252 100
D873V4, multiclass
       clus
vv      KCNH4 MUTATED KCNH4 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                9             252
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNH4 MUTATED    10   2   2   1
  KCNH4 WILD-TYPE 185 171  87  84
D873V5, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  N0            10             185
  N1             2             171
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V6, binary
                 cls
clus                0   1
  KCNH4 MUTATED    14   0
  KCNH4 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED     14    0
  KCNH4 WILD-TYPE  468   38
   clus
vv  KCNH4 MUTATED KCNH4 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D873V7, binary
                 cls
clus                0   1
  KCNH4 MUTATED     6   9
  KCNH4 WILD-TYPE 166 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      6    9
  KCNH4 WILD-TYPE  166  397
        clus
vv       KCNH4 MUTATED KCNH4 WILD-TYPE
  FEMALE             6             166
  MALE               9             397
[1] 2 2
[1] FALSE
D873V8, binary
                 cls
clus                0   1
  KCNH4 MUTATED    11   3
  KCNH4 WILD-TYPE 405  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED     11    3
  KCNH4 WILD-TYPE  405   99
     clus
vv    KCNH4 MUTATED KCNH4 WILD-TYPE
  NO             11             405
  YES             3              99
[1] 2 2
[1] FALSE
D873V9, continuous
[1] "Remove cluster labels:" "KCNH4 MUTATED"         
clus
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" "KCNH4 WILD-TYPE" 
D873V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH4 MUTATED       5                         1
  KCNH4 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH4 MUTATED                                           0     8
  KCNH4 WILD-TYPE                                         1   349
D873V11, multiclass
                                           clus
vv                                          KCNH4 MUTATED KCNH4 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V12, binary
                 cls
clus                0   1
  KCNH4 MUTATED     0  11
  KCNH4 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      0   11
  KCNH4 WILD-TYPE   10  387
                        clus
vv                       KCNH4 MUTATED KCNH4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(874) Variable = ZNF23 MUTATION ANALYSIS
D874V1, survival
                 sevent
clus2               0   1
  ZNF23 MUTATED     4   1
  ZNF23 WILD-TYPE 334 215
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              5             549 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              1             215 
$`ZNF23 MUTATED`
TCGA-IG-A97I TCGA-LN-A49W TCGA-BR-4256 TCGA-BR-8372 TCGA-FP-A4BE 
       12.16        13.25         9.34        31.27        11.08 

$`ZNF23 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZNF23 MUTATED ZNF23 WILD-TYPE 
           9.34            0.00 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
          31.27          122.30 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
          12.16           13.68 
[1] "9.3 - 31.3 (12.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.7"
D874V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF23 MUTATED         0        0        0        0         2         0
  ZNF23 WILD-TYPE      10       20       46       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF23 MUTATED           1          0          0          1        0         0
  ZNF23 WILD-TYPE        28         84         62         38       43         4
D874V3, multiclass
            clus
vv           ZNF23 MUTATED ZNF23 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZNF23 MUTATED       0   1   2   1
  ZNF23 WILD-TYPE    54 134 259 101
D874V4, multiclass
       clus
vv      ZNF23 MUTATED ZNF23 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZNF23 MUTATED     2   2   0   1
  ZNF23 WILD-TYPE 193 171  89  84
D874V5, multiclass
    clus
vv   ZNF23 MUTATED ZNF23 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V6, binary
                 cls
clus                0   1
  ZNF23 MUTATED     5   0
  ZNF23 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      5    0
  ZNF23 WILD-TYPE  477   38
   clus
vv  ZNF23 MUTATED ZNF23 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D874V7, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   5
  ZNF23 WILD-TYPE 172 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    5
  ZNF23 WILD-TYPE  172  401
        clus
vv       ZNF23 MUTATED ZNF23 WILD-TYPE
  FEMALE             0             172
  MALE               5             401
[1] 2 2
[1] FALSE
D874V8, binary
                 cls
clus                0   1
  ZNF23 MUTATED     2   3
  ZNF23 WILD-TYPE 414  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      2    3
  ZNF23 WILD-TYPE  414   99
     clus
vv    ZNF23 MUTATED ZNF23 WILD-TYPE
  NO              2             414
  YES             3              99
[1] 2 2
[1] FALSE
D874V9, continuous
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
D874V10, continuous
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ZNF23 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF23 MUTATED       1                         1
  ZNF23 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF23 MUTATED                                           0     3
  ZNF23 WILD-TYPE                                         1   354
D874V11, multiclass
                                           clus
vv                                          ZNF23 MUTATED ZNF23 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V12, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   4
  ZNF23 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    4
  ZNF23 WILD-TYPE   10  394
                        clus
vv                       ZNF23 MUTATED ZNF23 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(875) Variable = MYO3A MUTATION ANALYSIS
D875V1, survival
                 sevent
clus2               0   1
  MYO3A MUTATED    21  15
  MYO3A WILD-TYPE 317 201
  MYO3A MUTATED MYO3A WILD-TYPE 
             36             518 
  MYO3A MUTATED MYO3A WILD-TYPE 
             15             201 
$`MYO3A MUTATED`
TCGA-IC-A6RF TCGA-L5-A4OE TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A3QL 
       15.68        24.00        14.30         5.92         7.69        35.21 
TCGA-L5-A8NF TCGA-L5-A8NM TCGA-BR-6563 TCGA-BR-7196 TCGA-BR-8059 TCGA-BR-8080 
        2.66         7.76        39.12        21.90        14.43         9.60 
TCGA-BR-8081 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 
       32.25        14.04        14.79         1.12         9.34        28.14 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4QL TCGA-CD-8535 TCGA-CG-4462 TCGA-CG-5728 
       31.96         8.22        16.14        12.82         0.00        65.10 
TCGA-D7-5577 TCGA-D7-8579 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 
       25.71        20.91        11.08        30.51        26.47        22.32 
TCGA-HU-A4G6 TCGA-HU-A4GQ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-RD-A8N9 TCGA-VQ-A91V 
       24.26         0.10        13.35         6.44        35.61        42.64 

$`MYO3A WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       60.39        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8284 
       33.21        37.25        11.44         0.69        29.59         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79        27.12         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        52.21         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MYO3A MUTATED MYO3A WILD-TYPE 
           0.00            0.13 
  MYO3A MUTATED MYO3A WILD-TYPE 
           65.1           122.3 
  MYO3A MUTATED MYO3A WILD-TYPE 
         15.235          13.445 
[1] "0.0 - 65.1 (15.2)"  "0.1 - 122.3 (13.4)"
[1] "hr=" "1"  
D875V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYO3A MUTATED         1        2        3        1         3         6
  MYO3A WILD-TYPE       9       18       43       30        81        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3A MUTATED           3          5          3          7        3         1
  MYO3A WILD-TYPE        26         79         59         32       40         3
D875V3, multiclass
            clus
vv           MYO3A MUTATED MYO3A WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              6              77
  STAGE III              3              26
  STAGE IIIA             5              79
  STAGE IIIB             3              59
  STAGE IIIC             7              32
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYO3A MUTATED       7   9  12  11
  MYO3A WILD-TYPE    47 126 249  91
D875V4, multiclass
       clus
vv      MYO3A MUTATED MYO3A WILD-TYPE
  T0+T1             7              47
  T2                9             126
  T3               12             249
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYO3A MUTATED    11  11   7   9
  MYO3A WILD-TYPE 184 162  82  76
D875V5, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  N0            11             184
  N1            11             162
  N2             7              82
  N3             9              76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V6, binary
                 cls
clus                0   1
  MYO3A MUTATED    32   4
  MYO3A WILD-TYPE 450  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     32    4
  MYO3A WILD-TYPE  450   34
   clus
vv  MYO3A MUTATED MYO3A WILD-TYPE
  0            32             450
  1             4              34
[1] 2 2
[1] FALSE
D875V7, binary
                 cls
clus                0   1
  MYO3A MUTATED    18  21
  MYO3A WILD-TYPE 154 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     18   21
  MYO3A WILD-TYPE  154  385
        clus
vv       MYO3A MUTATED MYO3A WILD-TYPE
  FEMALE            18             154
  MALE              21             385
[1] 2 2
[1] FALSE
D875V8, binary
                 cls
clus                0   1
  MYO3A MUTATED    29   6
  MYO3A WILD-TYPE 387  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     29    6
  MYO3A WILD-TYPE  387   96
     clus
vv    MYO3A MUTATED MYO3A WILD-TYPE
  NO             29             387
  YES             6              96
[1] 2 2
[1] FALSE
D875V9, continuous
[1] "Remove cluster labels:" "MYO3A MUTATED"         
clus
  MYO3A MUTATED MYO3A WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MYO3A WILD-TYPE" "MYO3A WILD-TYPE" "MYO3A WILD-TYPE" 
D875V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYO3A MUTATED       6                         2
  MYO3A WILD-TYPE   127                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYO3A MUTATED                                           0    24
  MYO3A WILD-TYPE                                         1   333
D875V11, multiclass
                                           clus
vv                                          MYO3A MUTATED MYO3A WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                24             333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V12, binary
                 cls
clus                0   1
  MYO3A MUTATED     0  29
  MYO3A WILD-TYPE  10 369
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED      0   29
  MYO3A WILD-TYPE   10  369
                        clus
vv                       MYO3A MUTATED MYO3A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            29             369
[1] 2 2
[1] FALSE

Clustering(876) Variable = C7ORF49 MUTATION ANALYSIS
D876V1, survival
                   sevent
clus2                 0   1
  C7ORF49 MUTATED     7   1
  C7ORF49 WILD-TYPE 331 215
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                8               546 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                1               215 
$`C7ORF49 MUTATED`
TCGA-LN-A4A3 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-D7-A4YV 
       12.76        29.59         1.12        28.14        12.62         5.92 
TCGA-HU-A4G9 TCGA-HU-A4GU 
       24.20         6.58 

$`C7ORF49 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
             1.12              0.00 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            29.59            122.30 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            12.69             13.63 
[1] "1.1 - 29.6 (12.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.7"
D876V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF49 MUTATED         0        1        1        0         1         3
  C7ORF49 WILD-TYPE      10       19       45       31        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF49 MUTATED           1          0          0          1        0
  C7ORF49 WILD-TYPE        28         84         62         38       43
                   vv
clus                STAGE IVA
  C7ORF49 MUTATED           0
  C7ORF49 WILD-TYPE         4
D876V3, multiclass
            clus
vv           C7ORF49 MUTATED C7ORF49 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C7ORF49 MUTATED       1   1   4   2
  C7ORF49 WILD-TYPE    53 134 257 100
D876V4, multiclass
       clus
vv      C7ORF49 MUTATED C7ORF49 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C7ORF49 MUTATED     4   3   0   1
  C7ORF49 WILD-TYPE 191 170  89  84
D876V5, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V6, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     8   0
  C7ORF49 WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      8    0
  C7ORF49 WILD-TYPE  474   38
   clus
vv  C7ORF49 MUTATED C7ORF49 WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D876V7, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     4   4
  C7ORF49 WILD-TYPE 168 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      4    4
  C7ORF49 WILD-TYPE  168  402
        clus
vv       C7ORF49 MUTATED C7ORF49 WILD-TYPE
  FEMALE               4               168
  MALE                 4               402
[1] 2 2
[1] FALSE
D876V8, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     7   1
  C7ORF49 WILD-TYPE 409 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      7    1
  C7ORF49 WILD-TYPE  409  101
     clus
vv    C7ORF49 MUTATED C7ORF49 WILD-TYPE
  NO                7               409
  YES               1               101
[1] 2 2
[1] FALSE
D876V9, continuous
[1] "Remove cluster labels:" "C7ORF49 MUTATED"       
clus
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
D876V10, continuous
[1] "Remove cluster labels:" "C7ORF49 MUTATED"       
clus
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A6 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" "C7ORF49 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C7ORF49 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C7ORF49 MUTATED       4                         0
  C7ORF49 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C7ORF49 MUTATED                                           0     4
  C7ORF49 WILD-TYPE                                         1   353
D876V11, multiclass
                                           clus
vv                                          C7ORF49 MUTATED C7ORF49 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V12, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     0   8
  C7ORF49 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      0    8
  C7ORF49 WILD-TYPE   10  390
                        clus
vv                       C7ORF49 MUTATED C7ORF49 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(877) Variable = C1RL MUTATION ANALYSIS
D877V1, survival
                sevent
clus2              0   1
  C1RL MUTATED     5   1
  C1RL WILD-TYPE 333 215
  C1RL MUTATED C1RL WILD-TYPE 
             6            548 
  C1RL MUTATED C1RL WILD-TYPE 
             1            215 
$`C1RL MUTATED`
TCGA-L5-A4OP TCGA-XP-A8T7 TCGA-BR-6566 TCGA-BR-8487 TCGA-CD-A4MG TCGA-D7-A6F0 
        7.17        41.23        32.78         1.12         6.58        22.29 

$`C1RL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C1RL MUTATED C1RL WILD-TYPE 
          1.12           0.00 
  C1RL MUTATED C1RL WILD-TYPE 
         41.23         122.30 
  C1RL MUTATED C1RL WILD-TYPE 
        14.730         13.565 
[1] "1.1 - 41.2 (14.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.3"
D877V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1RL MUTATED         0        1        1        0         4         0
  C1RL WILD-TYPE      10       19       45       31        80        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1RL MUTATED           0          1          0          0        0         0
  C1RL WILD-TYPE        29         83         62         39       43         4
D877V3, multiclass
            clus
vv           C1RL MUTATED C1RL WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  C1RL MUTATED       1   2   3   1
  C1RL WILD-TYPE    53 133 258 101
D877V4, multiclass
       clus
vv      C1RL MUTATED C1RL WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  C1RL MUTATED     7   1   0   0
  C1RL WILD-TYPE 188 172  89  85
D877V5, multiclass
    clus
vv   C1RL MUTATED C1RL WILD-TYPE
  N0            7            188
  N1            1            172
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V6, binary
                cls
clus               0   1
  C1RL MUTATED     7   0
  C1RL WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      7    0
  C1RL WILD-TYPE  475   38
   clus
vv  C1RL MUTATED C1RL WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D877V7, binary
                cls
clus               0   1
  C1RL MUTATED     7   1
  C1RL WILD-TYPE 165 405
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      7    1
  C1RL WILD-TYPE  165  405
        clus
vv       C1RL MUTATED C1RL WILD-TYPE
  FEMALE            7            165
  MALE              1            405
[1] 2 2
[1] FALSE
D877V8, binary
                cls
clus               0   1
  C1RL MUTATED     5   0
  C1RL WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      5    0
  C1RL WILD-TYPE  411  102
     clus
vv    C1RL MUTATED C1RL WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D877V9, continuous
[1] "Remove cluster labels:" "C1RL MUTATED"          
clus
  C1RL MUTATED C1RL WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
D877V10, continuous
[1] "Remove cluster labels:" "C1RL MUTATED"          
clus
  C1RL MUTATED C1RL WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OQ 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" "C1RL WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  C1RL MUTATED       1                         0
  C1RL WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1RL MUTATED                                           0     7
  C1RL WILD-TYPE                                         1   350
D877V11, multiclass
                                           clus
vv                                          C1RL MUTATED C1RL WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V12, binary
                cls
clus               0   1
  C1RL MUTATED     1   6
  C1RL WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      1    6
  C1RL WILD-TYPE    9  392
                        clus
vv                       C1RL MUTATED C1RL WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(878) Variable = C9ORF25 MUTATION ANALYSIS
D878V1, survival
                   sevent
clus2                 0   1
  C9ORF25 MUTATED     2   3
  C9ORF25 WILD-TYPE 336 213
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               549 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                3               213 
$`C9ORF25 MUTATED`
TCGA-B7-A5TI TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4GQ 
       19.56        16.14         6.58         6.02         0.10 

$`C9ORF25 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
              0.1               0.0 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
            19.56            122.30 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
             6.58             13.58 
[1] "0.1 - 19.6 (6.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.9"
D878V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF25 MUTATED         0        0        0        0         1         0
  C9ORF25 WILD-TYPE      10       20       46       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF25 MUTATED           0          0          1          2        1
  C9ORF25 WILD-TYPE        29         84         61         37       42
                   vv
clus                STAGE IVA
  C9ORF25 MUTATED           0
  C9ORF25 WILD-TYPE         4
D878V3, multiclass
            clus
vv           C9ORF25 MUTATED C9ORF25 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C9ORF25 MUTATED       0   0   2   3
  C9ORF25 WILD-TYPE    54 135 259  99
D878V4, multiclass
       clus
vv      C9ORF25 MUTATED C9ORF25 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C9ORF25 MUTATED     1   1   1   2
  C9ORF25 WILD-TYPE 194 172  88  83
D878V5, multiclass
    clus
vv   C9ORF25 MUTATED C9ORF25 WILD-TYPE
  N0               1               194
  N1               1               172
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V6, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     5   0
  C9ORF25 WILD-TYPE 477  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      5    0
  C9ORF25 WILD-TYPE  477   38
   clus
vv  C9ORF25 MUTATED C9ORF25 WILD-TYPE
  0               5               477
  1               0                38
[1] 2 2
[1] FALSE
D878V7, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     1   4
  C9ORF25 WILD-TYPE 171 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      1    4
  C9ORF25 WILD-TYPE  171  402
        clus
vv       C9ORF25 MUTATED C9ORF25 WILD-TYPE
  FEMALE               1               171
  MALE                 4               402
[1] 2 2
[1] FALSE
D878V8, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     5   0
  C9ORF25 WILD-TYPE 411 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      5    0
  C9ORF25 WILD-TYPE  411  102
     clus
vv    C9ORF25 MUTATED C9ORF25 WILD-TYPE
  NO                5               411
  YES               0               102
[1] 2 2
[1] FALSE
D878V9, continuous
D878V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF25 MUTATED       2                         0
  C9ORF25 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF25 MUTATED                                           0     2
  C9ORF25 WILD-TYPE                                         1   355
D878V11, multiclass
                                           clus
vv                                          C9ORF25 MUTATED C9ORF25 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V12, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     0   4
  C9ORF25 WILD-TYPE  10 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      0    4
  C9ORF25 WILD-TYPE   10  394
                        clus
vv                       C9ORF25 MUTATED C9ORF25 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(879) Variable = LRFN3 MUTATION ANALYSIS
D879V1, survival
                 sevent
clus2               0   1
  LRFN3 MUTATED    16   4
  LRFN3 WILD-TYPE 322 212
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             20             534 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
              4             212 
$`LRFN3 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-CD-8529 
       34.68        44.94         6.18        31.10         1.12        12.30 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5726 
       12.82        12.43         6.58        11.77         1.02        28.96 
TCGA-F1-A448 TCGA-FP-A9TM TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4H0 TCGA-HU-A4H3 
       21.27         6.21        22.32         0.76         2.10        29.00 
TCGA-HU-A4H8 TCGA-MX-A5UJ 
       14.07        19.73 

$`LRFN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 
       29.42         2.66        19.96         2.20         7.40         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         0.26        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LRFN3 MUTATED LRFN3 WILD-TYPE 
           0.76            0.00 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
          44.94          122.30 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
         12.625          13.630 
[1] "0.8 - 44.9 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D879V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRFN3 MUTATED         0        2        1        1         5         1
  LRFN3 WILD-TYPE      10       18       45       30        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRFN3 MUTATED           0          3          1          3        2         0
  LRFN3 WILD-TYPE        29         81         61         36       41         4
D879V3, multiclass
            clus
vv           LRFN3 MUTATED LRFN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LRFN3 MUTATED       4   0  12   5
  LRFN3 WILD-TYPE    50 135 249  97
D879V4, multiclass
       clus
vv      LRFN3 MUTATED LRFN3 WILD-TYPE
  T0+T1             4              50
  T2                0             135
  T3               12             249
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LRFN3 MUTATED    10   4   3   3
  LRFN3 WILD-TYPE 185 169  86  82
D879V5, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  N0            10             185
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V6, binary
                 cls
clus                0   1
  LRFN3 MUTATED    19   2
  LRFN3 WILD-TYPE 463  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED     19    2
  LRFN3 WILD-TYPE  463   36
   clus
vv  LRFN3 MUTATED LRFN3 WILD-TYPE
  0            19             463
  1             2              36
[1] 2 2
[1] FALSE
D879V7, binary
                 cls
clus                0   1
  LRFN3 MUTATED     9  13
  LRFN3 WILD-TYPE 163 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      9   13
  LRFN3 WILD-TYPE  163  393
        clus
vv       LRFN3 MUTATED LRFN3 WILD-TYPE
  FEMALE             9             163
  MALE              13             393
[1] 2 2
[1] FALSE
D879V8, binary
                 cls
clus                0   1
  LRFN3 MUTATED    14   3
  LRFN3 WILD-TYPE 402  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED     14    3
  LRFN3 WILD-TYPE  402   99
     clus
vv    LRFN3 MUTATED LRFN3 WILD-TYPE
  NO             14             402
  YES             3              99
[1] 2 2
[1] FALSE
D879V9, continuous
D879V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRFN3 MUTATED      10                         0
  LRFN3 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRFN3 MUTATED                                           0    10
  LRFN3 WILD-TYPE                                         1   347
D879V11, multiclass
                                           clus
vv                                          LRFN3 MUTATED LRFN3 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V12, binary
                 cls
clus                0   1
  LRFN3 MUTATED     1  19
  LRFN3 WILD-TYPE   9 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      1   19
  LRFN3 WILD-TYPE    9  379
                        clus
vv                       LRFN3 MUTATED LRFN3 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(880) Variable = ING1 MUTATION ANALYSIS
D880V1, survival
                sevent
clus2              0   1
  ING1 MUTATED     4   3
  ING1 WILD-TYPE 334 213
  ING1 MUTATED ING1 WILD-TYPE 
             7            547 
  ING1 MUTATED ING1 WILD-TYPE 
             3            213 
$`ING1 MUTATED`
TCGA-2H-A9GO TCGA-L5-A88Z TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG 
       16.24         7.40        34.68         1.12        31.96         6.58 
TCGA-D7-A4YV 
        5.92 

$`ING1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ING1 MUTATED ING1 WILD-TYPE 
          1.12           0.00 
  ING1 MUTATED ING1 WILD-TYPE 
         34.68         122.30 
  ING1 MUTATED ING1 WILD-TYPE 
          7.40          13.58 
[1] "1.1 - 34.7 (7.4)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D880V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ING1 MUTATED         0        0        0        0         4         1
  ING1 WILD-TYPE      10       20       46       31        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ING1 MUTATED           0          0          0          0        2         1
  ING1 WILD-TYPE        29         84         62         39       41         3
D880V3, multiclass
            clus
vv           ING1 MUTATED ING1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ING1 MUTATED       1   0   5   2
  ING1 WILD-TYPE    53 135 256 100
D880V4, multiclass
       clus
vv      ING1 MUTATED ING1 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ING1 MUTATED     3   3   2   0
  ING1 WILD-TYPE 192 170  87  85
D880V5, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  N0            3            192
  N1            3            170
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V6, binary
                cls
clus               0   1
  ING1 MUTATED     6   2
  ING1 WILD-TYPE 476  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      6    2
  ING1 WILD-TYPE  476   36
   clus
vv  ING1 MUTATED ING1 WILD-TYPE
  0            6            476
  1            2             36
[1] 2 2
[1] FALSE
D880V7, binary
                cls
clus               0   1
  ING1 MUTATED     5   3
  ING1 WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      5    3
  ING1 WILD-TYPE  167  403
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D880V8, binary
                cls
clus               0   1
  ING1 MUTATED     7   0
  ING1 WILD-TYPE 409 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      7    0
  ING1 WILD-TYPE  409  102
     clus
vv    ING1 MUTATED ING1 WILD-TYPE
  NO             7            409
  YES            0            102
[1] 2 2
[1] FALSE
D880V9, continuous
D880V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ING1 MUTATED       2                         0
  ING1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ING1 MUTATED                                           0     5
  ING1 WILD-TYPE                                         1   352
D880V11, multiclass
                                           clus
vv                                          ING1 MUTATED ING1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V12, binary
                cls
clus               0   1
  ING1 MUTATED     0   6
  ING1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      0    6
  ING1 WILD-TYPE   10  392
                        clus
vv                       ING1 MUTATED ING1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(881) Variable = FAM26E MUTATION ANALYSIS
D881V1, survival
                  sevent
clus2                0   1
  FAM26E MUTATED     2   1
  FAM26E WILD-TYPE 336 215
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              551 
  FAM26E MUTATED FAM26E WILD-TYPE 
               1              215 
$`FAM26E MUTATED`
TCGA-BR-6566 TCGA-D7-A6EY TCGA-HU-8602 
       32.78        11.44        22.32 

$`FAM26E WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM26E MUTATED FAM26E WILD-TYPE 
           11.44             0.00 
  FAM26E MUTATED FAM26E WILD-TYPE 
           32.78           122.30 
  FAM26E MUTATED FAM26E WILD-TYPE 
           22.32            13.55 
[1] "11.4 - 32.8 (22.3)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D881V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM26E MUTATED         0        0        0        0         1         1
  FAM26E WILD-TYPE      10       20       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM26E MUTATED           0          0          1          0        0
  FAM26E WILD-TYPE        29         84         61         39       43
                  vv
clus               STAGE IVA
  FAM26E MUTATED           0
  FAM26E WILD-TYPE         4
D881V3, multiclass
            clus
vv           FAM26E MUTATED FAM26E WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM26E MUTATED       0   0   2   1
  FAM26E WILD-TYPE    54 135 259 101
D881V4, multiclass
       clus
vv      FAM26E MUTATED FAM26E WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 2              259
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM26E MUTATED     2   0   0   1
  FAM26E WILD-TYPE 193 173  89  84
D881V5, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  N0              2              193
  N1              0              173
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V6, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 479  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  479   38
   clus
vv  FAM26E MUTATED FAM26E WILD-TYPE
  0              3              479
  1              0               38
[1] 2 2
[1] FALSE
D881V7, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 169 406
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  169  406
        clus
vv       FAM26E MUTATED FAM26E WILD-TYPE
  FEMALE              3              169
  MALE                0              406
[1] 2 2
[1] FALSE
D881V8, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 413 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  413  102
     clus
vv    FAM26E MUTATED FAM26E WILD-TYPE
  NO               3              413
  YES              0              102
[1] 2 2
[1] FALSE
D881V9, continuous
D881V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM26E MUTATED       1                         0
  FAM26E WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM26E MUTATED                                           0     2
  FAM26E WILD-TYPE                                         1   355
D881V11, multiclass
                                           clus
vv                                          FAM26E MUTATED FAM26E WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V12, binary
                  cls
clus                 0   1
  FAM26E MUTATED     0   3
  FAM26E WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      0    3
  FAM26E WILD-TYPE   10  395
                        clus
vv                       FAM26E MUTATED FAM26E WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(882) Variable = USP1 MUTATION ANALYSIS
D882V1, survival
                sevent
clus2              0   1
  USP1 MUTATED     4   3
  USP1 WILD-TYPE 334 213
  USP1 MUTATED USP1 WILD-TYPE 
             7            547 
  USP1 MUTATED USP1 WILD-TYPE 
             3            213 
$`USP1 MUTATED`
TCGA-IG-A4P3 TCGA-L5-A4OW TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-5728 
       18.64         7.13        29.59        25.05        31.96        65.10 
TCGA-D7-A4YY 
       13.78 

$`USP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  USP1 MUTATED USP1 WILD-TYPE 
          7.13           0.00 
  USP1 MUTATED USP1 WILD-TYPE 
          65.1          122.3 
  USP1 MUTATED USP1 WILD-TYPE 
         25.05          13.51 
[1] "7.1 - 65.1 (25.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D882V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP1 MUTATED         0        0        1        0         0         3
  USP1 WILD-TYPE      10       20       45       31        84        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP1 MUTATED           0          0          1          1        1         0
  USP1 WILD-TYPE        29         84         61         38       42         4
D882V3, multiclass
            clus
vv           USP1 MUTATED USP1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  USP1 MUTATED       0   3   1   3
  USP1 WILD-TYPE    54 132 260  99
D882V4, multiclass
       clus
vv      USP1 MUTATED USP1 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               1            260
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  USP1 MUTATED     2   2   1   2
  USP1 WILD-TYPE 193 171  88  83
D882V5, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V6, binary
                cls
clus               0   1
  USP1 MUTATED     6   1
  USP1 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      6    1
  USP1 WILD-TYPE  476   37
   clus
vv  USP1 MUTATED USP1 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D882V7, binary
                cls
clus               0   1
  USP1 MUTATED     4   3
  USP1 WILD-TYPE 168 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      4    3
  USP1 WILD-TYPE  168  403
        clus
vv       USP1 MUTATED USP1 WILD-TYPE
  FEMALE            4            168
  MALE              3            403
[1] 2 2
[1] FALSE
D882V8, binary
                cls
clus               0   1
  USP1 MUTATED     4   2
  USP1 WILD-TYPE 412 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      4    2
  USP1 WILD-TYPE  412  100
     clus
vv    USP1 MUTATED USP1 WILD-TYPE
  NO             4            412
  YES            2            100
[1] 2 2
[1] FALSE
D882V9, continuous
D882V10, continuous
[1] "Remove cluster labels:" "USP1 MUTATED"          
clus
  USP1 MUTATED USP1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OX     TCGA-L5-A88S 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" "USP1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  USP1 MUTATED       1                         0
  USP1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP1 MUTATED                                           0     4
  USP1 WILD-TYPE                                         1   353
D882V11, multiclass
                                           clus
vv                                          USP1 MUTATED USP1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V12, binary
                cls
clus               0   1
  USP1 MUTATED     0   5
  USP1 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      0    5
  USP1 WILD-TYPE   10  393
                        clus
vv                       USP1 MUTATED USP1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(883) Variable = CRYBG3 MUTATION ANALYSIS
D883V1, survival
                  sevent
clus2                0   1
  CRYBG3 MUTATED    14   4
  CRYBG3 WILD-TYPE 324 212
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              18              536 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
               4              212 
$`CRYBG3 MUTATED`
TCGA-L5-A4OI TCGA-IG-A8O2 TCGA-LN-A9FO TCGA-VR-A8EP TCGA-BR-6452 TCGA-BR-8368 
       19.99         4.67         0.13        27.09        34.68         4.31 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5813 TCGA-CD-A4MJ TCGA-D7-A4YV 
       27.12        28.14        31.96        12.39        12.62         5.92 
TCGA-D7-A4YX TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-R5-A7ZI TCGA-VQ-AA6G 
       36.43        22.82        22.68         6.51        74.53        26.04 

$`CRYBG3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       16.44        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
            0.13             0.00 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
           74.53           122.30 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
           22.75            13.51 
[1] "0.1 - 74.5 (22.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D883V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYBG3 MUTATED         0        0        2        1         5         3
  CRYBG3 WILD-TYPE      10       20       44       30        79        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYBG3 MUTATED           0          0          3          2        2
  CRYBG3 WILD-TYPE        29         84         59         37       41
                  vv
clus               STAGE IVA
  CRYBG3 MUTATED           0
  CRYBG3 WILD-TYPE         4
D883V3, multiclass
            clus
vv           CRYBG3 MUTATED CRYBG3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               5               79
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              3               59
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CRYBG3 MUTATED       0   3  11   4
  CRYBG3 WILD-TYPE    54 132 250  98
D883V4, multiclass
       clus
vv      CRYBG3 MUTATED CRYBG3 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                11              250
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CRYBG3 MUTATED     8   5   3   2
  CRYBG3 WILD-TYPE 187 168  86  83
D883V5, multiclass
    clus
vv   CRYBG3 MUTATED CRYBG3 WILD-TYPE
  N0              8              187
  N1              5              168
  N2              3               86
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V6, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED    15   2
  CRYBG3 WILD-TYPE 467  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED     15    2
  CRYBG3 WILD-TYPE  467   36
   clus
vv  CRYBG3 MUTATED CRYBG3 WILD-TYPE
  0             15              467
  1              2               36
[1] 2 2
[1] FALSE
D883V7, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED     7  11
  CRYBG3 WILD-TYPE 165 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED      7   11
  CRYBG3 WILD-TYPE  165  395
        clus
vv       CRYBG3 MUTATED CRYBG3 WILD-TYPE
  FEMALE              7              165
  MALE               11              395
[1] 2 2
[1] FALSE
D883V8, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED    17   0
  CRYBG3 WILD-TYPE 399 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED     17    0
  CRYBG3 WILD-TYPE  399  102
     clus
vv    CRYBG3 MUTATED CRYBG3 WILD-TYPE
  NO              17              399
  YES              0              102
[1] 2 2
[1] FALSE
D883V9, continuous
[1] "Remove cluster labels:" "CRYBG3 MUTATED"        
clus
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" "CRYBG3 WILD-TYPE" 
D883V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CRYBG3 MUTATED       8                         0
  CRYBG3 WILD-TYPE   125                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYBG3 MUTATED                                           0    10
  CRYBG3 WILD-TYPE                                         1   347
D883V11, multiclass
                                           clus
vv                                          CRYBG3 MUTATED CRYBG3 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V12, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED     1  14
  CRYBG3 WILD-TYPE   9 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED      1   14
  CRYBG3 WILD-TYPE    9  384
                        clus
vv                       CRYBG3 MUTATED CRYBG3 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(884) Variable = HCFC1R1 MUTATION ANALYSIS
D884V1, survival
                   sevent
clus2                 0   1
  HCFC1R1 MUTATED     5   1
  HCFC1R1 WILD-TYPE 333 215
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               548 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                1               215 
$`HCFC1R1 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8487 TCGA-HF-A5NB TCGA-HU-A4G2 TCGA-HU-A4GN 
       30.90        29.59         1.12        30.51        24.30        29.98 

$`HCFC1R1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
             1.12              0.00 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
             30.9             122.3 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
           29.785            13.510 
[1] "1.1 - 30.9 (29.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.4"
D884V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HCFC1R1 MUTATED         0        0        0        0         2         2
  HCFC1R1 WILD-TYPE      10       20       46       31        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCFC1R1 MUTATED           0          0          0          1        0
  HCFC1R1 WILD-TYPE        29         84         62         38       43
                   vv
clus                STAGE IVA
  HCFC1R1 MUTATED           0
  HCFC1R1 WILD-TYPE         4
D884V3, multiclass
            clus
vv           HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  HCFC1R1 MUTATED       0   2   2   2
  HCFC1R1 WILD-TYPE    54 133 259 100
D884V4, multiclass
       clus
vv      HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HCFC1R1 MUTATED     2   2   0   1
  HCFC1R1 WILD-TYPE 193 171  89  84
D884V5, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  N0               2               193
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V6, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     6   0
  HCFC1R1 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      6    0
  HCFC1R1 WILD-TYPE  476   38
   clus
vv  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D884V7, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   2
  HCFC1R1 WILD-TYPE 168 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    2
  HCFC1R1 WILD-TYPE  168  404
        clus
vv       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  FEMALE               4               168
  MALE                 2               404
[1] 2 2
[1] FALSE
D884V8, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     5   1
  HCFC1R1 WILD-TYPE 411 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      5    1
  HCFC1R1 WILD-TYPE  411  101
     clus
vv    HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  NO                5               411
  YES               1               101
[1] 2 2
[1] FALSE
D884V9, continuous
D884V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HCFC1R1 MUTATED       2                         0
  HCFC1R1 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HCFC1R1 MUTATED                                           0     3
  HCFC1R1 WILD-TYPE                                         1   354
D884V11, multiclass
                                           clus
vv                                          HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V12, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     0   5
  HCFC1R1 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      0    5
  HCFC1R1 WILD-TYPE   10  393
                        clus
vv                       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(885) Variable = ZNF142 MUTATION ANALYSIS
D885V1, survival
                  sevent
clus2                0   1
  ZNF142 MUTATED    14  10
  ZNF142 WILD-TYPE 324 206
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              24              530 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              10              206 
$`ZNF142 MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NM TCGA-R6-A6DN TCGA-V5-A7RC TCGA-VR-AA4G TCGA-XP-A8T8 
       60.39         7.76         8.02         3.42        18.05        14.37 
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8372 
       26.70         6.97         6.61        34.68        14.43        31.27 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 
       28.14        31.96        16.14        12.43         6.58        15.95 
TCGA-CG-4306 TCGA-CG-5728 TCGA-HJ-7597 TCGA-HU-8602 TCGA-MX-A5UJ TCGA-VQ-A8P2 
        1.02        65.10        26.47        22.32        19.73        38.14 

$`ZNF142 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        27.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZNF142 MUTATED ZNF142 WILD-TYPE 
            1.02             0.00 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
            65.1            122.3 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
          17.095           13.445 
[1] "1.0 - 65.1 (17.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D885V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF142 MUTATED         2        0        2        2         2         4
  ZNF142 WILD-TYPE       8       20       44       29        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF142 MUTATED           2          4          1          2        2
  ZNF142 WILD-TYPE        27         80         61         37       41
                  vv
clus               STAGE IVA
  ZNF142 MUTATED           0
  ZNF142 WILD-TYPE         4
D885V3, multiclass
            clus
vv           ZNF142 MUTATED ZNF142 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               2               27
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF142 MUTATED       3   6   7   7
  ZNF142 WILD-TYPE    51 129 254  95
D885V4, multiclass
       clus
vv      ZNF142 MUTATED ZNF142 WILD-TYPE
  T0+T1              3               51
  T2                 6              129
  T3                 7              254
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF142 MUTATED     8   8   4   3
  ZNF142 WILD-TYPE 187 165  85  82
D885V5, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  N0              8              187
  N1              8              165
  N2              4               85
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V6, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    18   2
  ZNF142 WILD-TYPE 464  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     18    2
  ZNF142 WILD-TYPE  464   36
   clus
vv  ZNF142 MUTATED ZNF142 WILD-TYPE
  0             18              464
  1              2               36
[1] 2 2
[1] FALSE
D885V7, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    10  15
  ZNF142 WILD-TYPE 162 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     10   15
  ZNF142 WILD-TYPE  162  391
        clus
vv       ZNF142 MUTATED ZNF142 WILD-TYPE
  FEMALE             10              162
  MALE               15              391
[1] 2 2
[1] FALSE
D885V8, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    19   3
  ZNF142 WILD-TYPE 397  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     19    3
  ZNF142 WILD-TYPE  397   99
     clus
vv    ZNF142 MUTATED ZNF142 WILD-TYPE
  NO              19              397
  YES              3               99
[1] 2 2
[1] FALSE
D885V9, continuous
D885V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF142 MUTATED       4                         3
  ZNF142 WILD-TYPE   129                        11
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF142 MUTATED                                           0    15
  ZNF142 WILD-TYPE                                         1   342
D885V11, multiclass
                                           clus
vv                                          ZNF142 MUTATED ZNF142 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              3               11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V12, binary
                  cls
clus                 0   1
  ZNF142 MUTATED     1  17
  ZNF142 WILD-TYPE   9 381
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED      1   17
  ZNF142 WILD-TYPE    9  381
                        clus
vv                       ZNF142 MUTATED ZNF142 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             17              381
[1] 2 2
[1] FALSE

Clustering(886) Variable = POLE3 MUTATION ANALYSIS
D886V1, survival
                 sevent
clus2               0   1
  POLE3 MUTATED     1   1
  POLE3 WILD-TYPE 337 215
  POLE3 MUTATED POLE3 WILD-TYPE 
              2             552 
  POLE3 MUTATED POLE3 WILD-TYPE 
              1             215 
$`POLE3 MUTATED`
TCGA-BR-8078 TCGA-HU-A4GQ 
       29.59         0.10 

$`POLE3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  POLE3 MUTATED POLE3 WILD-TYPE 
            0.1             0.0 
  POLE3 MUTATED POLE3 WILD-TYPE 
          29.59          122.30 
  POLE3 MUTATED POLE3 WILD-TYPE 
         14.845          13.565 
[1] "0.1 - 29.6 (14.8)"  "0.0 - 122.3 (13.6)"
[1] "Remove cluster labels:" "POLE3 MUTATED"         
D886V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POLE3 MUTATED         1        0        0        0         0         1
  POLE3 WILD-TYPE       9       20       46       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLE3 MUTATED           0          0          0          1        0         0
  POLE3 WILD-TYPE        29         84         62         38       43         4
D886V3, multiclass
            clus
vv           POLE3 MUTATED POLE3 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  POLE3 MUTATED       1   0   0   2
  POLE3 WILD-TYPE    53 135 261 100
D886V4, multiclass
       clus
vv      POLE3 MUTATED POLE3 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                0             261
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  POLE3 MUTATED     1   1   1   0
  POLE3 WILD-TYPE 194 172  88  85
D886V5, multiclass
    clus
vv   POLE3 MUTATED POLE3 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V6, binary
                 cls
clus                0   1
  POLE3 MUTATED     2   0
  POLE3 WILD-TYPE 480  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      2    0
  POLE3 WILD-TYPE  480   38
   clus
vv  POLE3 MUTATED POLE3 WILD-TYPE
  0             2             480
  1             0              38
[1] 2 2
[1] FALSE
D886V7, binary
                 cls
clus                0   1
  POLE3 MUTATED     1   2
  POLE3 WILD-TYPE 171 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      1    2
  POLE3 WILD-TYPE  171  404
        clus
vv       POLE3 MUTATED POLE3 WILD-TYPE
  FEMALE             1             171
  MALE               2             404
[1] 2 2
[1] FALSE
D886V8, binary
                 cls
clus                0   1
  POLE3 MUTATED     3   0
  POLE3 WILD-TYPE 413 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      3    0
  POLE3 WILD-TYPE  413  102
     clus
vv    POLE3 MUTATED POLE3 WILD-TYPE
  NO              3             413
  YES             0             102
[1] 2 2
[1] FALSE
D886V9, continuous
D886V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  POLE3 MUTATED       1                         1
  POLE3 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POLE3 MUTATED                                           0     1
  POLE3 WILD-TYPE                                         1   356
D886V11, multiclass
                                           clus
vv                                          POLE3 MUTATED POLE3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V12, binary
                 cls
clus                0   1
  POLE3 MUTATED     0   3
  POLE3 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      0    3
  POLE3 WILD-TYPE   10  395
                        clus
vv                       POLE3 MUTATED POLE3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(887) Variable = HGF MUTATION ANALYSIS
D887V1, survival
               sevent
clus2             0   1
  HGF MUTATED    10   6
  HGF WILD-TYPE 328 210
  HGF MUTATED HGF WILD-TYPE 
           16           538 
  HGF MUTATED HGF WILD-TYPE 
            6           210 
$`HGF MUTATED`
TCGA-L5-A4OF TCGA-LN-A4A9 TCGA-BR-6452 TCGA-BR-8297 TCGA-BR-8485 TCGA-CD-5800 
       26.33        11.54        34.68         7.40         9.21        13.15 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A747 
        6.02       105.07        28.96        12.33        18.21         8.38 
TCGA-HU-A4GX TCGA-SW-A7EA TCGA-VQ-AA6K TCGA-ZA-A8F6 
       20.25        19.04        12.43        17.26 

$`HGF WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        26.04        16.14        27.55 

  HGF MUTATED HGF WILD-TYPE 
         6.02          0.00 
  HGF MUTATED HGF WILD-TYPE 
       105.07        122.30 
  HGF MUTATED HGF WILD-TYPE 
       15.205        13.565 
[1] "6.0 - 105.1 (15.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D887V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HGF MUTATED         0        2        4        2         2         2
  HGF WILD-TYPE      10       18       42       29        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HGF MUTATED           0          1          0          4        2         0
  HGF WILD-TYPE        29         83         62         35       41         4
D887V3, multiclass
            clus
vv           HGF MUTATED HGF WILD-TYPE
  STAGE I              0            10
  STAGE IA             2            18
  STAGE IB             4            42
  STAGE II             2            29
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           0            62
  STAGE IIIC           4            35
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  HGF MUTATED       3   6   4   6
  HGF WILD-TYPE    51 129 257  96
D887V4, multiclass
       clus
vv      HGF MUTATED HGF WILD-TYPE
  T0+T1           3            51
  T2              6           129
  T3              4           257
  T4              6            96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  HGF MUTATED     9   5   3   3
  HGF WILD-TYPE 186 168  86  82
D887V5, multiclass
    clus
vv   HGF MUTATED HGF WILD-TYPE
  N0           9           186
  N1           5           168
  N2           3            86
  N3           3            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V6, binary
               cls
clus              0   1
  HGF MUTATED    17   1
  HGF WILD-TYPE 465  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED     17    1
  HGF WILD-TYPE  465   37
   clus
vv  HGF MUTATED HGF WILD-TYPE
  0          17           465
  1           1            37
[1] 2 2
[1] FALSE
D887V7, binary
               cls
clus              0   1
  HGF MUTATED     8  12
  HGF WILD-TYPE 164 394
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED      8   12
  HGF WILD-TYPE  164  394
        clus
vv       HGF MUTATED HGF WILD-TYPE
  FEMALE           8           164
  MALE            12           394
[1] 2 2
[1] FALSE
D887V8, binary
               cls
clus              0   1
  HGF MUTATED    15   2
  HGF WILD-TYPE 401 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED     15    2
  HGF WILD-TYPE  401  100
     clus
vv    HGF MUTATED HGF WILD-TYPE
  NO           15           401
  YES           2           100
[1] 2 2
[1] FALSE
D887V9, continuous
[1] "Remove cluster labels:" "HGF MUTATED"           
clus
  HGF MUTATED HGF WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6    TCGA-LN-A5U7 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"HGF WILD-TYPE" "HGF WILD-TYPE" 
D887V10, continuous
[1] "Remove cluster labels:" "HGF MUTATED"           
clus
  HGF MUTATED HGF WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A4OX    TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A8NF    TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-L5-A8NS    TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A4A6    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" "HGF WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"HGF WILD-TYPE" "HGF WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  HGF MUTATED       4                         0
  HGF WILD-TYPE   129                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HGF MUTATED                                           0    12
  HGF WILD-TYPE                                         1   345
D887V11, multiclass
                                           clus
vv                                          HGF MUTATED HGF WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              12           345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V12, binary
               cls
clus              0   1
  HGF MUTATED     0  14
  HGF WILD-TYPE  10 384
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED      0   14
  HGF WILD-TYPE   10  384
                        clus
vv                       HGF MUTATED HGF WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          14           384
[1] 2 2
[1] FALSE

Clustering(888) Variable = PAM MUTATION ANALYSIS
D888V1, survival
               sevent
clus2             0   1
  PAM MUTATED     5   4
  PAM WILD-TYPE 333 212
  PAM MUTATED PAM WILD-TYPE 
            9           545 
  PAM MUTATED PAM WILD-TYPE 
            4           212 
$`PAM MUTATED`
TCGA-VR-AA7B TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6706 TCGA-BR-8078 TCGA-CG-4465 
       11.24        26.70         6.97        18.05        29.59         9.01 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-VQ-A94T 
       22.68        29.98        11.24 

$`PAM WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        25.61        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PAM MUTATED PAM WILD-TYPE 
         6.97          0.00 
  PAM MUTATED PAM WILD-TYPE 
        29.98        122.30 
  PAM MUTATED PAM WILD-TYPE 
        18.05         13.55 
[1] "7.0 - 30.0 (18.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D888V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAM MUTATED         0        0        0        0         1         3
  PAM WILD-TYPE      10       20       46       31        83        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAM MUTATED           0          2          1          0        2         0
  PAM WILD-TYPE        29         82         61         39       41         4
D888V3, multiclass
            clus
vv           PAM MUTATED PAM WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            1            83
  STAGE IIB            3            80
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           1            61
  STAGE IIIC           0            39
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  PAM MUTATED       0   1   5   3
  PAM WILD-TYPE    54 134 256  99
D888V4, multiclass
       clus
vv      PAM MUTATED PAM WILD-TYPE
  T0+T1           0            54
  T2              1           134
  T3              5           256
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  PAM MUTATED     2   4   1   2
  PAM WILD-TYPE 193 169  88  83
D888V5, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  N0           2           193
  N1           4           169
  N2           1            88
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V6, binary
               cls
clus              0   1
  PAM MUTATED     7   2
  PAM WILD-TYPE 475  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      7    2
  PAM WILD-TYPE  475   36
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           7           475
  1           2            36
[1] 2 2
[1] FALSE
D888V7, binary
               cls
clus              0   1
  PAM MUTATED     6   4
  PAM WILD-TYPE 166 402
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      6    4
  PAM WILD-TYPE  166  402
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           6           166
  MALE             4           402
[1] 2 2
[1] FALSE
D888V8, binary
               cls
clus              0   1
  PAM MUTATED     8   0
  PAM WILD-TYPE 408 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      8    0
  PAM WILD-TYPE  408  102
     clus
vv    PAM MUTATED PAM WILD-TYPE
  NO            8           408
  YES           0           102
[1] 2 2
[1] FALSE
D888V9, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-V5-AASW    TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-VR-A8ER    TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-VR-A8EY    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
D888V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  PAM MUTATED       2                         0
  PAM WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAM MUTATED                                           0     6
  PAM WILD-TYPE                                         1   351
D888V11, multiclass
                                           clus
vv                                          PAM MUTATED PAM WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               6           351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V12, binary
               cls
clus              0   1
  PAM MUTATED     0   7
  PAM WILD-TYPE  10 391
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    7
  PAM WILD-TYPE   10  391
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           7           391
[1] 2 2
[1] FALSE

Clustering(889) Variable = TMEM116 MUTATION ANALYSIS
D889V1, survival
                   sevent
clus2                 0   1
  TMEM116 MUTATED     0   3
  TMEM116 WILD-TYPE 338 213
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               551 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               213 
$`TMEM116 MUTATED`
TCGA-BR-4184 TCGA-BR-A4QL TCGA-VQ-A91U 
        6.97        16.14         1.71 

$`TMEM116 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        15.65        20.81        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TMEM116 MUTATED TMEM116 WILD-TYPE 
             1.71              0.00 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
            16.14            122.30 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
             6.97             13.58 
[1] "1.7 - 16.1 (7.0)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "5.8"
D889V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM116 MUTATED         0        0        0        0         0         0
  TMEM116 WILD-TYPE      10       20       46       31        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM116 MUTATED           0          2          1          0        0
  TMEM116 WILD-TYPE        29         82         61         39       43
                   vv
clus                STAGE IVA
  TMEM116 MUTATED           0
  TMEM116 WILD-TYPE         4
D889V3, multiclass
            clus
vv           TMEM116 MUTATED TMEM116 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM116 MUTATED       0   0   3   0
  TMEM116 WILD-TYPE    54 135 258 102
D889V4, multiclass
       clus
vv      TMEM116 MUTATED TMEM116 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  3               258
  T4                  0               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM116 MUTATED     0   2   0   1
  TMEM116 WILD-TYPE 195 171  89  84
D889V5, multiclass
    clus
vv   TMEM116 MUTATED TMEM116 WILD-TYPE
  N0               0               195
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D889V6, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     2   0
  TMEM116 WILD-TYPE 480  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      2    0
  TMEM116 WILD-TYPE  480   38
   clus
vv  TMEM116 MUTATED TMEM116 WILD-TYPE
  0               2               480
  1               0                38
[1] 2 2
[1] FALSE
D889V7, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     1   2
  TMEM116 WILD-TYPE 171 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      1    2
  TMEM116 WILD-TYPE  171  404
        clus
vv       TMEM116 MUTATED TMEM116 WILD-TYPE
  FEMALE               1               171
  MALE                 2               404
[1] 2 2
[1] FALSE
D889V8, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     3   0
  TMEM116 WILD-TYPE 413 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      3    0
  TMEM116 WILD-TYPE  413  102
     clus
vv    TMEM116 MUTATED TMEM116 WILD-TYPE
  NO                3               413
  YES               0               102
[1] 2 2
[1] FALSE
D889V9, continuous
D889V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM116 MUTATED       1                         0
  TMEM116 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM116 MUTATED                                           0     2
  TMEM116 WILD-TYPE                                         1   355
D889V11, multiclass
                                           clus
vv                                          TMEM116 MUTATED TMEM116 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D889V12, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     0   2
  TMEM116 WILD-TYPE  10 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      0    2
  TMEM116 WILD-TYPE   10  396
                        clus
vv                       TMEM116 MUTATED TMEM116 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               2               396
[1] 2 2
[1] FALSE

Clustering(890) Variable = DNER MUTATION ANALYSIS
D890V1, survival
                sevent
clus2              0   1
  DNER MUTATED    14   4
  DNER WILD-TYPE 324 212
  DNER MUTATED DNER WILD-TYPE 
            18            536 
  DNER MUTATED DNER WILD-TYPE 
             4            212 
$`DNER MUTATED`
TCGA-L5-A4OE TCGA-IC-A6RE TCGA-L5-A4OJ TCGA-L5-A893 TCGA-LN-A5U7 TCGA-R6-A8WC 
       24.00         7.69        21.01         3.02        25.25         2.30 
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-8483 TCGA-CD-5798 TCGA-CD-8530 TCGA-D7-A4YU 
        6.97        18.35         5.39        13.41        12.39        16.44 
TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-IN-A7NU TCGA-RD-A8N1 TCGA-VQ-A8P2 
       77.29        22.68         0.10        11.70       115.69        38.14 

$`DNER WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DNER MUTATED DNER WILD-TYPE 
           0.1            0.0 
  DNER MUTATED DNER WILD-TYPE 
        115.69         122.30 
  DNER MUTATED DNER WILD-TYPE 
        14.925         13.565 
[1] "0.1 - 115.7 (14.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D890V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNER MUTATED         2        0        0        3         1         2
  DNER WILD-TYPE       8       20       46       28        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNER MUTATED           0          3          4          1        0         0
  DNER WILD-TYPE        29         81         58         38       43         4
D890V3, multiclass
            clus
vv           DNER MUTATED DNER WILD-TYPE
  STAGE I               2              8
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              3             28
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            4             58
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DNER MUTATED       3   2   9   2
  DNER WILD-TYPE    51 133 252 100
D890V4, multiclass
       clus
vv      DNER MUTATED DNER WILD-TYPE
  T0+T1            3             51
  T2               2            133
  T3               9            252
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DNER MUTATED     5   6   4   2
  DNER WILD-TYPE 190 167  85  83
D890V5, multiclass
    clus
vv   DNER MUTATED DNER WILD-TYPE
  N0            5            190
  N1            6            167
  N2            4             85
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V6, binary
                cls
clus               0   1
  DNER MUTATED    15   0
  DNER WILD-TYPE 467  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED     15    0
  DNER WILD-TYPE  467   38
   clus
vv  DNER MUTATED DNER WILD-TYPE
  0           15            467
  1            0             38
[1] 2 2
[1] FALSE
D890V7, binary
                cls
clus               0   1
  DNER MUTATED     3  15
  DNER WILD-TYPE 169 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED      3   15
  DNER WILD-TYPE  169  391
        clus
vv       DNER MUTATED DNER WILD-TYPE
  FEMALE            3            169
  MALE             15            391
[1] 2 2
[1] FALSE
D890V8, binary
                cls
clus               0   1
  DNER MUTATED    13   4
  DNER WILD-TYPE 403  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED     13    4
  DNER WILD-TYPE  403   98
     clus
vv    DNER MUTATED DNER WILD-TYPE
  NO            13            403
  YES            4             98
[1] 2 2
[1] FALSE
D890V9, continuous
[1] "Remove cluster labels:" "DNER MUTATED"          
clus
  DNER MUTATED DNER WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A7HV 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"DNER WILD-TYPE" "DNER WILD-TYPE" "DNER WILD-TYPE" 
D890V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DNER MUTATED       5                         0
  DNER WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNER MUTATED                                           0    12
  DNER WILD-TYPE                                         1   345
D890V11, multiclass
                                           clus
vv                                          DNER MUTATED DNER WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V12, binary
                cls
clus               0   1
  DNER MUTATED     0  13
  DNER WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  DNER MUTATED      0   13
  DNER WILD-TYPE   10  385
                        clus
vv                       DNER MUTATED DNER WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(891) Variable = TEX15 MUTATION ANALYSIS
D891V1, survival
                 sevent
clus2               0   1
  TEX15 MUTATED    20   8
  TEX15 WILD-TYPE 318 208
  TEX15 MUTATED TEX15 WILD-TYPE 
             28             526 
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             208 
$`TEX15 MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-2H-A9GL TCGA-IC-A6RE TCGA-L5-A43E 
       21.99        22.98        16.24         5.92         7.69        30.25 
TCGA-LN-A7HX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-XP-A8T7 TCGA-B7-5816 TCGA-BR-6452 
       12.23        18.18        46.19        41.23        26.70        34.68 
TCGA-BR-8060 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4305 
       11.44        31.96        34.98        12.43        11.77        15.95 
TCGA-CG-4462 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN 
        0.00        11.44        14.47        22.32        22.68        29.98 
TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA68 
       23.84        19.73        38.14        43.66 

$`TEX15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX 
       27.12         5.16        20.02        47.05        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TEX15 MUTATED TEX15 WILD-TYPE 
            0.0             0.1 
  TEX15 MUTATED TEX15 WILD-TYPE 
          46.19          122.30 
  TEX15 MUTATED TEX15 WILD-TYPE 
         22.155          13.410 
[1] "0.0 - 46.2 (22.2)"  "0.1 - 122.3 (13.4)"
[1] "hr=" "1.8"
D891V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TEX15 MUTATED         1        0        2        2         5         9
  TEX15 WILD-TYPE       9       20       44       29        79        74
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX15 MUTATED           1          5          2          2        3         0
  TEX15 WILD-TYPE        28         79         60         37       40         4
D891V3, multiclass
            clus
vv           TEX15 MUTATED TEX15 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              5              79
  STAGE IIB              9              74
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TEX15 MUTATED       3   9  11  10
  TEX15 WILD-TYPE    51 126 250  92
D891V4, multiclass
       clus
vv      TEX15 MUTATED TEX15 WILD-TYPE
  T0+T1             3              51
  T2                9             126
  T3               11             250
  T4               10              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TEX15 MUTATED    12  12   4   4
  TEX15 WILD-TYPE 183 161  85  81
D891V5, multiclass
    clus
vv   TEX15 MUTATED TEX15 WILD-TYPE
  N0            12             183
  N1            12             161
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V6, binary
                 cls
clus                0   1
  TEX15 MUTATED    29   3
  TEX15 WILD-TYPE 453  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     29    3
  TEX15 WILD-TYPE  453   35
   clus
vv  TEX15 MUTATED TEX15 WILD-TYPE
  0            29             453
  1             3              35
[1] 2 2
[1] FALSE
D891V7, binary
                 cls
clus                0   1
  TEX15 MUTATED    16  18
  TEX15 WILD-TYPE 156 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     16   18
  TEX15 WILD-TYPE  156  388
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  FEMALE            16             156
  MALE              18             388
[1] 2 2
[1] FALSE
D891V8, binary
                 cls
clus                0   1
  TEX15 MUTATED    23   6
  TEX15 WILD-TYPE 393  96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     23    6
  TEX15 WILD-TYPE  393   96
     clus
vv    TEX15 MUTATED TEX15 WILD-TYPE
  NO             23             393
  YES             6              96
[1] 2 2
[1] FALSE
D891V9, continuous
D891V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TEX15 MUTATED       8                         0
  TEX15 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TEX15 MUTATED                                           0    20
  TEX15 WILD-TYPE                                         1   337
D891V11, multiclass
                                           clus
vv                                          TEX15 MUTATED TEX15 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                20             337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V12, binary
                 cls
clus                0   1
  TEX15 MUTATED     1  22
  TEX15 WILD-TYPE   9 376
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED      1   22
  TEX15 WILD-TYPE    9  376
                        clus
vv                       TEX15 MUTATED TEX15 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            22             376
[1] 2 2
[1] FALSE

Clustering(892) Variable = C1ORF63 MUTATION ANALYSIS
D892V1, survival
                   sevent
clus2                 0   1
  C1ORF63 MUTATED     2   1
  C1ORF63 WILD-TYPE 336 215
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
                3               551 
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
                1               215 
$`C1ORF63 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NF TCGA-BR-8081 
       19.99         2.66        32.25 

$`C1ORF63 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
             2.66              0.00 
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
            32.25            122.30 
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
            19.99             13.55 
[1] "2.7 - 32.2 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D892V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF63 MUTATED         0        0        0        0         0         1
  C1ORF63 WILD-TYPE      10       20       46       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF63 MUTATED           0          0          0          1        0
  C1ORF63 WILD-TYPE        29         84         62         38       43
                   vv
clus                STAGE IVA
  C1ORF63 MUTATED           1
  C1ORF63 WILD-TYPE         3
D892V3, multiclass
            clus
vv           C1ORF63 MUTATED C1ORF63 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C1ORF63 MUTATED       1   0   1   1
  C1ORF63 WILD-TYPE    53 135 260 101
D892V4, multiclass
       clus
vv      C1ORF63 MUTATED C1ORF63 WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  1               260
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C1ORF63 MUTATED     2   0   0   1
  C1ORF63 WILD-TYPE 193 173  89  84
D892V5, multiclass
    clus
vv   C1ORF63 MUTATED C1ORF63 WILD-TYPE
  N0               2               193
  N1               0               173
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V6, binary
                   cls
clus                  0   1
  C1ORF63 MUTATED     1   1
  C1ORF63 WILD-TYPE 481  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF63 MUTATED      1    1
  C1ORF63 WILD-TYPE  481   37
   clus
vv  C1ORF63 MUTATED C1ORF63 WILD-TYPE
  0               1               481
  1               1                37
[1] 2 2
[1] FALSE
D892V7, binary
                   cls
clus                  0   1
  C1ORF63 MUTATED     1   2
  C1ORF63 WILD-TYPE 171 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF63 MUTATED      1    2
  C1ORF63 WILD-TYPE  171  404
        clus
vv       C1ORF63 MUTATED C1ORF63 WILD-TYPE
  FEMALE               1               171
  MALE                 2               404
[1] 2 2
[1] FALSE
D892V8, binary
                   cls
clus                  0   1
  C1ORF63 MUTATED     3   0
  C1ORF63 WILD-TYPE 413 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF63 MUTATED      3    0
  C1ORF63 WILD-TYPE  413  102
     clus
vv    C1ORF63 MUTATED C1ORF63 WILD-TYPE
  NO                3               413
  YES               0               102
[1] 2 2
[1] FALSE
D892V9, continuous
D892V10, continuous
[1] "Remove cluster labels:" "C1ORF63 MUTATED"       
clus
  C1ORF63 MUTATED C1ORF63 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" "C1ORF63 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF63 MUTATED       0                         0
  C1ORF63 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF63 MUTATED                                           0     3
  C1ORF63 WILD-TYPE                                         1   354
D892V11, multiclass
                                           clus
vv                                          C1ORF63 MUTATED C1ORF63 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V12, binary
                   cls
clus                  0   1
  C1ORF63 MUTATED     0   1
  C1ORF63 WILD-TYPE  10 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF63 MUTATED      0    1
  C1ORF63 WILD-TYPE   10  397
                        clus
vv                       C1ORF63 MUTATED C1ORF63 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               1               397
[1] 2 2
[1] FALSE

Clustering(893) Variable = FOLH1 MUTATION ANALYSIS
D893V1, survival
                 sevent
clus2               0   1
  FOLH1 MUTATED    12  10
  FOLH1 WILD-TYPE 326 206
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             22             532 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
             10             206 
$`FOLH1 MUTATED`
TCGA-L5-A43I TCGA-L5-A4OG TCGA-2H-A9GI TCGA-2H-A9GR TCGA-L5-A4OW TCGA-L5-A8NM 
       18.28         4.70        14.30        32.45         7.13         7.76 
TCGA-L5-A8NQ TCGA-LN-A49M TCGA-LN-A49U TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8060 
       21.37        12.66        15.35         6.97        34.68        11.44 
TCGA-BR-8284 TCGA-BR-8370 TCGA-BR-A4PD TCGA-CD-A487 TCGA-CG-5721 TCGA-CG-5728 
        8.05         3.32        20.65        12.30         6.02        65.10 
TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GQ 
       14.47        30.51        22.68         0.10 

$`FOLH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.55        13.22         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        13.15        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  FOLH1 MUTATED FOLH1 WILD-TYPE 
            0.1             0.0 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
           65.1           122.3 
  FOLH1 MUTATED FOLH1 WILD-TYPE 
         13.480          13.565 
[1] "0.1 - 65.1 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D893V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FOLH1 MUTATED         1        0        3        0         5         6
  FOLH1 WILD-TYPE       9       20       43       31        79        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOLH1 MUTATED           1          3          1          3        1         0
  FOLH1 WILD-TYPE        28         81         61         36       42         4
D893V3, multiclass
            clus
vv           FOLH1 MUTATED FOLH1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FOLH1 MUTATED       1   8   9   6
  FOLH1 WILD-TYPE    53 127 252  96
D893V4, multiclass
       clus
vv      FOLH1 MUTATED FOLH1 WILD-TYPE
  T0+T1             1              53
  T2                8             127
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FOLH1 MUTATED    11   8   2   3
  FOLH1 WILD-TYPE 184 165  87  82
D893V5, multiclass
    clus
vv   FOLH1 MUTATED FOLH1 WILD-TYPE
  N0            11             184
  N1             8             165
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V6, binary
                 cls
clus                0   1
  FOLH1 MUTATED    22   0
  FOLH1 WILD-TYPE 460  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     22    0
  FOLH1 WILD-TYPE  460   38
   clus
vv  FOLH1 MUTATED FOLH1 WILD-TYPE
  0            22             460
  1             0              38
[1] 2 2
[1] FALSE
D893V7, binary
                 cls
clus                0   1
  FOLH1 MUTATED    11  13
  FOLH1 WILD-TYPE 161 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     11   13
  FOLH1 WILD-TYPE  161  393
        clus
vv       FOLH1 MUTATED FOLH1 WILD-TYPE
  FEMALE            11             161
  MALE              13             393
[1] 2 2
[1] FALSE
D893V8, binary
                 cls
clus                0   1
  FOLH1 MUTATED    17   4
  FOLH1 WILD-TYPE 399  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED     17    4
  FOLH1 WILD-TYPE  399   98
     clus
vv    FOLH1 MUTATED FOLH1 WILD-TYPE
  NO             17             399
  YES             4              98
[1] 2 2
[1] FALSE
D893V9, continuous
[1] "Remove cluster labels:" "FOLH1 MUTATED"         
clus
  FOLH1 MUTATED FOLH1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A49X 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2      TCGA-LN-A4A3 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"FOLH1 WILD-TYPE" "FOLH1 WILD-TYPE" 
D893V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FOLH1 MUTATED       5                         0
  FOLH1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FOLH1 MUTATED                                           0    12
  FOLH1 WILD-TYPE                                         1   345
D893V11, multiclass
                                           clus
vv                                          FOLH1 MUTATED FOLH1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V12, binary
                 cls
clus                0   1
  FOLH1 MUTATED     0  13
  FOLH1 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOLH1 MUTATED      0   13
  FOLH1 WILD-TYPE   10  385
                        clus
vv                       FOLH1 MUTATED FOLH1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(894) Variable = MOCS2 MUTATION ANALYSIS
D894V1, survival
                 sevent
clus2               0   1
  MOCS2 MUTATED     4   3
  MOCS2 WILD-TYPE 334 213
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              7             547 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              3             213 
$`MOCS2 MUTATED`
TCGA-L5-A8NM TCGA-LN-A9FO TCGA-V5-AASX TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-8361 
        7.76         0.13         8.98        18.35        30.90        31.10 
TCGA-HF-7132 
       77.29 

$`MOCS2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        4.64         7.43         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MOCS2 MUTATED MOCS2 WILD-TYPE 
           0.13            0.00 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          77.29          122.30 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          18.35           13.55 
[1] "0.1 - 77.3 (18.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D894V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MOCS2 MUTATED         0        0        0        1         1         1
  MOCS2 WILD-TYPE      10       20       46       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MOCS2 MUTATED           0          0          0          1        1         0
  MOCS2 WILD-TYPE        29         84         62         38       42         4
D894V3, multiclass
            clus
vv           MOCS2 MUTATED MOCS2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MOCS2 MUTATED       0   4   0   2
  MOCS2 WILD-TYPE    54 131 261 100
D894V4, multiclass
       clus
vv      MOCS2 MUTATED MOCS2 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                0             261
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MOCS2 MUTATED     1   3   2   0
  MOCS2 WILD-TYPE 194 170  87  85
D894V5, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  N0             1             194
  N1             3             170
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V6, binary
                 cls
clus                0   1
  MOCS2 MUTATED     7   0
  MOCS2 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      7    0
  MOCS2 WILD-TYPE  475   38
   clus
vv  MOCS2 MUTATED MOCS2 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D894V7, binary
                 cls
clus                0   1
  MOCS2 MUTATED     4   4
  MOCS2 WILD-TYPE 168 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      4    4
  MOCS2 WILD-TYPE  168  402
        clus
vv       MOCS2 MUTATED MOCS2 WILD-TYPE
  FEMALE             4             168
  MALE               4             402
[1] 2 2
[1] FALSE
D894V8, binary
                 cls
clus                0   1
  MOCS2 MUTATED     5   1
  MOCS2 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      5    1
  MOCS2 WILD-TYPE  411  101
     clus
vv    MOCS2 MUTATED MOCS2 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D894V9, continuous
[1] "Remove cluster labels:" "MOCS2 MUTATED"         
clus
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" "MOCS2 WILD-TYPE" 
D894V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MOCS2 MUTATED       1                         0
  MOCS2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MOCS2 MUTATED                                           0     6
  MOCS2 WILD-TYPE                                         1   351
D894V11, multiclass
                                           clus
vv                                          MOCS2 MUTATED MOCS2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V12, binary
                 cls
clus                0   1
  MOCS2 MUTATED     0   6
  MOCS2 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      0    6
  MOCS2 WILD-TYPE   10  392
                        clus
vv                       MOCS2 MUTATED MOCS2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(895) Variable = MICALL1 MUTATION ANALYSIS
D895V1, survival
                   sevent
clus2                 0   1
  MICALL1 MUTATED     7   3
  MICALL1 WILD-TYPE 331 213
  MICALL1 MUTATED MICALL1 WILD-TYPE 
               10               544 
  MICALL1 MUTATED MICALL1 WILD-TYPE 
                3               213 
$`MICALL1 MUTATED`
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-VR-A8ER TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-8483 
       10.36        10.45        12.43         2.10        11.01         5.39 
TCGA-BR-8591 TCGA-D7-A4YT TCGA-HU-A4GX TCGA-IN-7808 
       28.14        14.27        20.25         3.45 

$`MICALL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
       83.24        52.57        46.09        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40        36.36        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MICALL1 MUTATED MICALL1 WILD-TYPE 
              2.1               0.0 
  MICALL1 MUTATED MICALL1 WILD-TYPE 
            28.14            122.30 
  MICALL1 MUTATED MICALL1 WILD-TYPE 
            10.73             13.73 
[1] "2.1 - 28.1 (10.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D895V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MICALL1 MUTATED         0        0        0        0         1         1
  MICALL1 WILD-TYPE      10       20       46       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICALL1 MUTATED           1          3          0          3        0
  MICALL1 WILD-TYPE        28         81         62         36       43
                   vv
clus                STAGE IVA
  MICALL1 MUTATED           0
  MICALL1 WILD-TYPE         4
D895V3, multiclass
            clus
vv           MICALL1 MUTATED MICALL1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  MICALL1 MUTATED       0   2   4   4
  MICALL1 WILD-TYPE    54 133 257  98
D895V4, multiclass
       clus
vv      MICALL1 MUTATED MICALL1 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  4               257
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  MICALL1 MUTATED     1   2   2   4
  MICALL1 WILD-TYPE 194 171  87  81
D895V5, multiclass
    clus
vv   MICALL1 MUTATED MICALL1 WILD-TYPE
  N0               1               194
  N1               2               171
  N2               2                87
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V6, binary
                   cls
clus                  0   1
  MICALL1 MUTATED     8   1
  MICALL1 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALL1 MUTATED      8    1
  MICALL1 WILD-TYPE  474   37
   clus
vv  MICALL1 MUTATED MICALL1 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D895V7, binary
                   cls
clus                  0   1
  MICALL1 MUTATED     1   9
  MICALL1 WILD-TYPE 171 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALL1 MUTATED      1    9
  MICALL1 WILD-TYPE  171  397
        clus
vv       MICALL1 MUTATED MICALL1 WILD-TYPE
  FEMALE               1               171
  MALE                 9               397
[1] 2 2
[1] FALSE
D895V8, binary
                   cls
clus                  0   1
  MICALL1 MUTATED     7   3
  MICALL1 WILD-TYPE 409  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALL1 MUTATED      7    3
  MICALL1 WILD-TYPE  409   99
     clus
vv    MICALL1 MUTATED MICALL1 WILD-TYPE
  NO                7               409
  YES               3                99
[1] 2 2
[1] FALSE
D895V9, continuous
D895V10, continuous
[1] "Remove cluster labels:" "MICALL1 MUTATED"       
clus
  MICALL1 MUTATED MICALL1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" "MICALL1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"MICALL1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MICALL1 MUTATED       2                         0
  MICALL1 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MICALL1 MUTATED                                           0     7
  MICALL1 WILD-TYPE                                         1   350
D895V11, multiclass
                                           clus
vv                                          MICALL1 MUTATED MICALL1 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V12, binary
                   cls
clus                  0   1
  MICALL1 MUTATED     0   9
  MICALL1 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALL1 MUTATED      0    9
  MICALL1 WILD-TYPE   10  389
                        clus
vv                       MICALL1 MUTATED MICALL1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(896) Variable = CLCA4 MUTATION ANALYSIS
D896V1, survival
                 sevent
clus2               0   1
  CLCA4 MUTATED     9   9
  CLCA4 WILD-TYPE 329 207
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             18             536 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
              9             207 
$`CLCA4 MUTATED`
TCGA-IG-A7DP TCGA-JY-A6FE TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 
       14.86         3.68        26.70        30.90         6.61        34.68 
TCGA-BR-7704 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8382 TCGA-CD-8528 TCGA-CG-5717 
       35.24        31.10         0.26        25.05        12.33         6.97 
TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-FP-A4BE TCGA-VQ-A8P2 TCGA-VQ-A8PE 
      105.07         5.92        11.44        11.08        38.14        22.19 

$`CLCA4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CLCA4 MUTATED CLCA4 WILD-TYPE 
           0.26            0.00 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
         105.07          122.30 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
         18.525          13.530 
[1] "0.3 - 105.1 (18.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D896V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLCA4 MUTATED         0        0        1        3         2         2
  CLCA4 WILD-TYPE      10       20       45       28        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLCA4 MUTATED           2          3          2          2        0         0
  CLCA4 WILD-TYPE        27         81         60         37       43         4
D896V3, multiclass
            clus
vv           CLCA4 MUTATED CLCA4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CLCA4 MUTATED       0   5   7   6
  CLCA4 WILD-TYPE    54 130 254  96
D896V4, multiclass
       clus
vv      CLCA4 MUTATED CLCA4 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3                7             254
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CLCA4 MUTATED     6   7   1   3
  CLCA4 WILD-TYPE 189 166  88  82
D896V5, multiclass
    clus
vv   CLCA4 MUTATED CLCA4 WILD-TYPE
  N0             6             189
  N1             7             166
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V6, binary
                 cls
clus                0   1
  CLCA4 MUTATED    18   0
  CLCA4 WILD-TYPE 464  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     18    0
  CLCA4 WILD-TYPE  464   38
   clus
vv  CLCA4 MUTATED CLCA4 WILD-TYPE
  0            18             464
  1             0              38
[1] 2 2
[1] FALSE
D896V7, binary
                 cls
clus                0   1
  CLCA4 MUTATED    13   6
  CLCA4 WILD-TYPE 159 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     13    6
  CLCA4 WILD-TYPE  159  400
        clus
vv       CLCA4 MUTATED CLCA4 WILD-TYPE
  FEMALE            13             159
  MALE               6             400
[1] 2 2
[1] FALSE
D896V8, binary
                 cls
clus                0   1
  CLCA4 MUTATED    15   3
  CLCA4 WILD-TYPE 401  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     15    3
  CLCA4 WILD-TYPE  401   99
     clus
vv    CLCA4 MUTATED CLCA4 WILD-TYPE
  NO             15             401
  YES             3              99
[1] 2 2
[1] FALSE
D896V9, continuous
[1] "Remove cluster labels:" "CLCA4 MUTATED"         
clus
  CLCA4 MUTATED CLCA4 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
D896V10, continuous
[1] "Remove cluster labels:" "CLCA4 MUTATED"         
clus
  CLCA4 MUTATED CLCA4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" "CLCA4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CLCA4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CLCA4 MUTATED       1                         1
  CLCA4 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLCA4 MUTATED                                           0    15
  CLCA4 WILD-TYPE                                         1   342
D896V11, multiclass
                                           clus
vv                                          CLCA4 MUTATED CLCA4 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V12, binary
                 cls
clus                0   1
  CLCA4 MUTATED     0  14
  CLCA4 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED      0   14
  CLCA4 WILD-TYPE   10  384
                        clus
vv                       CLCA4 MUTATED CLCA4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(897) Variable = SMO MUTATION ANALYSIS
D897V1, survival
               sevent
clus2             0   1
  SMO MUTATED    14   4
  SMO WILD-TYPE 324 212
  SMO MUTATED SMO WILD-TYPE 
           18           536 
  SMO MUTATED SMO WILD-TYPE 
            4           212 
$`SMO MUTATED`
TCGA-IC-A6RF TCGA-CG-5727 TCGA-2H-A9GG TCGA-2H-A9GN TCGA-L5-A891 TCGA-BR-6452 
       15.68        79.07        20.05         8.94         3.75        34.68 
TCGA-BR-8078 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-CG-4306 
       29.59         9.21         1.12        12.79        31.96         1.02 
TCGA-CG-5723 TCGA-HF-7134 TCGA-HU-A4GX TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
      105.07        52.21        20.25        43.36        37.22        22.19 

$`SMO WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO 
        5.16        20.02        47.05        21.99        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.25        13.02        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       38.14        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SMO MUTATED SMO WILD-TYPE 
         1.02          0.00 
  SMO MUTATED SMO WILD-TYPE 
       105.07        122.30 
  SMO MUTATED SMO WILD-TYPE 
       21.220        13.495 
[1] "1.0 - 105.1 (21.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.6"
D897V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMO MUTATED         0        2        0        2         2         2
  SMO WILD-TYPE      10       18       46       29        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMO MUTATED           2          1          2          2        2         0
  SMO WILD-TYPE        27         83         60         37       41         4
D897V3, multiclass
            clus
vv           SMO MUTATED SMO WILD-TYPE
  STAGE I              0            10
  STAGE IA             2            18
  STAGE IB             0            46
  STAGE II             2            29
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            2            27
  STAGE IIIA           1            83
  STAGE IIIB           2            60
  STAGE IIIC           2            37
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  SMO MUTATED       2   1   9   6
  SMO WILD-TYPE    52 134 252  96
D897V4, multiclass
       clus
vv      SMO MUTATED SMO WILD-TYPE
  T0+T1           2            52
  T2              1           134
  T3              9           252
  T4              6            96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SMO MUTATED     7   5   4   2
  SMO WILD-TYPE 188 168  85  83
D897V5, multiclass
    clus
vv   SMO MUTATED SMO WILD-TYPE
  N0           7           188
  N1           5           168
  N2           4            85
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V6, binary
               cls
clus              0   1
  SMO MUTATED    16   2
  SMO WILD-TYPE 466  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED     16    2
  SMO WILD-TYPE  466   36
   clus
vv  SMO MUTATED SMO WILD-TYPE
  0          16           466
  1           2            36
[1] 2 2
[1] FALSE
D897V7, binary
               cls
clus              0   1
  SMO MUTATED     7  11
  SMO WILD-TYPE 165 395
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED      7   11
  SMO WILD-TYPE  165  395
        clus
vv       SMO MUTATED SMO WILD-TYPE
  FEMALE           7           165
  MALE            11           395
[1] 2 2
[1] FALSE
D897V8, binary
               cls
clus              0   1
  SMO MUTATED    14   2
  SMO WILD-TYPE 402 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED     14    2
  SMO WILD-TYPE  402  100
     clus
vv    SMO MUTATED SMO WILD-TYPE
  NO           14           402
  YES           2           100
[1] 2 2
[1] FALSE
D897V9, continuous
D897V10, continuous
[1] "Remove cluster labels:" "SMO MUTATED"           
clus
  SMO MUTATED SMO WILD-TYPE 
            1            97 
   TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG    TCGA-L5-A4OI 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" "SMO WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"SMO WILD-TYPE" "SMO WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  SMO MUTATED       3                         0
  SMO WILD-TYPE   130                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMO MUTATED                                           0     9
  SMO WILD-TYPE                                         1   348
D897V11, multiclass
                                           clus
vv                                          SMO MUTATED SMO WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               9           348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V12, binary
               cls
clus              0   1
  SMO MUTATED     0   8
  SMO WILD-TYPE  10 390
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED      0    8
  SMO WILD-TYPE   10  390
                        clus
vv                       SMO MUTATED SMO WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           8           390
[1] 2 2
[1] FALSE

Clustering(898) Variable = MSL1 MUTATION ANALYSIS
D898V1, survival
                sevent
clus2              0   1
  MSL1 MUTATED     4   3
  MSL1 WILD-TYPE 334 213
  MSL1 MUTATED MSL1 WILD-TYPE 
             7            547 
  MSL1 MUTATED MSL1 WILD-TYPE 
             3            213 
$`MSL1 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OO TCGA-L5-A8NM TCGA-BR-4201 TCGA-D7-A6EX TCGA-HU-A4G8 
       21.99         3.32         7.76        30.90        11.31        22.68 
TCGA-HU-A4H5 
       23.80 

$`MSL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MSL1 MUTATED MSL1 WILD-TYPE 
          3.32           0.00 
  MSL1 MUTATED MSL1 WILD-TYPE 
          30.9          122.3 
  MSL1 MUTATED MSL1 WILD-TYPE 
         21.99          13.55 
[1] "3.3 - 30.9 (22.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D898V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MSL1 MUTATED         0        0        1        0         0         2
  MSL1 WILD-TYPE      10       20       45       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSL1 MUTATED           0          1          0          1        1         0
  MSL1 WILD-TYPE        29         83         62         38       42         4
D898V3, multiclass
            clus
vv           MSL1 MUTATED MSL1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MSL1 MUTATED       0   3   3   1
  MSL1 WILD-TYPE    54 132 258 101
D898V4, multiclass
       clus
vv      MSL1 MUTATED MSL1 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MSL1 MUTATED     1   3   1   1
  MSL1 WILD-TYPE 194 170  88  84
D898V5, multiclass
    clus
vv   MSL1 MUTATED MSL1 WILD-TYPE
  N0            1            194
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V6, binary
                cls
clus               0   1
  MSL1 MUTATED     6   1
  MSL1 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL1 MUTATED      6    1
  MSL1 WILD-TYPE  476   37
   clus
vv  MSL1 MUTATED MSL1 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D898V7, binary
                cls
clus               0   1
  MSL1 MUTATED     5   2
  MSL1 WILD-TYPE 167 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL1 MUTATED      5    2
  MSL1 WILD-TYPE  167  404
        clus
vv       MSL1 MUTATED MSL1 WILD-TYPE
  FEMALE            5            167
  MALE              2            404
[1] 2 2
[1] FALSE
D898V8, binary
                cls
clus               0   1
  MSL1 MUTATED     6   0
  MSL1 WILD-TYPE 410 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL1 MUTATED      6    0
  MSL1 WILD-TYPE  410  102
     clus
vv    MSL1 MUTATED MSL1 WILD-TYPE
  NO             6            410
  YES            0            102
[1] 2 2
[1] FALSE
D898V9, continuous
D898V10, continuous
[1] "Remove cluster labels:" "MSL1 MUTATED"          
clus
  MSL1 MUTATED MSL1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" "MSL1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"MSL1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MSL1 MUTATED       2                         0
  MSL1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSL1 MUTATED                                           0     4
  MSL1 WILD-TYPE                                         1   353
D898V11, multiclass
                                           clus
vv                                          MSL1 MUTATED MSL1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V12, binary
                cls
clus               0   1
  MSL1 MUTATED     0   4
  MSL1 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL1 MUTATED      0    4
  MSL1 WILD-TYPE   10  394
                        clus
vv                       MSL1 MUTATED MSL1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(899) Variable = IRS4 MUTATION ANALYSIS
D899V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    16   8
  IRS4 WILD-TYPE 322 208
  IRS4 MUTATED IRS4 WILD-TYPE 
            24            530 
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            208 
$`IRS4 MUTATED`
TCGA-L5-A8NM TCGA-R6-A6L6 TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-B7-5818 TCGA-BR-4257 
        7.76         7.04         8.12        52.27        11.70         9.67 
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-5723 TCGA-CG-5733 
       34.68        35.84        25.05        31.96       105.07        21.07 
TCGA-D7-6526 TCGA-FP-7998 TCGA-HU-8602 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       17.19        22.29        22.32         8.98         0.10         6.51 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-IN-A6RJ TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
        2.10        29.00        12.46        19.73         5.46        38.14 

$`IRS4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        14.07        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58        20.25         0.26        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  IRS4 MUTATED IRS4 WILD-TYPE 
           0.1            0.0 
  IRS4 MUTATED IRS4 WILD-TYPE 
        105.07         122.30 
  IRS4 MUTATED IRS4 WILD-TYPE 
         18.46          13.53 
[1] "0.1 - 105.1 (18.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D899V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS4 MUTATED         0        1        2        1         3         2
  IRS4 WILD-TYPE      10       19       44       30        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRS4 MUTATED           0          7          1          6        1         0
  IRS4 WILD-TYPE        29         77         61         33       42         4
D899V3, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            7             77
  STAGE IIIB            1             61
  STAGE IIIC            6             33
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IRS4 MUTATED       2   6   7  10
  IRS4 WILD-TYPE    52 129 254  92
D899V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T0+T1            2             52
  T2               6            129
  T3               7            254
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IRS4 MUTATED     7   6   7   5
  IRS4 WILD-TYPE 188 167  82  80
D899V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            7            188
  N1            6            167
  N2            7             82
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V6, binary
                cls
clus               0   1
  IRS4 MUTATED    25   1
  IRS4 WILD-TYPE 457  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     25    1
  IRS4 WILD-TYPE  457   37
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           25            457
  1            1             37
[1] 2 2
[1] FALSE
D899V7, binary
                cls
clus               0   1
  IRS4 MUTATED    16  12
  IRS4 WILD-TYPE 156 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     16   12
  IRS4 WILD-TYPE  156  394
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           16            156
  MALE             12            394
[1] 2 2
[1] FALSE
D899V8, binary
                cls
clus               0   1
  IRS4 MUTATED    23   1
  IRS4 WILD-TYPE 393 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     23    1
  IRS4 WILD-TYPE  393  101
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO            23            393
  YES            1            101
[1] 2 2
[1] FALSE
D899V9, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
D899V10, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRS4 MUTATED       8                         0
  IRS4 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRS4 MUTATED                                           0    18
  IRS4 WILD-TYPE                                         1   339
D899V11, multiclass
                                           clus
vv                                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V12, binary
                cls
clus               0   1
  IRS4 MUTATED     1  20
  IRS4 WILD-TYPE   9 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1   20
  IRS4 WILD-TYPE    9  378
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           20            378
[1] 2 2
[1] FALSE

Clustering(900) Variable = AARS2 MUTATION ANALYSIS
D900V1, survival
                 sevent
clus2               0   1
  AARS2 MUTATED    13   8
  AARS2 WILD-TYPE 325 208
  AARS2 MUTATED AARS2 WILD-TYPE 
             21             533 
  AARS2 MUTATED AARS2 WILD-TYPE 
              8             208 
$`AARS2 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NM TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-AASV TCGA-X8-AAAR 
        4.31         7.76         2.89         2.30        15.35        18.21 
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8690 
       26.70        34.68        31.10         1.12        27.12        10.68 
TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4441 TCGA-CG-5723 TCGA-D7-A6EY 
       12.89        16.14         6.58        14.01       105.07        11.44 
TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-RD-A8MW 
       20.25        74.53        37.91 

$`AARS2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
       38.40         6.35        53.95         9.30        15.78        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        1.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  AARS2 MUTATED AARS2 WILD-TYPE 
           1.12            0.00 
  AARS2 MUTATED AARS2 WILD-TYPE 
         105.07          122.30 
  AARS2 MUTATED AARS2 WILD-TYPE 
          15.35           13.51 
[1] "1.1 - 105.1 (15.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D900V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AARS2 MUTATED         0        0        0        1         3         5
  AARS2 WILD-TYPE      10       20       46       30        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AARS2 MUTATED           0          1          5          2        1         0
  AARS2 WILD-TYPE        29         83         57         37       42         4
D900V3, multiclass
            clus
vv           AARS2 MUTATED AARS2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             5              57
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AARS2 MUTATED       1   3   9   6
  AARS2 WILD-TYPE    53 132 252  96
D900V4, multiclass
       clus
vv      AARS2 MUTATED AARS2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AARS2 MUTATED     7   5   4   3
  AARS2 WILD-TYPE 188 168  85  82
D900V5, multiclass
    clus
vv   AARS2 MUTATED AARS2 WILD-TYPE
  N0             7             188
  N1             5             168
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V6, binary
                 cls
clus                0   1
  AARS2 MUTATED    15   1
  AARS2 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED     15    1
  AARS2 WILD-TYPE  467   37
   clus
vv  AARS2 MUTATED AARS2 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D900V7, binary
                 cls
clus                0   1
  AARS2 MUTATED    10  11
  AARS2 WILD-TYPE 162 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED     10   11
  AARS2 WILD-TYPE  162  395
        clus
vv       AARS2 MUTATED AARS2 WILD-TYPE
  FEMALE            10             162
  MALE              11             395
[1] 2 2
[1] FALSE
D900V8, binary
                 cls
clus                0   1
  AARS2 MUTATED    16   2
  AARS2 WILD-TYPE 400 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED     16    2
  AARS2 WILD-TYPE  400  100
     clus
vv    AARS2 MUTATED AARS2 WILD-TYPE
  NO             16             400
  YES             2             100
[1] 2 2
[1] FALSE
D900V9, continuous
[1] "Remove cluster labels:" "AARS2 MUTATED"         
clus
  AARS2 MUTATED AARS2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"AARS2 WILD-TYPE" "AARS2 WILD-TYPE" "AARS2 WILD-TYPE" 
D900V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AARS2 MUTATED       3                         1
  AARS2 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AARS2 MUTATED                                           0    15
  AARS2 WILD-TYPE                                         1   342
D900V11, multiclass
                                           clus
vv                                          AARS2 MUTATED AARS2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V12, binary
                 cls
clus                0   1
  AARS2 MUTATED     1  16
  AARS2 WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      1   16
  AARS2 WILD-TYPE    9  382
                        clus
vv                       AARS2 MUTATED AARS2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(901) Variable = DDHD1 MUTATION ANALYSIS
D901V1, survival
                 sevent
clus2               0   1
  DDHD1 MUTATED     9   5
  DDHD1 WILD-TYPE 329 211
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             14             540 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              5             211 
$`DDHD1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A625 TCGA-L5-A8NM TCGA-LN-A7HZ TCGA-B7-5818 TCGA-BR-4184 
       19.99        12.82         7.76        13.18        11.70         6.97 
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8081 TCGA-CG-4438 TCGA-D7-A6EY TCGA-F1-6874 
       30.90        34.68        32.25        54.08        11.44        14.47 
TCGA-F1-A448 TCGA-HU-A4G8 
       21.27        22.68 

$`DDHD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DDHD1 MUTATED DDHD1 WILD-TYPE 
           6.97            0.00 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          54.08          122.30 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          17.23           13.53 
[1] "7.0 - 54.1 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D901V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDHD1 MUTATED         0        0        2        0         2         4
  DDHD1 WILD-TYPE      10       20       44       31        82        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDHD1 MUTATED           0          2          3          1        2         0
  DDHD1 WILD-TYPE        29         82         59         38       41         4
D901V3, multiclass
            clus
vv           DDHD1 MUTATED DDHD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DDHD1 MUTATED       0   5   7   5
  DDHD1 WILD-TYPE    54 130 254  97
D901V4, multiclass
       clus
vv      DDHD1 MUTATED DDHD1 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DDHD1 MUTATED     7   3   3   3
  DDHD1 WILD-TYPE 188 170  86  82
D901V5, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  N0             7             188
  N1             3             170
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V6, binary
                 cls
clus                0   1
  DDHD1 MUTATED    15   0
  DDHD1 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED     15    0
  DDHD1 WILD-TYPE  467   38
   clus
vv  DDHD1 MUTATED DDHD1 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D901V7, binary
                 cls
clus                0   1
  DDHD1 MUTATED     8   9
  DDHD1 WILD-TYPE 164 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      8    9
  DDHD1 WILD-TYPE  164  397
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  FEMALE             8             164
  MALE               9             397
[1] 2 2
[1] FALSE
D901V8, binary
                 cls
clus                0   1
  DDHD1 MUTATED    12   1
  DDHD1 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED     12    1
  DDHD1 WILD-TYPE  404  101
     clus
vv    DDHD1 MUTATED DDHD1 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D901V9, continuous
[1] "Remove cluster labels:" "DDHD1 MUTATED"         
clus
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
D901V10, continuous
[1] "Remove cluster labels:" "DDHD1 MUTATED"         
clus
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" "DDHD1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDHD1 MUTATED       3                         0
  DDHD1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDHD1 MUTATED                                           0    13
  DDHD1 WILD-TYPE                                         1   344
D901V11, multiclass
                                           clus
vv                                          DDHD1 MUTATED DDHD1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V12, binary
                 cls
clus                0   1
  DDHD1 MUTATED     1  13
  DDHD1 WILD-TYPE   9 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      1   13
  DDHD1 WILD-TYPE    9  385
                        clus
vv                       DDHD1 MUTATED DDHD1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(902) Variable = PSD MUTATION ANALYSIS
D902V1, survival
               sevent
clus2             0   1
  PSD MUTATED    13   5
  PSD WILD-TYPE 325 211
  PSD MUTATED PSD WILD-TYPE 
           18           536 
  PSD MUTATED PSD WILD-TYPE 
            5           211 
$`PSD MUTATED`
TCGA-L5-A88S TCGA-BR-4257 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8363 
       15.48         9.67        36.16        35.84        29.59         0.26 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5726 TCGA-D7-A6EX 
        1.12        27.12        31.96         6.58        28.96        11.31 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H3 
       77.29        26.47        24.20         6.58         2.10        29.00 

$`PSD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       44.94        21.90         9.21        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        20.22        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         0.10         6.51        20.25         0.26        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PSD MUTATED PSD WILD-TYPE 
         0.26          0.00 
  PSD MUTATED PSD WILD-TYPE 
        77.29        122.30 
  PSD MUTATED PSD WILD-TYPE 
       25.335        13.510 
[1] "0.3 - 77.3 (25.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D902V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSD MUTATED         1        3        4        1         2         2
  PSD WILD-TYPE       9       17       42       30        82        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSD MUTATED           0          1          1          2        1         0
  PSD WILD-TYPE        29         83         61         37       42         4
D902V3, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              1             9
  STAGE IA             3            17
  STAGE IB             4            42
  STAGE II             1            30
  STAGE IIA            2            82
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  PSD MUTATED       4   4   5   5
  PSD WILD-TYPE    50 131 256  97
D902V4, multiclass
       clus
vv      PSD MUTATED PSD WILD-TYPE
  T0+T1           4            50
  T2              4           131
  T3              5           256
  T4              5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  PSD MUTATED    10   4   2   2
  PSD WILD-TYPE 185 169  87  83
D902V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0          10           185
  N1           4           169
  N2           2            87
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V6, binary
               cls
clus              0   1
  PSD MUTATED    15   1
  PSD WILD-TYPE 467  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     15    1
  PSD WILD-TYPE  467   37
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          15           467
  1           1            37
[1] 2 2
[1] FALSE
D902V7, binary
               cls
clus              0   1
  PSD MUTATED     9  10
  PSD WILD-TYPE 163 396
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      9   10
  PSD WILD-TYPE  163  396
        clus
vv       PSD MUTATED PSD WILD-TYPE
  FEMALE           9           163
  MALE            10           396
[1] 2 2
[1] FALSE
D902V8, binary
               cls
clus              0   1
  PSD MUTATED    16   1
  PSD WILD-TYPE 400 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     16    1
  PSD WILD-TYPE  400  101
     clus
vv    PSD MUTATED PSD WILD-TYPE
  NO           16           400
  YES           1           101
[1] 2 2
[1] FALSE
D902V9, continuous
D902V10, continuous
[1] "Remove cluster labels:" "PSD MUTATED"           
clus
  PSD MUTATED PSD WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A4OX    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" "PSD WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"PSD WILD-TYPE" "PSD WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  PSD MUTATED       6                         1
  PSD WILD-TYPE   127                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSD MUTATED                                           0    10
  PSD WILD-TYPE                                         1   347
D902V11, multiclass
                                           clus
vv                                          PSD MUTATED PSD WILD-TYPE
  ASIAN                                               6           127
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              10           347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V12, binary
               cls
clus              0   1
  PSD MUTATED     0  16
  PSD WILD-TYPE  10 382
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      0   16
  PSD WILD-TYPE   10  382
                        clus
vv                       PSD MUTATED PSD WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          16           382
[1] 2 2
[1] FALSE

Clustering(903) Variable = NOP2 MUTATION ANALYSIS
D903V1, survival
                sevent
clus2              0   1
  NOP2 MUTATED     7   2
  NOP2 WILD-TYPE 331 214
  NOP2 MUTATED NOP2 WILD-TYPE 
             9            545 
  NOP2 MUTATED NOP2 WILD-TYPE 
             2            214 
$`NOP2 MUTATED`
TCGA-Z6-A8JD TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MI TCGA-HF-7132 
        3.42         3.32        31.27         1.12        11.77        77.29 
TCGA-HU-A4H8 TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       14.07        38.14        26.04 

$`NOP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31        14.04        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        16.14        27.55        12.43        17.26 

  NOP2 MUTATED NOP2 WILD-TYPE 
          1.12           0.00 
  NOP2 MUTATED NOP2 WILD-TYPE 
         77.29         122.30 
  NOP2 MUTATED NOP2 WILD-TYPE 
         14.07          13.55 
[1] "1.1 - 77.3 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D903V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOP2 MUTATED         0        0        1        1         2         1
  NOP2 WILD-TYPE      10       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOP2 MUTATED           0          2          1          1        0         0
  NOP2 WILD-TYPE        29         82         61         38       43         4
D903V3, multiclass
            clus
vv           NOP2 MUTATED NOP2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NOP2 MUTATED       1   1   5   2
  NOP2 WILD-TYPE    53 134 256 100
D903V4, multiclass
       clus
vv      NOP2 MUTATED NOP2 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NOP2 MUTATED     3   4   0   2
  NOP2 WILD-TYPE 192 169  89  83
D903V5, multiclass
    clus
vv   NOP2 MUTATED NOP2 WILD-TYPE
  N0            3            192
  N1            4            169
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V6, binary
                cls
clus               0   1
  NOP2 MUTATED     9   0
  NOP2 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      9    0
  NOP2 WILD-TYPE  473   38
   clus
vv  NOP2 MUTATED NOP2 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D903V7, binary
                cls
clus               0   1
  NOP2 MUTATED     1   8
  NOP2 WILD-TYPE 171 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      1    8
  NOP2 WILD-TYPE  171  398
        clus
vv       NOP2 MUTATED NOP2 WILD-TYPE
  FEMALE            1            171
  MALE              8            398
[1] 2 2
[1] FALSE
D903V8, binary
                cls
clus               0   1
  NOP2 MUTATED     7   2
  NOP2 WILD-TYPE 409 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      7    2
  NOP2 WILD-TYPE  409  100
     clus
vv    NOP2 MUTATED NOP2 WILD-TYPE
  NO             7            409
  YES            2            100
[1] 2 2
[1] FALSE
D903V9, continuous
[1] "Remove cluster labels:" "NOP2 MUTATED"          
clus
  NOP2 MUTATED NOP2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JE 
"NOP2 WILD-TYPE" "NOP2 WILD-TYPE" "NOP2 WILD-TYPE" 
D903V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOP2 MUTATED       2                         0
  NOP2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOP2 MUTATED                                           0     6
  NOP2 WILD-TYPE                                         1   351
D903V11, multiclass
                                           clus
vv                                          NOP2 MUTATED NOP2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V12, binary
                cls
clus               0   1
  NOP2 MUTATED     0   6
  NOP2 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      0    6
  NOP2 WILD-TYPE   10  392
                        clus
vv                       NOP2 MUTATED NOP2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(904) Variable = GPR45 MUTATION ANALYSIS
D904V1, survival
                 sevent
clus2               0   1
  GPR45 MUTATED    11   6
  GPR45 WILD-TYPE 327 210
  GPR45 MUTATED GPR45 WILD-TYPE 
             17             537 
  GPR45 MUTATED GPR45 WILD-TYPE 
              6             210 
$`GPR45 MUTATED`
TCGA-CG-4460 TCGA-MX-A663 TCGA-RE-A7BO TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-8284 
       21.99         9.86         7.00         6.97        30.90         8.05 
TCGA-BR-8360 TCGA-BR-8361 TCGA-CG-4305 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GT 
        6.18        31.10        15.95        22.68        11.77         6.51 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-A6RP TCGA-R5-A7ZI TCGA-RD-A8N6 
        6.58        23.84         6.44        74.53         8.94 

$`GPR45 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GPR45 MUTATED GPR45 WILD-TYPE 
           6.18            0.00 
  GPR45 MUTATED GPR45 WILD-TYPE 
          74.53          122.30 
  GPR45 MUTATED GPR45 WILD-TYPE 
           9.86           13.68 
[1] "6.2 - 74.5 (9.9)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D904V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR45 MUTATED         0        1        0        1         3         4
  GPR45 WILD-TYPE      10       19       46       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR45 MUTATED           0          3          0          3        2         0
  GPR45 WILD-TYPE        29         81         62         36       41         4
D904V3, multiclass
            clus
vv           GPR45 MUTATED GPR45 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GPR45 MUTATED       3   3   7   4
  GPR45 WILD-TYPE    51 132 254  98
D904V4, multiclass
       clus
vv      GPR45 MUTATED GPR45 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GPR45 MUTATED     4   7   4   2
  GPR45 WILD-TYPE 191 166  85  83
D904V5, multiclass
    clus
vv   GPR45 MUTATED GPR45 WILD-TYPE
  N0             4             191
  N1             7             166
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V6, binary
                 cls
clus                0   1
  GPR45 MUTATED    14   2
  GPR45 WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED     14    2
  GPR45 WILD-TYPE  468   36
   clus
vv  GPR45 MUTATED GPR45 WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D904V7, binary
                 cls
clus                0   1
  GPR45 MUTATED     9   8
  GPR45 WILD-TYPE 163 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED      9    8
  GPR45 WILD-TYPE  163  398
        clus
vv       GPR45 MUTATED GPR45 WILD-TYPE
  FEMALE             9             163
  MALE               8             398
[1] 2 2
[1] FALSE
D904V8, binary
                 cls
clus                0   1
  GPR45 MUTATED    16   1
  GPR45 WILD-TYPE 400 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED     16    1
  GPR45 WILD-TYPE  400  101
     clus
vv    GPR45 MUTATED GPR45 WILD-TYPE
  NO             16             400
  YES             1             101
[1] 2 2
[1] FALSE
D904V9, continuous
D904V10, continuous
[1] "Remove cluster labels:" "GPR45 MUTATED"         
clus
  GPR45 MUTATED GPR45 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-V5-A7RB 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" "GPR45 WILD-TYPE" 
     TCGA-Z6-AAPN 
"GPR45 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPR45 MUTATED       5                         0
  GPR45 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR45 MUTATED                                           0    10
  GPR45 WILD-TYPE                                         1   347
D904V11, multiclass
                                           clus
vv                                          GPR45 MUTATED GPR45 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V12, binary
                 cls
clus                0   1
  GPR45 MUTATED     1  14
  GPR45 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED      1   14
  GPR45 WILD-TYPE    9  384
                        clus
vv                       GPR45 MUTATED GPR45 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(905) Variable = IFI44 MUTATION ANALYSIS
D905V1, survival
                 sevent
clus2               0   1
  IFI44 MUTATED     3   2
  IFI44 WILD-TYPE 335 214
  IFI44 MUTATED IFI44 WILD-TYPE 
              5             549 
  IFI44 MUTATED IFI44 WILD-TYPE 
              2             214 
$`IFI44 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OW TCGA-BR-8680 TCGA-CD-8536 
        4.31        19.99         7.13        31.96        12.43 

$`IFI44 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IFI44 MUTATED IFI44 WILD-TYPE 
           4.31            0.00 
  IFI44 MUTATED IFI44 WILD-TYPE 
          31.96          122.30 
  IFI44 MUTATED IFI44 WILD-TYPE 
          12.43           13.58 
[1] "4.3 - 32.0 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D905V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFI44 MUTATED         0        0        0        1         0         2
  IFI44 WILD-TYPE      10       20       46       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFI44 MUTATED           0          0          0          1        1         0
  IFI44 WILD-TYPE        29         84         62         38       42         4
D905V3, multiclass
            clus
vv           IFI44 MUTATED IFI44 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IFI44 MUTATED       0   1   3   1
  IFI44 WILD-TYPE    54 134 258 101
D905V4, multiclass
       clus
vv      IFI44 MUTATED IFI44 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                3             258
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IFI44 MUTATED     2   2   1   1
  IFI44 WILD-TYPE 193 171  88  84
D905V5, multiclass
    clus
vv   IFI44 MUTATED IFI44 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V6, binary
                 cls
clus                0   1
  IFI44 MUTATED     3   1
  IFI44 WILD-TYPE 479  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      3    1
  IFI44 WILD-TYPE  479   37
   clus
vv  IFI44 MUTATED IFI44 WILD-TYPE
  0             3             479
  1             1              37
[1] 2 2
[1] FALSE
D905V7, binary
                 cls
clus                0   1
  IFI44 MUTATED     2   4
  IFI44 WILD-TYPE 170 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      2    4
  IFI44 WILD-TYPE  170  402
        clus
vv       IFI44 MUTATED IFI44 WILD-TYPE
  FEMALE             2             170
  MALE               4             402
[1] 2 2
[1] FALSE
D905V8, binary
                 cls
clus                0   1
  IFI44 MUTATED     4   0
  IFI44 WILD-TYPE 412 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      4    0
  IFI44 WILD-TYPE  412  102
     clus
vv    IFI44 MUTATED IFI44 WILD-TYPE
  NO              4             412
  YES             0             102
[1] 2 2
[1] FALSE
D905V9, continuous
D905V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IFI44 MUTATED       2                         0
  IFI44 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFI44 MUTATED                                           0     3
  IFI44 WILD-TYPE                                         1   354
D905V11, multiclass
                                           clus
vv                                          IFI44 MUTATED IFI44 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V12, binary
                 cls
clus                0   1
  IFI44 MUTATED     0   3
  IFI44 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI44 MUTATED      0    3
  IFI44 WILD-TYPE   10  395
                        clus
vv                       IFI44 MUTATED IFI44 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(906) Variable = BEST3 MUTATION ANALYSIS
D906V1, survival
                 sevent
clus2               0   1
  BEST3 MUTATED     7   6
  BEST3 WILD-TYPE 331 210
  BEST3 MUTATED BEST3 WILD-TYPE 
             13             541 
  BEST3 MUTATED BEST3 WILD-TYPE 
              6             210 
$`BEST3 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4P3 TCGA-VR-A8EY TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8371 
       19.99        18.64        33.70         6.97         6.61        11.80 
TCGA-CD-8529 TCGA-CG-4443 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GH 
       12.30        29.98        30.51        26.47        22.68        11.77 
TCGA-IN-A6RL 
       13.35 

$`BEST3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  BEST3 MUTATED BEST3 WILD-TYPE 
           6.61            0.00 
  BEST3 MUTATED BEST3 WILD-TYPE 
           33.7           122.3 
  BEST3 MUTATED BEST3 WILD-TYPE 
          18.64           13.55 
[1] "6.6 - 33.7 (18.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D906V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEST3 MUTATED         0        2        1        0         1         2
  BEST3 WILD-TYPE      10       18       45       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BEST3 MUTATED           1          2          1          2        1         0
  BEST3 WILD-TYPE        28         82         61         37       42         4
D906V3, multiclass
            clus
vv           BEST3 MUTATED BEST3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BEST3 MUTATED       2   5   5   2
  BEST3 WILD-TYPE    52 130 256 100
D906V4, multiclass
       clus
vv      BEST3 MUTATED BEST3 WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3                5             256
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BEST3 MUTATED     5   5   0   3
  BEST3 WILD-TYPE 190 168  89  82
D906V5, multiclass
    clus
vv   BEST3 MUTATED BEST3 WILD-TYPE
  N0             5             190
  N1             5             168
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V6, binary
                 cls
clus                0   1
  BEST3 MUTATED    10   1
  BEST3 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED     10    1
  BEST3 WILD-TYPE  472   37
   clus
vv  BEST3 MUTATED BEST3 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D906V7, binary
                 cls
clus                0   1
  BEST3 MUTATED     6   8
  BEST3 WILD-TYPE 166 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      6    8
  BEST3 WILD-TYPE  166  398
        clus
vv       BEST3 MUTATED BEST3 WILD-TYPE
  FEMALE             6             166
  MALE               8             398
[1] 2 2
[1] FALSE
D906V8, binary
                 cls
clus                0   1
  BEST3 MUTATED     9   3
  BEST3 WILD-TYPE 407  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      9    3
  BEST3 WILD-TYPE  407   99
     clus
vv    BEST3 MUTATED BEST3 WILD-TYPE
  NO              9             407
  YES             3              99
[1] 2 2
[1] FALSE
D906V9, continuous
[1] "Remove cluster labels:" "BEST3 MUTATED"         
clus
  BEST3 MUTATED BEST3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
D906V10, continuous
[1] "Remove cluster labels:" "BEST3 MUTATED"         
clus
  BEST3 MUTATED BEST3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4QT 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" "BEST3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BEST3 MUTATED       3                         0
  BEST3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BEST3 MUTATED                                           0     9
  BEST3 WILD-TYPE                                         1   348
D906V11, multiclass
                                           clus
vv                                          BEST3 MUTATED BEST3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V12, binary
                 cls
clus                0   1
  BEST3 MUTATED     0  10
  BEST3 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEST3 MUTATED      0   10
  BEST3 WILD-TYPE   10  388
                        clus
vv                       BEST3 MUTATED BEST3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(907) Variable = FLNB MUTATION ANALYSIS
D907V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    18  11
  FLNB WILD-TYPE 320 205
  FLNB MUTATED FLNB WILD-TYPE 
            29            525 
  FLNB MUTATED FLNB WILD-TYPE 
            11            205 
$`FLNB MUTATED`
TCGA-2H-A9GH TCGA-JY-A93C TCGA-JY-A93E TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-8059 
       31.27        23.18        25.22         2.10         6.97        14.43 
TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
        9.60         4.31        25.05         1.12        28.14        31.96 
TCGA-BR-A4CS TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5733 
        1.48        12.43         6.58        11.77         6.02        21.07 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       26.47        22.68        29.98         6.51        20.25        29.00 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.53         6.74        63.62        38.14        37.22 

$`FLNB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       37.25        11.44         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.58         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.35         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53         5.56        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.41        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FLNB MUTATED FLNB WILD-TYPE 
          1.12           0.00 
  FLNB MUTATED FLNB WILD-TYPE 
         63.62         122.30 
  FLNB MUTATED FLNB WILD-TYPE 
         20.25          13.51 
[1] "1.1 - 63.6 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D907V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FLNB MUTATED         0        0        3        1         5         3
  FLNB WILD-TYPE      10       20       43       30        79        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLNB MUTATED           1          9          1          6        2         0
  FLNB WILD-TYPE        28         75         61         33       41         4
D907V3, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            9             75
  STAGE IIIB            1             61
  STAGE IIIC            6             33
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FLNB MUTATED       3   4  11  13
  FLNB WILD-TYPE    51 131 250  89
D907V4, multiclass
       clus
vv      FLNB MUTATED FLNB WILD-TYPE
  T0+T1            3             51
  T2               4            131
  T3              11            250
  T4              13             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FLNB MUTATED     8  14   5   5
  FLNB WILD-TYPE 187 159  84  80
D907V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0            8            187
  N1           14            159
  N2            5             84
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V6, binary
                cls
clus               0   1
  FLNB MUTATED    29   1
  FLNB WILD-TYPE 453  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     29    1
  FLNB WILD-TYPE  453   37
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           29            453
  1            1             37
[1] 2 2
[1] FALSE
D907V7, binary
                cls
clus               0   1
  FLNB MUTATED    14  18
  FLNB WILD-TYPE 158 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     14   18
  FLNB WILD-TYPE  158  388
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  FEMALE           14            158
  MALE             18            388
[1] 2 2
[1] FALSE
D907V8, binary
                cls
clus               0   1
  FLNB MUTATED    26   3
  FLNB WILD-TYPE 390  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     26    3
  FLNB WILD-TYPE  390   99
     clus
vv    FLNB MUTATED FLNB WILD-TYPE
  NO            26            390
  YES            3             99
[1] 2 2
[1] FALSE
D907V9, continuous
[1] "Remove cluster labels:" "FLNB MUTATED"          
clus
  FLNB MUTATED FLNB WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
    TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-A8JD 
"FLNB WILD-TYPE" "FLNB WILD-TYPE" "FLNB WILD-TYPE" 
D907V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FLNB MUTATED      10                         0
  FLNB WILD-TYPE   123                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FLNB MUTATED                                           0    18
  FLNB WILD-TYPE                                         1   339
D907V11, multiclass
                                           clus
vv                                          FLNB MUTATED FLNB WILD-TYPE
  ASIAN                                               10            123
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V12, binary
                cls
clus               0   1
  FLNB MUTATED     0  24
  FLNB WILD-TYPE  10 374
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED      0   24
  FLNB WILD-TYPE   10  374
                        clus
vv                       FLNB MUTATED FLNB WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           24            374
[1] 2 2
[1] FALSE

Clustering(908) Variable = KCTD9 MUTATION ANALYSIS
D908V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     8   1
  KCTD9 WILD-TYPE 330 215
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              9             545 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              1             215 
$`KCTD9 MUTATED`
TCGA-B7-A5TI TCGA-BR-8370 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5733 
       19.56         3.32        12.43        15.95         6.02        21.07 
TCGA-D7-A4YU TCGA-HU-A4G8 TCGA-HU-A4GX 
       16.44        22.68        20.25 

$`KCTD9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KCTD9 MUTATED KCTD9 WILD-TYPE 
           3.32            0.00 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          22.68          122.30 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          16.44           13.51 
[1] "3.3 - 22.7 (16.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.2"
D908V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCTD9 MUTATED         0        0        0        2         0         1
  KCTD9 WILD-TYPE      10       20       46       29        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCTD9 MUTATED           0          1          2          2        2         0
  KCTD9 WILD-TYPE        29         83         60         37       41         4
D908V3, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               2              29
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCTD9 MUTATED       0   2   5   4
  KCTD9 WILD-TYPE    54 133 256  98
D908V4, multiclass
       clus
vv      KCTD9 MUTATED KCTD9 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCTD9 MUTATED     1   3   3   3
  KCTD9 WILD-TYPE 194 170  86  82
D908V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             1             194
  N1             3             170
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V6, binary
                 cls
clus                0   1
  KCTD9 MUTATED    10   0
  KCTD9 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED     10    0
  KCTD9 WILD-TYPE  472   38
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D908V7, binary
                 cls
clus                0   1
  KCTD9 MUTATED     5   6
  KCTD9 WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      5    6
  KCTD9 WILD-TYPE  167  400
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D908V8, binary
                 cls
clus                0   1
  KCTD9 MUTATED     9   0
  KCTD9 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      9    0
  KCTD9 WILD-TYPE  407  102
     clus
vv    KCTD9 MUTATED KCTD9 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D908V9, continuous
D908V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCTD9 MUTATED       3                         0
  KCTD9 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCTD9 MUTATED                                           0     5
  KCTD9 WILD-TYPE                                         1   352
D908V11, multiclass
                                           clus
vv                                          KCTD9 MUTATED KCTD9 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V12, binary
                 cls
clus                0   1
  KCTD9 MUTATED     0   8
  KCTD9 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      0    8
  KCTD9 WILD-TYPE   10  390
                        clus
vv                       KCTD9 MUTATED KCTD9 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(909) Variable = ERN2 MUTATION ANALYSIS
D909V1, survival
                sevent
clus2              0   1
  ERN2 MUTATED    10   6
  ERN2 WILD-TYPE 328 210
  ERN2 MUTATED ERN2 WILD-TYPE 
            16            538 
  ERN2 MUTATED ERN2 WILD-TYPE 
             6            210 
$`ERN2 MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-CG-4460 TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A8NK 
        4.31         8.94        21.99        41.52        24.03        13.55 
TCGA-LN-A4A2 TCGA-B7-5816 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5721 
       12.49        26.70        28.14        16.14        15.95         6.02 
TCGA-CG-5732 TCGA-F1-A448 TCGA-HU-8243 TCGA-VQ-AA69 
       69.04        21.27         5.92        28.41 

$`ERN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       25.22         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        15.02        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ERN2 MUTATED ERN2 WILD-TYPE 
          4.31           0.00 
  ERN2 MUTATED ERN2 WILD-TYPE 
         69.04         122.30 
  ERN2 MUTATED ERN2 WILD-TYPE 
        18.705         13.495 
[1] "4.3 - 69.0 (18.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D909V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERN2 MUTATED         0        0        2        1         2         2
  ERN2 WILD-TYPE      10       20       44       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERN2 MUTATED           1          1          2          2        3         0
  ERN2 WILD-TYPE        28         83         60         37       40         4
D909V3, multiclass
            clus
vv           ERN2 MUTATED ERN2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ERN2 MUTATED       0   4   8   5
  ERN2 WILD-TYPE    54 131 253  97
D909V4, multiclass
       clus
vv      ERN2 MUTATED ERN2 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ERN2 MUTATED     6   5   2   5
  ERN2 WILD-TYPE 189 168  87  80
D909V5, multiclass
    clus
vv   ERN2 MUTATED ERN2 WILD-TYPE
  N0            6            189
  N1            5            168
  N2            2             87
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V6, binary
                cls
clus               0   1
  ERN2 MUTATED    16   1
  ERN2 WILD-TYPE 466  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED     16    1
  ERN2 WILD-TYPE  466   37
   clus
vv  ERN2 MUTATED ERN2 WILD-TYPE
  0           16            466
  1            1             37
[1] 2 2
[1] FALSE
D909V7, binary
                cls
clus               0   1
  ERN2 MUTATED     8  11
  ERN2 WILD-TYPE 164 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED      8   11
  ERN2 WILD-TYPE  164  395
        clus
vv       ERN2 MUTATED ERN2 WILD-TYPE
  FEMALE            8            164
  MALE             11            395
[1] 2 2
[1] FALSE
D909V8, binary
                cls
clus               0   1
  ERN2 MUTATED    11   3
  ERN2 WILD-TYPE 405  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED     11    3
  ERN2 WILD-TYPE  405   99
     clus
vv    ERN2 MUTATED ERN2 WILD-TYPE
  NO            11            405
  YES            3             99
[1] 2 2
[1] FALSE
D909V9, continuous
[1] "Remove cluster labels:" "ERN2 MUTATED"          
clus
  ERN2 MUTATED ERN2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ERN2 WILD-TYPE" "ERN2 WILD-TYPE" "ERN2 WILD-TYPE" 
D909V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ERN2 MUTATED       2                         0
  ERN2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERN2 MUTATED                                           0    11
  ERN2 WILD-TYPE                                         1   346
D909V11, multiclass
                                           clus
vv                                          ERN2 MUTATED ERN2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V12, binary
                cls
clus               0   1
  ERN2 MUTATED     1   7
  ERN2 WILD-TYPE   9 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN2 MUTATED      1    7
  ERN2 WILD-TYPE    9  391
                        clus
vv                       ERN2 MUTATED ERN2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(910) Variable = PTGER4 MUTATION ANALYSIS
D910V1, survival
                  sevent
clus2                0   1
  PTGER4 MUTATED    10   4
  PTGER4 WILD-TYPE 328 212
  PTGER4 MUTATED PTGER4 WILD-TYPE 
              14              540 
  PTGER4 MUTATED PTGER4 WILD-TYPE 
               4              212 
$`PTGER4 MUTATED`
TCGA-KB-A93G TCGA-2H-A9GH TCGA-IG-A3YC TCGA-L5-A8NI TCGA-BR-4201 TCGA-BR-6452 
       20.15        31.27        20.12        13.48        30.90        34.68 
TCGA-BR-6566 TCGA-BR-7196 TCGA-BR-8369 TCGA-D7-A6EZ TCGA-FP-A4BE TCGA-HU-8238 
       32.78        21.90        14.04        20.32        11.08         1.51 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`PTGER4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24         0.23         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51        26.47         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PTGER4 MUTATED PTGER4 WILD-TYPE 
            1.51             0.00 
  PTGER4 MUTATED PTGER4 WILD-TYPE 
           38.14           122.30 
  PTGER4 MUTATED PTGER4 WILD-TYPE 
          20.285           13.410 
[1] "1.5 - 38.1 (20.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D910V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTGER4 MUTATED         0        0        2        0         3         1
  PTGER4 WILD-TYPE      10       20       44       31        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTGER4 MUTATED           1          3          1          1        1
  PTGER4 WILD-TYPE        28         81         61         38       42
                  vv
clus               STAGE IVA
  PTGER4 MUTATED           0
  PTGER4 WILD-TYPE         4
D910V3, multiclass
            clus
vv           PTGER4 MUTATED PTGER4 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PTGER4 MUTATED       1   3   9   2
  PTGER4 WILD-TYPE    53 132 252 100
D910V4, multiclass
       clus
vv      PTGER4 MUTATED PTGER4 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 9              252
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTGER4 MUTATED     5   4   3   2
  PTGER4 WILD-TYPE 190 169  86  83
D910V5, multiclass
    clus
vv   PTGER4 MUTATED PTGER4 WILD-TYPE
  N0              5              190
  N1              4              169
  N2              3               86
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V6, binary
                  cls
clus                 0   1
  PTGER4 MUTATED    14   1
  PTGER4 WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTGER4 MUTATED     14    1
  PTGER4 WILD-TYPE  468   37
   clus
vv  PTGER4 MUTATED PTGER4 WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D910V7, binary
                  cls
clus                 0   1
  PTGER4 MUTATED     6   9
  PTGER4 WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTGER4 MUTATED      6    9
  PTGER4 WILD-TYPE  166  397
        clus
vv       PTGER4 MUTATED PTGER4 WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D910V8, binary
                  cls
clus                 0   1
  PTGER4 MUTATED    13   2
  PTGER4 WILD-TYPE 403 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTGER4 MUTATED     13    2
  PTGER4 WILD-TYPE  403  100
     clus
vv    PTGER4 MUTATED PTGER4 WILD-TYPE
  NO              13              403
  YES              2              100
[1] 2 2
[1] FALSE
D910V9, continuous
[1] "Remove cluster labels:" "PTGER4 MUTATED"        
clus
  PTGER4 MUTATED PTGER4 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
D910V10, continuous
[1] "Remove cluster labels:" "PTGER4 MUTATED"        
clus
  PTGER4 MUTATED PTGER4 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A4P3 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" "PTGER4 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PTGER4 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTGER4 MUTATED       2                         1
  PTGER4 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTGER4 MUTATED                                           0    11
  PTGER4 WILD-TYPE                                         1   346
D910V11, multiclass
                                           clus
vv                                          PTGER4 MUTATED PTGER4 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V12, binary
                  cls
clus                 0   1
  PTGER4 MUTATED     0  11
  PTGER4 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTGER4 MUTATED      0   11
  PTGER4 WILD-TYPE   10  387
                        clus
vv                       PTGER4 MUTATED PTGER4 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(911) Variable = RUSC2 MUTATION ANALYSIS
D911V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    12   9
  RUSC2 WILD-TYPE 326 207
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             21             533 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              9             207 
$`RUSC2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A3Y9 TCGA-LN-A9FO TCGA-B7-5816 TCGA-BR-4280 
       19.99        21.99         0.85         0.13        26.70         6.61 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8487 TCGA-CD-A4MI TCGA-CG-4306 
       34.68        29.59         8.05         1.12        11.77         1.02 
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5579 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4G8 
        6.02        65.10        20.91        77.29        26.47        22.68 
TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-VQ-AA64 
        0.10        23.84        18.41 

$`RUSC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
            0.1             0.0 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          77.29          122.30 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          19.99           13.51 
[1] "0.1 - 77.3 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D911V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUSC2 MUTATED         1        0        2        1         3         4
  RUSC2 WILD-TYPE       9       20       44       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUSC2 MUTATED           1          3          1          3        3         0
  RUSC2 WILD-TYPE        28         81         61         36       40         4
D911V3, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RUSC2 MUTATED       1   6   9   7
  RUSC2 WILD-TYPE    53 129 252  95
D911V4, multiclass
       clus
vv      RUSC2 MUTATED RUSC2 WILD-TYPE
  T0+T1             1              53
  T2                6             129
  T3                9             252
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RUSC2 MUTATED     8   7   5   2
  RUSC2 WILD-TYPE 187 166  84  83
D911V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0             8             187
  N1             7             166
  N2             5              84
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V6, binary
                 cls
clus                0   1
  RUSC2 MUTATED    17   2
  RUSC2 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     17    2
  RUSC2 WILD-TYPE  465   36
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D911V7, binary
                 cls
clus                0   1
  RUSC2 MUTATED    12  11
  RUSC2 WILD-TYPE 160 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     12   11
  RUSC2 WILD-TYPE  160  395
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  FEMALE            12             160
  MALE              11             395
[1] 2 2
[1] FALSE
D911V8, binary
                 cls
clus                0   1
  RUSC2 MUTATED    18   2
  RUSC2 WILD-TYPE 398 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     18    2
  RUSC2 WILD-TYPE  398  100
     clus
vv    RUSC2 MUTATED RUSC2 WILD-TYPE
  NO             18             398
  YES             2             100
[1] 2 2
[1] FALSE
D911V9, continuous
[1] "Remove cluster labels:" "RUSC2 MUTATED"         
clus
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3YA      TCGA-IG-A3YB 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
D911V10, continuous
[1] "Remove cluster labels:" "RUSC2 MUTATED"         
clus
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" "RUSC2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RUSC2 MUTATED       5                         1
  RUSC2 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RUSC2 MUTATED                                           0    12
  RUSC2 WILD-TYPE                                         1   345
D911V11, multiclass
                                           clus
vv                                          RUSC2 MUTATED RUSC2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V12, binary
                 cls
clus                0   1
  RUSC2 MUTATED     0  16
  RUSC2 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      0   16
  RUSC2 WILD-TYPE   10  382
                        clus
vv                       RUSC2 MUTATED RUSC2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(912) Variable = IGF2BP3 MUTATION ANALYSIS
D912V1, survival
                   sevent
clus2                 0   1
  IGF2BP3 MUTATED     6   3
  IGF2BP3 WILD-TYPE 332 213
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                9               545 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                3               213 
$`IGF2BP3 MUTATED`
TCGA-2H-A9GI TCGA-L5-A893 TCGA-BR-8680 TCGA-CG-4437 TCGA-D7-A6EY TCGA-FP-A4BE 
       14.30         3.02        31.96         8.05        11.44        11.08 
TCGA-HU-A4GN TCGA-R5-A805 TCGA-VQ-A8P2 
       29.98         9.24        38.14 

$`IGF2BP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         6.08         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
             3.02              0.00 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
            38.14            122.30 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
            11.44             13.58 
[1] "3.0 - 38.1 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D912V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGF2BP3 MUTATED         1        0        0        1         2         0
  IGF2BP3 WILD-TYPE       9       20       46       30        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGF2BP3 MUTATED           1          1          2          0        1
  IGF2BP3 WILD-TYPE        28         83         60         39       42
                   vv
clus                STAGE IVA
  IGF2BP3 MUTATED           0
  IGF2BP3 WILD-TYPE         4
D912V3, multiclass
            clus
vv           IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  IGF2BP3 MUTATED       1   2   4   2
  IGF2BP3 WILD-TYPE    53 133 257 100
D912V4, multiclass
       clus
vv      IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  IGF2BP3 MUTATED     2   4   2   1
  IGF2BP3 WILD-TYPE 193 169  87  84
D912V5, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  N0               2               193
  N1               4               169
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V6, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     8   1
  IGF2BP3 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      8    1
  IGF2BP3 WILD-TYPE  474   37
   clus
vv  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D912V7, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     2   7
  IGF2BP3 WILD-TYPE 170 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      2    7
  IGF2BP3 WILD-TYPE  170  399
        clus
vv       IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  FEMALE               2               170
  MALE                 7               399
[1] 2 2
[1] FALSE
D912V8, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     6   2
  IGF2BP3 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      6    2
  IGF2BP3 WILD-TYPE  410  100
     clus
vv    IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D912V9, continuous
D912V10, continuous
[1] "Remove cluster labels:" "IGF2BP3 MUTATED"       
clus
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A8NE 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" "IGF2BP3 WILD-TYPE" 
       TCGA-Z6-AAPN 
"IGF2BP3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  IGF2BP3 MUTATED       2                         1
  IGF2BP3 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGF2BP3 MUTATED                                           0     4
  IGF2BP3 WILD-TYPE                                         1   353
D912V11, multiclass
                                           clus
vv                                          IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V12, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     0   5
  IGF2BP3 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      0    5
  IGF2BP3 WILD-TYPE   10  393
                        clus
vv                       IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(913) Variable = QRFPR MUTATION ANALYSIS
D913V1, survival
                 sevent
clus2               0   1
  QRFPR MUTATED     7   9
  QRFPR WILD-TYPE 331 207
  QRFPR MUTATED QRFPR WILD-TYPE 
             16             538 
  QRFPR MUTATED QRFPR WILD-TYPE 
              9             207 
$`QRFPR MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NG TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-ZR-A9CJ TCGA-B7-A5TI 
       19.99        35.97         4.67        47.93        19.73        19.56 
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8368 TCGA-CG-4465 
        6.97         9.67        34.68         0.26         4.31         9.01 
TCGA-D7-6822 TCGA-HU-A4H8 TCGA-RD-A7C1 TCGA-VQ-A91U 
       12.33        14.07        16.67         1.71 

$`QRFPR WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32         2.66        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  QRFPR MUTATED QRFPR WILD-TYPE 
           0.26            0.00 
  QRFPR MUTATED QRFPR WILD-TYPE 
          47.93          122.30 
  QRFPR MUTATED QRFPR WILD-TYPE 
         13.200          13.565 
[1] "0.3 - 47.9 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D913V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  QRFPR MUTATED         0        1        5        0         1         0
  QRFPR WILD-TYPE      10       19       41       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  QRFPR MUTATED           1          2          1          3        1         0
  QRFPR WILD-TYPE        28         82         61         36       42         4
D913V3, multiclass
            clus
vv           QRFPR MUTATED QRFPR WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  QRFPR MUTATED       2   4   8   2
  QRFPR WILD-TYPE    52 131 253 100
D913V4, multiclass
       clus
vv      QRFPR MUTATED QRFPR WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                8             253
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  QRFPR MUTATED     6   4   1   4
  QRFPR WILD-TYPE 189 169  88  81
D913V5, multiclass
    clus
vv   QRFPR MUTATED QRFPR WILD-TYPE
  N0             6             189
  N1             4             169
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V6, binary
                 cls
clus                0   1
  QRFPR MUTATED    11   1
  QRFPR WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED     11    1
  QRFPR WILD-TYPE  471   37
   clus
vv  QRFPR MUTATED QRFPR WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D913V7, binary
                 cls
clus                0   1
  QRFPR MUTATED     7  10
  QRFPR WILD-TYPE 165 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED      7   10
  QRFPR WILD-TYPE  165  396
        clus
vv       QRFPR MUTATED QRFPR WILD-TYPE
  FEMALE             7             165
  MALE              10             396
[1] 2 2
[1] FALSE
D913V8, binary
                 cls
clus                0   1
  QRFPR MUTATED    14   0
  QRFPR WILD-TYPE 402 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED     14    0
  QRFPR WILD-TYPE  402  102
     clus
vv    QRFPR MUTATED QRFPR WILD-TYPE
  NO             14             402
  YES             0             102
[1] 2 2
[1] FALSE
D913V9, continuous
D913V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  QRFPR MUTATED       3                         0
  QRFPR WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  QRFPR MUTATED                                           0    13
  QRFPR WILD-TYPE                                         1   344
D913V11, multiclass
                                           clus
vv                                          QRFPR MUTATED QRFPR WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V12, binary
                 cls
clus                0   1
  QRFPR MUTATED     0  12
  QRFPR WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED      0   12
  QRFPR WILD-TYPE   10  386
                        clus
vv                       QRFPR MUTATED QRFPR WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(914) Variable = GGT6 MUTATION ANALYSIS
D914V1, survival
                sevent
clus2              0   1
  GGT6 MUTATED     3   2
  GGT6 WILD-TYPE 335 214
  GGT6 MUTATED GGT6 WILD-TYPE 
             5            549 
  GGT6 MUTATED GGT6 WILD-TYPE 
             2            214 
$`GGT6 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-A4GH 
        6.61        34.68         6.58         6.02        11.77 

$`GGT6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GGT6 MUTATED GGT6 WILD-TYPE 
          6.02           0.00 
  GGT6 MUTATED GGT6 WILD-TYPE 
         34.68         122.30 
  GGT6 MUTATED GGT6 WILD-TYPE 
          6.61          13.68 
[1] "6.0 - 34.7 (6.6)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.5"
D914V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GGT6 MUTATED         0        1        0        0         2         0
  GGT6 WILD-TYPE      10       19       46       31        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGT6 MUTATED           1          1          0          0        1         0
  GGT6 WILD-TYPE        28         83         62         39       42         4
D914V3, multiclass
            clus
vv           GGT6 MUTATED GGT6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GGT6 MUTATED       1   1   2   2
  GGT6 WILD-TYPE    53 134 259 100
D914V4, multiclass
       clus
vv      GGT6 MUTATED GGT6 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GGT6 MUTATED     4   2   0   0
  GGT6 WILD-TYPE 191 171  89  85
D914V5, multiclass
    clus
vv   GGT6 MUTATED GGT6 WILD-TYPE
  N0            4            191
  N1            2            171
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V6, binary
                cls
clus               0   1
  GGT6 MUTATED     6   0
  GGT6 WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT6 MUTATED      6    0
  GGT6 WILD-TYPE  476   38
   clus
vv  GGT6 MUTATED GGT6 WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D914V7, binary
                cls
clus               0   1
  GGT6 MUTATED     3   3
  GGT6 WILD-TYPE 169 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT6 MUTATED      3    3
  GGT6 WILD-TYPE  169  403
        clus
vv       GGT6 MUTATED GGT6 WILD-TYPE
  FEMALE            3            169
  MALE              3            403
[1] 2 2
[1] FALSE
D914V8, binary
                cls
clus               0   1
  GGT6 MUTATED     5   0
  GGT6 WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT6 MUTATED      5    0
  GGT6 WILD-TYPE  411  102
     clus
vv    GGT6 MUTATED GGT6 WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D914V9, continuous
D914V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GGT6 MUTATED       2                         0
  GGT6 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GGT6 MUTATED                                           0     3
  GGT6 WILD-TYPE                                         1   354
D914V11, multiclass
                                           clus
vv                                          GGT6 MUTATED GGT6 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V12, binary
                cls
clus               0   1
  GGT6 MUTATED     0   5
  GGT6 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT6 MUTATED      0    5
  GGT6 WILD-TYPE   10  393
                        clus
vv                       GGT6 MUTATED GGT6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(915) Variable = SCIN MUTATION ANALYSIS
D915V1, survival
                sevent
clus2              0   1
  SCIN MUTATED     8   5
  SCIN WILD-TYPE 330 211
  SCIN MUTATED SCIN WILD-TYPE 
            13            541 
  SCIN MUTATED SCIN WILD-TYPE 
             5            211 
$`SCIN MUTATED`
TCGA-L5-A4OI TCGA-IG-A50L TCGA-L5-A4OT TCGA-LN-A49X TCGA-BR-4201 TCGA-BR-4256 
       19.99         0.53         4.90        12.62        30.90         9.34 
TCGA-BR-7704 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4306 
       35.24        28.14        31.96        12.30         6.58         1.02 
TCGA-R5-A7ZI 
       74.53 

$`SCIN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SCIN MUTATED SCIN WILD-TYPE 
          0.53           0.00 
  SCIN MUTATED SCIN WILD-TYPE 
         74.53         122.30 
  SCIN MUTATED SCIN WILD-TYPE 
         12.62          13.58 
[1] "0.5 - 74.5 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D915V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCIN MUTATED         0        0        0        1         2         0
  SCIN WILD-TYPE      10       20       46       30        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCIN MUTATED           0          2          0          2        5         0
  SCIN WILD-TYPE        29         82         62         37       38         4
D915V3, multiclass
            clus
vv           SCIN MUTATED SCIN WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SCIN MUTATED       0   1   7   5
  SCIN WILD-TYPE    54 134 254  97
D915V4, multiclass
       clus
vv      SCIN MUTATED SCIN WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               7            254
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SCIN MUTATED     5   4   2   2
  SCIN WILD-TYPE 190 169  87  83
D915V5, multiclass
    clus
vv   SCIN MUTATED SCIN WILD-TYPE
  N0            5            190
  N1            4            169
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V6, binary
                cls
clus               0   1
  SCIN MUTATED     8   5
  SCIN WILD-TYPE 474  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCIN MUTATED      8    5
  SCIN WILD-TYPE  474   33
   clus
vv  SCIN MUTATED SCIN WILD-TYPE
  0            8            474
  1            5             33
[1] 2 2
[1] FALSE
D915V7, binary
                cls
clus               0   1
  SCIN MUTATED     4  10
  SCIN WILD-TYPE 168 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCIN MUTATED      4   10
  SCIN WILD-TYPE  168  396
        clus
vv       SCIN MUTATED SCIN WILD-TYPE
  FEMALE            4            168
  MALE             10            396
[1] 2 2
[1] FALSE
D915V8, binary
                cls
clus               0   1
  SCIN MUTATED     9   2
  SCIN WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCIN MUTATED      9    2
  SCIN WILD-TYPE  407  100
     clus
vv    SCIN MUTATED SCIN WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D915V9, continuous
[1] "Remove cluster labels:" "SCIN MUTATED"          
clus
  SCIN MUTATED SCIN WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"SCIN WILD-TYPE" "SCIN WILD-TYPE" "SCIN WILD-TYPE" 
D915V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SCIN MUTATED       5                         0
  SCIN WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCIN MUTATED                                           0     8
  SCIN WILD-TYPE                                         1   349
D915V11, multiclass
                                           clus
vv                                          SCIN MUTATED SCIN WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V12, binary
                cls
clus               0   1
  SCIN MUTATED     1  10
  SCIN WILD-TYPE   9 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCIN MUTATED      1   10
  SCIN WILD-TYPE    9  388
                        clus
vv                       SCIN MUTATED SCIN WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(916) Variable = SLC6A11 MUTATION ANALYSIS
D916V1, survival
                   sevent
clus2                 0   1
  SLC6A11 MUTATED     6   5
  SLC6A11 WILD-TYPE 332 211
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
               11               543 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
                5               211 
$`SLC6A11 MUTATED`
TCGA-JY-A938 TCGA-CG-4460 TCGA-L5-A4OX TCGA-L5-A8NE TCGA-BR-8366 TCGA-CD-5801 
       34.85        21.99         7.43        55.50         0.95        13.18 
TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5733 TCGA-MX-A5UJ TCGA-RD-A8N5 
       29.98         6.02        21.07        19.73        57.44 

$`SLC6A11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
             0.95              0.00 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
            57.44            122.30 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
            21.07             13.51 
[1] "0.9 - 57.4 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D916V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC6A11 MUTATED         1        1        0        0         1         3
  SLC6A11 WILD-TYPE       9       19       46       31        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC6A11 MUTATED           0          5          0          0        2
  SLC6A11 WILD-TYPE        29         79         62         39       41
                   vv
clus                STAGE IVA
  SLC6A11 MUTATED           0
  SLC6A11 WILD-TYPE         4
D916V3, multiclass
            clus
vv           SLC6A11 MUTATED SLC6A11 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               5                79
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC6A11 MUTATED       2   3   5   3
  SLC6A11 WILD-TYPE    52 132 256  99
D916V4, multiclass
       clus
vv      SLC6A11 MUTATED SLC6A11 WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  5               256
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC6A11 MUTATED     4   7   2   0
  SLC6A11 WILD-TYPE 191 166  87  85
D916V5, multiclass
    clus
vv   SLC6A11 MUTATED SLC6A11 WILD-TYPE
  N0               4               191
  N1               7               166
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V6, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED    11   1
  SLC6A11 WILD-TYPE 471  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED     11    1
  SLC6A11 WILD-TYPE  471   37
   clus
vv  SLC6A11 MUTATED SLC6A11 WILD-TYPE
  0              11               471
  1               1                37
[1] 2 2
[1] FALSE
D916V7, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     5   8
  SLC6A11 WILD-TYPE 167 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      5    8
  SLC6A11 WILD-TYPE  167  398
        clus
vv       SLC6A11 MUTATED SLC6A11 WILD-TYPE
  FEMALE               5               167
  MALE                 8               398
[1] 2 2
[1] FALSE
D916V8, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED    10   1
  SLC6A11 WILD-TYPE 406 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED     10    1
  SLC6A11 WILD-TYPE  406  101
     clus
vv    SLC6A11 MUTATED SLC6A11 WILD-TYPE
  NO               10               406
  YES               1               101
[1] 2 2
[1] FALSE
D916V9, continuous
D916V10, continuous
[1] "Remove cluster labels:" "SLC6A11 MUTATED"       
clus
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NF 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" "SLC6A11 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC6A11 MUTATED       1                         1
  SLC6A11 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC6A11 MUTATED                                           0     7
  SLC6A11 WILD-TYPE                                         1   350
D916V11, multiclass
                                           clus
vv                                          SLC6A11 MUTATED SLC6A11 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V12, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     0   6
  SLC6A11 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      0    6
  SLC6A11 WILD-TYPE   10  392
                        clus
vv                       SLC6A11 MUTATED SLC6A11 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(917) Variable = SMCHD1 MUTATION ANALYSIS
D917V1, survival
                  sevent
clus2                0   1
  SMCHD1 MUTATED    12   3
  SMCHD1 WILD-TYPE 326 213
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              15              539 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
               3              213 
$`SMCHD1 MUTATED`
TCGA-EQ-A4SO TCGA-KH-A6WC TCGA-L5-A8NL TCGA-LN-A49R TCGA-BR-4184 TCGA-BR-4201 
       16.24         6.28        13.22        13.38         6.97        30.90 
TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-A4MG 
       35.84        32.25        24.79        31.96        20.42         6.58 
TCGA-CG-4437 TCGA-HU-A4G8 TCGA-HU-A4GH 
        8.05        22.68        11.77 

$`SMCHD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53        26.73        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
            6.28             0.00 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
           35.84           122.30 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
           16.24            13.55 
[1] "6.3 - 35.8 (16.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.1"
D917V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMCHD1 MUTATED         0        3        3        1         1         2
  SMCHD1 WILD-TYPE      10       17       43       30        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMCHD1 MUTATED           2          1          1          0        1
  SMCHD1 WILD-TYPE        27         83         61         39       42
                  vv
clus               STAGE IVA
  SMCHD1 MUTATED           0
  SMCHD1 WILD-TYPE         4
D917V3, multiclass
            clus
vv           SMCHD1 MUTATED SMCHD1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                3               17
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SMCHD1 MUTATED       3   5   5   3
  SMCHD1 WILD-TYPE    51 130 256  99
D917V4, multiclass
       clus
vv      SMCHD1 MUTATED SMCHD1 WILD-TYPE
  T0+T1              3               51
  T2                 5              130
  T3                 5              256
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SMCHD1 MUTATED     8   7   1   0
  SMCHD1 WILD-TYPE 187 166  88  85
D917V5, multiclass
    clus
vv   SMCHD1 MUTATED SMCHD1 WILD-TYPE
  N0              8              187
  N1              7              166
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V6, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED    14   1
  SMCHD1 WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED     14    1
  SMCHD1 WILD-TYPE  468   37
   clus
vv  SMCHD1 MUTATED SMCHD1 WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D917V7, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED     6  11
  SMCHD1 WILD-TYPE 166 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED      6   11
  SMCHD1 WILD-TYPE  166  395
        clus
vv       SMCHD1 MUTATED SMCHD1 WILD-TYPE
  FEMALE              6              166
  MALE               11              395
[1] 2 2
[1] FALSE
D917V8, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED    11   4
  SMCHD1 WILD-TYPE 405  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED     11    4
  SMCHD1 WILD-TYPE  405   98
     clus
vv    SMCHD1 MUTATED SMCHD1 WILD-TYPE
  NO              11              405
  YES              4               98
[1] 2 2
[1] FALSE
D917V9, continuous
[1] "Remove cluster labels:" "SMCHD1 MUTATED"        
clus
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49S 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A49X 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
D917V10, continuous
[1] "Remove cluster labels:" "SMCHD1 MUTATED"        
clus
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-L5-A43C 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" "SMCHD1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SMCHD1 MUTATED       6                         0
  SMCHD1 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMCHD1 MUTATED                                           0    10
  SMCHD1 WILD-TYPE                                         1   347
D917V11, multiclass
                                           clus
vv                                          SMCHD1 MUTATED SMCHD1 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V12, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED     0  15
  SMCHD1 WILD-TYPE  10 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED      0   15
  SMCHD1 WILD-TYPE   10  383
                        clus
vv                       SMCHD1 MUTATED SMCHD1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(918) Variable = PGCP MUTATION ANALYSIS
D918V1, survival
                sevent
clus2              0   1
  PGCP MUTATED     7   3
  PGCP WILD-TYPE 331 213
  PGCP MUTATED PGCP WILD-TYPE 
            10            544 
  PGCP MUTATED PGCP WILD-TYPE 
             3            213 
$`PGCP MUTATED`
TCGA-L5-A8NG TCGA-2H-A9GH TCGA-L5-A43C TCGA-BR-8059 TCGA-BR-8297 TCGA-BR-A4CQ 
       35.97        31.27         3.16        14.43         7.40        34.98 
TCGA-BR-A4PE TCGA-CG-5721 TCGA-CG-5733 TCGA-MX-A5UJ 
       20.42         6.02        21.07        19.73 

$`PGCP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PGCP MUTATED PGCP WILD-TYPE 
          3.16           0.00 
  PGCP MUTATED PGCP WILD-TYPE 
         35.97         122.30 
  PGCP MUTATED PGCP WILD-TYPE 
        20.075         13.510 
[1] "3.2 - 36.0 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D918V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGCP MUTATED         0        0        1        0         0         1
  PGCP WILD-TYPE      10       20       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGCP MUTATED           2          3          0          1        1         0
  PGCP WILD-TYPE        27         81         62         38       42         4
D918V3, multiclass
            clus
vv           PGCP MUTATED PGCP WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             2             27
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PGCP MUTATED       1   2   2   4
  PGCP WILD-TYPE    53 133 259  98
D918V4, multiclass
       clus
vv      PGCP MUTATED PGCP WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PGCP MUTATED     1   5   2   1
  PGCP WILD-TYPE 194 168  87  84
D918V5, multiclass
    clus
vv   PGCP MUTATED PGCP WILD-TYPE
  N0            1            194
  N1            5            168
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V6, binary
                cls
clus               0   1
  PGCP MUTATED     9   0
  PGCP WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGCP MUTATED      9    0
  PGCP WILD-TYPE  473   38
   clus
vv  PGCP MUTATED PGCP WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D918V7, binary
                cls
clus               0   1
  PGCP MUTATED     3   7
  PGCP WILD-TYPE 169 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGCP MUTATED      3    7
  PGCP WILD-TYPE  169  399
        clus
vv       PGCP MUTATED PGCP WILD-TYPE
  FEMALE            3            169
  MALE              7            399
[1] 2 2
[1] FALSE
D918V8, binary
                cls
clus               0   1
  PGCP MUTATED    10   0
  PGCP WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGCP MUTATED     10    0
  PGCP WILD-TYPE  406  102
     clus
vv    PGCP MUTATED PGCP WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D918V9, continuous
D918V10, continuous
[1] "Remove cluster labels:" "PGCP MUTATED"          
clus
  PGCP MUTATED PGCP WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43E 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" "PGCP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PGCP MUTATED       0                         0
  PGCP WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PGCP MUTATED                                           0     7
  PGCP WILD-TYPE                                         1   350
D918V11, multiclass
                                           clus
vv                                          PGCP MUTATED PGCP WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V12, binary
                cls
clus               0   1
  PGCP MUTATED     0   5
  PGCP WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGCP MUTATED      0    5
  PGCP WILD-TYPE   10  393
                        clus
vv                       PGCP MUTATED PGCP WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(919) Variable = TBL1XR1 MUTATION ANALYSIS
D919V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED     6   3
  TBL1XR1 WILD-TYPE 332 213
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                9               545 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                3               213 
$`TBL1XR1 MUTATED`
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-V5-AASV TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8680 
       16.47         7.76        15.35         9.34        29.59        31.96 
TCGA-CG-5726 TCGA-FP-A4BE TCGA-VQ-A8P2 
       28.96        11.08        38.14 

$`TBL1XR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
             7.76              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            38.14            122.30 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            16.47             13.51 
[1] "7.8 - 38.1 (16.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D919V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBL1XR1 MUTATED         0        1        0        0         1         3
  TBL1XR1 WILD-TYPE      10       19       46       31        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           1          2          0          0        2
  TBL1XR1 WILD-TYPE        28         82         62         39       41
                   vv
clus                STAGE IVA
  TBL1XR1 MUTATED           0
  TBL1XR1 WILD-TYPE         4
D919V3, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TBL1XR1 MUTATED       1   1   3   5
  TBL1XR1 WILD-TYPE    53 134 258  97
D919V4, multiclass
       clus
vv      TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  3               258
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TBL1XR1 MUTATED     5   4   2   0
  TBL1XR1 WILD-TYPE 190 169  87  85
D919V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V6, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     9   1
  TBL1XR1 WILD-TYPE 473  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      9    1
  TBL1XR1 WILD-TYPE  473   37
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0               9               473
  1               1                37
[1] 2 2
[1] FALSE
D919V7, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     4   7
  TBL1XR1 WILD-TYPE 168 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      4    7
  TBL1XR1 WILD-TYPE  168  399
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  FEMALE               4               168
  MALE                 7               399
[1] 2 2
[1] FALSE
D919V8, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     5   3
  TBL1XR1 WILD-TYPE 411  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      5    3
  TBL1XR1 WILD-TYPE  411   99
     clus
vv    TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  NO                5               411
  YES               3                99
[1] 2 2
[1] FALSE
D919V9, continuous
[1] "Remove cluster labels:" "TBL1XR1 MUTATED"       
clus
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
D919V10, continuous
[1] "Remove cluster labels:" "TBL1XR1 MUTATED"       
clus
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" "TBL1XR1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TBL1XR1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TBL1XR1 MUTATED       1                         2
  TBL1XR1 WILD-TYPE   132                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBL1XR1 MUTATED                                           0     7
  TBL1XR1 WILD-TYPE                                         1   350
D919V11, multiclass
                                           clus
vv                                          TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V12, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     0   7
  TBL1XR1 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      0    7
  TBL1XR1 WILD-TYPE   10  391
                        clus
vv                       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(920) Variable = TMEM127 MUTATION ANALYSIS
D920V1, survival
                   sevent
clus2                 0   1
  TMEM127 MUTATED     5   1
  TMEM127 WILD-TYPE 333 215
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                6               548 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                1               215 
$`TMEM127 MUTATED`
TCGA-L5-A4OM TCGA-BR-6452 TCGA-BR-6566 TCGA-CD-8531 TCGA-HF-A5NB TCGA-R5-A7ZI 
       47.93        34.68        32.78        12.59        30.51        74.53 

$`TMEM127 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TMEM127 MUTATED TMEM127 WILD-TYPE 
            12.59              0.00 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
            74.53            122.30 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
            33.73             13.51 
[1] "12.6 - 74.5 (33.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4.8"
D920V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM127 MUTATED         0        1        0        0         2         0
  TMEM127 WILD-TYPE      10       19       46       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM127 MUTATED           0          1          0          1        1
  TMEM127 WILD-TYPE        29         83         62         38       42
                   vv
clus                STAGE IVA
  TMEM127 MUTATED           0
  TMEM127 WILD-TYPE         4
D920V3, multiclass
            clus
vv           TMEM127 MUTATED TMEM127 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM127 MUTATED       1   0   3   2
  TMEM127 WILD-TYPE    53 135 258 100
D920V4, multiclass
       clus
vv      TMEM127 MUTATED TMEM127 WILD-TYPE
  T0+T1               1                53
  T2                  0               135
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM127 MUTATED     3   2   0   1
  TMEM127 WILD-TYPE 192 171  89  84
D920V5, multiclass
    clus
vv   TMEM127 MUTATED TMEM127 WILD-TYPE
  N0               3               192
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V6, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     4   1
  TMEM127 WILD-TYPE 478  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      4    1
  TMEM127 WILD-TYPE  478   37
   clus
vv  TMEM127 MUTATED TMEM127 WILD-TYPE
  0               4               478
  1               1                37
[1] 2 2
[1] FALSE
D920V7, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     6   0
  TMEM127 WILD-TYPE 166 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      6    0
  TMEM127 WILD-TYPE  166  406
        clus
vv       TMEM127 MUTATED TMEM127 WILD-TYPE
  FEMALE               6               166
  MALE                 0               406
[1] 2 2
[1] FALSE
D920V8, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     4   2
  TMEM127 WILD-TYPE 412 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      4    2
  TMEM127 WILD-TYPE  412  100
     clus
vv    TMEM127 MUTATED TMEM127 WILD-TYPE
  NO                4               412
  YES               2               100
[1] 2 2
[1] FALSE
D920V9, continuous
D920V10, continuous
[1] "Remove cluster labels:" "TMEM127 MUTATED"       
clus
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" "TMEM127 WILD-TYPE" 
       TCGA-Z6-AAPN 
"TMEM127 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM127 MUTATED       1                         0
  TMEM127 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM127 MUTATED                                           0     4
  TMEM127 WILD-TYPE                                         1   353
D920V11, multiclass
                                           clus
vv                                          TMEM127 MUTATED TMEM127 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V12, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     1   3
  TMEM127 WILD-TYPE   9 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      1    3
  TMEM127 WILD-TYPE    9  395
                        clus
vv                       TMEM127 MUTATED TMEM127 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(921) Variable = APITD1 MUTATION ANALYSIS
D921V1, survival
                  sevent
clus2                0   1
  APITD1 MUTATED     1   5
  APITD1 WILD-TYPE 337 211
  APITD1 MUTATED APITD1 WILD-TYPE 
               6              548 
  APITD1 MUTATED APITD1 WILD-TYPE 
               5              211 
$`APITD1 MUTATED`
TCGA-IG-A625 TCGA-BR-4257 TCGA-BR-8361 TCGA-BR-8382 TCGA-CD-A4MI TCGA-D7-A4YV 
       12.82         9.67        31.10        25.05        11.77         5.92 

$`APITD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  APITD1 MUTATED APITD1 WILD-TYPE 
            5.92             0.00 
  APITD1 MUTATED APITD1 WILD-TYPE 
            31.1            122.3 
  APITD1 MUTATED APITD1 WILD-TYPE 
          12.295           13.630 
[1] "5.9 - 31.1 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D921V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APITD1 MUTATED         0        0        0        0         0         1
  APITD1 WILD-TYPE      10       20       46       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APITD1 MUTATED           0          1          1          2        0
  APITD1 WILD-TYPE        29         83         61         37       43
                  vv
clus               STAGE IVA
  APITD1 MUTATED           0
  APITD1 WILD-TYPE         4
D921V3, multiclass
            clus
vv           APITD1 MUTATED APITD1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  APITD1 MUTATED       0   0   3   2
  APITD1 WILD-TYPE    54 135 258 100
D921V4, multiclass
       clus
vv      APITD1 MUTATED APITD1 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  APITD1 MUTATED     0   2   2   1
  APITD1 WILD-TYPE 195 171  87  84
D921V5, multiclass
    clus
vv   APITD1 MUTATED APITD1 WILD-TYPE
  N0              0              195
  N1              2              171
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V6, binary
                  cls
clus                 0   1
  APITD1 MUTATED     6   0
  APITD1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      6    0
  APITD1 WILD-TYPE  476   38
   clus
vv  APITD1 MUTATED APITD1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D921V7, binary
                  cls
clus                 0   1
  APITD1 MUTATED     4   2
  APITD1 WILD-TYPE 168 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      4    2
  APITD1 WILD-TYPE  168  404
        clus
vv       APITD1 MUTATED APITD1 WILD-TYPE
  FEMALE              4              168
  MALE                2              404
[1] 2 2
[1] FALSE
D921V8, binary
                  cls
clus                 0   1
  APITD1 MUTATED     5   0
  APITD1 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      5    0
  APITD1 WILD-TYPE  411  102
     clus
vv    APITD1 MUTATED APITD1 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D921V9, continuous
D921V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  APITD1 MUTATED       2                         0
  APITD1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APITD1 MUTATED                                           0     4
  APITD1 WILD-TYPE                                         1   353
D921V11, multiclass
                                           clus
vv                                          APITD1 MUTATED APITD1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V12, binary
                  cls
clus                 0   1
  APITD1 MUTATED     0   6
  APITD1 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      0    6
  APITD1 WILD-TYPE   10  392
                        clus
vv                       APITD1 MUTATED APITD1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(922) Variable = UGT2A3 MUTATION ANALYSIS
D922V1, survival
                  sevent
clus2                0   1
  UGT2A3 MUTATED     5   2
  UGT2A3 WILD-TYPE 333 214
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               7              547 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               2              214 
$`UGT2A3 MUTATED`
TCGA-LN-A8I0 TCGA-BR-4184 TCGA-CG-4465 TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4G8 
       13.38         6.97         9.01         6.02        22.32        22.68 
TCGA-HU-A4H2 
       12.95 

$`UGT2A3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
            6.02             0.00 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           22.68           122.30 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           12.95            13.68 
[1] "6.0 - 22.7 (12.9)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D922V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGT2A3 MUTATED         0        0        0        0         1         2
  UGT2A3 WILD-TYPE      10       20       46       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT2A3 MUTATED           0          1          1          0        3
  UGT2A3 WILD-TYPE        29         83         61         39       40
                  vv
clus               STAGE IVA
  UGT2A3 MUTATED           0
  UGT2A3 WILD-TYPE         4
D922V3, multiclass
            clus
vv           UGT2A3 MUTATED UGT2A3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  UGT2A3 MUTATED       0   1   3   4
  UGT2A3 WILD-TYPE    54 134 258  98
D922V4, multiclass
       clus
vv      UGT2A3 MUTATED UGT2A3 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  UGT2A3 MUTATED     2   3   1   2
  UGT2A3 WILD-TYPE 193 170  88  83
D922V5, multiclass
    clus
vv   UGT2A3 MUTATED UGT2A3 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V6, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     6   1
  UGT2A3 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      6    1
  UGT2A3 WILD-TYPE  476   37
   clus
vv  UGT2A3 MUTATED UGT2A3 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D922V7, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     5   3
  UGT2A3 WILD-TYPE 167 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      5    3
  UGT2A3 WILD-TYPE  167  403
        clus
vv       UGT2A3 MUTATED UGT2A3 WILD-TYPE
  FEMALE              5              167
  MALE                3              403
[1] 2 2
[1] FALSE
D922V8, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     6   0
  UGT2A3 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      6    0
  UGT2A3 WILD-TYPE  410  102
     clus
vv    UGT2A3 MUTATED UGT2A3 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D922V9, continuous
D922V10, continuous
[1] "Remove cluster labels:" "UGT2A3 MUTATED"        
clus
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"UGT2A3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UGT2A3 MUTATED       4                         0
  UGT2A3 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGT2A3 MUTATED                                           0     2
  UGT2A3 WILD-TYPE                                         1   355
D922V11, multiclass
                                           clus
vv                                          UGT2A3 MUTATED UGT2A3 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V12, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     0   6
  UGT2A3 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      0    6
  UGT2A3 WILD-TYPE   10  392
                        clus
vv                       UGT2A3 MUTATED UGT2A3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(923) Variable = ATP8B1 MUTATION ANALYSIS
D923V1, survival
                  sevent
clus2                0   1
  ATP8B1 MUTATED    13   4
  ATP8B1 WILD-TYPE 325 212
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              17              537 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               4              212 
$`ATP8B1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NL TCGA-L5-A8NW TCGA-LN-A8I1 TCGA-VR-A8EW TCGA-B7-5818 
       60.39        13.22        46.09        13.18         8.12        11.70 
TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4449 TCGA-D7-A6F0 
        9.67        35.24        31.96         6.58        19.07        22.29 
TCGA-F1-6874 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-AA68 
       14.47         6.51        20.25        38.14        43.66 

$`ATP8B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            6.51             0.00 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
           60.39           122.30 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
           19.07            13.51 
[1] "6.5 - 60.4 (19.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D923V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP8B1 MUTATED         2        0        4        2         3         0
  ATP8B1 WILD-TYPE       8       20       42       29        81        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B1 MUTATED           1          2          1          2        1
  ATP8B1 WILD-TYPE        28         82         61         37       42
                  vv
clus               STAGE IVA
  ATP8B1 MUTATED           0
  ATP8B1 WILD-TYPE         4
D923V3, multiclass
            clus
vv           ATP8B1 MUTATED ATP8B1 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                2               29
  STAGE IIA               3               81
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATP8B1 MUTATED       3   6   5   5
  ATP8B1 WILD-TYPE    51 129 256  97
D923V4, multiclass
       clus
vv      ATP8B1 MUTATED ATP8B1 WILD-TYPE
  T0+T1              3               51
  T2                 6              129
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP8B1 MUTATED     9   5   3   1
  ATP8B1 WILD-TYPE 186 168  86  84
D923V5, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  N0              9              186
  N1              5              168
  N2              3               86
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V6, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    19   1
  ATP8B1 WILD-TYPE 463  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     19    1
  ATP8B1 WILD-TYPE  463   37
   clus
vv  ATP8B1 MUTATED ATP8B1 WILD-TYPE
  0             19              463
  1              1               37
[1] 2 2
[1] FALSE
D923V7, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    10  11
  ATP8B1 WILD-TYPE 162 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     10   11
  ATP8B1 WILD-TYPE  162  395
        clus
vv       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  FEMALE             10              162
  MALE               11              395
[1] 2 2
[1] FALSE
D923V8, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    14   3
  ATP8B1 WILD-TYPE 402  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     14    3
  ATP8B1 WILD-TYPE  402   99
     clus
vv    ATP8B1 MUTATED ATP8B1 WILD-TYPE
  NO              14              402
  YES              3               99
[1] 2 2
[1] FALSE
D923V9, continuous
[1] "Remove cluster labels:" "ATP8B1 MUTATED"        
clus
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
D923V10, continuous
[1] "Remove cluster labels:" "ATP8B1 MUTATED"        
clus
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-LN-A49O 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" "ATP8B1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP8B1 MUTATED       6                         1
  ATP8B1 WILD-TYPE   127                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP8B1 MUTATED                                           0    13
  ATP8B1 WILD-TYPE                                         1   344
D923V11, multiclass
                                           clus
vv                                          ATP8B1 MUTATED ATP8B1 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V12, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED     0  14
  ATP8B1 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED      0   14
  ATP8B1 WILD-TYPE   10  384
                        clus
vv                       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(924) Variable = HIVEP1 MUTATION ANALYSIS
D924V1, survival
                  sevent
clus2                0   1
  HIVEP1 MUTATED    22   7
  HIVEP1 WILD-TYPE 316 209
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              29              525 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
               7              209 
$`HIVEP1 MUTATED`
TCGA-JY-A6FB TCGA-EQ-A4SO TCGA-IG-A4P3 TCGA-L5-A88V TCGA-L5-A8NS TCGA-LN-A49M 
       60.39        16.24        18.64         2.60        13.41        12.66 
TCGA-LN-A4A2 TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8081 
       12.49         9.67        30.90        35.24        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
        8.05         3.32        25.05         1.12        28.14        31.96 
TCGA-BR-A4QL TCGA-CD-8528 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5726 
       16.14        12.33         6.58         8.05         6.02        28.96 
TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-HU-A4H8 
       52.21        22.32         6.51        23.84        14.07 

$`HIVEP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
        5.92        10.45        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31        14.04        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
       11.08         5.52         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        2.10        12.95        29.00        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
            1.12             0.00 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           60.39           122.30 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           16.14            13.51 
[1] "1.1 - 60.4 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D924V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP1 MUTATED         1        2        1        2         5         6
  HIVEP1 WILD-TYPE       9       18       45       29        79        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP1 MUTATED           1          2          3          3        2
  HIVEP1 WILD-TYPE        28         82         59         36       41
                  vv
clus               STAGE IVA
  HIVEP1 MUTATED           0
  HIVEP1 WILD-TYPE         4
D924V3, multiclass
            clus
vv           HIVEP1 MUTATED HIVEP1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               5               79
  STAGE IIB               6               77
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              3               59
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HIVEP1 MUTATED       4   4  11  10
  HIVEP1 WILD-TYPE    50 131 250  92
D924V4, multiclass
       clus
vv      HIVEP1 MUTATED HIVEP1 WILD-TYPE
  T0+T1              4               50
  T2                 4              131
  T3                11              250
  T4                10               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HIVEP1 MUTATED    14   6   3   5
  HIVEP1 WILD-TYPE 181 167  86  80
D924V5, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  N0             14              181
  N1              6              167
  N2              3               86
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V6, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    26   1
  HIVEP1 WILD-TYPE 456  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     26    1
  HIVEP1 WILD-TYPE  456   37
   clus
vv  HIVEP1 MUTATED HIVEP1 WILD-TYPE
  0             26              456
  1              1               37
[1] 2 2
[1] FALSE
D924V7, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    13  17
  HIVEP1 WILD-TYPE 159 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     13   17
  HIVEP1 WILD-TYPE  159  389
        clus
vv       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  FEMALE             13              159
  MALE               17              389
[1] 2 2
[1] FALSE
D924V8, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    22   6
  HIVEP1 WILD-TYPE 394  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     22    6
  HIVEP1 WILD-TYPE  394   96
     clus
vv    HIVEP1 MUTATED HIVEP1 WILD-TYPE
  NO              22              394
  YES              6               96
[1] 2 2
[1] FALSE
D924V9, continuous
[1] "Remove cluster labels:" "HIVEP1 MUTATED"        
clus
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A3 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"HIVEP1 WILD-TYPE" "HIVEP1 WILD-TYPE" 
D924V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HIVEP1 MUTATED       9                         0
  HIVEP1 WILD-TYPE   124                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIVEP1 MUTATED                                           0    17
  HIVEP1 WILD-TYPE                                         1   340
D924V11, multiclass
                                           clus
vv                                          HIVEP1 MUTATED HIVEP1 WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V12, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED     0  23
  HIVEP1 WILD-TYPE  10 375
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED      0   23
  HIVEP1 WILD-TYPE   10  375
                        clus
vv                       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             23              375
[1] 2 2
[1] FALSE

Clustering(925) Variable = RINT1 MUTATION ANALYSIS
D925V1, survival
                 sevent
clus2               0   1
  RINT1 MUTATED     4   4
  RINT1 WILD-TYPE 334 212
  RINT1 MUTATED RINT1 WILD-TYPE 
              8             546 
  RINT1 MUTATED RINT1 WILD-TYPE 
              4             212 
$`RINT1 MUTATED`
TCGA-LN-A4A2 TCGA-LN-A7HY TCGA-VR-A8EQ TCGA-BR-6709 TCGA-BR-8078 TCGA-BR-8680 
       12.49        12.03        22.82        12.16        29.59        31.96 
TCGA-CD-A4MG TCGA-CG-5726 
        6.58        28.96 

$`RINT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RINT1 MUTATED RINT1 WILD-TYPE 
           6.58            0.00 
  RINT1 MUTATED RINT1 WILD-TYPE 
          31.96          122.30 
  RINT1 MUTATED RINT1 WILD-TYPE 
         17.655          13.565 
[1] "6.6 - 32.0 (17.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D925V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RINT1 MUTATED         1        2        0        0         2         1
  RINT1 WILD-TYPE       9       18       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RINT1 MUTATED           2          0          1          0        1         0
  RINT1 WILD-TYPE        27         84         61         39       42         4
D925V3, multiclass
            clus
vv           RINT1 MUTATED RINT1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RINT1 MUTATED       3   0   5   2
  RINT1 WILD-TYPE    51 135 256 100
D925V4, multiclass
       clus
vv      RINT1 MUTATED RINT1 WILD-TYPE
  T0+T1             3              51
  T2                0             135
  T3                5             256
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RINT1 MUTATED     5   3   1   1
  RINT1 WILD-TYPE 190 170  88  84
D925V5, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V6, binary
                 cls
clus                0   1
  RINT1 MUTATED     8   1
  RINT1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      8    1
  RINT1 WILD-TYPE  474   37
   clus
vv  RINT1 MUTATED RINT1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D925V7, binary
                 cls
clus                0   1
  RINT1 MUTATED     2   8
  RINT1 WILD-TYPE 170 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      2    8
  RINT1 WILD-TYPE  170  398
        clus
vv       RINT1 MUTATED RINT1 WILD-TYPE
  FEMALE             2             170
  MALE               8             398
[1] 2 2
[1] FALSE
D925V8, binary
                 cls
clus                0   1
  RINT1 MUTATED     6   3
  RINT1 WILD-TYPE 410  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      6    3
  RINT1 WILD-TYPE  410   99
     clus
vv    RINT1 MUTATED RINT1 WILD-TYPE
  NO              6             410
  YES             3              99
[1] 2 2
[1] FALSE
D925V9, continuous
D925V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RINT1 MUTATED       5                         1
  RINT1 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RINT1 MUTATED                                           0     3
  RINT1 WILD-TYPE                                         1   354
D925V11, multiclass
                                           clus
vv                                          RINT1 MUTATED RINT1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V12, binary
                 cls
clus                0   1
  RINT1 MUTATED     0   8
  RINT1 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      0    8
  RINT1 WILD-TYPE   10  390
                        clus
vv                       RINT1 MUTATED RINT1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(926) Variable = H2AFY MUTATION ANALYSIS
D926V1, survival
                 sevent
clus2               0   1
  H2AFY MUTATED     7   1
  H2AFY WILD-TYPE 331 215
  H2AFY MUTATED H2AFY WILD-TYPE 
              8             546 
  H2AFY MUTATED H2AFY WILD-TYPE 
              1             215 
$`H2AFY MUTATED`
TCGA-IG-A3QL TCGA-L5-A8NN TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8361 
       35.21         5.49        26.70        34.68        29.59        31.10 
TCGA-HU-A4GQ TCGA-HU-A4GX 
        0.10        20.25 

$`H2AFY WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  H2AFY MUTATED H2AFY WILD-TYPE 
            0.1             0.0 
  H2AFY MUTATED H2AFY WILD-TYPE 
          35.21          122.30 
  H2AFY MUTATED H2AFY WILD-TYPE 
         28.145          13.510 
[1] "0.1 - 35.2 (28.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.2"
D926V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  H2AFY MUTATED         0        0        0        0         2         2
  H2AFY WILD-TYPE      10       20       46       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  H2AFY MUTATED           1          1          0          3        0         0
  H2AFY WILD-TYPE        28         83         62         36       43         4
D926V3, multiclass
            clus
vv           H2AFY MUTATED H2AFY WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  H2AFY MUTATED       0   1   2   6
  H2AFY WILD-TYPE    54 134 259  96
D926V4, multiclass
       clus
vv      H2AFY MUTATED H2AFY WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  H2AFY MUTATED     5   1   3   0
  H2AFY WILD-TYPE 190 172  86  85
D926V5, multiclass
    clus
vv   H2AFY MUTATED H2AFY WILD-TYPE
  N0             5             190
  N1             1             172
  N2             3              86
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V6, binary
                 cls
clus                0   1
  H2AFY MUTATED     9   0
  H2AFY WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      9    0
  H2AFY WILD-TYPE  473   38
   clus
vv  H2AFY MUTATED H2AFY WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D926V7, binary
                 cls
clus                0   1
  H2AFY MUTATED     6   3
  H2AFY WILD-TYPE 166 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      6    3
  H2AFY WILD-TYPE  166  403
        clus
vv       H2AFY MUTATED H2AFY WILD-TYPE
  FEMALE             6             166
  MALE               3             403
[1] 2 2
[1] FALSE
D926V8, binary
                 cls
clus                0   1
  H2AFY MUTATED     8   0
  H2AFY WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      8    0
  H2AFY WILD-TYPE  408  102
     clus
vv    H2AFY MUTATED H2AFY WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D926V9, continuous
[1] "Remove cluster labels:" "H2AFY MUTATED"         
clus
  H2AFY MUTATED H2AFY WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
D926V10, continuous
[1] "Remove cluster labels:" "H2AFY MUTATED"         
clus
  H2AFY MUTATED H2AFY WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" "H2AFY WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  H2AFY MUTATED       2                         0
  H2AFY WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  H2AFY MUTATED                                           0     7
  H2AFY WILD-TYPE                                         1   350
D926V11, multiclass
                                           clus
vv                                          H2AFY MUTATED H2AFY WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V12, binary
                 cls
clus                0   1
  H2AFY MUTATED     0   8
  H2AFY WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      0    8
  H2AFY WILD-TYPE   10  390
                        clus
vv                       H2AFY MUTATED H2AFY WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(927) Variable = TAF1L MUTATION ANALYSIS
D927V1, survival
                 sevent
clus2               0   1
  TAF1L MUTATED    23  13
  TAF1L WILD-TYPE 315 203
  TAF1L MUTATED TAF1L WILD-TYPE 
             36             518 
  TAF1L MUTATED TAF1L WILD-TYPE 
             13             203 
$`TAF1L MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-IG-A3YB TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OX 
       25.78         7.63         2.63        30.25        21.01         7.43 
TCGA-LN-A8I1 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-6802 
       13.18        11.70        30.90        34.68        25.61        30.90 
TCGA-BR-7707 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8591 TCGA-BR-8680 
       35.84         8.05         7.40         9.21        28.14        31.96 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4477 TCGA-D7-6521 TCGA-D7-A4YX TCGA-F1-A448 
       16.14        15.95        30.97        18.54        36.43        21.27 
TCGA-FP-A9TM TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-RD-A8N1 
        6.21        11.77         0.10        14.07        13.35       115.69 
TCGA-RD-A8N5 TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A91U TCGA-VQ-A94T 
       57.44        13.02        37.41        38.14         1.71        11.24 

$`TAF1L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        29.59         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       20.81        42.64        66.81        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TAF1L MUTATED TAF1L WILD-TYPE 
            0.1             0.0 
  TAF1L MUTATED TAF1L WILD-TYPE 
         115.69          122.30 
  TAF1L MUTATED TAF1L WILD-TYPE 
         17.340          13.495 
[1] "0.1 - 115.7 (17.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D927V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF1L MUTATED         3        1        4        1         2         2
  TAF1L WILD-TYPE       7       19       42       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1L MUTATED           2          6          5          5        3         0
  TAF1L WILD-TYPE        27         78         57         34       40         4
D927V3, multiclass
            clus
vv           TAF1L MUTATED TAF1L WILD-TYPE
  STAGE I                3               7
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             6              78
  STAGE IIIB             5              57
  STAGE IIIC             5              34
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TAF1L MUTATED       6  10  14   8
  TAF1L WILD-TYPE    48 125 247  94
D927V4, multiclass
       clus
vv      TAF1L MUTATED TAF1L WILD-TYPE
  T0+T1             6              48
  T2               10             125
  T3               14             247
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TAF1L MUTATED     8  14   6   8
  TAF1L WILD-TYPE 187 159  83  77
D927V5, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  N0             8             187
  N1            14             159
  N2             6              83
  N3             8              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V6, binary
                 cls
clus                0   1
  TAF1L MUTATED    34   3
  TAF1L WILD-TYPE 448  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     34    3
  TAF1L WILD-TYPE  448   35
   clus
vv  TAF1L MUTATED TAF1L WILD-TYPE
  0            34             448
  1             3              35
[1] 2 2
[1] FALSE
D927V7, binary
                 cls
clus                0   1
  TAF1L MUTATED    10  28
  TAF1L WILD-TYPE 162 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     10   28
  TAF1L WILD-TYPE  162  378
        clus
vv       TAF1L MUTATED TAF1L WILD-TYPE
  FEMALE            10             162
  MALE              28             378
[1] 2 2
[1] FALSE
D927V8, binary
                 cls
clus                0   1
  TAF1L MUTATED    29   8
  TAF1L WILD-TYPE 387  94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     29    8
  TAF1L WILD-TYPE  387   94
     clus
vv    TAF1L MUTATED TAF1L WILD-TYPE
  NO             29             387
  YES             8              94
[1] 2 2
[1] FALSE
D927V9, continuous
[1] "Remove cluster labels:" "TAF1L MUTATED"         
clus
  TAF1L MUTATED TAF1L WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
D927V10, continuous
[1] "Remove cluster labels:" "TAF1L MUTATED"         
clus
  TAF1L MUTATED TAF1L WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A88S 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" "TAF1L WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF1L MUTATED       6                         2
  TAF1L WILD-TYPE   127                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF1L MUTATED                                           0    25
  TAF1L WILD-TYPE                                         1   332
D927V11, multiclass
                                           clus
vv                                          TAF1L MUTATED TAF1L WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                25             332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V12, binary
                 cls
clus                0   1
  TAF1L MUTATED     1  25
  TAF1L WILD-TYPE   9 373
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      1   25
  TAF1L WILD-TYPE    9  373
                        clus
vv                       TAF1L MUTATED TAF1L WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            25             373
[1] 2 2
[1] FALSE

Clustering(928) Variable = C1ORF177 MUTATION ANALYSIS
D928V1, survival
                    sevent
clus2                  0   1
  C1ORF177 MUTATED     8   4
  C1ORF177 WILD-TYPE 330 212
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                542 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 4                212 
$`C1ORF177 MUTATED`
TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7722 TCGA-BR-8363 TCGA-BR-8487 
        9.34        32.78        44.94        15.32         0.26         1.12 
TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-R5-A7ZI TCGA-SW-A7EA 
       11.44        77.29         6.51         6.58        74.53        19.04 

$`C1ORF177 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
              0.26               0.00 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
             77.29             122.30 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
            13.380             13.565 
[1] "0.3 - 77.3 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D928V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF177 MUTATED         0        0        2        1         4         2
  C1ORF177 WILD-TYPE      10       20       44       30        80        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF177 MUTATED           0          0          1          0        1
  C1ORF177 WILD-TYPE        29         84         61         39       42
                    vv
clus                 STAGE IVA
  C1ORF177 MUTATED           0
  C1ORF177 WILD-TYPE         4
D928V3, multiclass
            clus
vv           C1ORF177 MUTATED C1ORF177 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  1                 30
  STAGE IIA                 4                 80
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  C1ORF177 MUTATED       0   3   7   1
  C1ORF177 WILD-TYPE    54 132 254 101
D928V4, multiclass
       clus
vv      C1ORF177 MUTATED C1ORF177 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   7                254
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  C1ORF177 MUTATED     6   5   0   1
  C1ORF177 WILD-TYPE 189 168  89  84
D928V5, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  N0                6                189
  N1                5                168
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V6, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED    11   1
  C1ORF177 WILD-TYPE 471  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED     11    1
  C1ORF177 WILD-TYPE  471   37
   clus
vv  C1ORF177 MUTATED C1ORF177 WILD-TYPE
  0               11                471
  1                1                 37
[1] 2 2
[1] FALSE
D928V7, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     8   4
  C1ORF177 WILD-TYPE 164 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      8    4
  C1ORF177 WILD-TYPE  164  402
        clus
vv       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  FEMALE                8                164
  MALE                  4                402
[1] 2 2
[1] FALSE
D928V8, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED    11   1
  C1ORF177 WILD-TYPE 405 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED     11    1
  C1ORF177 WILD-TYPE  405  101
     clus
vv    C1ORF177 MUTATED C1ORF177 WILD-TYPE
  NO                11                405
  YES                1                101
[1] 2 2
[1] FALSE
D928V9, continuous
D928V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF177 MUTATED       2                         0
  C1ORF177 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF177 MUTATED                                           0     9
  C1ORF177 WILD-TYPE                                         1   348
D928V11, multiclass
                                           clus
vv                                          C1ORF177 MUTATED C1ORF177 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V12, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     1  10
  C1ORF177 WILD-TYPE   9 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      1   10
  C1ORF177 WILD-TYPE    9  388
                        clus
vv                       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               10                388
[1] 2 2
[1] FALSE

Clustering(929) Variable = DGKD MUTATION ANALYSIS
D929V1, survival
                sevent
clus2              0   1
  DGKD MUTATED     4   4
  DGKD WILD-TYPE 334 212
  DGKD MUTATED DGKD WILD-TYPE 
             8            546 
  DGKD MUTATED DGKD WILD-TYPE 
             4            212 
$`DGKD MUTATED`
TCGA-2H-A9GL TCGA-L5-A8NQ TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8525 TCGA-HF-7134 
        5.92        21.37        30.90         1.12        12.59        52.21 
TCGA-HU-8602 TCGA-HU-A4GQ 
       22.32         0.10 

$`DGKD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DGKD MUTATED DGKD WILD-TYPE 
           0.1            0.0 
  DGKD MUTATED DGKD WILD-TYPE 
         52.21         122.30 
  DGKD MUTATED DGKD WILD-TYPE 
        16.980         13.565 
[1] "0.1 - 52.2 (17.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D929V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DGKD MUTATED         0        1        0        0         2         1
  DGKD WILD-TYPE      10       19       46       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DGKD MUTATED           1          1          0          1        0         0
  DGKD WILD-TYPE        28         83         62         38       43         4
D929V3, multiclass
            clus
vv           DGKD MUTATED DGKD WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DGKD MUTATED       1   2   3   2
  DGKD WILD-TYPE    53 133 258 100
D929V4, multiclass
       clus
vv      DGKD MUTATED DGKD WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DGKD MUTATED     4   2   1   0
  DGKD WILD-TYPE 191 171  88  85
D929V5, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  N0            4            191
  N1            2            171
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V6, binary
                cls
clus               0   1
  DGKD MUTATED     8   0
  DGKD WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      8    0
  DGKD WILD-TYPE  474   38
   clus
vv  DGKD MUTATED DGKD WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D929V7, binary
                cls
clus               0   1
  DGKD MUTATED     4   4
  DGKD WILD-TYPE 168 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      4    4
  DGKD WILD-TYPE  168  402
        clus
vv       DGKD MUTATED DGKD WILD-TYPE
  FEMALE            4            168
  MALE              4            402
[1] 2 2
[1] FALSE
D929V8, binary
                cls
clus               0   1
  DGKD MUTATED     7   1
  DGKD WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      7    1
  DGKD WILD-TYPE  409  101
     clus
vv    DGKD MUTATED DGKD WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D929V9, continuous
D929V10, continuous
[1] "Remove cluster labels:" "DGKD MUTATED"          
clus
  DGKD MUTATED DGKD WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" "DGKD WILD-TYPE" 
    TCGA-Z6-AAPN 
"DGKD WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DGKD MUTATED       3                         0
  DGKD WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DGKD MUTATED                                           0     3
  DGKD WILD-TYPE                                         1   354
D929V11, multiclass
                                           clus
vv                                          DGKD MUTATED DGKD WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V12, binary
                cls
clus               0   1
  DGKD MUTATED     0   5
  DGKD WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      0    5
  DGKD WILD-TYPE   10  393
                        clus
vv                       DGKD MUTATED DGKD WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(930) Variable = TNFRSF25 MUTATION ANALYSIS
D930V1, survival
                    sevent
clus2                  0   1
  TNFRSF25 MUTATED     3   5
  TNFRSF25 WILD-TYPE 335 211
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
                 8                546 
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
                 5                211 
$`TNFRSF25 MUTATED`
TCGA-L5-A4OI TCGA-R6-A6DN TCGA-VR-A8EX TCGA-Z6-A9VB TCGA-BR-A4QL TCGA-CG-5721 
       19.99         8.02        28.11         1.32        16.14         6.02 
TCGA-HU-A4GQ TCGA-IN-A6RR 
        0.10         6.74 

$`TNFRSF25 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
               0.1                0.0 
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
             28.11             122.30 
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
              7.38              13.63 
[1] "0.1 - 28.1 (7.4)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.6"
D930V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFRSF25 MUTATED         0        0        0        0         0         0
  TNFRSF25 WILD-TYPE      10       20       46       31        84        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF25 MUTATED           0          2          1          2        1
  TNFRSF25 WILD-TYPE        29         82         61         37       42
                    vv
clus                 STAGE IVA
  TNFRSF25 MUTATED           1
  TNFRSF25 WILD-TYPE         3
D930V3, multiclass
            clus
vv           TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                1                 61
  STAGE IIIC                2                 37
  STAGE IV                  1                 42
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TNFRSF25 MUTATED       1   0   4   2
  TNFRSF25 WILD-TYPE    53 135 257 100
D930V4, multiclass
       clus
vv      TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  T0+T1                1                 53
  T2                   0                135
  T3                   4                257
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TNFRSF25 MUTATED     0   4   1   2
  TNFRSF25 WILD-TYPE 195 169  88  83
D930V5, multiclass
    clus
vv   TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  N0                0                195
  N1                4                169
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V6, binary
                    cls
clus                   0   1
  TNFRSF25 MUTATED     5   1
  TNFRSF25 WILD-TYPE 477  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNFRSF25 MUTATED      5    1
  TNFRSF25 WILD-TYPE  477   37
   clus
vv  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  0                5                477
  1                1                 37
[1] 2 2
[1] FALSE
D930V7, binary
                    cls
clus                   0   1
  TNFRSF25 MUTATED     1   7
  TNFRSF25 WILD-TYPE 171 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNFRSF25 MUTATED      1    7
  TNFRSF25 WILD-TYPE  171  399
        clus
vv       TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  FEMALE                1                171
  MALE                  7                399
[1] 2 2
[1] FALSE
D930V8, binary
                    cls
clus                   0   1
  TNFRSF25 MUTATED     7   0
  TNFRSF25 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNFRSF25 MUTATED      7    0
  TNFRSF25 WILD-TYPE  409  102
     clus
vv    TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D930V9, continuous
[1] "Remove cluster labels:" "TNFRSF25 MUTATED"      
clus
  TNFRSF25 MUTATED TNFRSF25 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" "TNFRSF25 WILD-TYPE" 
        TCGA-Z6-A8JE 
"TNFRSF25 WILD-TYPE" 
D930V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TNFRSF25 MUTATED       1                         0
  TNFRSF25 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFRSF25 MUTATED                                           0     5
  TNFRSF25 WILD-TYPE                                         1   352
D930V11, multiclass
                                           clus
vv                                          TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V12, binary
                    cls
clus                   0   1
  TNFRSF25 MUTATED     0   5
  TNFRSF25 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNFRSF25 MUTATED      0    5
  TNFRSF25 WILD-TYPE   10  393
                        clus
vv                       TNFRSF25 MUTATED TNFRSF25 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(931) Variable = CFI MUTATION ANALYSIS
D931V1, survival
               sevent
clus2             0   1
  CFI MUTATED    10   3
  CFI WILD-TYPE 328 213
  CFI MUTATED CFI WILD-TYPE 
           13           541 
  CFI MUTATED CFI WILD-TYPE 
            3           213 
$`CFI MUTATED`
TCGA-L5-A43J TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7715 
        4.31         9.34         9.67        34.68        30.90        33.63 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8529 TCGA-CG-4305 TCGA-HU-A4GU TCGA-HU-A4H3 
        1.12        31.96        12.30        15.95         6.58        29.00 
TCGA-VQ-A8P2 
       38.14 

$`CFI WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         4.08         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CFI MUTATED CFI WILD-TYPE 
         1.12          0.00 
  CFI MUTATED CFI WILD-TYPE 
        38.14        122.30 
  CFI MUTATED CFI WILD-TYPE 
        15.95         13.55 
[1] "1.1 - 38.1 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D931V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CFI MUTATED         0        0        0        1         3         2
  CFI WILD-TYPE      10       20       46       30        81        81
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CFI MUTATED           0          2          0          1        2         0
  CFI WILD-TYPE        29         82         62         38       41         4
D931V3, multiclass
            clus
vv           CFI MUTATED CFI WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             1            30
  STAGE IIA            3            81
  STAGE IIB            2            81
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           0            62
  STAGE IIIC           1            38
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  CFI MUTATED       0   1   6   4
  CFI WILD-TYPE    54 134 255  98
D931V4, multiclass
       clus
vv      CFI MUTATED CFI WILD-TYPE
  T0+T1           0            54
  T2              1           134
  T3              6           255
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  CFI MUTATED     5   5   2   1
  CFI WILD-TYPE 190 168  87  84
D931V5, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  N0           5           190
  N1           5           168
  N2           2            87
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V6, binary
               cls
clus              0   1
  CFI MUTATED    11   2
  CFI WILD-TYPE 471  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED     11    2
  CFI WILD-TYPE  471   36
   clus
vv  CFI MUTATED CFI WILD-TYPE
  0          11           471
  1           2            36
[1] 2 2
[1] FALSE
D931V7, binary
               cls
clus              0   1
  CFI MUTATED     5   9
  CFI WILD-TYPE 167 397
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      5    9
  CFI WILD-TYPE  167  397
        clus
vv       CFI MUTATED CFI WILD-TYPE
  FEMALE           5           167
  MALE             9           397
[1] 2 2
[1] FALSE
D931V8, binary
               cls
clus              0   1
  CFI MUTATED     9   2
  CFI WILD-TYPE 407 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      9    2
  CFI WILD-TYPE  407  100
     clus
vv    CFI MUTATED CFI WILD-TYPE
  NO            9           407
  YES           2           100
[1] 2 2
[1] FALSE
D931V9, continuous
D931V10, continuous
[1] "Remove cluster labels:" "CFI MUTATED"           
clus
  CFI MUTATED CFI WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A4OE    TCGA-L5-A4OG    TCGA-L5-A4OI 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NS 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-LN-A7HX    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" "CFI WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"CFI WILD-TYPE" "CFI WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CFI MUTATED       4                         0
  CFI WILD-TYPE   129                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CFI MUTATED                                           0     9
  CFI WILD-TYPE                                         1   348
D931V11, multiclass
                                           clus
vv                                          CFI MUTATED CFI WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               9           348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V12, binary
               cls
clus              0   1
  CFI MUTATED     0  11
  CFI WILD-TYPE  10 387
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      0   11
  CFI WILD-TYPE   10  387
                        clus
vv                       CFI MUTATED CFI WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          11           387
[1] 2 2
[1] FALSE

Clustering(932) Variable = EMILIN3 MUTATION ANALYSIS
D932V1, survival
                   sevent
clus2                 0   1
  EMILIN3 MUTATED     9   5
  EMILIN3 WILD-TYPE 329 211
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               14               540 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
                5               211 
$`EMILIN3 MUTATED`
TCGA-VR-A8Q7 TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-5802 
       52.27         6.97        35.84        31.96        13.18        13.35 
TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5730 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-A4GQ 
       11.77         6.02         4.01         5.92        21.27         0.10 
TCGA-IN-A6RS TCGA-VQ-A8P2 
       12.59        38.14 

$`EMILIN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.02        13.15        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44         6.74         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
              0.1               0.0 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
            52.27            122.30 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
           12.885            13.730 
[1] "0.1 - 52.3 (12.9)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D932V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EMILIN3 MUTATED         0        1        1        1         0         1
  EMILIN3 WILD-TYPE      10       19       45       30        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EMILIN3 MUTATED           0          6          1          1        3
  EMILIN3 WILD-TYPE        29         78         61         38       40
                   vv
clus                STAGE IVA
  EMILIN3 MUTATED           0
  EMILIN3 WILD-TYPE         4
D932V3, multiclass
            clus
vv           EMILIN3 MUTATED EMILIN3 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               6                78
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  EMILIN3 MUTATED       1   2   7   5
  EMILIN3 WILD-TYPE    53 133 254  97
D932V4, multiclass
       clus
vv      EMILIN3 MUTATED EMILIN3 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  7               254
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  EMILIN3 MUTATED     4   8   2   1
  EMILIN3 WILD-TYPE 191 165  87  84
D932V5, multiclass
    clus
vv   EMILIN3 MUTATED EMILIN3 WILD-TYPE
  N0               4               191
  N1               8               165
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V6, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED    12   2
  EMILIN3 WILD-TYPE 470  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED     12    2
  EMILIN3 WILD-TYPE  470   36
   clus
vv  EMILIN3 MUTATED EMILIN3 WILD-TYPE
  0              12               470
  1               2                36
[1] 2 2
[1] FALSE
D932V7, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED     4  11
  EMILIN3 WILD-TYPE 168 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED      4   11
  EMILIN3 WILD-TYPE  168  395
        clus
vv       EMILIN3 MUTATED EMILIN3 WILD-TYPE
  FEMALE               4               168
  MALE                11               395
[1] 2 2
[1] FALSE
D932V8, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED    10   3
  EMILIN3 WILD-TYPE 406  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED     10    3
  EMILIN3 WILD-TYPE  406   99
     clus
vv    EMILIN3 MUTATED EMILIN3 WILD-TYPE
  NO               10               406
  YES               3                99
[1] 2 2
[1] FALSE
D932V9, continuous
[1] "Remove cluster labels:" "EMILIN3 MUTATED"       
clus
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
D932V10, continuous
[1] "Remove cluster labels:" "EMILIN3 MUTATED"       
clus
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" "EMILIN3 WILD-TYPE" 
       TCGA-Z6-AAPN 
"EMILIN3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EMILIN3 MUTATED       5                         0
  EMILIN3 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EMILIN3 MUTATED                                           0     8
  EMILIN3 WILD-TYPE                                         1   349
D932V11, multiclass
                                           clus
vv                                          EMILIN3 MUTATED EMILIN3 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V12, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED     1  10
  EMILIN3 WILD-TYPE   9 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED      1   10
  EMILIN3 WILD-TYPE    9  388
                        clus
vv                       EMILIN3 MUTATED EMILIN3 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(933) Variable = EHBP1 MUTATION ANALYSIS
D933V1, survival
                 sevent
clus2               0   1
  EHBP1 MUTATED    14   4
  EHBP1 WILD-TYPE 324 212
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             18             536 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              4             212 
$`EHBP1 MUTATED`
TCGA-L5-A4OJ TCGA-LN-A49V TCGA-LN-A4A1 TCGA-S8-A6BW TCGA-VR-A8EU TCGA-BR-4201 
       21.01        12.59        12.59        20.38        18.31        30.90 
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8683 TCGA-CG-5721 
       34.68        29.59         7.40         5.39         9.86         6.02 
TCGA-CG-5723 TCGA-IN-A6RN TCGA-IN-A7NU TCGA-R5-A805 TCGA-SW-A7EA TCGA-VQ-A8P2 
      105.07        19.53        11.70         9.24        19.04        38.14 

$`EHBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
        6.44         6.74        12.59         6.51        10.62        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EHBP1 MUTATED EHBP1 WILD-TYPE 
           5.39            0.00 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         105.07          122.30 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         18.675          13.530 
[1] "5.4 - 105.1 (18.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.1"
D933V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EHBP1 MUTATED         1        0        3        1         4         1
  EHBP1 WILD-TYPE       9       20       43       30        80        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EHBP1 MUTATED           0          2          3          1        2         0
  EHBP1 WILD-TYPE        29         82         59         38       41         4
D933V3, multiclass
            clus
vv           EHBP1 MUTATED EHBP1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EHBP1 MUTATED       3   5   6   5
  EHBP1 WILD-TYPE    51 130 255  97
D933V4, multiclass
       clus
vv      EHBP1 MUTATED EHBP1 WILD-TYPE
  T0+T1             3              51
  T2                5             130
  T3                6             255
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EHBP1 MUTATED     8   4   4   2
  EHBP1 WILD-TYPE 187 169  85  83
D933V5, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  N0             8             187
  N1             4             169
  N2             4              85
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V6, binary
                 cls
clus                0   1
  EHBP1 MUTATED    17   1
  EHBP1 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     17    1
  EHBP1 WILD-TYPE  465   37
   clus
vv  EHBP1 MUTATED EHBP1 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D933V7, binary
                 cls
clus                0   1
  EHBP1 MUTATED     6  13
  EHBP1 WILD-TYPE 166 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED      6   13
  EHBP1 WILD-TYPE  166  393
        clus
vv       EHBP1 MUTATED EHBP1 WILD-TYPE
  FEMALE             6             166
  MALE              13             393
[1] 2 2
[1] FALSE
D933V8, binary
                 cls
clus                0   1
  EHBP1 MUTATED    14   3
  EHBP1 WILD-TYPE 402  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     14    3
  EHBP1 WILD-TYPE  402   99
     clus
vv    EHBP1 MUTATED EHBP1 WILD-TYPE
  NO             14             402
  YES             3              99
[1] 2 2
[1] FALSE
D933V9, continuous
D933V10, continuous
[1] "Remove cluster labels:" "EHBP1 MUTATED"         
clus
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" "EHBP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EHBP1 MUTATED       3                         0
  EHBP1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EHBP1 MUTATED                                           0    13
  EHBP1 WILD-TYPE                                         1   344
D933V11, multiclass
                                           clus
vv                                          EHBP1 MUTATED EHBP1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V12, binary
                 cls
clus                0   1
  EHBP1 MUTATED     0  13
  EHBP1 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED      0   13
  EHBP1 WILD-TYPE   10  385
                        clus
vv                       EHBP1 MUTATED EHBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(934) Variable = HIC2 MUTATION ANALYSIS
D934V1, survival
                sevent
clus2              0   1
  HIC2 MUTATED    12   4
  HIC2 WILD-TYPE 326 212
  HIC2 MUTATED HIC2 WILD-TYPE 
            16            538 
  HIC2 MUTATED HIC2 WILD-TYPE 
             4            212 
$`HIC2 MUTATED`
TCGA-LN-A49V TCGA-RE-A7BO TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 
       12.59         7.00         6.97        34.68        44.94        29.59 
TCGA-BR-8372 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 
       31.27        12.43         6.58        11.77         6.02        65.10 
TCGA-D7-A4YY TCGA-D7-A6EV TCGA-HU-8602 TCGA-HU-A4GU 
       13.78        11.24        22.32         6.58 

$`HIC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        36.43        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HIC2 MUTATED HIC2 WILD-TYPE 
          6.02           0.00 
  HIC2 MUTATED HIC2 WILD-TYPE 
          65.1          122.3 
  HIC2 MUTATED HIC2 WILD-TYPE 
         12.51          13.63 
[1] "6.0 - 65.1 (12.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D934V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIC2 MUTATED         0        0        1        1         4         5
  HIC2 WILD-TYPE      10       20       45       30        80        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIC2 MUTATED           0          3          1          1        2         0
  HIC2 WILD-TYPE        29         81         61         38       41         4
D934V3, multiclass
            clus
vv           HIC2 MUTATED HIC2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HIC2 MUTATED       1   2   9   6
  HIC2 WILD-TYPE    53 133 252  96
D934V4, multiclass
       clus
vv      HIC2 MUTATED HIC2 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               9            252
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HIC2 MUTATED     9   5   2   2
  HIC2 WILD-TYPE 186 168  87  83
D934V5, multiclass
    clus
vv   HIC2 MUTATED HIC2 WILD-TYPE
  N0            9            186
  N1            5            168
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V6, binary
                cls
clus               0   1
  HIC2 MUTATED    18   0
  HIC2 WILD-TYPE 464  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIC2 MUTATED     18    0
  HIC2 WILD-TYPE  464   38
   clus
vv  HIC2 MUTATED HIC2 WILD-TYPE
  0           18            464
  1            0             38
[1] 2 2
[1] FALSE
D934V7, binary
                cls
clus               0   1
  HIC2 MUTATED    10   9
  HIC2 WILD-TYPE 162 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIC2 MUTATED     10    9
  HIC2 WILD-TYPE  162  397
        clus
vv       HIC2 MUTATED HIC2 WILD-TYPE
  FEMALE           10            162
  MALE              9            397
[1] 2 2
[1] FALSE
D934V8, binary
                cls
clus               0   1
  HIC2 MUTATED    13   2
  HIC2 WILD-TYPE 403 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIC2 MUTATED     13    2
  HIC2 WILD-TYPE  403  100
     clus
vv    HIC2 MUTATED HIC2 WILD-TYPE
  NO            13            403
  YES            2            100
[1] 2 2
[1] FALSE
D934V9, continuous
[1] "Remove cluster labels:" "HIC2 MUTATED"          
clus
  HIC2 MUTATED HIC2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49W 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
D934V10, continuous
[1] "Remove cluster labels:" "HIC2 MUTATED"          
clus
  HIC2 MUTATED HIC2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-V5-A7RB     TCGA-V5-A7RC 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" "HIC2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HIC2 MUTATED       6                         0
  HIC2 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIC2 MUTATED                                           0    11
  HIC2 WILD-TYPE                                         1   346
D934V11, multiclass
                                           clus
vv                                          HIC2 MUTATED HIC2 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V12, binary
                cls
clus               0   1
  HIC2 MUTATED     0  17
  HIC2 WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIC2 MUTATED      0   17
  HIC2 WILD-TYPE   10  381
                        clus
vv                       HIC2 MUTATED HIC2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(935) Variable = C9ORF86 MUTATION ANALYSIS
D935V1, survival
                   sevent
clus2                 0   1
  C9ORF86 MUTATED     9   3
  C9ORF86 WILD-TYPE 329 213
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
               12               542 
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
                3               213 
$`C9ORF86 MUTATED`
TCGA-L5-A43H TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4465 
        0.30        26.70        44.94        28.14        16.14         9.01 
TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4GT TCGA-SW-A7EA TCGA-VQ-A8P2 
      105.07        14.47        22.32         6.51        19.04        38.14 

$`C9ORF86 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
              0.3               0.0 
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
           105.07            122.30 
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
           20.680            13.495 
[1] "0.3 - 105.1 (20.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D935V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF86 MUTATED         0        0        2        1         2         2
  C9ORF86 WILD-TYPE      10       20       44       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF86 MUTATED           1          1          1          1        1
  C9ORF86 WILD-TYPE        28         83         61         38       42
                   vv
clus                STAGE IVA
  C9ORF86 MUTATED           0
  C9ORF86 WILD-TYPE         4
D935V3, multiclass
            clus
vv           C9ORF86 MUTATED C9ORF86 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C9ORF86 MUTATED       0   3   5   5
  C9ORF86 WILD-TYPE    54 132 256  97
D935V4, multiclass
       clus
vv      C9ORF86 MUTATED C9ORF86 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  5               256
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C9ORF86 MUTATED     6   3   0   3
  C9ORF86 WILD-TYPE 189 170  89  82
D935V5, multiclass
    clus
vv   C9ORF86 MUTATED C9ORF86 WILD-TYPE
  N0               6               189
  N1               3               170
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V6, binary
                   cls
clus                  0   1
  C9ORF86 MUTATED    11   1
  C9ORF86 WILD-TYPE 471  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF86 MUTATED     11    1
  C9ORF86 WILD-TYPE  471   37
   clus
vv  C9ORF86 MUTATED C9ORF86 WILD-TYPE
  0              11               471
  1               1                37
[1] 2 2
[1] FALSE
D935V7, binary
                   cls
clus                  0   1
  C9ORF86 MUTATED     7   6
  C9ORF86 WILD-TYPE 165 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF86 MUTATED      7    6
  C9ORF86 WILD-TYPE  165  400
        clus
vv       C9ORF86 MUTATED C9ORF86 WILD-TYPE
  FEMALE               7               165
  MALE                 6               400
[1] 2 2
[1] FALSE
D935V8, binary
                   cls
clus                  0   1
  C9ORF86 MUTATED    10   1
  C9ORF86 WILD-TYPE 406 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF86 MUTATED     10    1
  C9ORF86 WILD-TYPE  406  101
     clus
vv    C9ORF86 MUTATED C9ORF86 WILD-TYPE
  NO               10               406
  YES               1               101
[1] 2 2
[1] FALSE
D935V9, continuous
D935V10, continuous
[1] "Remove cluster labels:" "C9ORF86 MUTATED"       
clus
  C9ORF86 MUTATED C9ORF86 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A4OH        TCGA-L5-A4OM 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" "C9ORF86 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C9ORF86 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF86 MUTATED       2                         0
  C9ORF86 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF86 MUTATED                                           0     9
  C9ORF86 WILD-TYPE                                         1   348
D935V11, multiclass
                                           clus
vv                                          C9ORF86 MUTATED C9ORF86 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V12, binary
                   cls
clus                  0   1
  C9ORF86 MUTATED     0   9
  C9ORF86 WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF86 MUTATED      0    9
  C9ORF86 WILD-TYPE   10  389
                        clus
vv                       C9ORF86 MUTATED C9ORF86 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(936) Variable = ABCC1 MUTATION ANALYSIS
D936V1, survival
                 sevent
clus2               0   1
  ABCC1 MUTATED     8   8
  ABCC1 WILD-TYPE 330 208
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             16             538 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
              8             208 
$`ABCC1 MUTATED`
TCGA-IC-A6RE TCGA-IG-A4QS TCGA-R6-A6L6 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7707 
        7.69         3.88         7.04         6.97        30.90        35.84 
TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI 
       33.63         8.05        31.27        16.14         6.58        11.77 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       22.32         0.10         6.51         6.58 

$`ABCC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06        16.31        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       11.44         0.69        29.59         9.60        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         8.98        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ABCC1 MUTATED ABCC1 WILD-TYPE 
            0.1             0.0 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
          35.84          122.30 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
           7.87           13.73 
[1] "0.1 - 35.8 (7.9)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.6"
D936V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC1 MUTATED         0        0        2        0         3         3
  ABCC1 WILD-TYPE      10       20       44       31        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCC1 MUTATED           0          3          2          3        0         0
  ABCC1 WILD-TYPE        29         81         60         36       43         4
D936V3, multiclass
            clus
vv           ABCC1 MUTATED ABCC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCC1 MUTATED       1   2   9   4
  ABCC1 WILD-TYPE    53 133 252  98
D936V4, multiclass
       clus
vv      ABCC1 MUTATED ABCC1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                9             252
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCC1 MUTATED     6   4   3   3
  ABCC1 WILD-TYPE 189 169  86  82
D936V5, multiclass
    clus
vv   ABCC1 MUTATED ABCC1 WILD-TYPE
  N0             6             189
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V6, binary
                 cls
clus                0   1
  ABCC1 MUTATED    15   0
  ABCC1 WILD-TYPE 467  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED     15    0
  ABCC1 WILD-TYPE  467   38
   clus
vv  ABCC1 MUTATED ABCC1 WILD-TYPE
  0            15             467
  1             0              38
[1] 2 2
[1] FALSE
D936V7, binary
                 cls
clus                0   1
  ABCC1 MUTATED     5  12
  ABCC1 WILD-TYPE 167 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED      5   12
  ABCC1 WILD-TYPE  167  394
        clus
vv       ABCC1 MUTATED ABCC1 WILD-TYPE
  FEMALE             5             167
  MALE              12             394
[1] 2 2
[1] FALSE
D936V8, binary
                 cls
clus                0   1
  ABCC1 MUTATED    16   0
  ABCC1 WILD-TYPE 400 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED     16    0
  ABCC1 WILD-TYPE  400  102
     clus
vv    ABCC1 MUTATED ABCC1 WILD-TYPE
  NO             16             400
  YES             0             102
[1] 2 2
[1] FALSE
D936V9, continuous
D936V10, continuous
[1] "Remove cluster labels:" "ABCC1 MUTATED"         
clus
  ABCC1 MUTATED ABCC1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" "ABCC1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ABCC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC1 MUTATED       6                         0
  ABCC1 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC1 MUTATED                                           0    10
  ABCC1 WILD-TYPE                                         1   347
D936V11, multiclass
                                           clus
vv                                          ABCC1 MUTATED ABCC1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V12, binary
                 cls
clus                0   1
  ABCC1 MUTATED     0  16
  ABCC1 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED      0   16
  ABCC1 WILD-TYPE   10  382
                        clus
vv                       ABCC1 MUTATED ABCC1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(937) Variable = ZNF750 MUTATION ANALYSIS
D937V1, survival
                  sevent
clus2                0   1
  ZNF750 MUTATED    14   2
  ZNF750 WILD-TYPE 324 214
  ZNF750 MUTATED ZNF750 WILD-TYPE 
              16              538 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
               2              214 
$`ZNF750 MUTATED`
TCGA-S8-A6BV TCGA-IG-A8O2 TCGA-LN-A49S TCGA-LN-A49Y TCGA-LN-A4A9 TCGA-LN-A7HV 
       20.02         4.67        13.15        12.46        11.54        10.52 
TCGA-LN-A7HX TCGA-LN-A9FP TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-BR-8589 TCGA-BR-8680 
       12.23        12.03         3.42         2.10        27.12        31.96 
TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-VQ-A8P2 
       77.29        22.68         6.51        38.14 

$`ZNF750 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        25.25        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZNF750 MUTATED ZNF750 WILD-TYPE 
             2.1              0.0 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
           77.29           122.30 
  ZNF750 MUTATED ZNF750 WILD-TYPE 
          12.345           13.730 
[1] "2.1 - 77.3 (12.3)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "3.2"
D937V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF750 MUTATED         1        0        0        1         7         2
  ZNF750 WILD-TYPE       9       20       46       30        77        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF750 MUTATED           0          3          2          0        1
  ZNF750 WILD-TYPE        29         81         60         39       42
                  vv
clus               STAGE IVA
  ZNF750 MUTATED           0
  ZNF750 WILD-TYPE         4
D937V3, multiclass
            clus
vv           ZNF750 MUTATED ZNF750 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               7               77
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF750 MUTATED       1   5   8   3
  ZNF750 WILD-TYPE    53 130 253  99
D937V4, multiclass
       clus
vv      ZNF750 MUTATED ZNF750 WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 8              253
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF750 MUTATED     8   7   2   0
  ZNF750 WILD-TYPE 187 166  87  85
D937V5, multiclass
    clus
vv   ZNF750 MUTATED ZNF750 WILD-TYPE
  N0              8              187
  N1              7              166
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V6, binary
                  cls
clus                 0   1
  ZNF750 MUTATED    14   1
  ZNF750 WILD-TYPE 468  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED     14    1
  ZNF750 WILD-TYPE  468   37
   clus
vv  ZNF750 MUTATED ZNF750 WILD-TYPE
  0             14              468
  1              1               37
[1] 2 2
[1] FALSE
D937V7, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     3  14
  ZNF750 WILD-TYPE 169 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      3   14
  ZNF750 WILD-TYPE  169  392
        clus
vv       ZNF750 MUTATED ZNF750 WILD-TYPE
  FEMALE              3              169
  MALE               14              392
[1] 2 2
[1] FALSE
D937V8, binary
                  cls
clus                 0   1
  ZNF750 MUTATED    10   6
  ZNF750 WILD-TYPE 406  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED     10    6
  ZNF750 WILD-TYPE  406   96
     clus
vv    ZNF750 MUTATED ZNF750 WILD-TYPE
  NO              10              406
  YES              6               96
[1] 2 2
[1] FALSE
D937V9, continuous
D937V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF750 MUTATED      10                         1
  ZNF750 WILD-TYPE   123                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF750 MUTATED                                           0     5
  ZNF750 WILD-TYPE                                         1   352
D937V11, multiclass
                                           clus
vv                                          ZNF750 MUTATED ZNF750 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V12, binary
                  cls
clus                 0   1
  ZNF750 MUTATED     0  15
  ZNF750 WILD-TYPE  10 383
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF750 MUTATED      0   15
  ZNF750 WILD-TYPE   10  383
                        clus
vv                       ZNF750 MUTATED ZNF750 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             15              383
[1] 2 2
[1] FALSE

Clustering(938) Variable = ZNF7 MUTATION ANALYSIS
D938V1, survival
                sevent
clus2              0   1
  ZNF7 MUTATED     7   1
  ZNF7 WILD-TYPE 331 215
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             8            546 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             1            215 
$`ZNF7 MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-CG-4305 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-A4G9 
       30.90        35.84        15.95         6.02        11.08        24.20 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`ZNF7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF7 MUTATED ZNF7 WILD-TYPE 
          6.02           0.00 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
         38.14         122.30 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
        22.225         13.510 
[1] "6.0 - 38.1 (22.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4"  
D938V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF7 MUTATED         1        1        1        1         1         0
  ZNF7 WILD-TYPE       9       19       45       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF7 MUTATED           0          1          0          1        1         0
  ZNF7 WILD-TYPE        29         83         62         38       42         4
D938V3, multiclass
            clus
vv           ZNF7 MUTATED ZNF7 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ZNF7 MUTATED       2   3   1   3
  ZNF7 WILD-TYPE    52 132 260  99
D938V4, multiclass
       clus
vv      ZNF7 MUTATED ZNF7 WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3               1            260
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ZNF7 MUTATED     3   4   1   0
  ZNF7 WILD-TYPE 192 169  88  85
D938V5, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  N0            3            192
  N1            4            169
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V6, binary
                cls
clus               0   1
  ZNF7 MUTATED     8   0
  ZNF7 WILD-TYPE 474  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      8    0
  ZNF7 WILD-TYPE  474   38
   clus
vv  ZNF7 MUTATED ZNF7 WILD-TYPE
  0            8            474
  1            0             38
[1] 2 2
[1] FALSE
D938V7, binary
                cls
clus               0   1
  ZNF7 MUTATED     4   5
  ZNF7 WILD-TYPE 168 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      4    5
  ZNF7 WILD-TYPE  168  401
        clus
vv       ZNF7 MUTATED ZNF7 WILD-TYPE
  FEMALE            4            168
  MALE              5            401
[1] 2 2
[1] FALSE
D938V8, binary
                cls
clus               0   1
  ZNF7 MUTATED     7   2
  ZNF7 WILD-TYPE 409 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      7    2
  ZNF7 WILD-TYPE  409  100
     clus
vv    ZNF7 MUTATED ZNF7 WILD-TYPE
  NO             7            409
  YES            2            100
[1] 2 2
[1] FALSE
D938V9, continuous
D938V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ZNF7 MUTATED       2                         2
  ZNF7 WILD-TYPE   131                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF7 MUTATED                                           0     3
  ZNF7 WILD-TYPE                                         1   354
D938V11, multiclass
                                           clus
vv                                          ZNF7 MUTATED ZNF7 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V12, binary
                cls
clus               0   1
  ZNF7 MUTATED     0   6
  ZNF7 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      0    6
  ZNF7 WILD-TYPE   10  392
                        clus
vv                       ZNF7 MUTATED ZNF7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(939) Variable = TMEM64 MUTATION ANALYSIS
D939V1, survival
                  sevent
clus2                0   1
  TMEM64 MUTATED     7   1
  TMEM64 WILD-TYPE 331 215
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               8              546 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               1              215 
$`TMEM64 MUTATED`
TCGA-LN-A49O TCGA-BR-6452 TCGA-BR-7707 TCGA-CD-8525 TCGA-CD-8536 TCGA-CG-4300 
       13.41        34.68        35.84        12.59        12.43        20.02 
TCGA-MX-A5UJ TCGA-VQ-AA6J 
       19.73        27.55 

$`TMEM64 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 
       13.35        11.21        12.10        12.39        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 

  TMEM64 MUTATED TMEM64 WILD-TYPE 
           12.43             0.00 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
           35.84           122.30 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
          19.875           13.530 
[1] "12.4 - 35.8 (19.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4"  
D939V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM64 MUTATED         0        0        1        1         2         0
  TMEM64 WILD-TYPE      10       20       45       30        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM64 MUTATED           0          2          2          0        0
  TMEM64 WILD-TYPE        29         82         60         39       43
                  vv
clus               STAGE IVA
  TMEM64 MUTATED           0
  TMEM64 WILD-TYPE         4
D939V3, multiclass
            clus
vv           TMEM64 MUTATED TMEM64 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TMEM64 MUTATED       0   1   6   1
  TMEM64 WILD-TYPE    54 134 255 101
D939V4, multiclass
       clus
vv      TMEM64 MUTATED TMEM64 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 6              255
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TMEM64 MUTATED     4   1   3   0
  TMEM64 WILD-TYPE 191 172  86  85
D939V5, multiclass
    clus
vv   TMEM64 MUTATED TMEM64 WILD-TYPE
  N0              4              191
  N1              1              172
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V6, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     8   0
  TMEM64 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      8    0
  TMEM64 WILD-TYPE  474   38
   clus
vv  TMEM64 MUTATED TMEM64 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D939V7, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     4   4
  TMEM64 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      4    4
  TMEM64 WILD-TYPE  168  402
        clus
vv       TMEM64 MUTATED TMEM64 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D939V8, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     5   2
  TMEM64 WILD-TYPE 411 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      5    2
  TMEM64 WILD-TYPE  411  100
     clus
vv    TMEM64 MUTATED TMEM64 WILD-TYPE
  NO               5              411
  YES              2              100
[1] 2 2
[1] FALSE
D939V9, continuous
[1] "Remove cluster labels:" "TMEM64 MUTATED"        
clus
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49P       TCGA-LN-A49R 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
D939V10, continuous
[1] "Remove cluster labels:" "TMEM64 MUTATED"        
clus
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" "TMEM64 WILD-TYPE" 
      TCGA-Z6-AAPN 
"TMEM64 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TMEM64 MUTATED       3                         1
  TMEM64 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM64 MUTATED                                           0     3
  TMEM64 WILD-TYPE                                         1   354
D939V11, multiclass
                                           clus
vv                                          TMEM64 MUTATED TMEM64 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V12, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     0   6
  TMEM64 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      0    6
  TMEM64 WILD-TYPE   10  392
                        clus
vv                       TMEM64 MUTATED TMEM64 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(940) Variable = HSP90B1 MUTATION ANALYSIS
D940V1, survival
                   sevent
clus2                 0   1
  HSP90B1 MUTATED     6   5
  HSP90B1 WILD-TYPE 332 211
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
               11               543 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                5               211 
$`HSP90B1 MUTATED`
TCGA-L5-A43J TCGA-CG-4460 TCGA-IG-A97I TCGA-BR-4184 TCGA-BR-8680 TCGA-CG-5721 
        4.31        21.99        12.16         6.97        31.96         6.02 
TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.44        26.47        22.82        22.68        24.20 

$`HSP90B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD 
        0.76        24.30         5.59        24.26         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
             4.31              0.00 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
            31.96            122.30 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
            21.99             13.55 
[1] "4.3 - 32.0 (22.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D940V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSP90B1 MUTATED         0        1        1        0         2         2
  HSP90B1 WILD-TYPE      10       19       45       31        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90B1 MUTATED           0          1          1          0        3
  HSP90B1 WILD-TYPE        29         83         61         39       40
                   vv
clus                STAGE IVA
  HSP90B1 MUTATED           0
  HSP90B1 WILD-TYPE         4
D940V3, multiclass
            clus
vv           HSP90B1 MUTATED HSP90B1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  HSP90B1 MUTATED       1   2   5   3
  HSP90B1 WILD-TYPE    53 133 256  99
D940V4, multiclass
       clus
vv      HSP90B1 MUTATED HSP90B1 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  5               256
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HSP90B1 MUTATED     5   4   1   1
  HSP90B1 WILD-TYPE 190 169  88  84
D940V5, multiclass
    clus
vv   HSP90B1 MUTATED HSP90B1 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V6, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     6   2
  HSP90B1 WILD-TYPE 476  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      6    2
  HSP90B1 WILD-TYPE  476   36
   clus
vv  HSP90B1 MUTATED HSP90B1 WILD-TYPE
  0               6               476
  1               2                36
[1] 2 2
[1] FALSE
D940V7, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     6   5
  HSP90B1 WILD-TYPE 166 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      6    5
  HSP90B1 WILD-TYPE  166  401
        clus
vv       HSP90B1 MUTATED HSP90B1 WILD-TYPE
  FEMALE               6               166
  MALE                 5               401
[1] 2 2
[1] FALSE
D940V8, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     9   1
  HSP90B1 WILD-TYPE 407 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      9    1
  HSP90B1 WILD-TYPE  407  101
     clus
vv    HSP90B1 MUTATED HSP90B1 WILD-TYPE
  NO                9               407
  YES               1               101
[1] 2 2
[1] FALSE
D940V9, continuous
D940V10, continuous
[1] "Remove cluster labels:" "HSP90B1 MUTATED"       
clus
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A4OE        TCGA-L5-A4OG 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" "HSP90B1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"HSP90B1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HSP90B1 MUTATED       4                         0
  HSP90B1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSP90B1 MUTATED                                           0     5
  HSP90B1 WILD-TYPE                                         1   352
D940V11, multiclass
                                           clus
vv                                          HSP90B1 MUTATED HSP90B1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V12, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     0   8
  HSP90B1 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      0    8
  HSP90B1 WILD-TYPE   10  390
                        clus
vv                       HSP90B1 MUTATED HSP90B1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(941) Variable = OR10J1 MUTATION ANALYSIS
D941V1, survival
                  sevent
clus2                0   1
  OR10J1 MUTATED     7   6
  OR10J1 WILD-TYPE 331 210
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              541 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               6              210 
$`OR10J1 MUTATED`
TCGA-2H-A9GI TCGA-L5-A4OT TCGA-L5-A8NV TCGA-XP-A8T7 TCGA-B7-5816 TCGA-BR-4184 
       14.30         4.90        52.57        41.23        26.70         6.97 
TCGA-BR-8297 TCGA-CD-8526 TCGA-D7-5579 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-RD-A7BT 
        7.40        12.53        20.91        22.68        11.77         8.61 
TCGA-VQ-A8PQ 
       15.65 

$`OR10J1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19        17.85         1.87        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  OR10J1 MUTATED OR10J1 WILD-TYPE 
             4.9              0.0 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           52.57           122.30 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           14.30            13.55 
[1] "4.9 - 52.6 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D941V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR10J1 MUTATED         0        1        0        0         2         2
  OR10J1 WILD-TYPE      10       19       46       31        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10J1 MUTATED           1          4          0          1        3
  OR10J1 WILD-TYPE        28         80         62         38       40
                  vv
clus               STAGE IVA
  OR10J1 MUTATED           0
  OR10J1 WILD-TYPE         4
D941V3, multiclass
            clus
vv           OR10J1 MUTATED OR10J1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OR10J1 MUTATED       1   1   9   3
  OR10J1 WILD-TYPE    53 134 252  99
D941V4, multiclass
       clus
vv      OR10J1 MUTATED OR10J1 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 9              252
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR10J1 MUTATED     4   7   1   2
  OR10J1 WILD-TYPE 191 166  88  83
D941V5, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  N0              4              191
  N1              7              166
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V6, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  471   36
   clus
vv  OR10J1 MUTATED OR10J1 WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D941V7, binary
                  cls
clus                 0   1
  OR10J1 MUTATED     5   9
  OR10J1 WILD-TYPE 167 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED      5    9
  OR10J1 WILD-TYPE  167  397
        clus
vv       OR10J1 MUTATED OR10J1 WILD-TYPE
  FEMALE              5              167
  MALE                9              397
[1] 2 2
[1] FALSE
D941V8, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    13   1
  OR10J1 WILD-TYPE 403 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     13    1
  OR10J1 WILD-TYPE  403  101
     clus
vv    OR10J1 MUTATED OR10J1 WILD-TYPE
  NO              13              403
  YES              1              101
[1] 2 2
[1] FALSE
D941V9, continuous
[1] "Remove cluster labels:" "OR10J1 MUTATED"        
clus
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
D941V10, continuous
[1] "Remove cluster labels:" "OR10J1 MUTATED"        
clus
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" "OR10J1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OR10J1 MUTATED       3                         0
  OR10J1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR10J1 MUTATED                                           1     8
  OR10J1 WILD-TYPE                                         0   349
D941V11, multiclass
                                           clus
vv                                          OR10J1 MUTATED OR10J1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V12, binary
                  cls
clus                 0   1
  OR10J1 MUTATED     1   8
  OR10J1 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED      1    8
  OR10J1 WILD-TYPE    9  390
                        clus
vv                       OR10J1 MUTATED OR10J1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(942) Variable = CPSF2 MUTATION ANALYSIS
D942V1, survival
                 sevent
clus2               0   1
  CPSF2 MUTATED     3   6
  CPSF2 WILD-TYPE 335 210
  CPSF2 MUTATED CPSF2 WILD-TYPE 
              9             545 
  CPSF2 MUTATED CPSF2 WILD-TYPE 
              6             210 
$`CPSF2 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NM TCGA-L5-A8NV TCGA-LN-A8HZ TCGA-BR-8078 TCGA-CD-A4MI 
       21.99         7.76        52.57        12.33        29.59        11.77 
TCGA-CG-5725 TCGA-D7-A6EX TCGA-HU-A4GQ 
       15.02        11.31         0.10 

$`CPSF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        12.03        13.18        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CPSF2 MUTATED CPSF2 WILD-TYPE 
            0.1             0.0 
  CPSF2 MUTATED CPSF2 WILD-TYPE 
          52.57          122.30 
  CPSF2 MUTATED CPSF2 WILD-TYPE 
          12.33           13.58 
[1] "0.1 - 52.6 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D942V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CPSF2 MUTATED         0        0        2        0         2         2
  CPSF2 WILD-TYPE      10       20       44       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPSF2 MUTATED           0          2          0          1        1         0
  CPSF2 WILD-TYPE        29         82         62         38       42         4
D942V3, multiclass
            clus
vv           CPSF2 MUTATED CPSF2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CPSF2 MUTATED       0   4   3   3
  CPSF2 WILD-TYPE    54 131 258  99
D942V4, multiclass
       clus
vv      CPSF2 MUTATED CPSF2 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CPSF2 MUTATED     5   3   2   0
  CPSF2 WILD-TYPE 190 170  87  85
D942V5, multiclass
    clus
vv   CPSF2 MUTATED CPSF2 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V6, binary
                 cls
clus                0   1
  CPSF2 MUTATED     9   1
  CPSF2 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPSF2 MUTATED      9    1
  CPSF2 WILD-TYPE  473   37
   clus
vv  CPSF2 MUTATED CPSF2 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D942V7, binary
                 cls
clus                0   1
  CPSF2 MUTATED     4   6
  CPSF2 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPSF2 MUTATED      4    6
  CPSF2 WILD-TYPE  168  400
        clus
vv       CPSF2 MUTATED CPSF2 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D942V8, binary
                 cls
clus                0   1
  CPSF2 MUTATED     8   1
  CPSF2 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPSF2 MUTATED      8    1
  CPSF2 WILD-TYPE  408  101
     clus
vv    CPSF2 MUTATED CPSF2 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D942V9, continuous
D942V10, continuous
[1] "Remove cluster labels:" "CPSF2 MUTATED"         
clus
  CPSF2 MUTATED CPSF2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" "CPSF2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CPSF2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CPSF2 MUTATED       3                         0
  CPSF2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CPSF2 MUTATED                                           0     4
  CPSF2 WILD-TYPE                                         1   353
D942V11, multiclass
                                           clus
vv                                          CPSF2 MUTATED CPSF2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V12, binary
                 cls
clus                0   1
  CPSF2 MUTATED     0   5
  CPSF2 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPSF2 MUTATED      0    5
  CPSF2 WILD-TYPE   10  393
                        clus
vv                       CPSF2 MUTATED CPSF2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(943) Variable = ZBTB40 MUTATION ANALYSIS
D943V1, survival
                  sevent
clus2                0   1
  ZBTB40 MUTATED     9   4
  ZBTB40 WILD-TYPE 329 212
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              13              541 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               4              212 
$`ZBTB40 MUTATED`
TCGA-IG-A97H TCGA-VR-A8EZ TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8370 TCGA-BR-8676 
       14.50        18.18        30.90        34.68         3.32         7.53 
TCGA-CD-A48C TCGA-CG-5733 TCGA-F1-A448 TCGA-HF-7132 TCGA-HU-A4GU TCGA-IN-A6RJ 
       11.61        21.07        21.27        77.29         6.58        12.46 
TCGA-VQ-A8P2 
       38.14 

$`ZBTB40 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
            3.32             0.00 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           77.29           122.30 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           18.18            13.51 
[1] "3.3 - 77.3 (18.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D943V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB40 MUTATED         0        1        0        1         2         2
  ZBTB40 WILD-TYPE      10       19       46       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB40 MUTATED           0          2          3          1        0
  ZBTB40 WILD-TYPE        29         82         59         38       43
                  vv
clus               STAGE IVA
  ZBTB40 MUTATED           0
  ZBTB40 WILD-TYPE         4
D943V3, multiclass
            clus
vv           ZBTB40 MUTATED ZBTB40 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZBTB40 MUTATED       1   3   8   1
  ZBTB40 WILD-TYPE    53 132 253 101
D943V4, multiclass
       clus
vv      ZBTB40 MUTATED ZBTB40 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 8              253
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB40 MUTATED     2   4   1   4
  ZBTB40 WILD-TYPE 193 169  88  81
D943V5, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  N0              2              193
  N1              4              169
  N2              1               88
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V6, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED    13   0
  ZBTB40 WILD-TYPE 469  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED     13    0
  ZBTB40 WILD-TYPE  469   38
   clus
vv  ZBTB40 MUTATED ZBTB40 WILD-TYPE
  0             13              469
  1              0               38
[1] 2 2
[1] FALSE
D943V7, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     4   9
  ZBTB40 WILD-TYPE 168 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      4    9
  ZBTB40 WILD-TYPE  168  397
        clus
vv       ZBTB40 MUTATED ZBTB40 WILD-TYPE
  FEMALE              4              168
  MALE                9              397
[1] 2 2
[1] FALSE
D943V8, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     9   3
  ZBTB40 WILD-TYPE 407  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      9    3
  ZBTB40 WILD-TYPE  407   99
     clus
vv    ZBTB40 MUTATED ZBTB40 WILD-TYPE
  NO               9              407
  YES              3               99
[1] 2 2
[1] FALSE
D943V9, continuous
[1] "Remove cluster labels:" "ZBTB40 MUTATED"        
clus
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
D943V10, continuous
[1] "Remove cluster labels:" "ZBTB40 MUTATED"        
clus
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8Q7 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" "ZBTB40 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB40 MUTATED       3                         0
  ZBTB40 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB40 MUTATED                                           0     8
  ZBTB40 WILD-TYPE                                         1   349
D943V11, multiclass
                                           clus
vv                                          ZBTB40 MUTATED ZBTB40 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V12, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     1   8
  ZBTB40 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      1    8
  ZBTB40 WILD-TYPE    9  390
                        clus
vv                       ZBTB40 MUTATED ZBTB40 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(944) Variable = RPS6KA6 MUTATION ANALYSIS
D944V1, survival
                   sevent
clus2                 0   1
  RPS6KA6 MUTATED    15   7
  RPS6KA6 WILD-TYPE 323 209
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               22               532 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
                7               209 
$`RPS6KA6 MUTATED`
TCGA-2H-A9GO TCGA-L5-A43C TCGA-LN-A49M TCGA-R6-A6DN TCGA-BR-6452 TCGA-BR-7703 
       16.24         3.16        12.66         8.02        34.68        36.16 
TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4J8 TCGA-CD-8528 TCGA-CD-A4MI TCGA-CG-4465 
       31.27        28.14        13.51        12.33        11.77         9.01 
TCGA-CG-4477 TCGA-CG-5721 TCGA-D7-5579 TCGA-D7-6519 TCGA-FP-7916 TCGA-HU-A4GQ 
       30.97         6.02        20.91        20.55        14.07         0.10 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 TCGA-VQ-A8P2 
       19.73        74.53         4.60        38.14 

$`RPS6KA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 
       12.03         0.00        18.97         7.07         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       25.71        12.66        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        8.52         6.08         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
              0.1               0.0 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
            74.53            122.30 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
           15.155            13.530 
[1] "0.1 - 74.5 (15.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D944V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RPS6KA6 MUTATED         0        1        1        0         2         0
  RPS6KA6 WILD-TYPE      10       19       45       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA6 MUTATED           0          5          1          4        4
  RPS6KA6 WILD-TYPE        29         79         61         35       39
                   vv
clus                STAGE IVA
  RPS6KA6 MUTATED           1
  RPS6KA6 WILD-TYPE         3
D944V3, multiclass
            clus
vv           RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               5                79
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 4                39
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  RPS6KA6 MUTATED       1   3   7   9
  RPS6KA6 WILD-TYPE    53 132 254  93
D944V4, multiclass
       clus
vv      RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  7               254
  T4                  9                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  RPS6KA6 MUTATED     5   6   4   5
  RPS6KA6 WILD-TYPE 190 167  85  80
D944V5, multiclass
    clus
vv   RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  N0               5               190
  N1               6               167
  N2               4                85
  N3               5                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V6, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED    15   4
  RPS6KA6 WILD-TYPE 467  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED     15    4
  RPS6KA6 WILD-TYPE  467   34
   clus
vv  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  0              15               467
  1               4                34
[1] 2 2
[1] FALSE
D944V7, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED     8  14
  RPS6KA6 WILD-TYPE 164 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED      8   14
  RPS6KA6 WILD-TYPE  164  392
        clus
vv       RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  FEMALE               8               164
  MALE                14               392
[1] 2 2
[1] FALSE
D944V8, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED    15   5
  RPS6KA6 WILD-TYPE 401  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED     15    5
  RPS6KA6 WILD-TYPE  401   97
     clus
vv    RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  NO               15               401
  YES               5                97
[1] 2 2
[1] FALSE
D944V9, continuous
[1] "Remove cluster labels:" "RPS6KA6 MUTATED"       
clus
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
D944V10, continuous
[1] "Remove cluster labels:" "RPS6KA6 MUTATED"       
clus
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6L4 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" "RPS6KA6 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RPS6KA6 MUTATED       5                         1
  RPS6KA6 WILD-TYPE   128                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPS6KA6 MUTATED                                           0    12
  RPS6KA6 WILD-TYPE                                         1   345
D944V11, multiclass
                                           clus
vv                                          RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V12, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED     1  15
  RPS6KA6 WILD-TYPE   9 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED      1   15
  RPS6KA6 WILD-TYPE    9  383
                        clus
vv                       RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              15               383
[1] 2 2
[1] FALSE

Clustering(945) Variable = ICAM3 MUTATION ANALYSIS
D945V1, survival
                 sevent
clus2               0   1
  ICAM3 MUTATED     2   3
  ICAM3 WILD-TYPE 336 213
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              5             549 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              3             213 
$`ICAM3 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GF TCGA-Q9-A6FW TCGA-BR-4191 TCGA-HF-A5NB 
       21.99        25.78         7.82        18.35        30.51 

$`ICAM3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ICAM3 MUTATED ICAM3 WILD-TYPE 
           7.82            0.00 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
          30.51          122.30 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
          21.99           13.51 
[1] "7.8 - 30.5 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D945V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ICAM3 MUTATED         0        0        0        0         0         0
  ICAM3 WILD-TYPE      10       20       46       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICAM3 MUTATED           1          0          1          1        2         0
  ICAM3 WILD-TYPE        28         84         61         38       41         4
D945V3, multiclass
            clus
vv           ICAM3 MUTATED ICAM3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ICAM3 MUTATED       0   0   2   3
  ICAM3 WILD-TYPE    54 135 259  99
D945V4, multiclass
       clus
vv      ICAM3 MUTATED ICAM3 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ICAM3 MUTATED     0   3   2   1
  ICAM3 WILD-TYPE 195 170  87  84
D945V5, multiclass
    clus
vv   ICAM3 MUTATED ICAM3 WILD-TYPE
  N0             0             195
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V6, binary
                 cls
clus                0   1
  ICAM3 MUTATED     5   1
  ICAM3 WILD-TYPE 477  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      5    1
  ICAM3 WILD-TYPE  477   37
   clus
vv  ICAM3 MUTATED ICAM3 WILD-TYPE
  0             5             477
  1             1              37
[1] 2 2
[1] FALSE
D945V7, binary
                 cls
clus                0   1
  ICAM3 MUTATED     3   3
  ICAM3 WILD-TYPE 169 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      3    3
  ICAM3 WILD-TYPE  169  403
        clus
vv       ICAM3 MUTATED ICAM3 WILD-TYPE
  FEMALE             3             169
  MALE               3             403
[1] 2 2
[1] FALSE
D945V8, binary
                 cls
clus                0   1
  ICAM3 MUTATED     4   1
  ICAM3 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      4    1
  ICAM3 WILD-TYPE  412  101
     clus
vv    ICAM3 MUTATED ICAM3 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D945V9, continuous
D945V10, continuous
[1] "Remove cluster labels:" "ICAM3 MUTATED"         
clus
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-R6-A6DN 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ICAM3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ICAM3 MUTATED       0                         0
  ICAM3 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ICAM3 MUTATED                                           0     3
  ICAM3 WILD-TYPE                                         1   354
D945V11, multiclass
                                           clus
vv                                          ICAM3 MUTATED ICAM3 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V12, binary
                 cls
clus                0   1
  ICAM3 MUTATED     0   3
  ICAM3 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      0    3
  ICAM3 WILD-TYPE   10  395
                        clus
vv                       ICAM3 MUTATED ICAM3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(946) Variable = PAX4 MUTATION ANALYSIS
D946V1, survival
                sevent
clus2              0   1
  PAX4 MUTATED     8   4
  PAX4 WILD-TYPE 330 212
  PAX4 MUTATED PAX4 WILD-TYPE 
            12            542 
  PAX4 MUTATED PAX4 WILD-TYPE 
             4            212 
$`PAX4 MUTATED`
TCGA-L5-A8NT TCGA-JY-A6FG TCGA-L5-A8NK TCGA-L5-A8NV TCGA-V5-A7RB TCGA-CD-8529 
       27.12        41.52        13.55        52.57         5.29        12.30 
TCGA-CD-8536 TCGA-CD-A4MJ TCGA-D7-A6EY TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-VQ-A8P2 
       12.43        12.62        11.44         6.51        23.84        38.14 

$`PAX4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PAX4 MUTATED PAX4 WILD-TYPE 
          5.29           0.00 
  PAX4 MUTATED PAX4 WILD-TYPE 
         52.57         122.30 
  PAX4 MUTATED PAX4 WILD-TYPE 
        13.085         13.630 
[1] "5.3 - 52.6 (13.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D946V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX4 MUTATED         0        1        1        1         3         2
  PAX4 WILD-TYPE      10       19       45       30        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX4 MUTATED           1          1          1          0        1         0
  PAX4 WILD-TYPE        28         83         61         39       42         4
D946V3, multiclass
            clus
vv           PAX4 MUTATED PAX4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PAX4 MUTATED       2   2   7   2
  PAX4 WILD-TYPE    52 133 254 100
D946V4, multiclass
       clus
vv      PAX4 MUTATED PAX4 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               7            254
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PAX4 MUTATED     8   4   1   1
  PAX4 WILD-TYPE 187 169  88  84
D946V5, multiclass
    clus
vv   PAX4 MUTATED PAX4 WILD-TYPE
  N0            8            187
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V6, binary
                cls
clus               0   1
  PAX4 MUTATED    12   1
  PAX4 WILD-TYPE 470  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX4 MUTATED     12    1
  PAX4 WILD-TYPE  470   37
   clus
vv  PAX4 MUTATED PAX4 WILD-TYPE
  0           12            470
  1            1             37
[1] 2 2
[1] FALSE
D946V7, binary
                cls
clus               0   1
  PAX4 MUTATED     5   9
  PAX4 WILD-TYPE 167 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX4 MUTATED      5    9
  PAX4 WILD-TYPE  167  397
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  FEMALE            5            167
  MALE              9            397
[1] 2 2
[1] FALSE
D946V8, binary
                cls
clus               0   1
  PAX4 MUTATED     8   4
  PAX4 WILD-TYPE 408  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX4 MUTATED      8    4
  PAX4 WILD-TYPE  408   98
     clus
vv    PAX4 MUTATED PAX4 WILD-TYPE
  NO             8            408
  YES            4             98
[1] 2 2
[1] FALSE
D946V9, continuous
[1] "Remove cluster labels:" "PAX4 MUTATED"          
clus
  PAX4 MUTATED PAX4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
D946V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PAX4 MUTATED       6                         0
  PAX4 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAX4 MUTATED                                           0     7
  PAX4 WILD-TYPE                                         1   350
D946V11, multiclass
                                           clus
vv                                          PAX4 MUTATED PAX4 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V12, binary
                cls
clus               0   1
  PAX4 MUTATED     1   8
  PAX4 WILD-TYPE   9 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX4 MUTATED      1    8
  PAX4 WILD-TYPE    9  390
                        clus
vv                       PAX4 MUTATED PAX4 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(947) Variable = ZNF514 MUTATION ANALYSIS
D947V1, survival
                  sevent
clus2                0   1
  ZNF514 MUTATED     2   6
  ZNF514 WILD-TYPE 336 210
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               8              546 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               6              210 
$`ZNF514 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4469 
        6.97         9.34        34.68        31.96         6.58         7.07 
TCGA-CG-5726 TCGA-VQ-AA64 
       28.96        18.41 

$`ZNF514 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF514 MUTATED ZNF514 WILD-TYPE 
            6.58             0.00 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
           34.68           122.30 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
          13.875           13.565 
[1] "6.6 - 34.7 (13.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D947V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF514 MUTATED         0        1        0        0         2         0
  ZNF514 WILD-TYPE      10       19       46       31        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF514 MUTATED           0          1          1          0        2
  ZNF514 WILD-TYPE        29         83         61         39       41
                  vv
clus               STAGE IVA
  ZNF514 MUTATED           0
  ZNF514 WILD-TYPE         4
D947V3, multiclass
            clus
vv           ZNF514 MUTATED ZNF514 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF514 MUTATED       1   0   5   1
  ZNF514 WILD-TYPE    53 135 256 101
D947V4, multiclass
       clus
vv      ZNF514 MUTATED ZNF514 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 5              256
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF514 MUTATED     3   2   2   1
  ZNF514 WILD-TYPE 192 171  87  84
D947V5, multiclass
    clus
vv   ZNF514 MUTATED ZNF514 WILD-TYPE
  N0              3              192
  N1              2              171
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V6, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     7   1
  ZNF514 WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      7    1
  ZNF514 WILD-TYPE  475   37
   clus
vv  ZNF514 MUTATED ZNF514 WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D947V7, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     2   7
  ZNF514 WILD-TYPE 170 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      2    7
  ZNF514 WILD-TYPE  170  399
        clus
vv       ZNF514 MUTATED ZNF514 WILD-TYPE
  FEMALE              2              170
  MALE                7              399
[1] 2 2
[1] FALSE
D947V8, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     5   1
  ZNF514 WILD-TYPE 411 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      5    1
  ZNF514 WILD-TYPE  411  101
     clus
vv    ZNF514 MUTATED ZNF514 WILD-TYPE
  NO               5              411
  YES              1              101
[1] 2 2
[1] FALSE
D947V9, continuous
D947V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF514 MUTATED       2                         0
  ZNF514 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF514 MUTATED                                           0     5
  ZNF514 WILD-TYPE                                         1   352
D947V11, multiclass
                                           clus
vv                                          ZNF514 MUTATED ZNF514 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V12, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     0   6
  ZNF514 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      0    6
  ZNF514 WILD-TYPE   10  392
                        clus
vv                       ZNF514 MUTATED ZNF514 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(948) Variable = MSN MUTATION ANALYSIS
D948V1, survival
               sevent
clus2             0   1
  MSN MUTATED     8   8
  MSN WILD-TYPE 330 208
  MSN MUTATED MSN WILD-TYPE 
           16           538 
  MSN MUTATED MSN WILD-TYPE 
            8           208 
$`MSN MUTATED`
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-2H-A9GI TCGA-IG-A5B8 TCGA-L5-A893 TCGA-V5-AASV 
        4.70        19.99        14.30         0.79         3.02        15.35 
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8680 TCGA-BR-A4QI TCGA-CG-5726 
       34.68        32.25         8.05        31.96        21.44        28.96 
TCGA-D7-6525 TCGA-HU-A4GU TCGA-MX-A5UG TCGA-VQ-A8DU 
       13.35         6.58         3.72         5.46 

$`MSN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69        29.59         9.60         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MSN MUTATED MSN WILD-TYPE 
         0.79          0.00 
  MSN MUTATED MSN WILD-TYPE 
        34.68        122.30 
  MSN MUTATED MSN WILD-TYPE 
       13.825        13.565 
[1] "0.8 - 34.7 (13.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D948V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MSN MUTATED         2        1        1        0         2         3
  MSN WILD-TYPE       8       19       45       31        82        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSN MUTATED           1          3          0          2        1         0
  MSN WILD-TYPE        28         81         62         37       42         4
D948V3, multiclass
            clus
vv           MSN MUTATED MSN WILD-TYPE
  STAGE I              2             8
  STAGE IA             1            19
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            3            80
  STAGE III            1            28
  STAGE IIIA           3            81
  STAGE IIIB           0            62
  STAGE IIIC           2            37
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  MSN MUTATED       3   1   9   3
  MSN WILD-TYPE    51 134 252  99
D948V4, multiclass
       clus
vv      MSN MUTATED MSN WILD-TYPE
  T0+T1           3            51
  T2              1           134
  T3              9           252
  T4              3            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  MSN MUTATED     8   3   3   2
  MSN WILD-TYPE 187 170  86  83
D948V5, multiclass
    clus
vv   MSN MUTATED MSN WILD-TYPE
  N0           8           187
  N1           3           170
  N2           3            86
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V6, binary
               cls
clus              0   1
  MSN MUTATED    13   1
  MSN WILD-TYPE 469  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED     13    1
  MSN WILD-TYPE  469   37
   clus
vv  MSN MUTATED MSN WILD-TYPE
  0          13           469
  1           1            37
[1] 2 2
[1] FALSE
D948V7, binary
               cls
clus              0   1
  MSN MUTATED     6  10
  MSN WILD-TYPE 166 396
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      6   10
  MSN WILD-TYPE  166  396
        clus
vv       MSN MUTATED MSN WILD-TYPE
  FEMALE           6           166
  MALE            10           396
[1] 2 2
[1] FALSE
D948V8, binary
               cls
clus              0   1
  MSN MUTATED    14   1
  MSN WILD-TYPE 402 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED     14    1
  MSN WILD-TYPE  402  101
     clus
vv    MSN MUTATED MSN WILD-TYPE
  NO           14           402
  YES           1           101
[1] 2 2
[1] FALSE
D948V9, continuous
[1] "Remove cluster labels:" "MSN MUTATED"           
clus
  MSN MUTATED MSN WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASW 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" "MSN WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"MSN WILD-TYPE" "MSN WILD-TYPE" 
D948V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  MSN MUTATED       3                         1
  MSN WILD-TYPE   130                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSN MUTATED                                           0    10
  MSN WILD-TYPE                                         1   347
D948V11, multiclass
                                           clus
vv                                          MSN MUTATED MSN WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              10           347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V12, binary
               cls
clus              0   1
  MSN MUTATED     0  10
  MSN WILD-TYPE  10 388
[1] "tbl2"
               cls
clus            [,1] [,2]
  MSN MUTATED      0   10
  MSN WILD-TYPE   10  388
                        clus
vv                       MSN MUTATED MSN WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO          10           388
[1] 2 2
[1] FALSE

Clustering(949) Variable = ANKRD36 MUTATION ANALYSIS
D949V1, survival
                   sevent
clus2                 0   1
  ANKRD36 MUTATED    15   8
  ANKRD36 WILD-TYPE 323 208
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               23               531 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
                8               208 
$`ANKRD36 MUTATED`
TCGA-CG-4460 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-L5-A43C TCGA-L5-A4OX TCGA-L5-A8NE 
       21.99         4.67        14.50         3.16         7.43        55.50 
TCGA-LN-A4MQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-Z6-A8JD TCGA-BR-4184 TCGA-BR-6802 
       12.33         7.82         8.02         3.42         6.97        30.90 
TCGA-BR-6803 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 
       31.20         6.18        31.10         0.26        28.14        31.96 
TCGA-BR-A4CS TCGA-CD-8529 TCGA-CD-8532 TCGA-HF-A5NB TCGA-HU-8602 
        1.48        12.30        11.64        30.51        22.32 

$`ANKRD36 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
             0.26              0.00 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
             55.5             122.3 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
            12.30             13.68 
[1] "0.3 - 55.5 (12.3)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D949V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD36 MUTATED         0        0        1        1         3         4
  ANKRD36 WILD-TYPE      10       20       45       30        81        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD36 MUTATED           1          2          2          4        3
  ANKRD36 WILD-TYPE        28         82         60         35       40
                   vv
clus                STAGE IVA
  ANKRD36 MUTATED           0
  ANKRD36 WILD-TYPE         4
D949V3, multiclass
            clus
vv           ANKRD36 MUTATED ANKRD36 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                4                79
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               4                35
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ANKRD36 MUTATED       0   3  10   8
  ANKRD36 WILD-TYPE    54 132 251  94
D949V4, multiclass
       clus
vv      ANKRD36 MUTATED ANKRD36 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                 10               251
  T4                  8                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ANKRD36 MUTATED     7   5   5   3
  ANKRD36 WILD-TYPE 188 168  84  82
D949V5, multiclass
    clus
vv   ANKRD36 MUTATED ANKRD36 WILD-TYPE
  N0               7               188
  N1               5               168
  N2               5                84
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V6, binary
                   cls
clus                  0   1
  ANKRD36 MUTATED    17   3
  ANKRD36 WILD-TYPE 465  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED     17    3
  ANKRD36 WILD-TYPE  465   35
   clus
vv  ANKRD36 MUTATED ANKRD36 WILD-TYPE
  0              17               465
  1               3                35
[1] 2 2
[1] FALSE
D949V7, binary
                   cls
clus                  0   1
  ANKRD36 MUTATED     6  17
  ANKRD36 WILD-TYPE 166 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      6   17
  ANKRD36 WILD-TYPE  166  389
        clus
vv       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  FEMALE               6               166
  MALE                17               389
[1] 2 2
[1] FALSE
D949V8, binary
                   cls
clus                  0   1
  ANKRD36 MUTATED    18   2
  ANKRD36 WILD-TYPE 398 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED     18    2
  ANKRD36 WILD-TYPE  398  100
     clus
vv    ANKRD36 MUTATED ANKRD36 WILD-TYPE
  NO               18               398
  YES               2               100
[1] 2 2
[1] FALSE
D949V9, continuous
[1] "Remove cluster labels:" "ANKRD36 MUTATED"       
clus
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MR 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JE 
"ANKRD36 WILD-TYPE" "ANKRD36 WILD-TYPE" 
D949V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD36 MUTATED       7                         0
  ANKRD36 WILD-TYPE   126                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD36 MUTATED                                           0    14
  ANKRD36 WILD-TYPE                                         1   343
D949V11, multiclass
                                           clus
vv                                          ANKRD36 MUTATED ANKRD36 WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V12, binary
                   cls
clus                  0   1
  ANKRD36 MUTATED     0  18
  ANKRD36 WILD-TYPE  10 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      0   18
  ANKRD36 WILD-TYPE   10  380
                        clus
vv                       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(950) Variable = SIGLEC1 MUTATION ANALYSIS
D950V1, survival
                   sevent
clus2                 0   1
  SIGLEC1 MUTATED    18  10
  SIGLEC1 WILD-TYPE 320 206
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
               28               526 
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
               10               206 
$`SIGLEC1 MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-JY-A6F8 
       24.00        19.99        21.99         0.79        23.41       122.10 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-V5-A7RC TCGA-V5-AASW TCGA-B7-A5TJ TCGA-BR-4184 
        7.82         7.59         3.42         9.27        11.01         6.97 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-8527 TCGA-CD-8536 
       36.16        35.84        29.59         0.26         7.17        12.43 
TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-A747 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4G9 
       65.10        20.91         8.38        11.08        77.29        24.20 
TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA6B 
       11.77         0.10        38.14        32.94 

$`SIGLEC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.53        17.03        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         8.02         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29        15.65         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        38.93        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
              0.1               0.0 
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
            122.1             122.3 
  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE 
           16.210            13.565 
[1] "0.1 - 122.1 (16.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D950V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SIGLEC1 MUTATED         2        3        4        3         1         4
  SIGLEC1 WILD-TYPE       8       17       42       28        83        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC1 MUTATED           0          3          3          2        1
  SIGLEC1 WILD-TYPE        29         81         59         37       42
                   vv
clus                STAGE IVA
  SIGLEC1 MUTATED           0
  SIGLEC1 WILD-TYPE         4
D950V3, multiclass
            clus
vv           SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 3                17
  STAGE IB                 4                42
  STAGE II                 3                28
  STAGE IIA                1                83
  STAGE IIB                4                79
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               3                59
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SIGLEC1 MUTATED       5   5  11   5
  SIGLEC1 WILD-TYPE    49 130 250  97
D950V4, multiclass
       clus
vv      SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  T0+T1               5                49
  T2                  5               130
  T3                 11               250
  T4                  5                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SIGLEC1 MUTATED    12   7   5   1
  SIGLEC1 WILD-TYPE 183 166  84  84
D950V5, multiclass
    clus
vv   SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  N0              12               183
  N1               7               166
  N2               5                84
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V6, binary
                   cls
clus                  0   1
  SIGLEC1 MUTATED    21   1
  SIGLEC1 WILD-TYPE 461  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC1 MUTATED     21    1
  SIGLEC1 WILD-TYPE  461   37
   clus
vv  SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  0              21               461
  1               1                37
[1] 2 2
[1] FALSE
D950V7, binary
                   cls
clus                  0   1
  SIGLEC1 MUTATED     9  20
  SIGLEC1 WILD-TYPE 163 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC1 MUTATED      9   20
  SIGLEC1 WILD-TYPE  163  386
        clus
vv       SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  FEMALE               9               163
  MALE                20               386
[1] 2 2
[1] FALSE
D950V8, binary
                   cls
clus                  0   1
  SIGLEC1 MUTATED    21   6
  SIGLEC1 WILD-TYPE 395  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC1 MUTATED     21    6
  SIGLEC1 WILD-TYPE  395   96
     clus
vv    SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  NO               21               395
  YES               6                96
[1] 2 2
[1] FALSE
D950V9, continuous
D950V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SIGLEC1 MUTATED       5                         3
  SIGLEC1 WILD-TYPE   128                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIGLEC1 MUTATED                                           0    18
  SIGLEC1 WILD-TYPE                                         1   339
D950V11, multiclass
                                           clus
vv                                          SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               3                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V12, binary
                   cls
clus                  0   1
  SIGLEC1 MUTATED     0  21
  SIGLEC1 WILD-TYPE  10 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC1 MUTATED      0   21
  SIGLEC1 WILD-TYPE   10  377
                        clus
vv                       SIGLEC1 MUTATED SIGLEC1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              21               377
[1] 2 2
[1] FALSE

Clustering(951) Variable = CLGN MUTATION ANALYSIS
D951V1, survival
                sevent
clus2              0   1
  CLGN MUTATED     4   4
  CLGN WILD-TYPE 334 212
  CLGN MUTATED CLGN WILD-TYPE 
             8            546 
  CLGN MUTATED CLGN WILD-TYPE 
             4            212 
$`CLGN MUTATED`
TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 
        7.76         6.97         6.61        34.68         6.18        31.10 
TCGA-CD-A4MI TCGA-CG-5721 
       11.77         6.02 

$`CLGN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CLGN MUTATED CLGN WILD-TYPE 
          6.02           0.00 
  CLGN MUTATED CLGN WILD-TYPE 
         34.68         122.30 
  CLGN MUTATED CLGN WILD-TYPE 
         7.365         13.730 
[1] "6.0 - 34.7 (7.4)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.7"
D951V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLGN MUTATED         0        0        0        0         2         1
  CLGN WILD-TYPE      10       20       46       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLGN MUTATED           1          3          0          1        1         0
  CLGN WILD-TYPE        28         81         62         38       42         4
D951V3, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CLGN MUTATED       0   2   4   3
  CLGN WILD-TYPE    54 133 257  99
D951V4, multiclass
       clus
vv      CLGN MUTATED CLGN WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CLGN MUTATED     3   5   1   0
  CLGN WILD-TYPE 192 168  88  85
D951V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0            3            192
  N1            5            168
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V6, binary
                cls
clus               0   1
  CLGN MUTATED     9   0
  CLGN WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      9    0
  CLGN WILD-TYPE  473   38
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D951V7, binary
                cls
clus               0   1
  CLGN MUTATED     6   4
  CLGN WILD-TYPE 166 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      6    4
  CLGN WILD-TYPE  166  402
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  FEMALE            6            166
  MALE              4            402
[1] 2 2
[1] FALSE
D951V8, binary
                cls
clus               0   1
  CLGN MUTATED     8   0
  CLGN WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      8    0
  CLGN WILD-TYPE  408  102
     clus
vv    CLGN MUTATED CLGN WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D951V9, continuous
D951V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CLGN MUTATED       1                         0
  CLGN WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLGN MUTATED                                           0     8
  CLGN WILD-TYPE                                         1   349
D951V11, multiclass
                                           clus
vv                                          CLGN MUTATED CLGN WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V12, binary
                cls
clus               0   1
  CLGN MUTATED     0   8
  CLGN WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      0    8
  CLGN WILD-TYPE   10  390
                        clus
vv                       CLGN MUTATED CLGN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(952) Variable = IL7R MUTATION ANALYSIS
D952V1, survival
                sevent
clus2              0   1
  IL7R MUTATED    11   5
  IL7R WILD-TYPE 327 211
  IL7R MUTATED IL7R WILD-TYPE 
            16            538 
  IL7R MUTATED IL7R WILD-TYPE 
             5            211 
$`IL7R MUTATED`
TCGA-JY-A6FB TCGA-IG-A3YA TCGA-IG-A3YC TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7197 
       60.39        20.78        20.12        30.90        34.68         9.21 
TCGA-BR-7704 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-A4MG 
       35.24        28.14        31.96         0.53        16.14         6.58 
TCGA-CG-4465 TCGA-CG-5733 TCGA-HU-A4GH TCGA-VQ-A8P2 
        9.01        21.07        11.77        38.14 

$`IL7R WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       35.21         0.85         2.63        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  IL7R MUTATED IL7R WILD-TYPE 
          0.53           0.00 
  IL7R MUTATED IL7R WILD-TYPE 
         60.39         122.30 
  IL7R MUTATED IL7R WILD-TYPE 
        20.925         13.495 
[1] "0.5 - 60.4 (20.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D952V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL7R MUTATED         1        1        0        2         2         0
  IL7R WILD-TYPE       9       19       46       29        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL7R MUTATED           0          4          2          1        2         0
  IL7R WILD-TYPE        29         80         60         38       41         4
D952V3, multiclass
            clus
vv           IL7R MUTATED IL7R WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IL7R MUTATED       2   2   7   6
  IL7R WILD-TYPE    52 133 254  96
D952V4, multiclass
       clus
vv      IL7R MUTATED IL7R WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               7            254
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IL7R MUTATED     7   2   3   3
  IL7R WILD-TYPE 188 171  86  82
D952V5, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  N0            7            188
  N1            2            171
  N2            3             86
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V6, binary
                cls
clus               0   1
  IL7R MUTATED    14   2
  IL7R WILD-TYPE 468  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     14    2
  IL7R WILD-TYPE  468   36
   clus
vv  IL7R MUTATED IL7R WILD-TYPE
  0           14            468
  1            2             36
[1] 2 2
[1] FALSE
D952V7, binary
                cls
clus               0   1
  IL7R MUTATED     6  11
  IL7R WILD-TYPE 166 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      6   11
  IL7R WILD-TYPE  166  395
        clus
vv       IL7R MUTATED IL7R WILD-TYPE
  FEMALE            6            166
  MALE             11            395
[1] 2 2
[1] FALSE
D952V8, binary
                cls
clus               0   1
  IL7R MUTATED    13   1
  IL7R WILD-TYPE 403 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     13    1
  IL7R WILD-TYPE  403  101
     clus
vv    IL7R MUTATED IL7R WILD-TYPE
  NO            13            403
  YES            1            101
[1] 2 2
[1] FALSE
D952V9, continuous
[1] "Remove cluster labels:" "IL7R MUTATED"          
clus
  IL7R MUTATED IL7R WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YB 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-IG-A51D     TCGA-IG-A5S3     TCGA-IG-A7DP     TCGA-KH-A6WC 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M     TCGA-LN-A49N 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A49X 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2     TCGA-LN-A4A3 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6     TCGA-LN-A4A8 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" 
D952V10, continuous
[1] "Remove cluster labels:" "IL7R MUTATED"          
clus
  IL7R MUTATED IL7R WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A4P3     TCGA-IG-A4QT 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS     TCGA-IG-A8O2 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE     TCGA-JY-A6FG 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C     TCGA-L5-A43E 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM     TCGA-L5-A4ON 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ     TCGA-L5-A4OT 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX     TCGA-L5-A88S 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE     TCGA-L5-A8NF 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ     TCGA-L5-A8NR 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" "IL7R WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IL7R MUTATED       4                         0
  IL7R WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL7R MUTATED                                           0    11
  IL7R WILD-TYPE                                         1   346
D952V11, multiclass
                                           clus
vv                                          IL7R MUTATED IL7R WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V12, binary
                cls
clus               0   1
  IL7R MUTATED     0  13
  IL7R WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      0   13
  IL7R WILD-TYPE   10  385
                        clus
vv                       IL7R MUTATED IL7R WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(953) Variable = AVEN MUTATION ANALYSIS
D953V1, survival
                sevent
clus2              0   1
  AVEN MUTATED     5   2
  AVEN WILD-TYPE 333 214
  AVEN MUTATED AVEN WILD-TYPE 
             7            547 
  AVEN MUTATED AVEN WILD-TYPE 
             2            214 
$`AVEN MUTATED`
TCGA-B7-A5TJ TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-7707 TCGA-HF-A5NB TCGA-HU-A4G6 
       11.01        30.90         9.67        35.84        30.51        24.26 
TCGA-VQ-A8P2 
       38.14 

$`AVEN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  AVEN MUTATED AVEN WILD-TYPE 
          9.67           0.00 
  AVEN MUTATED AVEN WILD-TYPE 
         38.14         122.30 
  AVEN MUTATED AVEN WILD-TYPE 
         30.51          13.51 
[1] "9.7 - 38.1 (30.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D953V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AVEN MUTATED         0        1        1        0         0         1
  AVEN WILD-TYPE      10       19       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AVEN MUTATED           0          1          0          1        0         0
  AVEN WILD-TYPE        29         83         62         38       43         4
D953V3, multiclass
            clus
vv           AVEN MUTATED AVEN WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  AVEN MUTATED       1   2   0   3
  AVEN WILD-TYPE    53 133 261  99
D953V4, multiclass
       clus
vv      AVEN MUTATED AVEN WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               0            261
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  AVEN MUTATED     2   1   0   1
  AVEN WILD-TYPE 193 172  89  84
D953V5, multiclass
    clus
vv   AVEN MUTATED AVEN WILD-TYPE
  N0            2            193
  N1            1            172
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V6, binary
                cls
clus               0   1
  AVEN MUTATED     7   0
  AVEN WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      7    0
  AVEN WILD-TYPE  475   38
   clus
vv  AVEN MUTATED AVEN WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D953V7, binary
                cls
clus               0   1
  AVEN MUTATED     4   3
  AVEN WILD-TYPE 168 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      4    3
  AVEN WILD-TYPE  168  403
        clus
vv       AVEN MUTATED AVEN WILD-TYPE
  FEMALE            4            168
  MALE              3            403
[1] 2 2
[1] FALSE
D953V8, binary
                cls
clus               0   1
  AVEN MUTATED     5   2
  AVEN WILD-TYPE 411 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      5    2
  AVEN WILD-TYPE  411  100
     clus
vv    AVEN MUTATED AVEN WILD-TYPE
  NO             5            411
  YES            2            100
[1] 2 2
[1] FALSE
D953V9, continuous
D953V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AVEN MUTATED       1                         0
  AVEN WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AVEN MUTATED                                           0     5
  AVEN WILD-TYPE                                         1   352
D953V11, multiclass
                                           clus
vv                                          AVEN MUTATED AVEN WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V12, binary
                cls
clus               0   1
  AVEN MUTATED     0   5
  AVEN WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      0    5
  AVEN WILD-TYPE   10  393
                        clus
vv                       AVEN MUTATED AVEN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(954) Variable = CCDC37 MUTATION ANALYSIS
D954V1, survival
                  sevent
clus2                0   1
  CCDC37 MUTATED     9   5
  CCDC37 WILD-TYPE 329 211
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              14              540 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
               5              211 
$`CCDC37 MUTATED`
TCGA-L5-A4OW TCGA-LN-A49L TCGA-R6-A6XG TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
        7.13        10.45        38.40         6.97        30.90        34.68 
TCGA-BR-8081 TCGA-BR-8372 TCGA-CG-5721 TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-A4GT 
       32.25        31.27         6.02        21.07        11.08         6.51 
TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.58        38.14 

$`CCDC37 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CCDC37 MUTATED CCDC37 WILD-TYPE 
            6.02             0.00 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
            38.4            122.3 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
          16.075           13.565 
[1] "6.0 - 38.4 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D954V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC37 MUTATED         0        0        1        0         4         4
  CCDC37 WILD-TYPE      10       20       45       31        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC37 MUTATED           0          3          0          1        1
  CCDC37 WILD-TYPE        29         81         62         38       42
                  vv
clus               STAGE IVA
  CCDC37 MUTATED           0
  CCDC37 WILD-TYPE         4
D954V3, multiclass
            clus
vv           CCDC37 MUTATED CCDC37 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CCDC37 MUTATED       0   5   5   5
  CCDC37 WILD-TYPE    54 130 256  97
D954V4, multiclass
       clus
vv      CCDC37 MUTATED CCDC37 WILD-TYPE
  T0+T1              0               54
  T2                 5              130
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CCDC37 MUTATED     7   5   1   1
  CCDC37 WILD-TYPE 188 168  88  84
D954V5, multiclass
    clus
vv   CCDC37 MUTATED CCDC37 WILD-TYPE
  N0              7              188
  N1              5              168
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V6, binary
                  cls
clus                 0   1
  CCDC37 MUTATED    15   0
  CCDC37 WILD-TYPE 467  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED     15    0
  CCDC37 WILD-TYPE  467   38
   clus
vv  CCDC37 MUTATED CCDC37 WILD-TYPE
  0             15              467
  1              0               38
[1] 2 2
[1] FALSE
D954V7, binary
                  cls
clus                 0   1
  CCDC37 MUTATED     7  10
  CCDC37 WILD-TYPE 165 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED      7   10
  CCDC37 WILD-TYPE  165  396
        clus
vv       CCDC37 MUTATED CCDC37 WILD-TYPE
  FEMALE              7              165
  MALE               10              396
[1] 2 2
[1] FALSE
D954V8, binary
                  cls
clus                 0   1
  CCDC37 MUTATED    12   3
  CCDC37 WILD-TYPE 404  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED     12    3
  CCDC37 WILD-TYPE  404   99
     clus
vv    CCDC37 MUTATED CCDC37 WILD-TYPE
  NO              12              404
  YES              3               99
[1] 2 2
[1] FALSE
D954V9, continuous
[1] "Remove cluster labels:" "CCDC37 MUTATED"        
clus
  CCDC37 MUTATED CCDC37 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49M 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
D954V10, continuous
[1] "Remove cluster labels:" "CCDC37 MUTATED"        
clus
  CCDC37 MUTATED CCDC37 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OX 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" "CCDC37 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CCDC37 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC37 MUTATED       3                         1
  CCDC37 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC37 MUTATED                                           0     9
  CCDC37 WILD-TYPE                                         1   348
D954V11, multiclass
                                           clus
vv                                          CCDC37 MUTATED CCDC37 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V12, binary
                  cls
clus                 0   1
  CCDC37 MUTATED     0  12
  CCDC37 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED      0   12
  CCDC37 WILD-TYPE   10  386
                        clus
vv                       CCDC37 MUTATED CCDC37 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(955) Variable = SPATA5L1 MUTATION ANALYSIS
D955V1, survival
                    sevent
clus2                  0   1
  SPATA5L1 MUTATED     7   1
  SPATA5L1 WILD-TYPE 331 215
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 8                546 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 1                215 
$`SPATA5L1 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FH TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8680 TCGA-CG-5728 
       19.99        47.38        44.94        29.59        31.96        65.10 
TCGA-HU-A4GQ TCGA-HU-A4H0 
        0.10         2.10 

$`SPATA5L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
               0.1                0.0 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
              65.1              122.3 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
            30.775             13.510 
[1] "0.1 - 65.1 (30.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.8"
D955V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA5L1 MUTATED         0        0        1        0         1         2
  SPATA5L1 WILD-TYPE      10       20       45       31        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA5L1 MUTATED           0          0          0          3        1
  SPATA5L1 WILD-TYPE        29         84         62         36       42
                    vv
clus                 STAGE IVA
  SPATA5L1 MUTATED           0
  SPATA5L1 WILD-TYPE         4
D955V3, multiclass
            clus
vv           SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SPATA5L1 MUTATED       0   2   2   4
  SPATA5L1 WILD-TYPE    54 133 259  98
D955V4, multiclass
       clus
vv      SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  T0+T1                0                 54
  T2                   2                133
  T3                   2                259
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SPATA5L1 MUTATED     3   1   2   2
  SPATA5L1 WILD-TYPE 192 172  87  83
D955V5, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  N0                3                192
  N1                1                172
  N2                2                 87
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V6, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     6   1
  SPATA5L1 WILD-TYPE 476  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      6    1
  SPATA5L1 WILD-TYPE  476   37
   clus
vv  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  0                6                476
  1                1                 37
[1] 2 2
[1] FALSE
D955V7, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     3   5
  SPATA5L1 WILD-TYPE 169 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      3    5
  SPATA5L1 WILD-TYPE  169  401
        clus
vv       SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  FEMALE                3                169
  MALE                  5                401
[1] 2 2
[1] FALSE
D955V8, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     7   0
  SPATA5L1 WILD-TYPE 409 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      7    0
  SPATA5L1 WILD-TYPE  409  102
     clus
vv    SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  NO                 7                409
  YES                0                102
[1] 2 2
[1] FALSE
D955V9, continuous
D955V10, continuous
[1] "Remove cluster labels:" "SPATA5L1 MUTATED"      
clus
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A88T 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-KH-A6WC         TCGA-L5-A43C 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A43E         TCGA-L5-A43H         TCGA-L5-A4OH 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A4OM         TCGA-L5-A4ON         TCGA-L5-A4OO 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A4OP         TCGA-L5-A4OQ         TCGA-L5-A4OT 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A4OU         TCGA-L5-A4OW         TCGA-L5-A4OX 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" "SPATA5L1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SPATA5L1 MUTATED       3                         0
  SPATA5L1 WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA5L1 MUTATED                                           0     4
  SPATA5L1 WILD-TYPE                                         1   353
D955V11, multiclass
                                           clus
vv                                          SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V12, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     0   5
  SPATA5L1 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      0    5
  SPATA5L1 WILD-TYPE   10  393
                        clus
vv                       SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(956) Variable = SERPINB10 MUTATION ANALYSIS
D956V1, survival
                     sevent
clus2                   0   1
  SERPINB10 MUTATED     7   3
  SERPINB10 WILD-TYPE 331 213
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 10                 544 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  3                 213 
$`SERPINB10 MUTATED`
TCGA-R6-A8W5 TCGA-XP-A8T6 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG 
       15.78        25.08        44.94        29.59        31.96         6.58 
TCGA-CG-5721 TCGA-D7-A4Z0 TCGA-HF-7132 TCGA-HU-A4H8 
        6.02        14.76        77.29        14.07 

$`SERPINB10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
               6.02                0.00 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
              77.29              122.30 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
             20.430              13.495 
[1] "6.0 - 77.3 (20.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D956V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB10 MUTATED         0        0        1        1         2         3
  SERPINB10 WILD-TYPE      10       20       45       30        82        80
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB10 MUTATED           0          0          0          0        2
  SERPINB10 WILD-TYPE        29         84         62         39       41
                     vv
clus                  STAGE IVA
  SERPINB10 MUTATED           1
  SERPINB10 WILD-TYPE         3
D956V3, multiclass
            clus
vv           SERPINB10 MUTATED SERPINB10 WILD-TYPE
  STAGE I                    0                  10
  STAGE IA                   0                  20
  STAGE IB                   1                  45
  STAGE II                   1                  30
  STAGE IIA                  2                  82
  STAGE IIB                  3                  80
  STAGE III                  0                  29
  STAGE IIIA                 0                  84
  STAGE IIIB                 0                  62
  STAGE IIIC                 0                  39
  STAGE IV                   2                  41
  STAGE IVA                  1                   3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  SERPINB10 MUTATED       1   3   3   3
  SERPINB10 WILD-TYPE    53 132 258  99
D956V4, multiclass
       clus
vv      SERPINB10 MUTATED SERPINB10 WILD-TYPE
  T0+T1                 1                  53
  T2                    3                 132
  T3                    3                 258
  T4                    3                  99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  SERPINB10 MUTATED     3   5   2   0
  SERPINB10 WILD-TYPE 192 168  87  85
D956V5, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  N0                 3                 192
  N1                 5                 168
  N2                 2                  87
  N3                 0                  85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V6, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     8   2
  SERPINB10 WILD-TYPE 474  36
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      8    2
  SERPINB10 WILD-TYPE  474   36
   clus
vv  SERPINB10 MUTATED SERPINB10 WILD-TYPE
  0                 8                 474
  1                 2                  36
[1] 2 2
[1] FALSE
D956V7, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     3   7
  SERPINB10 WILD-TYPE 169 399
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      3    7
  SERPINB10 WILD-TYPE  169  399
        clus
vv       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  FEMALE                 3                 169
  MALE                   7                 399
[1] 2 2
[1] FALSE
D956V8, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     8   2
  SERPINB10 WILD-TYPE 408 100
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      8    2
  SERPINB10 WILD-TYPE  408  100
     clus
vv    SERPINB10 MUTATED SERPINB10 WILD-TYPE
  NO                  8                 408
  YES                 2                 100
[1] 2 2
[1] FALSE
D956V9, continuous
[1] "Remove cluster labels:" "SERPINB10 MUTATED"     
clus
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  1                  67 
         TCGA-IG-A3I8          TCGA-IG-A3QL          TCGA-IG-A3Y9 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A3YA          TCGA-IG-A3YB          TCGA-IG-A3YC 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A51D          TCGA-IG-A5S3          TCGA-IG-A7DP 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-KH-A6WC          TCGA-LN-A49K          TCGA-LN-A49L 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49M          TCGA-LN-A49N          TCGA-LN-A49O 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49P          TCGA-LN-A49R          TCGA-LN-A49S 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49U          TCGA-LN-A49V          TCGA-LN-A49W 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49X          TCGA-LN-A49Y          TCGA-LN-A4A1 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A4A2          TCGA-LN-A4A3          TCGA-LN-A4A4 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A4A5          TCGA-LN-A4A6          TCGA-LN-A4A8 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A4A9          TCGA-LN-A4MQ          TCGA-LN-A4MR 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A5U5          TCGA-LN-A5U6          TCGA-LN-A5U7 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A7HV          TCGA-LN-A7HW          TCGA-LN-A7HX 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A7HY          TCGA-LN-A7HZ          TCGA-V5-A7RB 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-V5-A7RC          TCGA-V5-A7RE          TCGA-V5-AASV 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-V5-AASW          TCGA-V5-AASX          TCGA-VR-A8EO 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8EP          TCGA-VR-A8EQ          TCGA-VR-A8ER 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8ET          TCGA-VR-A8EU          TCGA-VR-A8EW 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8EX          TCGA-VR-A8EY          TCGA-VR-A8EZ 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8Q7          TCGA-VR-AA4D          TCGA-VR-AA4G 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-AA7B          TCGA-VR-AA7D          TCGA-VR-AA7I 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-XP-A8T7          TCGA-XP-A8T8          TCGA-Z6-A8JD 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-Z6-A8JE 
"SERPINB10 WILD-TYPE" 
D956V10, continuous
[1] "Remove cluster labels:" "SERPINB10 MUTATED"     
clus
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  2                  96 
         TCGA-IC-A6RF          TCGA-L5-A43I          TCGA-L5-A43J 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A4OE          TCGA-L5-A4OG          TCGA-L5-A4OI 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A88T          TCGA-L5-A88Y          TCGA-L5-A8NG 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A8NT          TCGA-Q9-A6FU          TCGA-IC-A6RE 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A3QL          TCGA-IG-A3Y9          TCGA-IG-A3YA 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A3YC          TCGA-IG-A4P3          TCGA-IG-A4QT 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A50L          TCGA-IG-A5B8          TCGA-IG-A6QS 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-IG-A8O2          TCGA-IG-A97H          TCGA-JY-A6FA 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-JY-A6FE          TCGA-JY-A6FG          TCGA-JY-A6FH 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-KH-A6WC          TCGA-L5-A43C          TCGA-L5-A43E 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A43H          TCGA-L5-A4OH          TCGA-L5-A4OM 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A4ON          TCGA-L5-A4OO          TCGA-L5-A4OP 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A4OQ          TCGA-L5-A4OT          TCGA-L5-A4OU 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A4OW          TCGA-L5-A4OX          TCGA-L5-A88S 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A88V          TCGA-L5-A893          TCGA-L5-A8NE 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A8NF          TCGA-L5-A8NK          TCGA-L5-A8NN 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A8NQ          TCGA-L5-A8NR          TCGA-L5-A8NS 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-L5-A8NW          TCGA-LN-A49O          TCGA-LN-A49P 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49R          TCGA-LN-A49S          TCGA-LN-A49U 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A49V          TCGA-LN-A49W          TCGA-LN-A4A3 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A4A6          TCGA-LN-A4A9          TCGA-LN-A5U6 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A5U7          TCGA-LN-A7HV          TCGA-LN-A7HW 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A7HX          TCGA-LN-A7HZ          TCGA-LN-A8HZ 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-LN-A8I0          TCGA-M9-A5M8          TCGA-Q9-A6FW 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-R6-A6DN          TCGA-R6-A6L4          TCGA-R6-A6XQ 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-R6-A6Y2          TCGA-R6-A8W8          TCGA-R6-A8WC 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-RE-A7BO          TCGA-V5-A7RB          TCGA-V5-A7RC 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-V5-AASV          TCGA-VR-A8EP          TCGA-VR-A8ER 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8EU          TCGA-VR-A8EW          TCGA-VR-A8EX 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-A8EZ          TCGA-VR-A8Q7          TCGA-VR-AA4G 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-VR-AA7D          TCGA-VR-AA7I          TCGA-X8-AAAR 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
         TCGA-XP-A8T7          TCGA-XP-A8T8          TCGA-Z6-AAPN 
"SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" "SERPINB10 WILD-TYPE" 
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB10 MUTATED       3                         1
  SERPINB10 WILD-TYPE   130                        13
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB10 MUTATED                                           0     4
  SERPINB10 WILD-TYPE                                         1   353
D956V11, multiclass
                                           clus
vv                                          SERPINB10 MUTATED
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     4
                                           clus
vv                                          SERPINB10 WILD-TYPE
  ASIAN                                                     130
  BLACK OR AFRICAN AMERICAN                                  13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V12, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     1   7
  SERPINB10 WILD-TYPE   9 391
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      1    7
  SERPINB10 WILD-TYPE    9  391
                        clus
vv                       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  HISPANIC OR LATINO                     1                   9
  NOT HISPANIC OR LATINO                 7                 391
[1] 2 2
[1] FALSE

Clustering(957) Variable = PIWIL2 MUTATION ANALYSIS
D957V1, survival
                  sevent
clus2                0   1
  PIWIL2 MUTATED     7   5
  PIWIL2 WILD-TYPE 331 211
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
              12              542 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               5              211 
$`PIWIL2 MUTATED`
TCGA-L5-A88T TCGA-2H-A9GO TCGA-L5-A4OW TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-A4QL 
       22.82        16.24         7.13        30.90         4.31        16.14 
TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4GT TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.02        11.44         6.51        74.53        19.04        38.14 

$`PIWIL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
            4.31             0.00 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           74.53           122.30 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           16.19            13.53 
[1] "4.3 - 74.5 (16.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D957V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIWIL2 MUTATED         0        0        2        0         1         2
  PIWIL2 WILD-TYPE      10       20       44       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIWIL2 MUTATED           0          1          2          0        2
  PIWIL2 WILD-TYPE        29         83         60         39       41
                  vv
clus               STAGE IVA
  PIWIL2 MUTATED           1
  PIWIL2 WILD-TYPE         3
D957V3, multiclass
            clus
vv           PIWIL2 MUTATED PIWIL2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PIWIL2 MUTATED       0   5   4   3
  PIWIL2 WILD-TYPE    54 130 257  99
D957V4, multiclass
       clus
vv      PIWIL2 MUTATED PIWIL2 WILD-TYPE
  T0+T1              0               54
  T2                 5              130
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PIWIL2 MUTATED     3   6   0   2
  PIWIL2 WILD-TYPE 192 167  89  83
D957V5, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  N0              3              192
  N1              6              167
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V6, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED    10   2
  PIWIL2 WILD-TYPE 472  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED     10    2
  PIWIL2 WILD-TYPE  472   36
   clus
vv  PIWIL2 MUTATED PIWIL2 WILD-TYPE
  0             10              472
  1              2               36
[1] 2 2
[1] FALSE
D957V7, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     8   4
  PIWIL2 WILD-TYPE 164 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      8    4
  PIWIL2 WILD-TYPE  164  402
        clus
vv       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  FEMALE              8              164
  MALE                4              402
[1] 2 2
[1] FALSE
D957V8, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED    11   1
  PIWIL2 WILD-TYPE 405 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED     11    1
  PIWIL2 WILD-TYPE  405  101
     clus
vv    PIWIL2 MUTATED PIWIL2 WILD-TYPE
  NO              11              405
  YES              1              101
[1] 2 2
[1] FALSE
D957V9, continuous
D957V10, continuous
[1] "Remove cluster labels:" "PIWIL2 MUTATED"        
clus
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88Y       TCGA-L5-A8NG 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OX       TCGA-L5-A88S 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" "PIWIL2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIWIL2 MUTATED       1                         0
  PIWIL2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIWIL2 MUTATED                                           0     8
  PIWIL2 WILD-TYPE                                         1   349
D957V11, multiclass
                                           clus
vv                                          PIWIL2 MUTATED PIWIL2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V12, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     1   6
  PIWIL2 WILD-TYPE   9 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      1    6
  PIWIL2 WILD-TYPE    9  392
                        clus
vv                       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(958) Variable = FAM46D MUTATION ANALYSIS
D958V1, survival
                  sevent
clus2                0   1
  FAM46D MUTATED    10   3
  FAM46D WILD-TYPE 328 213
  FAM46D MUTATED FAM46D WILD-TYPE 
              13              541 
  FAM46D MUTATED FAM46D WILD-TYPE 
               3              213 
$`FAM46D MUTATED`
TCGA-IG-A51D TCGA-L5-A4OX TCGA-LN-A9FO TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-8369 
       17.03         7.43         0.13        15.95        39.12        14.04 
TCGA-BR-8485 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6822 TCGA-F1-6874 
        9.21         6.58       105.07        21.07        12.33        14.47 
TCGA-VQ-A8P2 
       38.14 

$`FAM46D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        19.33        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FAM46D MUTATED FAM46D WILD-TYPE 
            0.13             0.00 
  FAM46D MUTATED FAM46D WILD-TYPE 
          105.07           122.30 
  FAM46D MUTATED FAM46D WILD-TYPE 
           14.47            13.51 
[1] "0.1 - 105.1 (14.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D958V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM46D MUTATED         0        0        2        1         3         3
  FAM46D WILD-TYPE      10       20       44       30        81        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM46D MUTATED           0          2          1          1        0
  FAM46D WILD-TYPE        29         82         61         38       43
                  vv
clus               STAGE IVA
  FAM46D MUTATED           0
  FAM46D WILD-TYPE         4
D958V3, multiclass
            clus
vv           FAM46D MUTATED FAM46D WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM46D MUTATED       1   7   3   2
  FAM46D WILD-TYPE    53 128 258 100
D958V4, multiclass
       clus
vv      FAM46D MUTATED FAM46D WILD-TYPE
  T0+T1              1               53
  T2                 7              128
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM46D MUTATED     4   6   1   2
  FAM46D WILD-TYPE 191 167  88  83
D958V5, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  N0              4              191
  N1              6              167
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V6, binary
                  cls
clus                 0   1
  FAM46D MUTATED    13   0
  FAM46D WILD-TYPE 469  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED     13    0
  FAM46D WILD-TYPE  469   38
   clus
vv  FAM46D MUTATED FAM46D WILD-TYPE
  0             13              469
  1              0               38
[1] 2 2
[1] FALSE
D958V7, binary
                  cls
clus                 0   1
  FAM46D MUTATED     3  10
  FAM46D WILD-TYPE 169 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      3   10
  FAM46D WILD-TYPE  169  396
        clus
vv       FAM46D MUTATED FAM46D WILD-TYPE
  FEMALE              3              169
  MALE               10              396
[1] 2 2
[1] FALSE
D958V8, binary
                  cls
clus                 0   1
  FAM46D MUTATED    12   1
  FAM46D WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED     12    1
  FAM46D WILD-TYPE  404  101
     clus
vv    FAM46D MUTATED FAM46D WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D958V9, continuous
[1] "Remove cluster labels:" "FAM46D MUTATED"        
clus
  FAM46D MUTATED FAM46D WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A5S3       TCGA-IG-A7DP 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
D958V10, continuous
[1] "Remove cluster labels:" "FAM46D MUTATED"        
clus
  FAM46D MUTATED FAM46D WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" "FAM46D WILD-TYPE" 
      TCGA-Z6-AAPN 
"FAM46D WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM46D MUTATED       2                         0
  FAM46D WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM46D MUTATED                                           0     9
  FAM46D WILD-TYPE                                         1   348
D958V11, multiclass
                                           clus
vv                                          FAM46D MUTATED FAM46D WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V12, binary
                  cls
clus                 0   1
  FAM46D MUTATED     0   9
  FAM46D WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      0    9
  FAM46D WILD-TYPE   10  389
                        clus
vv                       FAM46D MUTATED FAM46D WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(959) Variable = LIPH MUTATION ANALYSIS
D959V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     6   3
  LIPH WILD-TYPE 332 213
  LIPH MUTATED LIPH WILD-TYPE 
             9            545 
  LIPH MUTATED LIPH WILD-TYPE 
             3            213 
$`LIPH MUTATED`
TCGA-LN-A7HY TCGA-VR-A8EQ TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-8363 TCGA-F1-6874 
       12.03        22.82        26.70        19.56         0.26        14.47 
TCGA-HU-8602 TCGA-KB-A93J TCGA-VQ-AA6K 
       22.32        36.95        12.43 

$`LIPH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        17.26 

  LIPH MUTATED LIPH WILD-TYPE 
          0.26           0.00 
  LIPH MUTATED LIPH WILD-TYPE 
         36.95         122.30 
  LIPH MUTATED LIPH WILD-TYPE 
         19.56          13.51 
[1] "0.3 - 37.0 (19.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D959V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LIPH MUTATED         0        0        2        1         0         2
  LIPH WILD-TYPE      10       20       44       30        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIPH MUTATED           2          0          0          2        0         0
  LIPH WILD-TYPE        27         84         62         37       43         4
D959V3, multiclass
            clus
vv           LIPH MUTATED LIPH WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             2             27
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  LIPH MUTATED       0   3   2   4
  LIPH WILD-TYPE    54 132 259  98
D959V4, multiclass
       clus
vv      LIPH MUTATED LIPH WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  LIPH MUTATED     4   3   0   2
  LIPH WILD-TYPE 191 170  89  83
D959V5, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            4            191
  N1            3            170
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V6, binary
                cls
clus               0   1
  LIPH MUTATED     9   0
  LIPH WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      9    0
  LIPH WILD-TYPE  473   38
   clus
vv  LIPH MUTATED LIPH WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D959V7, binary
                cls
clus               0   1
  LIPH MUTATED     3   6
  LIPH WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      3    6
  LIPH WILD-TYPE  169  400
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D959V8, binary
                cls
clus               0   1
  LIPH MUTATED     6   3
  LIPH WILD-TYPE 410  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      6    3
  LIPH WILD-TYPE  410   99
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             6            410
  YES            3             99
[1] 2 2
[1] FALSE
D959V9, continuous
[1] "Remove cluster labels:" "LIPH MUTATED"          
clus
  LIPH MUTATED LIPH WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" "LIPH WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"LIPH WILD-TYPE" "LIPH WILD-TYPE" 
D959V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  LIPH MUTATED       2                         0
  LIPH WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIPH MUTATED                                           0     7
  LIPH WILD-TYPE                                         1   350
D959V11, multiclass
                                           clus
vv                                          LIPH MUTATED LIPH WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V12, binary
                cls
clus               0   1
  LIPH MUTATED     0   6
  LIPH WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      0    6
  LIPH WILD-TYPE   10  392
                        clus
vv                       LIPH MUTATED LIPH WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(960) Variable = GOLT1B MUTATION ANALYSIS
D960V1, survival
                  sevent
clus2                0   1
  GOLT1B MUTATED     4   1
  GOLT1B WILD-TYPE 334 215
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              549 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               1              215 
$`GOLT1B MUTATED`
TCGA-CG-4460 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8591 
       21.99        30.90        35.84        29.59        28.14 

$`GOLT1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GOLT1B MUTATED GOLT1B WILD-TYPE 
           21.99             0.00 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
           35.84           122.30 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
           29.59            13.51 
[1] "22.0 - 35.8 (29.6)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.4"
D960V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GOLT1B MUTATED         0        0        1        0         0         1
  GOLT1B WILD-TYPE      10       20       45       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLT1B MUTATED           0          1          0          1        1
  GOLT1B WILD-TYPE        29         83         62         38       42
                  vv
clus               STAGE IVA
  GOLT1B MUTATED           0
  GOLT1B WILD-TYPE         4
D960V3, multiclass
            clus
vv           GOLT1B MUTATED GOLT1B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GOLT1B MUTATED       0   1   1   3
  GOLT1B WILD-TYPE    54 134 260  99
D960V4, multiclass
       clus
vv      GOLT1B MUTATED GOLT1B WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 1              260
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GOLT1B MUTATED     2   1   1   1
  GOLT1B WILD-TYPE 193 172  88  84
D960V5, multiclass
    clus
vv   GOLT1B MUTATED GOLT1B WILD-TYPE
  N0              2              193
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V6, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     4   1
  GOLT1B WILD-TYPE 478  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      4    1
  GOLT1B WILD-TYPE  478   37
   clus
vv  GOLT1B MUTATED GOLT1B WILD-TYPE
  0              4              478
  1              1               37
[1] 2 2
[1] FALSE
D960V7, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     3   2
  GOLT1B WILD-TYPE 169 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      3    2
  GOLT1B WILD-TYPE  169  404
        clus
vv       GOLT1B MUTATED GOLT1B WILD-TYPE
  FEMALE              3              169
  MALE                2              404
[1] 2 2
[1] FALSE
D960V8, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     5   0
  GOLT1B WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      5    0
  GOLT1B WILD-TYPE  411  102
     clus
vv    GOLT1B MUTATED GOLT1B WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D960V9, continuous
D960V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GOLT1B MUTATED       0                         0
  GOLT1B WILD-TYPE   133                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GOLT1B MUTATED                                           0     4
  GOLT1B WILD-TYPE                                         1   353
D960V11, multiclass
                                           clus
vv                                          GOLT1B MUTATED GOLT1B WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V12, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     0   4
  GOLT1B WILD-TYPE  10 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      0    4
  GOLT1B WILD-TYPE   10  394
                        clus
vv                       GOLT1B MUTATED GOLT1B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(961) Variable = HMCN1 MUTATION ANALYSIS
D961V1, survival
                 sevent
clus2               0   1
  HMCN1 MUTATED    68  32
  HMCN1 WILD-TYPE 270 184
  HMCN1 MUTATED HMCN1 WILD-TYPE 
            100             454 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             32             184 
$`HMCN1 MUTATED`
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4460 
        8.94        24.00        19.99        35.97        20.02        21.99 
TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-JY-A6FE 
       31.27        16.24         7.69         0.85        18.64         3.68 
TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OR TCGA-L5-A8NE TCGA-L5-A8NM 
       21.70        30.25        21.01         3.16        55.50         7.76 
TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A8HZ 
       13.41        10.36        12.46        15.52        13.22        12.33 
TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC 
       33.11         5.06        16.31        53.95        15.78         2.30 
TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-B7-5818 TCGA-B7-A5TJ 
        5.29         8.98        28.11        18.18        11.70        11.01 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7707 
        6.97        30.90        34.68        12.16         9.21        35.84 
TCGA-BR-7717 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8297 
       18.15        29.59        32.25         0.56         2.66         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8367 TCGA-BR-8382 TCGA-BR-8485 TCGA-BR-8486 
       31.10         0.26        26.33        25.05         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4PE TCGA-BR-A4PF 
        1.12        12.79        31.96        12.89        20.42         1.15 
TCGA-CD-5813 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4469 
       12.39        12.62        15.95         8.05        54.08         7.07 
TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-5579 
        6.02        28.96        65.10         4.01        21.07        20.91 
TCGA-D7-6519 TCGA-D7-6822 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.55        12.33        21.14         5.92        13.78        14.76 
TCGA-D7-A6EY TCGA-FP-7735 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 
       11.44         3.48        11.08        77.29        30.51        26.47 
TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       22.32         5.59        22.68        25.81        11.77         6.58 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ 
        0.26        23.84        14.07        33.40        18.81        12.46 
TCGA-IN-A7NU TCGA-RD-A8MV TCGA-SW-A7EB TCGA-VQ-A8P2 
       11.70       122.30         5.79        38.14 

$`HMCN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         4.31         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 
       22.82         0.36        27.12         5.16        47.05        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        8.94         4.21        32.45        33.27        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55        13.22         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        22.39        12.85        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.26         7.82         8.02         7.59         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        6.35         9.30         2.89        12.69         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
        1.32         2.66        19.73        26.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 
       11.44         0.69         9.60         8.05        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 
        2.20         6.18        22.19        17.52         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         5.39        25.18        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         7.99         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       15.02        69.04         7.99        25.71        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV 
       20.91        14.27        16.44        36.43        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 
       22.82        21.07         0.76        24.30        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        20.25         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       21.17        15.68        36.36         3.45         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HMCN1 MUTATED HMCN1 WILD-TYPE 
           0.26            0.00 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
          122.3           122.1 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         15.140          13.495 
[1] "0.3 - 122.3 (15.1)" "0.0 - 122.1 (13.5)"
[1] "hr=" "1.3"
D961V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HMCN1 MUTATED         2        6       12        5         9        21
  HMCN1 WILD-TYPE       8       14       34       26        75        62
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMCN1 MUTATED           2         10          8          9        9         3
  HMCN1 WILD-TYPE        27         74         54         30       34         1
D961V3, multiclass
            clus
vv           HMCN1 MUTATED HMCN1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               6              14
  STAGE IB              12              34
  STAGE II               5              26
  STAGE IIA              9              75
  STAGE IIB             21              62
  STAGE III              2              27
  STAGE IIIA            10              74
  STAGE IIIB             8              54
  STAGE IIIC             9              30
  STAGE IV               9              34
  STAGE IVA              3               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HMCN1 MUTATED      14  28  33  25
  HMCN1 WILD-TYPE    40 107 228  77
D961V4, multiclass
       clus
vv      HMCN1 MUTATED HMCN1 WILD-TYPE
  T0+T1            14              40
  T2               28             107
  T3               33             228
  T4               25              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HMCN1 MUTATED    39  29  15  15
  HMCN1 WILD-TYPE 156 144  74  70
D961V5, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  N0            39             156
  N1            29             144
  N2            15              74
  N3            15              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V6, binary
                 cls
clus                0   1
  HMCN1 MUTATED    83   7
  HMCN1 WILD-TYPE 399  31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     83    7
  HMCN1 WILD-TYPE  399   31
   clus
vv  HMCN1 MUTATED HMCN1 WILD-TYPE
  0            83             399
  1             7              31
[1] 2 2
[1] FALSE
D961V7, binary
                 cls
clus                0   1
  HMCN1 MUTATED    34  71
  HMCN1 WILD-TYPE 138 335
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     34   71
  HMCN1 WILD-TYPE  138  335
        clus
vv       HMCN1 MUTATED HMCN1 WILD-TYPE
  FEMALE            34             138
  MALE              71             335
[1] 2 2
[1] FALSE
D961V8, binary
                 cls
clus                0   1
  HMCN1 MUTATED    82  13
  HMCN1 WILD-TYPE 334  89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     82   13
  HMCN1 WILD-TYPE  334   89
     clus
vv    HMCN1 MUTATED HMCN1 WILD-TYPE
  NO             82             334
  YES            13              89
[1] 2 2
[1] FALSE
D961V9, continuous
D961V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HMCN1 MUTATED      19                         2
  HMCN1 WILD-TYPE   114                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HMCN1 MUTATED                                           0    65
  HMCN1 WILD-TYPE                                         1   292
D961V11, multiclass
                                           clus
vv                                          HMCN1 MUTATED HMCN1 WILD-TYPE
  ASIAN                                                19             114
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                65             292
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V12, binary
                 cls
clus                0   1
  HMCN1 MUTATED     1  73
  HMCN1 WILD-TYPE   9 325
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED      1   73
  HMCN1 WILD-TYPE    9  325
                        clus
vv                       HMCN1 MUTATED HMCN1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            73             325
[1] 2 2
[1] FALSE

Clustering(962) Variable = SERPINB7 MUTATION ANALYSIS
D962V1, survival
                    sevent
clus2                  0   1
  SERPINB7 MUTATED     3   3
  SERPINB7 WILD-TYPE 335 213
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                548 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 3                213 
$`SERPINB7 MUTATED`
TCGA-BR-6452 TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4PD TCGA-CD-A4MG TCGA-CG-4455 
       34.68         9.86         1.48        20.65         6.58        12.03 

$`SERPINB7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
              1.48               0.00 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             34.68             122.30 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
            10.945             13.630 
[1] "1.5 - 34.7 (10.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D962V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB7 MUTATED         0        0        0        1         2         1
  SERPINB7 WILD-TYPE      10       20       46       30        82        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB7 MUTATED           0          0          1          1        0
  SERPINB7 WILD-TYPE        29         84         61         38       43
                    vv
clus                 STAGE IVA
  SERPINB7 MUTATED           0
  SERPINB7 WILD-TYPE         4
D962V3, multiclass
            clus
vv           SERPINB7 MUTATED SERPINB7 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 2                 82
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SERPINB7 MUTATED       0   1   2   3
  SERPINB7 WILD-TYPE    54 134 259  99
D962V4, multiclass
       clus
vv      SERPINB7 MUTATED SERPINB7 WILD-TYPE
  T0+T1                0                 54
  T2                   1                134
  T3                   2                259
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SERPINB7 MUTATED     3   1   1   1
  SERPINB7 WILD-TYPE 192 172  88  84
D962V5, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  N0                3                192
  N1                1                172
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V6, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   0
  SERPINB7 WILD-TYPE 476  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    0
  SERPINB7 WILD-TYPE  476   38
   clus
vv  SERPINB7 MUTATED SERPINB7 WILD-TYPE
  0                6                476
  1                0                 38
[1] 2 2
[1] FALSE
D962V7, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     2   4
  SERPINB7 WILD-TYPE 170 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      2    4
  SERPINB7 WILD-TYPE  170  402
        clus
vv       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  FEMALE                2                170
  MALE                  4                402
[1] 2 2
[1] FALSE
D962V8, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   0
  SERPINB7 WILD-TYPE 410 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    0
  SERPINB7 WILD-TYPE  410  102
     clus
vv    SERPINB7 MUTATED SERPINB7 WILD-TYPE
  NO                 6                410
  YES                0                102
[1] 2 2
[1] FALSE
D962V9, continuous
D962V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB7 MUTATED       2                         0
  SERPINB7 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB7 MUTATED                                           0     3
  SERPINB7 WILD-TYPE                                         1   354
D962V11, multiclass
                                           clus
vv                                          SERPINB7 MUTATED SERPINB7 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V12, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     0   5
  SERPINB7 WILD-TYPE  10 393
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      0    5
  SERPINB7 WILD-TYPE   10  393
                        clus
vv                       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                5                393
[1] 2 2
[1] FALSE

Clustering(963) Variable = TLE1 MUTATION ANALYSIS
D963V1, survival
                sevent
clus2              0   1
  TLE1 MUTATED    11   2
  TLE1 WILD-TYPE 327 214
  TLE1 MUTATED TLE1 WILD-TYPE 
            13            541 
  TLE1 MUTATED TLE1 WILD-TYPE 
             2            214 
$`TLE1 MUTATED`
TCGA-CG-4460 TCGA-L5-A4OU TCGA-LN-A7HY TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 
       21.99        29.00        12.03         6.61        34.68        35.84 
TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 TCGA-HF-A5NB TCGA-HU-8602 
        6.18        31.27         1.12        27.12        30.51        22.32 
TCGA-VQ-A8E2 
       43.36 

$`TLE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TLE1 MUTATED TLE1 WILD-TYPE 
          1.12           0.00 
  TLE1 MUTATED TLE1 WILD-TYPE 
         43.36         122.30 
  TLE1 MUTATED TLE1 WILD-TYPE 
         27.12          13.51 
[1] "1.1 - 43.4 (27.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.4"
D963V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TLE1 MUTATED         0        0        1        0         4         1
  TLE1 WILD-TYPE      10       20       45       31        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TLE1 MUTATED           2          0          2          2        2         0
  TLE1 WILD-TYPE        27         84         60         37       41         4
D963V3, multiclass
            clus
vv           TLE1 MUTATED TLE1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             2             27
  STAGE IIIA            0             84
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TLE1 MUTATED       0   2   6   6
  TLE1 WILD-TYPE    54 133 255  96
D963V4, multiclass
       clus
vv      TLE1 MUTATED TLE1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               6            255
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TLE1 MUTATED     6   4   2   2
  TLE1 WILD-TYPE 189 169  87  83
D963V5, multiclass
    clus
vv   TLE1 MUTATED TLE1 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V6, binary
                cls
clus               0   1
  TLE1 MUTATED    13   1
  TLE1 WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED     13    1
  TLE1 WILD-TYPE  469   37
   clus
vv  TLE1 MUTATED TLE1 WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D963V7, binary
                cls
clus               0   1
  TLE1 MUTATED     8   6
  TLE1 WILD-TYPE 164 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED      8    6
  TLE1 WILD-TYPE  164  400
        clus
vv       TLE1 MUTATED TLE1 WILD-TYPE
  FEMALE            8            164
  MALE              6            400
[1] 2 2
[1] FALSE
D963V8, binary
                cls
clus               0   1
  TLE1 MUTATED    11   2
  TLE1 WILD-TYPE 405 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED     11    2
  TLE1 WILD-TYPE  405  100
     clus
vv    TLE1 MUTATED TLE1 WILD-TYPE
  NO            11            405
  YES            2            100
[1] 2 2
[1] FALSE
D963V9, continuous
[1] "Remove cluster labels:" "TLE1 MUTATED"          
clus
  TLE1 MUTATED TLE1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
D963V10, continuous
[1] "Remove cluster labels:" "TLE1 MUTATED"          
clus
  TLE1 MUTATED TLE1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" "TLE1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"TLE1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TLE1 MUTATED       3                         0
  TLE1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TLE1 MUTATED                                           0     9
  TLE1 WILD-TYPE                                         1   348
D963V11, multiclass
                                           clus
vv                                          TLE1 MUTATED TLE1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V12, binary
                cls
clus               0   1
  TLE1 MUTATED     0  10
  TLE1 WILD-TYPE  10 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED      0   10
  TLE1 WILD-TYPE   10  388
                        clus
vv                       TLE1 MUTATED TLE1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(964) Variable = BRMS1 MUTATION ANALYSIS
D964V1, survival
                 sevent
clus2               0   1
  BRMS1 MUTATED     4   2
  BRMS1 WILD-TYPE 334 214
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             548 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              2             214 
$`BRMS1 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8078 TCGA-EQ-8122 TCGA-HU-A4GN TCGA-HU-A4H8 
        9.34        34.68        29.59         7.99        29.98        14.07 

$`BRMS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BRMS1 MUTATED BRMS1 WILD-TYPE 
           7.99            0.00 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
          34.68          122.30 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
          21.83           13.53 
[1] "8.0 - 34.7 (21.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D964V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRMS1 MUTATED         0        0        1        0         2         2
  BRMS1 WILD-TYPE      10       20       45       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRMS1 MUTATED           0          0          0          0        0         0
  BRMS1 WILD-TYPE        29         84         62         39       43         4
D964V3, multiclass
            clus
vv           BRMS1 MUTATED BRMS1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BRMS1 MUTATED       1   1   2   1
  BRMS1 WILD-TYPE    53 134 259 101
D964V4, multiclass
       clus
vv      BRMS1 MUTATED BRMS1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BRMS1 MUTATED     2   4   0   0
  BRMS1 WILD-TYPE 193 169  89  85
D964V5, multiclass
    clus
vv   BRMS1 MUTATED BRMS1 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V6, binary
                 cls
clus                0   1
  BRMS1 MUTATED     5   0
  BRMS1 WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      5    0
  BRMS1 WILD-TYPE  477   38
   clus
vv  BRMS1 MUTATED BRMS1 WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D964V7, binary
                 cls
clus                0   1
  BRMS1 MUTATED     3   3
  BRMS1 WILD-TYPE 169 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      3    3
  BRMS1 WILD-TYPE  169  403
        clus
vv       BRMS1 MUTATED BRMS1 WILD-TYPE
  FEMALE             3             169
  MALE               3             403
[1] 2 2
[1] FALSE
D964V8, binary
                 cls
clus                0   1
  BRMS1 MUTATED     5   1
  BRMS1 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      5    1
  BRMS1 WILD-TYPE  411  101
     clus
vv    BRMS1 MUTATED BRMS1 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D964V9, continuous
D964V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRMS1 MUTATED       2                         0
  BRMS1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRMS1 MUTATED                                           0     4
  BRMS1 WILD-TYPE                                         1   353
D964V11, multiclass
                                           clus
vv                                          BRMS1 MUTATED BRMS1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V12, binary
                 cls
clus                0   1
  BRMS1 MUTATED     0   6
  BRMS1 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      0    6
  BRMS1 WILD-TYPE   10  392
                        clus
vv                       BRMS1 MUTATED BRMS1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(965) Variable = GATA3 MUTATION ANALYSIS
D965V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED    10   8
  GATA3 WILD-TYPE 328 208
  GATA3 MUTATED GATA3 WILD-TYPE 
             18             536 
  GATA3 MUTATED GATA3 WILD-TYPE 
              8             208 
$`GATA3 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-R6-A6DN TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7958 
       19.99         7.76         8.02        34.68        36.16        29.56 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
        0.26         4.31        25.05         1.12        28.14        31.96 
TCGA-BR-8687 TCGA-CG-4469 TCGA-EQ-5647 TCGA-HU-8244 TCGA-HU-A4GQ TCGA-VQ-A8P2 
        8.22         7.07         0.62        24.39         0.10        38.14 

$`GATA3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GATA3 MUTATED GATA3 WILD-TYPE 
            0.1             0.0 
  GATA3 MUTATED GATA3 WILD-TYPE 
          38.14          122.30 
  GATA3 MUTATED GATA3 WILD-TYPE 
         14.105          13.565 
[1] "0.1 - 38.1 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D965V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GATA3 MUTATED         0        2        2        0         2         1
  GATA3 WILD-TYPE      10       18       44       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA3 MUTATED           0          1          1          6        3         0
  GATA3 WILD-TYPE        29         83         61         33       40         4
D965V3, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             6              33
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GATA3 MUTATED       3   3   4   9
  GATA3 WILD-TYPE    51 132 257  93
D965V4, multiclass
       clus
vv      GATA3 MUTATED GATA3 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                4             257
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GATA3 MUTATED     7   2   3   6
  GATA3 WILD-TYPE 188 171  86  79
D965V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0             7             188
  N1             2             171
  N2             3              86
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V6, binary
                 cls
clus                0   1
  GATA3 MUTATED    17   2
  GATA3 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     17    2
  GATA3 WILD-TYPE  465   36
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D965V7, binary
                 cls
clus                0   1
  GATA3 MUTATED    11  10
  GATA3 WILD-TYPE 161 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     11   10
  GATA3 WILD-TYPE  161  396
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  FEMALE            11             161
  MALE              10             396
[1] 2 2
[1] FALSE
D965V8, binary
                 cls
clus                0   1
  GATA3 MUTATED    16   1
  GATA3 WILD-TYPE 400 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     16    1
  GATA3 WILD-TYPE  400  101
     clus
vv    GATA3 MUTATED GATA3 WILD-TYPE
  NO             16             400
  YES             1             101
[1] 2 2
[1] FALSE
D965V9, continuous
D965V10, continuous
[1] "Remove cluster labels:" "GATA3 MUTATED"         
clus
  GATA3 MUTATED GATA3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6L4 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" "GATA3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GATA3 MUTATED       3                         0
  GATA3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GATA3 MUTATED                                           0    17
  GATA3 WILD-TYPE                                         1   340
D965V11, multiclass
                                           clus
vv                                          GATA3 MUTATED GATA3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V12, binary
                 cls
clus                0   1
  GATA3 MUTATED     0  17
  GATA3 WILD-TYPE  10 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      0   17
  GATA3 WILD-TYPE   10  381
                        clus
vv                       GATA3 MUTATED GATA3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(966) Variable = FAM18A MUTATION ANALYSIS
D966V1, survival
                  sevent
clus2                0   1
  FAM18A MUTATED     3   1
  FAM18A WILD-TYPE 335 215
  FAM18A MUTATED FAM18A WILD-TYPE 
               4              550 
  FAM18A MUTATED FAM18A WILD-TYPE 
               1              215 
$`FAM18A MUTATED`
TCGA-L5-A8NJ TCGA-BR-4257 TCGA-BR-8081 TCGA-HU-A4GX 
       16.47         9.67        32.25        20.25 

$`FAM18A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  FAM18A MUTATED FAM18A WILD-TYPE 
            9.67             0.00 
  FAM18A MUTATED FAM18A WILD-TYPE 
           32.25           122.30 
  FAM18A MUTATED FAM18A WILD-TYPE 
           18.36            13.53 
[1] "9.7 - 32.2 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D966V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM18A MUTATED         0        0        0        0         0         1
  FAM18A WILD-TYPE      10       20       46       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM18A MUTATED           1          0          0          1        0
  FAM18A WILD-TYPE        28         84         62         38       43
                  vv
clus               STAGE IVA
  FAM18A MUTATED           0
  FAM18A WILD-TYPE         4
D966V3, multiclass
            clus
vv           FAM18A MUTATED FAM18A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FAM18A MUTATED       0   0   1   2
  FAM18A WILD-TYPE    54 135 260 100
D966V4, multiclass
       clus
vv      FAM18A MUTATED FAM18A WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 1              260
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FAM18A MUTATED     1   1   1   0
  FAM18A WILD-TYPE 194 172  88  85
D966V5, multiclass
    clus
vv   FAM18A MUTATED FAM18A WILD-TYPE
  N0              1              194
  N1              1              172
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V6, binary
                  cls
clus                 0   1
  FAM18A MUTATED     4   0
  FAM18A WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      4    0
  FAM18A WILD-TYPE  478   38
   clus
vv  FAM18A MUTATED FAM18A WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D966V7, binary
                  cls
clus                 0   1
  FAM18A MUTATED     3   1
  FAM18A WILD-TYPE 169 405
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      3    1
  FAM18A WILD-TYPE  169  405
        clus
vv       FAM18A MUTATED FAM18A WILD-TYPE
  FEMALE              3              169
  MALE                1              405
[1] 2 2
[1] FALSE
D966V8, binary
                  cls
clus                 0   1
  FAM18A MUTATED     4   0
  FAM18A WILD-TYPE 412 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      4    0
  FAM18A WILD-TYPE  412  102
     clus
vv    FAM18A MUTATED FAM18A WILD-TYPE
  NO               4              412
  YES              0              102
[1] 2 2
[1] FALSE
D966V9, continuous
D966V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM18A MUTATED       1                         0
  FAM18A WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM18A MUTATED                                           0     3
  FAM18A WILD-TYPE                                         1   354
D966V11, multiclass
                                           clus
vv                                          FAM18A MUTATED FAM18A WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V12, binary
                  cls
clus                 0   1
  FAM18A MUTATED     0   3
  FAM18A WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      0    3
  FAM18A WILD-TYPE   10  395
                        clus
vv                       FAM18A MUTATED FAM18A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(967) Variable = GPATCH2 MUTATION ANALYSIS
D967V1, survival
                   sevent
clus2                 0   1
  GPATCH2 MUTATED     4   3
  GPATCH2 WILD-TYPE 334 213
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                7               547 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                3               213 
$`GPATCH2 MUTATED`
TCGA-2H-A9GJ TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8060 TCGA-CG-5721 TCGA-HU-A4GQ 
       58.55        34.68        44.94        11.44         6.02         0.10 
TCGA-KB-A93J 
       36.95 

$`GPATCH2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
              0.1               0.0 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            58.55            122.30 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            34.68             13.55 
[1] "0.1 - 58.5 (34.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D967V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH2 MUTATED         2        0        1        1         2         1
  GPATCH2 WILD-TYPE       8       20       45       30        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH2 MUTATED           0          0          0          1        1
  GPATCH2 WILD-TYPE        29         84         62         38       42
                   vv
clus                STAGE IVA
  GPATCH2 MUTATED           0
  GPATCH2 WILD-TYPE         4
D967V3, multiclass
            clus
vv           GPATCH2 MUTATED GPATCH2 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GPATCH2 MUTATED       3   3   2   2
  GPATCH2 WILD-TYPE    51 132 259 100
D967V4, multiclass
       clus
vv      GPATCH2 MUTATED GPATCH2 WILD-TYPE
  T0+T1               3                51
  T2                  3               132
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GPATCH2 MUTATED     4   3   2   0
  GPATCH2 WILD-TYPE 191 170  87  85
D967V5, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V6, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     9   0
  GPATCH2 WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      9    0
  GPATCH2 WILD-TYPE  473   38
   clus
vv  GPATCH2 MUTATED GPATCH2 WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D967V7, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     4   6
  GPATCH2 WILD-TYPE 168 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      4    6
  GPATCH2 WILD-TYPE  168  400
        clus
vv       GPATCH2 MUTATED GPATCH2 WILD-TYPE
  FEMALE               4               168
  MALE                 6               400
[1] 2 2
[1] FALSE
D967V8, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     7   1
  GPATCH2 WILD-TYPE 409 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      7    1
  GPATCH2 WILD-TYPE  409  101
     clus
vv    GPATCH2 MUTATED GPATCH2 WILD-TYPE
  NO                7               409
  YES               1               101
[1] 2 2
[1] FALSE
D967V9, continuous
D967V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPATCH2 MUTATED       1                         1
  GPATCH2 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPATCH2 MUTATED                                           0     5
  GPATCH2 WILD-TYPE                                         1   352
D967V11, multiclass
                                           clus
vv                                          GPATCH2 MUTATED GPATCH2 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V12, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     0   6
  GPATCH2 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      0    6
  GPATCH2 WILD-TYPE   10  392
                        clus
vv                       GPATCH2 MUTATED GPATCH2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(968) Variable = OR6C70 MUTATION ANALYSIS
D968V1, survival
                  sevent
clus2                0   1
  OR6C70 MUTATED     2   2
  OR6C70 WILD-TYPE 336 214
  OR6C70 MUTATED OR6C70 WILD-TYPE 
               4              550 
  OR6C70 MUTATED OR6C70 WILD-TYPE 
               2              214 
$`OR6C70 MUTATED`
TCGA-L5-A4OI TCGA-BR-4256 TCGA-CG-5733 TCGA-D7-5578 
       19.99         9.34        21.07        12.66 

$`OR6C70 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OR6C70 MUTATED OR6C70 WILD-TYPE 
            9.34             0.00 
  OR6C70 MUTATED OR6C70 WILD-TYPE 
           21.07           122.30 
  OR6C70 MUTATED OR6C70 WILD-TYPE 
          16.325           13.565 
[1] "9.3 - 21.1 (16.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D968V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR6C70 MUTATED         1        0        1        0         0         0
  OR6C70 WILD-TYPE       9       20       45       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR6C70 MUTATED           0          2          0          1        0
  OR6C70 WILD-TYPE        29         82         62         38       43
                  vv
clus               STAGE IVA
  OR6C70 MUTATED           0
  OR6C70 WILD-TYPE         4
D968V3, multiclass
            clus
vv           OR6C70 MUTATED OR6C70 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OR6C70 MUTATED       1   2   2   0
  OR6C70 WILD-TYPE    53 133 259 102
D968V4, multiclass
       clus
vv      OR6C70 MUTATED OR6C70 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 2              259
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR6C70 MUTATED     1   2   2   1
  OR6C70 WILD-TYPE 194 171  87  84
D968V5, multiclass
    clus
vv   OR6C70 MUTATED OR6C70 WILD-TYPE
  N0              1              194
  N1              2              171
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V6, binary
                  cls
clus                 0   1
  OR6C70 MUTATED     4   0
  OR6C70 WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C70 MUTATED      4    0
  OR6C70 WILD-TYPE  478   38
   clus
vv  OR6C70 MUTATED OR6C70 WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D968V7, binary
                  cls
clus                 0   1
  OR6C70 MUTATED     1   5
  OR6C70 WILD-TYPE 171 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C70 MUTATED      1    5
  OR6C70 WILD-TYPE  171  401
        clus
vv       OR6C70 MUTATED OR6C70 WILD-TYPE
  FEMALE              1              171
  MALE                5              401
[1] 2 2
[1] FALSE
D968V8, binary
                  cls
clus                 0   1
  OR6C70 MUTATED     5   0
  OR6C70 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C70 MUTATED      5    0
  OR6C70 WILD-TYPE  411  102
     clus
vv    OR6C70 MUTATED OR6C70 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D968V9, continuous
D968V10, continuous
[1] "Remove cluster labels:" "OR6C70 MUTATED"        
clus
  OR6C70 MUTATED OR6C70 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" "OR6C70 WILD-TYPE" 
      TCGA-Z6-AAPN 
"OR6C70 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OR6C70 MUTATED       0                         1
  OR6C70 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR6C70 MUTATED                                           0     3
  OR6C70 WILD-TYPE                                         1   354
D968V11, multiclass
                                           clus
vv                                          OR6C70 MUTATED OR6C70 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V12, binary
                  cls
clus                 0   1
  OR6C70 MUTATED     0   3
  OR6C70 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C70 MUTATED      0    3
  OR6C70 WILD-TYPE   10  395
                        clus
vv                       OR6C70 MUTATED OR6C70 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(969) Variable = SPIB MUTATION ANALYSIS
D969V1, survival
                sevent
clus2              0   1
  SPIB MUTATED     7   2
  SPIB WILD-TYPE 331 214
  SPIB MUTATED SPIB WILD-TYPE 
             9            545 
  SPIB MUTATED SPIB WILD-TYPE 
             2            214 
$`SPIB MUTATED`
TCGA-M9-A5M8 TCGA-BR-4201 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8690 TCGA-CD-A4MI 
       33.11        30.90        28.14        31.96        10.68        11.77 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-VQ-A8P2 
       23.84        33.40        38.14 

$`SPIB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SPIB MUTATED SPIB WILD-TYPE 
         10.68           0.00 
  SPIB MUTATED SPIB WILD-TYPE 
         38.14         122.30 
  SPIB MUTATED SPIB WILD-TYPE 
         30.90          13.51 
[1] "10.7 - 38.1 (30.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D969V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPIB MUTATED         0        0        0        0         1         1
  SPIB WILD-TYPE      10       20       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPIB MUTATED           0          3          1          1        1         0
  SPIB WILD-TYPE        29         81         61         38       42         4
D969V3, multiclass
            clus
vv           SPIB MUTATED SPIB WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SPIB MUTATED       0   2   4   3
  SPIB WILD-TYPE    54 133 257  99
D969V4, multiclass
       clus
vv      SPIB MUTATED SPIB WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SPIB MUTATED     1   2   3   2
  SPIB WILD-TYPE 194 171  86  83
D969V5, multiclass
    clus
vv   SPIB MUTATED SPIB WILD-TYPE
  N0            1            194
  N1            2            171
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V6, binary
                cls
clus               0   1
  SPIB MUTATED     8   1
  SPIB WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPIB MUTATED      8    1
  SPIB WILD-TYPE  474   37
   clus
vv  SPIB MUTATED SPIB WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D969V7, binary
                cls
clus               0   1
  SPIB MUTATED     3   6
  SPIB WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPIB MUTATED      3    6
  SPIB WILD-TYPE  169  400
        clus
vv       SPIB MUTATED SPIB WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D969V8, binary
                cls
clus               0   1
  SPIB MUTATED     8   1
  SPIB WILD-TYPE 408 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPIB MUTATED      8    1
  SPIB WILD-TYPE  408  101
     clus
vv    SPIB MUTATED SPIB WILD-TYPE
  NO             8            408
  YES            1            101
[1] 2 2
[1] FALSE
D969V9, continuous
D969V10, continuous
[1] "Remove cluster labels:" "SPIB MUTATED"          
clus
  SPIB MUTATED SPIB WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" "SPIB WILD-TYPE" 
    TCGA-Z6-AAPN 
"SPIB WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SPIB MUTATED       4                         0
  SPIB WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPIB MUTATED                                           0     4
  SPIB WILD-TYPE                                         1   353
D969V11, multiclass
                                           clus
vv                                          SPIB MUTATED SPIB WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V12, binary
                cls
clus               0   1
  SPIB MUTATED     0   7
  SPIB WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPIB MUTATED      0    7
  SPIB WILD-TYPE   10  391
                        clus
vv                       SPIB MUTATED SPIB WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(970) Variable = SULF1 MUTATION ANALYSIS
D970V1, survival
                 sevent
clus2               0   1
  SULF1 MUTATED    25   4
  SULF1 WILD-TYPE 313 212
  SULF1 MUTATED SULF1 WILD-TYPE 
             29             525 
  SULF1 MUTATED SULF1 WILD-TYPE 
              4             212 
$`SULF1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OG TCGA-L5-A8NG TCGA-CG-5727 TCGA-2H-A9GO TCGA-L5-A4OW 
       60.39         4.70        35.97        79.07        16.24         7.13 
TCGA-LN-A49V TCGA-V5-AASX TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6453 TCGA-BR-6802 
       12.59         8.98        26.70         9.67        15.95        30.90 
TCGA-BR-7703 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4J8 
       36.16        37.25        29.59         1.12        28.14        13.51 
TCGA-CD-5802 TCGA-CD-8534 TCGA-CG-5721 TCGA-D7-5578 TCGA-D7-A6EY TCGA-F1-6874 
       13.35        12.07         6.02        12.66        11.44        14.47 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GX TCGA-HU-A4H3 
       22.68        24.20         3.25        20.25        29.00 

$`SULF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       40.21        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD 
       14.17         0.53        28.34         0.66        32.52        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.18        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SULF1 MUTATED SULF1 WILD-TYPE 
           1.12            0.00 
  SULF1 MUTATED SULF1 WILD-TYPE 
          79.07          122.30 
  SULF1 MUTATED SULF1 WILD-TYPE 
          15.95           13.51 
[1] "1.1 - 79.1 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.4"
D970V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SULF1 MUTATED         2        2        1        3         3         4
  SULF1 WILD-TYPE       8       18       45       28        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SULF1 MUTATED           1          2          4          3        2         1
  SULF1 WILD-TYPE        28         82         58         36       41         3
D970V3, multiclass
            clus
vv           SULF1 MUTATED SULF1 WILD-TYPE
  STAGE I                2               8
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               3              28
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             4              58
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SULF1 MUTATED       4   3  12   9
  SULF1 WILD-TYPE    50 132 249  93
D970V4, multiclass
       clus
vv      SULF1 MUTATED SULF1 WILD-TYPE
  T0+T1             4              50
  T2                3             132
  T3               12             249
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SULF1 MUTATED    12   6   6   4
  SULF1 WILD-TYPE 183 167  83  81
D970V5, multiclass
    clus
vv   SULF1 MUTATED SULF1 WILD-TYPE
  N0            12             183
  N1             6             167
  N2             6              83
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V6, binary
                 cls
clus                0   1
  SULF1 MUTATED    29   1
  SULF1 WILD-TYPE 453  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     29    1
  SULF1 WILD-TYPE  453   37
   clus
vv  SULF1 MUTATED SULF1 WILD-TYPE
  0            29             453
  1             1              37
[1] 2 2
[1] FALSE
D970V7, binary
                 cls
clus                0   1
  SULF1 MUTATED    15  16
  SULF1 WILD-TYPE 157 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     15   16
  SULF1 WILD-TYPE  157  390
        clus
vv       SULF1 MUTATED SULF1 WILD-TYPE
  FEMALE            15             157
  MALE              16             390
[1] 2 2
[1] FALSE
D970V8, binary
                 cls
clus                0   1
  SULF1 MUTATED    25   2
  SULF1 WILD-TYPE 391 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     25    2
  SULF1 WILD-TYPE  391  100
     clus
vv    SULF1 MUTATED SULF1 WILD-TYPE
  NO             25             391
  YES             2             100
[1] 2 2
[1] FALSE
D970V9, continuous
[1] "Remove cluster labels:" "SULF1 MUTATED"         
clus
  SULF1 MUTATED SULF1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49W 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SULF1 WILD-TYPE" "SULF1 WILD-TYPE" 
D970V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SULF1 MUTATED       8                         0
  SULF1 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SULF1 MUTATED                                           0    19
  SULF1 WILD-TYPE                                         1   338
D970V11, multiclass
                                           clus
vv                                          SULF1 MUTATED SULF1 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V12, binary
                 cls
clus                0   1
  SULF1 MUTATED     0  24
  SULF1 WILD-TYPE  10 374
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED      0   24
  SULF1 WILD-TYPE   10  374
                        clus
vv                       SULF1 MUTATED SULF1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            24             374
[1] 2 2
[1] FALSE

Clustering(971) Variable = LPHN2 MUTATION ANALYSIS
D971V1, survival
                 sevent
clus2               0   1
  LPHN2 MUTATED    14  12
  LPHN2 WILD-TYPE 324 204
  LPHN2 MUTATED LPHN2 WILD-TYPE 
             26             528 
  LPHN2 MUTATED LPHN2 WILD-TYPE 
             12             204 
$`LPHN2 MUTATED`
TCGA-L5-A4OE TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A8O2 
       24.00        25.78         7.63        13.94        32.45         4.67 
TCGA-L5-A8NR TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 
        8.71        53.95        12.69        34.68        15.95        13.68 
TCGA-BR-7717 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 
       18.15         9.60         7.40        25.18         9.21        27.12 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4469 TCGA-CG-5721 TCGA-HU-8238 TCGA-HU-A4GU 
       31.96        11.77         7.07         6.02         1.51         6.58 
TCGA-IN-A6RI TCGA-VQ-A8P2 
       18.38        38.14 

$`LPHN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         5.92         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 
        9.34         9.67         6.18         9.57         6.61        13.87 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         3.72         5.39        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  LPHN2 MUTATED LPHN2 WILD-TYPE 
           1.51            0.00 
  LPHN2 MUTATED LPHN2 WILD-TYPE 
          53.95          122.30 
  LPHN2 MUTATED LPHN2 WILD-TYPE 
          13.81           13.53 
[1] "1.5 - 54.0 (13.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D971V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LPHN2 MUTATED         1        0        0        0         4         2
  LPHN2 WILD-TYPE       9       20       46       31        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LPHN2 MUTATED           3          3          3          3        4         0
  LPHN2 WILD-TYPE        26         81         59         36       39         4
D971V3, multiclass
            clus
vv           LPHN2 MUTATED LPHN2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              3              26
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             3              36
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LPHN2 MUTATED       2   1  12   9
  LPHN2 WILD-TYPE    52 134 249  93
D971V4, multiclass
       clus
vv      LPHN2 MUTATED LPHN2 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3               12             249
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LPHN2 MUTATED     4  12   4   4
  LPHN2 WILD-TYPE 191 161  85  81
D971V5, multiclass
    clus
vv   LPHN2 MUTATED LPHN2 WILD-TYPE
  N0             4             191
  N1            12             161
  N2             4              85
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V6, binary
                 cls
clus                0   1
  LPHN2 MUTATED    22   1
  LPHN2 WILD-TYPE 460  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPHN2 MUTATED     22    1
  LPHN2 WILD-TYPE  460   37
   clus
vv  LPHN2 MUTATED LPHN2 WILD-TYPE
  0            22             460
  1             1              37
[1] 2 2
[1] FALSE
D971V7, binary
                 cls
clus                0   1
  LPHN2 MUTATED     4  22
  LPHN2 WILD-TYPE 168 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPHN2 MUTATED      4   22
  LPHN2 WILD-TYPE  168  384
        clus
vv       LPHN2 MUTATED LPHN2 WILD-TYPE
  FEMALE             4             168
  MALE              22             384
[1] 2 2
[1] FALSE
D971V8, binary
                 cls
clus                0   1
  LPHN2 MUTATED    23   1
  LPHN2 WILD-TYPE 393 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPHN2 MUTATED     23    1
  LPHN2 WILD-TYPE  393  101
     clus
vv    LPHN2 MUTATED LPHN2 WILD-TYPE
  NO             23             393
  YES             1             101
[1] 2 2
[1] FALSE
D971V9, continuous
D971V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LPHN2 MUTATED       5                         0
  LPHN2 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LPHN2 MUTATED                                           0    14
  LPHN2 WILD-TYPE                                         1   343
D971V11, multiclass
                                           clus
vv                                          LPHN2 MUTATED LPHN2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V12, binary
                 cls
clus                0   1
  LPHN2 MUTATED     1  16
  LPHN2 WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPHN2 MUTATED      1   16
  LPHN2 WILD-TYPE    9  382
                        clus
vv                       LPHN2 MUTATED LPHN2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(972) Variable = TMEM161A MUTATION ANALYSIS
D972V1, survival
                    sevent
clus2                  0   1
  TMEM161A MUTATED     5   1
  TMEM161A WILD-TYPE 333 215
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                 6                548 
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                 1                215 
$`TMEM161A MUTATED`
TCGA-JY-A6FG TCGA-LN-A49V TCGA-BR-6452 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4H3 
       41.52        12.59        34.68        11.08        30.51        29.00 

$`TMEM161A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TMEM161A MUTATED TMEM161A WILD-TYPE 
             11.08               0.00 
  TMEM161A MUTATED TMEM161A WILD-TYPE 
             41.52             122.30 
  TMEM161A MUTATED TMEM161A WILD-TYPE 
            29.755             13.530 
[1] "11.1 - 41.5 (29.8)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.5"
D972V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM161A MUTATED         1        0        1        0         3         0
  TMEM161A WILD-TYPE       9       20       45       31        81        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM161A MUTATED           1          0          0          2        1
  TMEM161A WILD-TYPE        28         84         62         37       42
                    vv
clus                 STAGE IVA
  TMEM161A MUTATED           0
  TMEM161A WILD-TYPE         4
D972V3, multiclass
            clus
vv           TMEM161A MUTATED TMEM161A WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  0                 31
  STAGE IIA                 3                 81
  STAGE IIB                 0                 83
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                2                 37
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TMEM161A MUTATED       2   1   4   3
  TMEM161A WILD-TYPE    52 134 257  99
D972V4, multiclass
       clus
vv      TMEM161A MUTATED TMEM161A WILD-TYPE
  T0+T1                2                 52
  T2                   1                134
  T3                   4                257
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TMEM161A MUTATED     4   2   1   2
  TMEM161A WILD-TYPE 191 171  88  83
D972V5, multiclass
    clus
vv   TMEM161A MUTATED TMEM161A WILD-TYPE
  N0                4                191
  N1                2                171
  N2                1                 88
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V6, binary
                    cls
clus                   0   1
  TMEM161A MUTATED     9   0
  TMEM161A WILD-TYPE 473  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM161A MUTATED      9    0
  TMEM161A WILD-TYPE  473   38
   clus
vv  TMEM161A MUTATED TMEM161A WILD-TYPE
  0                9                473
  1                0                 38
[1] 2 2
[1] FALSE
D972V7, binary
                    cls
clus                   0   1
  TMEM161A MUTATED     5   5
  TMEM161A WILD-TYPE 167 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM161A MUTATED      5    5
  TMEM161A WILD-TYPE  167  401
        clus
vv       TMEM161A MUTATED TMEM161A WILD-TYPE
  FEMALE                5                167
  MALE                  5                401
[1] 2 2
[1] FALSE
D972V8, binary
                    cls
clus                   0   1
  TMEM161A MUTATED     3   3
  TMEM161A WILD-TYPE 413  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM161A MUTATED      3    3
  TMEM161A WILD-TYPE  413   99
     clus
vv    TMEM161A MUTATED TMEM161A WILD-TYPE
  NO                 3                413
  YES                3                 99
[1] 2 2
[1] FALSE
D972V9, continuous
[1] "Remove cluster labels:" "TMEM161A MUTATED"      
clus
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49W         TCGA-LN-A49X 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HY 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-V5-A7RB         TCGA-V5-A7RC 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-V5-A7RE         TCGA-V5-AASV         TCGA-V5-AASW 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-V5-AASX         TCGA-VR-A8EO         TCGA-VR-A8EP 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8EQ         TCGA-VR-A8ER         TCGA-VR-A8ET 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8EY         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-AA4D         TCGA-VR-AA4G         TCGA-VR-AA7B 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-XP-A8T6 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-Z6-A8JE 
"TMEM161A WILD-TYPE" 
D972V10, continuous
[1] "Remove cluster labels:" "TMEM161A MUTATED"      
clus
  TMEM161A MUTATED TMEM161A WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FH         TCGA-KH-A6WC 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49W 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" "TMEM161A WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TMEM161A MUTATED       2                         2
  TMEM161A WILD-TYPE   131                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM161A MUTATED                                           0     4
  TMEM161A WILD-TYPE                                         1   353
D972V11, multiclass
                                           clus
vv                                          TMEM161A MUTATED TMEM161A WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V12, binary
                    cls
clus                   0   1
  TMEM161A MUTATED     0   7
  TMEM161A WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM161A MUTATED      0    7
  TMEM161A WILD-TYPE   10  391
                        clus
vv                       TMEM161A MUTATED TMEM161A WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(973) Variable = PLXNB1 MUTATION ANALYSIS
D973V1, survival
                  sevent
clus2                0   1
  PLXNB1 MUTATED    19  11
  PLXNB1 WILD-TYPE 319 205
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
              30              524 
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
              11              205 
$`PLXNB1 MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GF TCGA-L5-A4OX TCGA-LN-A5U7 
       18.28         4.31        19.99        25.78         7.43        25.25 
TCGA-R6-A8WG TCGA-Z6-A8JD TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 
       12.69         3.42        26.70         6.97         9.67        34.68 
TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ 
       32.78        29.59         1.12        31.96         6.58        12.62 
TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.44        26.47        22.32        22.68         0.10        20.25 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-A6RP TCGA-KB-A93J TCGA-R5-A7ZI TCGA-VQ-A8P2 
       23.80        14.07         6.44        36.95        74.53        38.14 

$`PLXNB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15         9.86        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
       14.37         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.84        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53         5.56        63.62         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
             0.1              0.0 
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
           74.53           122.30 
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
          20.120           13.495 
[1] "0.1 - 74.5 (20.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D973V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLXNB1 MUTATED         1        0        4        1         5         7
  PLXNB1 WILD-TYPE       9       20       42       30        79        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNB1 MUTATED           1          3          1          4        2
  PLXNB1 WILD-TYPE        28         81         61         35       41
                  vv
clus               STAGE IVA
  PLXNB1 MUTATED           0
  PLXNB1 WILD-TYPE         4
D973V3, multiclass
            clus
vv           PLXNB1 MUTATED PLXNB1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               5               79
  STAGE IIB               7               76
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PLXNB1 MUTATED       3   6  12   8
  PLXNB1 WILD-TYPE    51 129 249  94
D973V4, multiclass
       clus
vv      PLXNB1 MUTATED PLXNB1 WILD-TYPE
  T0+T1              3               51
  T2                 6              129
  T3                12              249
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PLXNB1 MUTATED    13  10   3   3
  PLXNB1 WILD-TYPE 182 163  86  82
D973V5, multiclass
    clus
vv   PLXNB1 MUTATED PLXNB1 WILD-TYPE
  N0             13              182
  N1             10              163
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V6, binary
                  cls
clus                 0   1
  PLXNB1 MUTATED    22   2
  PLXNB1 WILD-TYPE 460  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB1 MUTATED     22    2
  PLXNB1 WILD-TYPE  460   36
   clus
vv  PLXNB1 MUTATED PLXNB1 WILD-TYPE
  0             22              460
  1              2               36
[1] 2 2
[1] FALSE
D973V7, binary
                  cls
clus                 0   1
  PLXNB1 MUTATED    12  19
  PLXNB1 WILD-TYPE 160 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB1 MUTATED     12   19
  PLXNB1 WILD-TYPE  160  387
        clus
vv       PLXNB1 MUTATED PLXNB1 WILD-TYPE
  FEMALE             12              160
  MALE               19              387
[1] 2 2
[1] FALSE
D973V8, binary
                  cls
clus                 0   1
  PLXNB1 MUTATED    26   4
  PLXNB1 WILD-TYPE 390  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB1 MUTATED     26    4
  PLXNB1 WILD-TYPE  390   98
     clus
vv    PLXNB1 MUTATED PLXNB1 WILD-TYPE
  NO              26              390
  YES              4               98
[1] 2 2
[1] FALSE
D973V9, continuous
[1] "Remove cluster labels:" "PLXNB1 MUTATED"        
clus
  PLXNB1 MUTATED PLXNB1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A7HV 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JE 
"PLXNB1 WILD-TYPE" "PLXNB1 WILD-TYPE" 
D973V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PLXNB1 MUTATED      10                         1
  PLXNB1 WILD-TYPE   123                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLXNB1 MUTATED                                           0    19
  PLXNB1 WILD-TYPE                                         1   338
D973V11, multiclass
                                           clus
vv                                          PLXNB1 MUTATED PLXNB1 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 19              338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V12, binary
                  cls
clus                 0   1
  PLXNB1 MUTATED     2  22
  PLXNB1 WILD-TYPE   8 376
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNB1 MUTATED      2   22
  PLXNB1 WILD-TYPE    8  376
                        clus
vv                       PLXNB1 MUTATED PLXNB1 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             22              376
[1] 2 2
[1] FALSE

Clustering(974) Variable = MYOCD MUTATION ANALYSIS
D974V1, survival
                 sevent
clus2               0   1
  MYOCD MUTATED     9   7
  MYOCD WILD-TYPE 329 209
  MYOCD MUTATED MYOCD WILD-TYPE 
             16             538 
  MYOCD MUTATED MYOCD WILD-TYPE 
              7             209 
$`MYOCD MUTATED`
TCGA-IG-A4QS TCGA-BR-4201 TCGA-BR-6802 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8591 
        3.88        30.90        30.90         0.26         0.95        28.14 
TCGA-BR-8686 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CG-5721 TCGA-D7-A4YV 
       20.88         0.53        16.14        12.30         6.02         5.92 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4GX TCGA-VQ-A8E2 
       11.44        14.47        20.25        43.36 

$`MYOCD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.25        13.02        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MYOCD MUTATED MYOCD WILD-TYPE 
           0.26            0.00 
  MYOCD MUTATED MYOCD WILD-TYPE 
          43.36          122.30 
  MYOCD MUTATED MYOCD WILD-TYPE 
         13.385          13.565 
[1] "0.3 - 43.4 (13.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D974V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYOCD MUTATED         1        0        2        0         1         1
  MYOCD WILD-TYPE       9       20       44       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYOCD MUTATED           0          1          6          2        2         0
  MYOCD WILD-TYPE        29         83         56         37       41         4
D974V3, multiclass
            clus
vv           MYOCD MUTATED MYOCD WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             6              56
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYOCD MUTATED       1   3   7   6
  MYOCD WILD-TYPE    53 132 254  96
D974V4, multiclass
       clus
vv      MYOCD MUTATED MYOCD WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYOCD MUTATED     4   5   5   3
  MYOCD WILD-TYPE 191 168  84  82
D974V5, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  N0             4             191
  N1             5             168
  N2             5              84
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V6, binary
                 cls
clus                0   1
  MYOCD MUTATED    16   1
  MYOCD WILD-TYPE 466  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED     16    1
  MYOCD WILD-TYPE  466   37
   clus
vv  MYOCD MUTATED MYOCD WILD-TYPE
  0            16             466
  1             1              37
[1] 2 2
[1] FALSE
D974V7, binary
                 cls
clus                0   1
  MYOCD MUTATED     8  10
  MYOCD WILD-TYPE 164 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      8   10
  MYOCD WILD-TYPE  164  396
        clus
vv       MYOCD MUTATED MYOCD WILD-TYPE
  FEMALE             8             164
  MALE              10             396
[1] 2 2
[1] FALSE
D974V8, binary
                 cls
clus                0   1
  MYOCD MUTATED    14   2
  MYOCD WILD-TYPE 402 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED     14    2
  MYOCD WILD-TYPE  402  100
     clus
vv    MYOCD MUTATED MYOCD WILD-TYPE
  NO             14             402
  YES             2             100
[1] 2 2
[1] FALSE
D974V9, continuous
D974V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYOCD MUTATED       5                         1
  MYOCD WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYOCD MUTATED                                           0    11
  MYOCD WILD-TYPE                                         1   346
D974V11, multiclass
                                           clus
vv                                          MYOCD MUTATED MYOCD WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V12, binary
                 cls
clus                0   1
  MYOCD MUTATED     0  16
  MYOCD WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      0   16
  MYOCD WILD-TYPE   10  382
                        clus
vv                       MYOCD MUTATED MYOCD WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(975) Variable = EIF4E1B MUTATION ANALYSIS
D975V1, survival
                   sevent
clus2                 0   1
  EIF4E1B MUTATED     4   3
  EIF4E1B WILD-TYPE 334 213
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
                7               547 
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
                3               213 
$`EIF4E1B MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-BR-4257 TCGA-CD-A4MJ TCGA-CG-5717 TCGA-F1-A448 
       19.99        21.99         9.67        12.62         6.97        21.27 
TCGA-VQ-A8P2 
       38.14 

$`EIF4E1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
             6.97              0.00 
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
            38.14            122.30 
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
            19.99             13.55 
[1] "7.0 - 38.1 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D975V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4E1B MUTATED         0        0        1        1         0         1
  EIF4E1B WILD-TYPE      10       20       45       30        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4E1B MUTATED           0          1          1          1        2
  EIF4E1B WILD-TYPE        29         83         61         38       41
                   vv
clus                STAGE IVA
  EIF4E1B MUTATED           0
  EIF4E1B WILD-TYPE         4
D975V3, multiclass
            clus
vv           EIF4E1B MUTATED EIF4E1B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  EIF4E1B MUTATED       0   2   2   4
  EIF4E1B WILD-TYPE    54 133 259  98
D975V4, multiclass
       clus
vv      EIF4E1B MUTATED EIF4E1B WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  2               259
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  EIF4E1B MUTATED     2   3   1   2
  EIF4E1B WILD-TYPE 193 170  88  83
D975V5, multiclass
    clus
vv   EIF4E1B MUTATED EIF4E1B WILD-TYPE
  N0               2               193
  N1               3               170
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V6, binary
                   cls
clus                  0   1
  EIF4E1B MUTATED     7   1
  EIF4E1B WILD-TYPE 475  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF4E1B MUTATED      7    1
  EIF4E1B WILD-TYPE  475   37
   clus
vv  EIF4E1B MUTATED EIF4E1B WILD-TYPE
  0               7               475
  1               1                37
[1] 2 2
[1] FALSE
D975V7, binary
                   cls
clus                  0   1
  EIF4E1B MUTATED     3   6
  EIF4E1B WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF4E1B MUTATED      3    6
  EIF4E1B WILD-TYPE  169  400
        clus
vv       EIF4E1B MUTATED EIF4E1B WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D975V8, binary
                   cls
clus                  0   1
  EIF4E1B MUTATED     6   2
  EIF4E1B WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF4E1B MUTATED      6    2
  EIF4E1B WILD-TYPE  410  100
     clus
vv    EIF4E1B MUTATED EIF4E1B WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D975V9, continuous
D975V10, continuous
[1] "Remove cluster labels:" "EIF4E1B MUTATED"       
clus
  EIF4E1B MUTATED EIF4E1B WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" "EIF4E1B WILD-TYPE" 
       TCGA-Z6-AAPN 
"EIF4E1B WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EIF4E1B MUTATED       1                         0
  EIF4E1B WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4E1B MUTATED                                           0     6
  EIF4E1B WILD-TYPE                                         1   351
D975V11, multiclass
                                           clus
vv                                          EIF4E1B MUTATED EIF4E1B WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V12, binary
                   cls
clus                  0   1
  EIF4E1B MUTATED     1   4
  EIF4E1B WILD-TYPE   9 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF4E1B MUTATED      1    4
  EIF4E1B WILD-TYPE    9  394
                        clus
vv                       EIF4E1B MUTATED EIF4E1B WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               4               394
[1] 2 2
[1] FALSE

Clustering(976) Variable = PKD2 MUTATION ANALYSIS
D976V1, survival
                sevent
clus2              0   1
  PKD2 MUTATED     9   3
  PKD2 WILD-TYPE 329 213
  PKD2 MUTATED PKD2 WILD-TYPE 
            12            542 
  PKD2 MUTATED PKD2 WILD-TYPE 
             3            213 
$`PKD2 MUTATED`
TCGA-IG-A4P3 TCGA-L5-A8NL TCGA-L5-A8NS TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A8 
       18.64        13.22        13.41        12.59        12.49        15.52 
TCGA-LN-A9FQ TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-HU-A4GQ TCGA-IN-7806 TCGA-VQ-A8P2 
       12.85        13.78        20.32         0.10        36.36        38.14 

$`PKD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PKD2 MUTATED PKD2 WILD-TYPE 
           0.1            0.0 
  PKD2 MUTATED PKD2 WILD-TYPE 
         38.14         122.30 
  PKD2 MUTATED PKD2 WILD-TYPE 
        13.595         13.565 
[1] "0.1 - 38.1 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D976V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKD2 MUTATED         0        0        1        0         4         3
  PKD2 WILD-TYPE      10       20       45       31        80        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKD2 MUTATED           1          2          1          1        0         0
  PKD2 WILD-TYPE        28         82         61         38       43         4
D976V3, multiclass
            clus
vv           PKD2 MUTATED PKD2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PKD2 MUTATED       0   3   8   2
  PKD2 WILD-TYPE    54 132 253 100
D976V4, multiclass
       clus
vv      PKD2 MUTATED PKD2 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               8            253
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PKD2 MUTATED     6   4   2   1
  PKD2 WILD-TYPE 189 169  87  84
D976V5, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  N0            6            189
  N1            4            169
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V6, binary
                cls
clus               0   1
  PKD2 MUTATED    13   0
  PKD2 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED     13    0
  PKD2 WILD-TYPE  469   38
   clus
vv  PKD2 MUTATED PKD2 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D976V7, binary
                cls
clus               0   1
  PKD2 MUTATED     0  13
  PKD2 WILD-TYPE 172 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      0   13
  PKD2 WILD-TYPE  172  393
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  FEMALE            0            172
  MALE             13            393
[1] 2 2
[1] FALSE
D976V8, binary
                cls
clus               0   1
  PKD2 MUTATED     5   6
  PKD2 WILD-TYPE 411  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      5    6
  PKD2 WILD-TYPE  411   96
     clus
vv    PKD2 MUTATED PKD2 WILD-TYPE
  NO             5            411
  YES            6             96
[1] 2 2
[1] FALSE
D976V9, continuous
D976V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKD2 MUTATED       5                         0
  PKD2 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKD2 MUTATED                                           0     7
  PKD2 WILD-TYPE                                         1   350
D976V11, multiclass
                                           clus
vv                                          PKD2 MUTATED PKD2 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V12, binary
                cls
clus               0   1
  PKD2 MUTATED     0   9
  PKD2 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      0    9
  PKD2 WILD-TYPE   10  389
                        clus
vv                       PKD2 MUTATED PKD2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(977) Variable = APOA1BP MUTATION ANALYSIS
D977V1, survival
                   sevent
clus2                 0   1
  APOA1BP MUTATED     4   1
  APOA1BP WILD-TYPE 334 215
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                5               549 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                1               215 
$`APOA1BP MUTATED`
TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-A4J8 TCGA-CD-A489 TCGA-CG-4477 
       26.70        32.78        13.51        11.31        30.97 

$`APOA1BP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  APOA1BP MUTATED APOA1BP WILD-TYPE 
            11.31              0.00 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
            32.78            122.30 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
            26.70             13.55 
[1] "11.3 - 32.8 (26.7)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.7"
D977V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APOA1BP MUTATED         0        0        1        0         2         1
  APOA1BP WILD-TYPE      10       20       45       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APOA1BP MUTATED           0          0          1          0        0
  APOA1BP WILD-TYPE        29         84         61         39       43
                   vv
clus                STAGE IVA
  APOA1BP MUTATED           0
  APOA1BP WILD-TYPE         4
D977V3, multiclass
            clus
vv           APOA1BP MUTATED APOA1BP WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  APOA1BP MUTATED       0   1   3   1
  APOA1BP WILD-TYPE    54 134 258 101
D977V4, multiclass
       clus
vv      APOA1BP MUTATED APOA1BP WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  APOA1BP MUTATED     4   1   0   1
  APOA1BP WILD-TYPE 191 172  89  84
D977V5, multiclass
    clus
vv   APOA1BP MUTATED APOA1BP WILD-TYPE
  N0               4               191
  N1               1               172
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V6, binary
                   cls
clus                  0   1
  APOA1BP MUTATED     6   0
  APOA1BP WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      6    0
  APOA1BP WILD-TYPE  476   38
   clus
vv  APOA1BP MUTATED APOA1BP WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D977V7, binary
                   cls
clus                  0   1
  APOA1BP MUTATED     5   1
  APOA1BP WILD-TYPE 167 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      5    1
  APOA1BP WILD-TYPE  167  405
        clus
vv       APOA1BP MUTATED APOA1BP WILD-TYPE
  FEMALE               5               167
  MALE                 1               405
[1] 2 2
[1] FALSE
D977V8, binary
                   cls
clus                  0   1
  APOA1BP MUTATED     4   1
  APOA1BP WILD-TYPE 412 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      4    1
  APOA1BP WILD-TYPE  412  101
     clus
vv    APOA1BP MUTATED APOA1BP WILD-TYPE
  NO                4               412
  YES               1               101
[1] 2 2
[1] FALSE
D977V9, continuous
D977V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  APOA1BP MUTATED       1                         0
  APOA1BP WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APOA1BP MUTATED                                           0     4
  APOA1BP WILD-TYPE                                         1   353
D977V11, multiclass
                                           clus
vv                                          APOA1BP MUTATED APOA1BP WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V12, binary
                   cls
clus                  0   1
  APOA1BP MUTATED     0   5
  APOA1BP WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      0    5
  APOA1BP WILD-TYPE   10  393
                        clus
vv                       APOA1BP MUTATED APOA1BP WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(978) Variable = ATP2C1 MUTATION ANALYSIS
D978V1, survival
                  sevent
clus2                0   1
  ATP2C1 MUTATED    10   9
  ATP2C1 WILD-TYPE 328 207
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              19              535 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               9              207 
$`ATP2C1 MUTATED`
TCGA-L5-A43I TCGA-Q9-A6FU TCGA-CG-4475 TCGA-JY-A939 TCGA-L5-A4OF TCGA-L5-A88W 
       18.28         5.16        22.98        21.70        26.33        25.12 
TCGA-LN-A49P TCGA-LN-A4A4 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 
       12.33        12.59        26.70         6.97        34.68        31.10 
TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-A4IY TCGA-CD-A4MG TCGA-CG-4306 TCGA-VQ-A8P2 
        0.26         1.12        12.89         6.58         1.02        38.14 
TCGA-VQ-AA64 
       18.41 

$`ATP2C1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        21.99        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43        15.48         2.60         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
            0.26             0.00 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           38.14           122.30 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           18.28            13.55 
[1] "0.3 - 38.1 (18.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D978V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2C1 MUTATED         0        0        1        0         5         5
  ATP2C1 WILD-TYPE      10       20       45       31        79        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2C1 MUTATED           1          4          2          1        1
  ATP2C1 WILD-TYPE        28         80         60         38       42
                  vv
clus               STAGE IVA
  ATP2C1 MUTATED           0
  ATP2C1 WILD-TYPE         4
D978V3, multiclass
            clus
vv           ATP2C1 MUTATED ATP2C1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              4               80
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATP2C1 MUTATED       2   1  12   5
  ATP2C1 WILD-TYPE    52 134 249  97
D978V4, multiclass
       clus
vv      ATP2C1 MUTATED ATP2C1 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                12              249
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP2C1 MUTATED     9   7   4   0
  ATP2C1 WILD-TYPE 186 166  85  85
D978V5, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  N0              9              186
  N1              7              166
  N2              4               85
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D978V6, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED    15   1
  ATP2C1 WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED     15    1
  ATP2C1 WILD-TYPE  467   37
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D978V7, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     7  13
  ATP2C1 WILD-TYPE 165 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      7   13
  ATP2C1 WILD-TYPE  165  393
        clus
vv       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  FEMALE              7              165
  MALE               13              393
[1] 2 2
[1] FALSE
D978V8, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED    12   6
  ATP2C1 WILD-TYPE 404  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED     12    6
  ATP2C1 WILD-TYPE  404   96
     clus
vv    ATP2C1 MUTATED ATP2C1 WILD-TYPE
  NO              12              404
  YES              6               96
[1] 2 2
[1] FALSE
D978V9, continuous
[1] "Remove cluster labels:" "ATP2C1 MUTATED"        
clus
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49R 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ATP2C1 WILD-TYPE" "ATP2C1 WILD-TYPE" 
D978V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP2C1 MUTATED       4                         0
  ATP2C1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP2C1 MUTATED                                           0    14
  ATP2C1 WILD-TYPE                                         1   343
D978V11, multiclass
                                           clus
vv                                          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D978V12, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     0  12
  ATP2C1 WILD-TYPE  10 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0   12
  ATP2C1 WILD-TYPE   10  386
                        clus
vv                       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             12              386
[1] 2 2
[1] FALSE

Clustering(979) Variable = FER1L6 MUTATION ANALYSIS
D979V1, survival
                  sevent
clus2                0   1
  FER1L6 MUTATED    20   9
  FER1L6 WILD-TYPE 318 207
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              29              525 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
               9              207 
$`FER1L6 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A6QS TCGA-JY-A6FA TCGA-L5-A8NE TCGA-L5-A8NM 
       19.99        21.99         9.96        44.75        55.50         7.76 
TCGA-LN-A49M TCGA-LN-A7HX TCGA-R6-A8WG TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7703 
       12.66        12.23        12.69        34.68        18.05        36.16 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MG 
       31.10        31.27         1.12        31.96        12.30         6.58 
TCGA-CG-5723 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HF-7133 TCGA-HU-A4G8 TCGA-HU-A4GN 
      105.07        11.31        11.44        63.06        22.68        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-SW-A7EA TCGA-VQ-A8P2 
        0.10        23.84        23.80        19.04        38.14 

$`FER1L6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
       36.43        13.78        14.76        26.43        11.24        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       25.81        11.77        21.37         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        29.00        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FER1L6 MUTATED FER1L6 WILD-TYPE 
             0.1              0.0 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
          105.07           122.30 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
           21.99            13.48 
[1] "0.1 - 105.1 (22.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D979V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FER1L6 MUTATED         0        1        3        1         6         6
  FER1L6 WILD-TYPE      10       19       43       30        78        77
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FER1L6 MUTATED           0          3          1          4        4
  FER1L6 WILD-TYPE        29         81         61         35       39
                  vv
clus               STAGE IVA
  FER1L6 MUTATED           0
  FER1L6 WILD-TYPE         4
D979V3, multiclass
            clus
vv           FER1L6 MUTATED FER1L6 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               6               78
  STAGE IIB               6               77
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FER1L6 MUTATED       2  13   8   7
  FER1L6 WILD-TYPE    52 122 253  95
D979V4, multiclass
       clus
vv      FER1L6 MUTATED FER1L6 WILD-TYPE
  T0+T1              2               52
  T2                13              122
  T3                 8              253
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FER1L6 MUTATED    10  10   5   4
  FER1L6 WILD-TYPE 185 163  84  81
D979V5, multiclass
    clus
vv   FER1L6 MUTATED FER1L6 WILD-TYPE
  N0             10              185
  N1             10              163
  N2              5               84
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V6, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    26   3
  FER1L6 WILD-TYPE 456  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     26    3
  FER1L6 WILD-TYPE  456   35
   clus
vv  FER1L6 MUTATED FER1L6 WILD-TYPE
  0             26              456
  1              3               35
[1] 2 2
[1] FALSE
D979V7, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    12  19
  FER1L6 WILD-TYPE 160 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     12   19
  FER1L6 WILD-TYPE  160  387
        clus
vv       FER1L6 MUTATED FER1L6 WILD-TYPE
  FEMALE             12              160
  MALE               19              387
[1] 2 2
[1] FALSE
D979V8, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    24   5
  FER1L6 WILD-TYPE 392  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     24    5
  FER1L6 WILD-TYPE  392   97
     clus
vv    FER1L6 MUTATED FER1L6 WILD-TYPE
  NO              24              392
  YES              5               97
[1] 2 2
[1] FALSE
D979V9, continuous
[1] "Remove cluster labels:" "FER1L6 MUTATED"        
clus
  FER1L6 MUTATED FER1L6 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FER1L6 WILD-TYPE" "FER1L6 WILD-TYPE" 
D979V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FER1L6 MUTATED      11                         0
  FER1L6 WILD-TYPE   122                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FER1L6 MUTATED                                           0    16
  FER1L6 WILD-TYPE                                         1   341
D979V11, multiclass
                                           clus
vv                                          FER1L6 MUTATED FER1L6 WILD-TYPE
  ASIAN                                                 11              122
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V12, binary
                  cls
clus                 0   1
  FER1L6 MUTATED     1  21
  FER1L6 WILD-TYPE   9 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED      1   21
  FER1L6 WILD-TYPE    9  377
                        clus
vv                       FER1L6 MUTATED FER1L6 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(980) Variable = MGA MUTATION ANALYSIS
D980V1, survival
               sevent
clus2             0   1
  MGA MUTATED    24  15
  MGA WILD-TYPE 314 201
  MGA MUTATED MGA WILD-TYPE 
           39           515 
  MGA MUTATED MGA WILD-TYPE 
           15           201 
$`MGA MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A4OH TCGA-L5-A88W 
       31.27        14.30        14.50        47.38        32.61        25.12 
TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NS TCGA-R6-A6XG TCGA-VR-A8EQ TCGA-VR-A8EW 
        2.66        13.55        13.41        38.40        22.82         8.12 
TCGA-XP-A8T8 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 
       14.37        11.70         6.97        30.90        34.68        30.90 
TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8531 
       44.94         6.18        27.12        31.96        13.18        12.59 
TCGA-CG-4465 TCGA-CG-5725 TCGA-CG-5726 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 
        9.01        15.02        28.96        13.78        14.47        21.27 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 
       11.08        26.47        22.32         0.10        29.00        14.07 
TCGA-IN-A6RL TCGA-SW-A7EA TCGA-VQ-A8P2 
       13.35        19.04        38.14 

$`MGA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       20.05        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43        15.48         2.60         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MGA MUTATED MGA WILD-TYPE 
          0.1           0.0 
  MGA MUTATED MGA WILD-TYPE 
        47.38        122.30 
  MGA MUTATED MGA WILD-TYPE 
        15.02         13.38 
[1] "0.1 - 47.4 (15.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.2"
D980V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGA MUTATED         1        2        6        0         7         5
  MGA WILD-TYPE       9       18       40       31        77        78
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGA MUTATED           2          6          4          2        2         1
  MGA WILD-TYPE        27         78         58         37       41         3
D980V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              1             9
  STAGE IA             2            18
  STAGE IB             6            40
  STAGE II             0            31
  STAGE IIA            7            77
  STAGE IIB            5            78
  STAGE III            2            27
  STAGE IIIA           6            78
  STAGE IIIB           4            58
  STAGE IIIC           2            37
  STAGE IV             2            41
  STAGE IVA            1             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  MGA MUTATED       7   8  17   7
  MGA WILD-TYPE    47 127 244  95
D980V4, multiclass
       clus
vv      MGA MUTATED MGA WILD-TYPE
  T0+T1           7            47
  T2              8           127
  T3             17           244
  T4              7            95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  MGA MUTATED    17  13   4   4
  MGA WILD-TYPE 178 160  85  81
D980V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0          17           178
  N1          13           160
  N2           4            85
  N3           4            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V6, binary
               cls
clus              0   1
  MGA MUTATED    34   3
  MGA WILD-TYPE 448  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     34    3
  MGA WILD-TYPE  448   35
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          34           448
  1           3            35
[1] 2 2
[1] FALSE
D980V7, binary
               cls
clus              0   1
  MGA MUTATED    11  30
  MGA WILD-TYPE 161 376
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     11   30
  MGA WILD-TYPE  161  376
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          11           161
  MALE            30           376
[1] 2 2
[1] FALSE
D980V8, binary
               cls
clus              0   1
  MGA MUTATED    25  10
  MGA WILD-TYPE 391  92
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     25   10
  MGA WILD-TYPE  391   92
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           25           391
  YES          10            92
[1] 2 2
[1] FALSE
D980V9, continuous
D980V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  MGA MUTATED      10                         2
  MGA WILD-TYPE   123                        12
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MGA MUTATED                                           0    24
  MGA WILD-TYPE                                         1   333
D980V11, multiclass
                                           clus
vv                                          MGA MUTATED MGA WILD-TYPE
  ASIAN                                              10           123
  BLACK OR AFRICAN AMERICAN                           2            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              24           333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V12, binary
               cls
clus              0   1
  MGA MUTATED     2  25
  MGA WILD-TYPE   8 373
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      2   25
  MGA WILD-TYPE    8  373
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               2             8
  NOT HISPANIC OR LATINO          25           373
[1] 2 2
[1] FALSE

Clustering(981) Variable = MYCT1 MUTATION ANALYSIS
D981V1, survival
                 sevent
clus2               0   1
  MYCT1 MUTATED     7   3
  MYCT1 WILD-TYPE 331 213
  MYCT1 MUTATED MYCT1 WILD-TYPE 
             10             544 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              3             213 
$`MYCT1 MUTATED`
TCGA-L5-A8NH TCGA-LN-A7HZ TCGA-R6-A8WC TCGA-BR-6452 TCGA-BR-8485 TCGA-CD-8527 
       12.92        13.18         2.30        34.68         9.21         7.17 
TCGA-CG-4469 TCGA-FP-8099 TCGA-IN-A6RP TCGA-VQ-A91V 
        7.07        17.06         6.44        42.64 

$`MYCT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       12.10        12.39        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MYCT1 MUTATED MYCT1 WILD-TYPE 
            2.3             0.0 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
          42.64          122.30 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
         11.065          13.730 
[1] "2.3 - 42.6 (11.1)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D981V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYCT1 MUTATED         0        0        0        1         3         0
  MYCT1 WILD-TYPE      10       20       46       30        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYCT1 MUTATED           0          1          0          2        2         0
  MYCT1 WILD-TYPE        29         83         62         37       41         4
D981V3, multiclass
            clus
vv           MYCT1 MUTATED MYCT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MYCT1 MUTATED       2   2   4   1
  MYCT1 WILD-TYPE    52 133 257 101
D981V4, multiclass
       clus
vv      MYCT1 MUTATED MYCT1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MYCT1 MUTATED     4   2   1   3
  MYCT1 WILD-TYPE 191 171  88  82
D981V5, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  N0             4             191
  N1             2             171
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V6, binary
                 cls
clus                0   1
  MYCT1 MUTATED     8   1
  MYCT1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      8    1
  MYCT1 WILD-TYPE  474   37
   clus
vv  MYCT1 MUTATED MYCT1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D981V7, binary
                 cls
clus                0   1
  MYCT1 MUTATED     4   7
  MYCT1 WILD-TYPE 168 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      4    7
  MYCT1 WILD-TYPE  168  399
        clus
vv       MYCT1 MUTATED MYCT1 WILD-TYPE
  FEMALE             4             168
  MALE               7             399
[1] 2 2
[1] FALSE
D981V8, binary
                 cls
clus                0   1
  MYCT1 MUTATED     5   2
  MYCT1 WILD-TYPE 411 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      5    2
  MYCT1 WILD-TYPE  411  100
     clus
vv    MYCT1 MUTATED MYCT1 WILD-TYPE
  NO              5             411
  YES             2             100
[1] 2 2
[1] FALSE
D981V9, continuous
[1] "Remove cluster labels:" "MYCT1 MUTATED"         
clus
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
D981V10, continuous
[1] "Remove cluster labels:" "MYCT1 MUTATED"         
clus
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A8HZ 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" "MYCT1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYCT1 MUTATED       2                         0
  MYCT1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYCT1 MUTATED                                           0     7
  MYCT1 WILD-TYPE                                         1   350
D981V11, multiclass
                                           clus
vv                                          MYCT1 MUTATED MYCT1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V12, binary
                 cls
clus                0   1
  MYCT1 MUTATED     0   8
  MYCT1 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      0    8
  MYCT1 WILD-TYPE   10  390
                        clus
vv                       MYCT1 MUTATED MYCT1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(982) Variable = KCNQ1 MUTATION ANALYSIS
D982V1, survival
                 sevent
clus2               0   1
  KCNQ1 MUTATED     5   1
  KCNQ1 WILD-TYPE 333 215
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             548 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              1             215 
$`KCNQ1 MUTATED`
TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 TCGA-HF-A5NB TCGA-VQ-A8P2 
        0.95        31.27        31.96         1.02        30.51        38.14 

$`KCNQ1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
           0.95            0.00 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
          38.14          122.30 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
          30.89           13.53 
[1] "0.9 - 38.1 (30.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3"  
D982V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNQ1 MUTATED         0        0        0        0         1         0
  KCNQ1 WILD-TYPE      10       20       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNQ1 MUTATED           0          1          0          2        2         0
  KCNQ1 WILD-TYPE        29         83         62         37       41         4
D982V3, multiclass
            clus
vv           KCNQ1 MUTATED KCNQ1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNQ1 MUTATED       0   0   2   4
  KCNQ1 WILD-TYPE    54 135 259  98
D982V4, multiclass
       clus
vv      KCNQ1 MUTATED KCNQ1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNQ1 MUTATED     1   1   2   2
  KCNQ1 WILD-TYPE 194 172  87  83
D982V5, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V6, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     4   2
  KCNQ1 WILD-TYPE 478  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      4    2
  KCNQ1 WILD-TYPE  478   36
   clus
vv  KCNQ1 MUTATED KCNQ1 WILD-TYPE
  0             4             478
  1             2              36
[1] 2 2
[1] FALSE
D982V7, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     2   4
  KCNQ1 WILD-TYPE 170 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      2    4
  KCNQ1 WILD-TYPE  170  402
        clus
vv       KCNQ1 MUTATED KCNQ1 WILD-TYPE
  FEMALE             2             170
  MALE               4             402
[1] 2 2
[1] FALSE
D982V8, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     3   2
  KCNQ1 WILD-TYPE 413 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      3    2
  KCNQ1 WILD-TYPE  413  100
     clus
vv    KCNQ1 MUTATED KCNQ1 WILD-TYPE
  NO              3             413
  YES             2             100
[1] 2 2
[1] FALSE
D982V9, continuous
D982V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNQ1 MUTATED       1                         0
  KCNQ1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNQ1 MUTATED                                           0     3
  KCNQ1 WILD-TYPE                                         1   354
D982V11, multiclass
                                           clus
vv                                          KCNQ1 MUTATED KCNQ1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V12, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     0   3
  KCNQ1 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      0    3
  KCNQ1 WILD-TYPE   10  395
                        clus
vv                       KCNQ1 MUTATED KCNQ1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(983) Variable = LIMCH1 MUTATION ANALYSIS
D983V1, survival
                  sevent
clus2                0   1
  LIMCH1 MUTATED    11   5
  LIMCH1 WILD-TYPE 327 211
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              16              538 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               5              211 
$`LIMCH1 MUTATED`
TCGA-IC-A6RE TCGA-IG-A5S3 TCGA-L5-A4OP TCGA-LN-A4A8 TCGA-B7-5816 TCGA-BR-7707 
        7.69        23.41         7.17        15.52        26.70        35.84 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A48C TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-6525 
        1.12        16.14        11.61        11.77        65.10        13.35 
TCGA-D7-A6EY TCGA-IN-7806 TCGA-IN-A6RJ TCGA-MX-A5UJ 
       11.44        36.36        12.46        19.73 

$`LIMCH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       23.80        21.17        14.07        15.68        33.40         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            1.12             0.00 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            65.1            122.3 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
          14.435           13.565 
[1] "1.1 - 65.1 (14.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D983V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LIMCH1 MUTATED         0        2        2        0         2         5
  LIMCH1 WILD-TYPE      10       18       44       31        82        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIMCH1 MUTATED           0          3          2          0        0
  LIMCH1 WILD-TYPE        29         81         60         39       43
                  vv
clus               STAGE IVA
  LIMCH1 MUTATED           0
  LIMCH1 WILD-TYPE         4
D983V3, multiclass
            clus
vv           LIMCH1 MUTATED LIMCH1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  LIMCH1 MUTATED       3   4   8   1
  LIMCH1 WILD-TYPE    51 131 253 101
D983V4, multiclass
       clus
vv      LIMCH1 MUTATED LIMCH1 WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                 8              253
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LIMCH1 MUTATED     8   4   2   2
  LIMCH1 WILD-TYPE 187 169  87  83
D983V5, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  N0              8              187
  N1              4              169
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V6, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    15   0
  LIMCH1 WILD-TYPE 467  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     15    0
  LIMCH1 WILD-TYPE  467   38
   clus
vv  LIMCH1 MUTATED LIMCH1 WILD-TYPE
  0             15              467
  1              0               38
[1] 2 2
[1] FALSE
D983V7, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    10   6
  LIMCH1 WILD-TYPE 162 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     10    6
  LIMCH1 WILD-TYPE  162  400
        clus
vv       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  FEMALE             10              162
  MALE                6              400
[1] 2 2
[1] FALSE
D983V8, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    14   0
  LIMCH1 WILD-TYPE 402 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     14    0
  LIMCH1 WILD-TYPE  402  102
     clus
vv    LIMCH1 MUTATED LIMCH1 WILD-TYPE
  NO              14              402
  YES              0              102
[1] 2 2
[1] FALSE
D983V9, continuous
[1] "Remove cluster labels:" "LIMCH1 MUTATED"        
clus
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A7DP 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-V5-A7RB 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
D983V10, continuous
[1] "Remove cluster labels:" "LIMCH1 MUTATED"        
clus
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IG-A3QL 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" "LIMCH1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LIMCH1 MUTATED       3                         0
  LIMCH1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIMCH1 MUTATED                                           0    12
  LIMCH1 WILD-TYPE                                         1   345
D983V11, multiclass
                                           clus
vv                                          LIMCH1 MUTATED LIMCH1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V12, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED     0  14
  LIMCH1 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED      0   14
  LIMCH1 WILD-TYPE   10  384
                        clus
vv                       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(984) Variable = KRTAP5-1 MUTATION ANALYSIS
D984V1, survival
                    sevent
clus2                  0   1
  KRTAP5-1 MUTATED     6   3
  KRTAP5-1 WILD-TYPE 332 213
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
                 9                545 
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
                 3                213 
$`KRTAP5-1 MUTATED`
TCGA-L5-A4OX TCGA-BR-8487 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-HF-7132 TCGA-HU-A4GT 
        7.43         1.12         6.58         5.92        77.29         6.51 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       29.00        14.07        38.14 

$`KRTAP5-1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
              1.12               0.00 
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
             77.29             122.30 
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
              7.43              13.58 
[1] "1.1 - 77.3 (7.4)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D984V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP5-1 MUTATED         0        0        1        1         3         2
  KRTAP5-1 WILD-TYPE      10       20       45       30        81        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP5-1 MUTATED           0          1          0          1        0
  KRTAP5-1 WILD-TYPE        29         83         62         38       43
                    vv
clus                 STAGE IVA
  KRTAP5-1 MUTATED           0
  KRTAP5-1 WILD-TYPE         4
D984V3, multiclass
            clus
vv           KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 3                 81
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                1                 83
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KRTAP5-1 MUTATED       1   2   4   2
  KRTAP5-1 WILD-TYPE    53 133 257 100
D984V4, multiclass
       clus
vv      KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  T0+T1                1                 53
  T2                   2                133
  T3                   4                257
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KRTAP5-1 MUTATED     3   5   0   1
  KRTAP5-1 WILD-TYPE 192 168  89  84
D984V5, multiclass
    clus
vv   KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  N0                3                192
  N1                5                168
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V6, binary
                    cls
clus                   0   1
  KRTAP5-1 MUTATED    10   0
  KRTAP5-1 WILD-TYPE 472  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-1 MUTATED     10    0
  KRTAP5-1 WILD-TYPE  472   38
   clus
vv  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  0               10                472
  1                0                 38
[1] 2 2
[1] FALSE
D984V7, binary
                    cls
clus                   0   1
  KRTAP5-1 MUTATED     5   5
  KRTAP5-1 WILD-TYPE 167 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-1 MUTATED      5    5
  KRTAP5-1 WILD-TYPE  167  401
        clus
vv       KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  FEMALE                5                167
  MALE                  5                401
[1] 2 2
[1] FALSE
D984V8, binary
                    cls
clus                   0   1
  KRTAP5-1 MUTATED     6   2
  KRTAP5-1 WILD-TYPE 410 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-1 MUTATED      6    2
  KRTAP5-1 WILD-TYPE  410  100
     clus
vv    KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  NO                 6                410
  YES                2                100
[1] 2 2
[1] FALSE
D984V9, continuous
D984V10, continuous
[1] "Remove cluster labels:" "KRTAP5-1 MUTATED"      
clus
  KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A88S         TCGA-L5-A88V 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" "KRTAP5-1 WILD-TYPE" 
        TCGA-Z6-AAPN 
"KRTAP5-1 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KRTAP5-1 MUTATED       4                         0
  KRTAP5-1 WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRTAP5-1 MUTATED                                           0     5
  KRTAP5-1 WILD-TYPE                                         1   352
D984V11, multiclass
                                           clus
vv                                          KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V12, binary
                    cls
clus                   0   1
  KRTAP5-1 MUTATED     0   7
  KRTAP5-1 WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-1 MUTATED      0    7
  KRTAP5-1 WILD-TYPE   10  391
                        clus
vv                       KRTAP5-1 MUTATED KRTAP5-1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(985) Variable = C20ORF7 MUTATION ANALYSIS
D985V1, survival
                   sevent
clus2                 0   1
  C20ORF7 MUTATED     4   2
  C20ORF7 WILD-TYPE 334 214
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               548 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                2               214 
$`C20ORF7 MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8591 TCGA-CD-5804 TCGA-MX-A5UG TCGA-VQ-A8P2 
        6.61        29.59        28.14        12.10         3.72        38.14 

$`C20ORF7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62        36.95        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
             3.72              0.00 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
            38.14            122.30 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
           20.120            13.565 
[1] "3.7 - 38.1 (20.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D985V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C20ORF7 MUTATED         0        0        0        0         0         1
  C20ORF7 WILD-TYPE      10       20       46       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF7 MUTATED           1          2          0          1        0
  C20ORF7 WILD-TYPE        28         82         62         38       43
                   vv
clus                STAGE IVA
  C20ORF7 MUTATED           0
  C20ORF7 WILD-TYPE         4
D985V3, multiclass
            clus
vv           C20ORF7 MUTATED C20ORF7 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C20ORF7 MUTATED       0   1   2   3
  C20ORF7 WILD-TYPE    54 134 259  99
D985V4, multiclass
       clus
vv      C20ORF7 MUTATED C20ORF7 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C20ORF7 MUTATED     1   4   0   1
  C20ORF7 WILD-TYPE 194 169  89  84
D985V5, multiclass
    clus
vv   C20ORF7 MUTATED C20ORF7 WILD-TYPE
  N0               1               194
  N1               4               169
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V6, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     6   0
  C20ORF7 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      6    0
  C20ORF7 WILD-TYPE  476   38
   clus
vv  C20ORF7 MUTATED C20ORF7 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D985V7, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     2   4
  C20ORF7 WILD-TYPE 170 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      2    4
  C20ORF7 WILD-TYPE  170  402
        clus
vv       C20ORF7 MUTATED C20ORF7 WILD-TYPE
  FEMALE               2               170
  MALE                 4               402
[1] 2 2
[1] FALSE
D985V8, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     5   1
  C20ORF7 WILD-TYPE 411 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      5    1
  C20ORF7 WILD-TYPE  411  101
     clus
vv    C20ORF7 MUTATED C20ORF7 WILD-TYPE
  NO                5               411
  YES               1               101
[1] 2 2
[1] FALSE
D985V9, continuous
D985V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C20ORF7 MUTATED       2                         0
  C20ORF7 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C20ORF7 MUTATED                                           0     4
  C20ORF7 WILD-TYPE                                         1   353
D985V11, multiclass
                                           clus
vv                                          C20ORF7 MUTATED C20ORF7 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V12, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     0   5
  C20ORF7 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      0    5
  C20ORF7 WILD-TYPE   10  393
                        clus
vv                       C20ORF7 MUTATED C20ORF7 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(986) Variable = KCNH2 MUTATION ANALYSIS
D986V1, survival
                 sevent
clus2               0   1
  KCNH2 MUTATED     9   5
  KCNH2 WILD-TYPE 329 211
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             14             540 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
              5             211 
$`KCNH2 MUTATED`
TCGA-IG-A4QS TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4257 
        3.88        26.70        19.56         6.97        18.35         9.67 
TCGA-BR-8077 TCGA-BR-8487 TCGA-CG-4469 TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G8 
        0.69         1.12         7.07       105.07        22.32        22.68 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`KCNH2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KCNH2 MUTATED KCNH2 WILD-TYPE 
           0.69            0.00 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
         105.07          122.30 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
         18.955          13.530 
[1] "0.7 - 105.1 (19.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D986V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH2 MUTATED         0        0        0        1         1         4
  KCNH2 WILD-TYPE      10       20       46       30        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNH2 MUTATED           0          2          2          2        1         0
  KCNH2 WILD-TYPE        29         82         60         37       42         4
D986V3, multiclass
            clus
vv           KCNH2 MUTATED KCNH2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNH2 MUTATED       0   1   5   7
  KCNH2 WILD-TYPE    54 134 256  95
D986V4, multiclass
       clus
vv      KCNH2 MUTATED KCNH2 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                5             256
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNH2 MUTATED     4   6   2   2
  KCNH2 WILD-TYPE 191 167  87  83
D986V5, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  N0             4             191
  N1             6             167
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V6, binary
                 cls
clus                0   1
  KCNH2 MUTATED    14   0
  KCNH2 WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED     14    0
  KCNH2 WILD-TYPE  468   38
   clus
vv  KCNH2 MUTATED KCNH2 WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D986V7, binary
                 cls
clus                0   1
  KCNH2 MUTATED     7   8
  KCNH2 WILD-TYPE 165 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      7    8
  KCNH2 WILD-TYPE  165  398
        clus
vv       KCNH2 MUTATED KCNH2 WILD-TYPE
  FEMALE             7             165
  MALE               8             398
[1] 2 2
[1] FALSE
D986V8, binary
                 cls
clus                0   1
  KCNH2 MUTATED    12   1
  KCNH2 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED     12    1
  KCNH2 WILD-TYPE  404  101
     clus
vv    KCNH2 MUTATED KCNH2 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D986V9, continuous
D986V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH2 MUTATED       3                         0
  KCNH2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH2 MUTATED                                           0    10
  KCNH2 WILD-TYPE                                         1   347
D986V11, multiclass
                                           clus
vv                                          KCNH2 MUTATED KCNH2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V12, binary
                 cls
clus                0   1
  KCNH2 MUTATED     0  12
  KCNH2 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      0   12
  KCNH2 WILD-TYPE   10  386
                        clus
vv                       KCNH2 MUTATED KCNH2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(987) Variable = XRCC2 MUTATION ANALYSIS
D987V1, survival
                 sevent
clus2               0   1
  XRCC2 MUTATED     4   1
  XRCC2 WILD-TYPE 334 215
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              5             549 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              1             215 
$`XRCC2 MUTATED`
TCGA-CG-4460 TCGA-VR-A8Q7 TCGA-BR-6452 TCGA-HU-A4GN TCGA-HU-A4GT 
       21.99        52.27        34.68        29.98         6.51 

$`XRCC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  XRCC2 MUTATED XRCC2 WILD-TYPE 
           6.51            0.00 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
          52.27          122.30 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
          29.98           13.51 
[1] "6.5 - 52.3 (30.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3"  
D987V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XRCC2 MUTATED         0        0        0        0         3         0
  XRCC2 WILD-TYPE      10       20       46       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRCC2 MUTATED           0          2          0          0        1         0
  XRCC2 WILD-TYPE        29         82         62         39       42         4
D987V3, multiclass
            clus
vv           XRCC2 MUTATED XRCC2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  XRCC2 MUTATED       0   1   3   2
  XRCC2 WILD-TYPE    54 134 258 100
D987V4, multiclass
       clus
vv      XRCC2 MUTATED XRCC2 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  XRCC2 MUTATED     3   4   0   0
  XRCC2 WILD-TYPE 192 169  89  85
D987V5, multiclass
    clus
vv   XRCC2 MUTATED XRCC2 WILD-TYPE
  N0             3             192
  N1             4             169
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V6, binary
                 cls
clus                0   1
  XRCC2 MUTATED     6   1
  XRCC2 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      6    1
  XRCC2 WILD-TYPE  476   37
   clus
vv  XRCC2 MUTATED XRCC2 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D987V7, binary
                 cls
clus                0   1
  XRCC2 MUTATED     5   2
  XRCC2 WILD-TYPE 167 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      5    2
  XRCC2 WILD-TYPE  167  404
        clus
vv       XRCC2 MUTATED XRCC2 WILD-TYPE
  FEMALE             5             167
  MALE               2             404
[1] 2 2
[1] FALSE
D987V8, binary
                 cls
clus                0   1
  XRCC2 MUTATED     5   0
  XRCC2 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      5    0
  XRCC2 WILD-TYPE  411  102
     clus
vv    XRCC2 MUTATED XRCC2 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D987V9, continuous
[1] "Remove cluster labels:" "XRCC2 MUTATED"         
clus
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
D987V10, continuous
[1] "Remove cluster labels:" "XRCC2 MUTATED"         
clus
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" "XRCC2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"XRCC2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XRCC2 MUTATED       2                         0
  XRCC2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XRCC2 MUTATED                                           0     4
  XRCC2 WILD-TYPE                                         1   353
D987V11, multiclass
                                           clus
vv                                          XRCC2 MUTATED XRCC2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V12, binary
                 cls
clus                0   1
  XRCC2 MUTATED     0   5
  XRCC2 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      0    5
  XRCC2 WILD-TYPE   10  393
                        clus
vv                       XRCC2 MUTATED XRCC2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(988) Variable = EIF4G1 MUTATION ANALYSIS
D988V1, survival
                  sevent
clus2                0   1
  EIF4G1 MUTATED    17   7
  EIF4G1 WILD-TYPE 321 209
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
              24              530 
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
               7              209 
$`EIF4G1 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GO TCGA-IG-A6QS TCGA-KH-A6WC TCGA-L5-A88W TCGA-BR-4184 
       19.99        16.24         9.96         6.28        25.12         6.97 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8372 
        6.61        34.68        32.78        30.90        31.10        31.27 
TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-D7-5579 TCGA-D7-6815 TCGA-F1-A448 
       25.05        28.14        31.96        20.91        15.98        21.27 
TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-IN-A6RP TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.08         0.10        20.25         6.44        19.73        38.14 

$`EIF4G1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48         2.60         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80        14.79         7.36         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       21.37        29.98         8.98         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
             0.1              0.0 
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
           38.14           122.30 
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
           20.58            13.41 
[1] "0.1 - 38.1 (20.6)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D988V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4G1 MUTATED         0        1        1        0         4         3
  EIF4G1 WILD-TYPE      10       19       45       31        80        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G1 MUTATED           1          5          1          8        1
  EIF4G1 WILD-TYPE        28         79         61         31       42
                  vv
clus               STAGE IVA
  EIF4G1 MUTATED           1
  EIF4G1 WILD-TYPE         3
D988V3, multiclass
            clus
vv           EIF4G1 MUTATED EIF4G1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               3               80
  STAGE III               1               28
  STAGE IIIA              5               79
  STAGE IIIB              1               61
  STAGE IIIC              8               31
  STAGE IV                1               42
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  EIF4G1 MUTATED       2   4  11   9
  EIF4G1 WILD-TYPE    52 131 250  93
D988V4, multiclass
       clus
vv      EIF4G1 MUTATED EIF4G1 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                11              250
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  EIF4G1 MUTATED     7   5   8   6
  EIF4G1 WILD-TYPE 188 168  81  79
D988V5, multiclass
    clus
vv   EIF4G1 MUTATED EIF4G1 WILD-TYPE
  N0              7              188
  N1              5              168
  N2              8               81
  N3              6               79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V6, binary
                  cls
clus                 0   1
  EIF4G1 MUTATED    21   2
  EIF4G1 WILD-TYPE 461  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G1 MUTATED     21    2
  EIF4G1 WILD-TYPE  461   36
   clus
vv  EIF4G1 MUTATED EIF4G1 WILD-TYPE
  0             21              461
  1              2               36
[1] 2 2
[1] FALSE
D988V7, binary
                  cls
clus                 0   1
  EIF4G1 MUTATED     8  18
  EIF4G1 WILD-TYPE 164 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G1 MUTATED      8   18
  EIF4G1 WILD-TYPE  164  388
        clus
vv       EIF4G1 MUTATED EIF4G1 WILD-TYPE
  FEMALE              8              164
  MALE               18              388
[1] 2 2
[1] FALSE
D988V8, binary
                  cls
clus                 0   1
  EIF4G1 MUTATED    19   6
  EIF4G1 WILD-TYPE 397  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G1 MUTATED     19    6
  EIF4G1 WILD-TYPE  397   96
     clus
vv    EIF4G1 MUTATED EIF4G1 WILD-TYPE
  NO              19              397
  YES              6               96
[1] 2 2
[1] FALSE
D988V9, continuous
[1] "Remove cluster labels:" "EIF4G1 MUTATED"        
clus
  EIF4G1 MUTATED EIF4G1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" "EIF4G1 WILD-TYPE" 
D988V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EIF4G1 MUTATED       3                         1
  EIF4G1 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4G1 MUTATED                                           0    20
  EIF4G1 WILD-TYPE                                         1   337
D988V11, multiclass
                                           clus
vv                                          EIF4G1 MUTATED EIF4G1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V12, binary
                  cls
clus                 0   1
  EIF4G1 MUTATED     1  20
  EIF4G1 WILD-TYPE   9 378
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G1 MUTATED      1   20
  EIF4G1 WILD-TYPE    9  378
                        clus
vv                       EIF4G1 MUTATED EIF4G1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             20              378
[1] 2 2
[1] FALSE

Clustering(989) Variable = PTPN3 MUTATION ANALYSIS
D989V1, survival
                 sevent
clus2               0   1
  PTPN3 MUTATED     9   8
  PTPN3 WILD-TYPE 329 208
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             17             537 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              8             208 
$`PTPN3 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OE TCGA-2H-A9GK TCGA-LN-A7HV TCGA-XP-A8T7 TCGA-BR-4256 
       34.85        24.00         7.63        10.52        41.23         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8382 TCGA-D7-A4YV TCGA-F1-A448 TCGA-FP-A4BE 
        9.67        34.68        25.05         5.92        21.27        11.08 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8PM 
       22.32         0.10        19.73        74.53         1.87 

$`PTPN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         4.08         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        37.22        22.19        17.85        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PTPN3 MUTATED PTPN3 WILD-TYPE 
            0.1             0.0 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
          74.53          122.30 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
          19.73           13.55 
[1] "0.1 - 74.5 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D989V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN3 MUTATED         0        0        0        0         4         4
  PTPN3 WILD-TYPE      10       20       46       31        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN3 MUTATED           1          1          2          2        2         0
  PTPN3 WILD-TYPE        28         83         60         37       41         4
D989V3, multiclass
            clus
vv           PTPN3 MUTATED PTPN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPN3 MUTATED       0   2   9   6
  PTPN3 WILD-TYPE    54 133 252  96
D989V4, multiclass
       clus
vv      PTPN3 MUTATED PTPN3 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPN3 MUTATED     7   4   3   3
  PTPN3 WILD-TYPE 188 169  86  82
D989V5, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  N0             7             188
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V6, binary
                 cls
clus                0   1
  PTPN3 MUTATED    17   1
  PTPN3 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     17    1
  PTPN3 WILD-TYPE  465   37
   clus
vv  PTPN3 MUTATED PTPN3 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D989V7, binary
                 cls
clus                0   1
  PTPN3 MUTATED    10  10
  PTPN3 WILD-TYPE 162 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     10   10
  PTPN3 WILD-TYPE  162  396
        clus
vv       PTPN3 MUTATED PTPN3 WILD-TYPE
  FEMALE            10             162
  MALE              10             396
[1] 2 2
[1] FALSE
D989V8, binary
                 cls
clus                0   1
  PTPN3 MUTATED    15   3
  PTPN3 WILD-TYPE 401  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     15    3
  PTPN3 WILD-TYPE  401   99
     clus
vv    PTPN3 MUTATED PTPN3 WILD-TYPE
  NO             15             401
  YES             3              99
[1] 2 2
[1] FALSE
D989V9, continuous
[1] "Remove cluster labels:" "PTPN3 MUTATED"         
clus
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T8 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PTPN3 WILD-TYPE" "PTPN3 WILD-TYPE" 
D989V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPN3 MUTATED       3                         1
  PTPN3 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN3 MUTATED                                           0    15
  PTPN3 WILD-TYPE                                         1   342
D989V11, multiclass
                                           clus
vv                                          PTPN3 MUTATED PTPN3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V12, binary
                 cls
clus                0   1
  PTPN3 MUTATED     3  13
  PTPN3 WILD-TYPE   7 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED      3   13
  PTPN3 WILD-TYPE    7  385
                        clus
vv                       PTPN3 MUTATED PTPN3 WILD-TYPE
  HISPANIC OR LATINO                 3               7
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(990) Variable = CRYBB1 MUTATION ANALYSIS
D990V1, survival
                  sevent
clus2                0   1
  CRYBB1 MUTATED     9   2
  CRYBB1 WILD-TYPE 329 214
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
              11              543 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
               2              214 
$`CRYBB1 MUTATED`
TCGA-L5-A88V TCGA-LN-A4A1 TCGA-V5-AASX TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7704 
        2.60        12.59         8.98        30.90        44.94        35.24 
TCGA-BR-A4QL TCGA-D7-A6F2 TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-VQ-A8P2 
       16.14        15.65         6.58        23.80        38.14 

$`CRYBB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       15.48        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
             2.6              0.0 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
           44.94           122.30 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
           16.14            13.51 
[1] "2.6 - 44.9 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D990V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYBB1 MUTATED         0        0        2        1         2         1
  CRYBB1 WILD-TYPE      10       20       44       30        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYBB1 MUTATED           1          1          1          0        1
  CRYBB1 WILD-TYPE        28         83         61         39       42
                  vv
clus               STAGE IVA
  CRYBB1 MUTATED           0
  CRYBB1 WILD-TYPE         4
D990V3, multiclass
            clus
vv           CRYBB1 MUTATED CRYBB1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CRYBB1 MUTATED       1   3   6   2
  CRYBB1 WILD-TYPE    53 132 255 100
D990V4, multiclass
       clus
vv      CRYBB1 MUTATED CRYBB1 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 6              255
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CRYBB1 MUTATED     5   3   1   1
  CRYBB1 WILD-TYPE 190 170  88  84
D990V5, multiclass
    clus
vv   CRYBB1 MUTATED CRYBB1 WILD-TYPE
  N0              5              190
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V6, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED    11   0
  CRYBB1 WILD-TYPE 471  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED     11    0
  CRYBB1 WILD-TYPE  471   38
   clus
vv  CRYBB1 MUTATED CRYBB1 WILD-TYPE
  0             11              471
  1              0               38
[1] 2 2
[1] FALSE
D990V7, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     6   7
  CRYBB1 WILD-TYPE 166 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      6    7
  CRYBB1 WILD-TYPE  166  399
        clus
vv       CRYBB1 MUTATED CRYBB1 WILD-TYPE
  FEMALE              6              166
  MALE                7              399
[1] 2 2
[1] FALSE
D990V8, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     9   1
  CRYBB1 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      9    1
  CRYBB1 WILD-TYPE  407  101
     clus
vv    CRYBB1 MUTATED CRYBB1 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D990V9, continuous
[1] "Remove cluster labels:" "CRYBB1 MUTATED"        
clus
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A2 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
D990V10, continuous
[1] "Remove cluster labels:" "CRYBB1 MUTATED"        
clus
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A893       TCGA-L5-A8NE 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" "CRYBB1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CRYBB1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CRYBB1 MUTATED       3                         0
  CRYBB1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYBB1 MUTATED                                           0    10
  CRYBB1 WILD-TYPE                                         1   347
D990V11, multiclass
                                           clus
vv                                          CRYBB1 MUTATED CRYBB1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V12, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     0  11
  CRYBB1 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      0   11
  CRYBB1 WILD-TYPE   10  387
                        clus
vv                       CRYBB1 MUTATED CRYBB1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(991) Variable = DHX9 MUTATION ANALYSIS
D991V1, survival
                sevent
clus2              0   1
  DHX9 MUTATED    11   9
  DHX9 WILD-TYPE 327 207
  DHX9 MUTATED DHX9 WILD-TYPE 
            20            534 
  DHX9 MUTATED DHX9 WILD-TYPE 
             9            207 
$`DHX9 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GR TCGA-L5-A8NE TCGA-L5-A8NM TCGA-LN-A4A1 TCGA-R6-A8WG 
       21.99        32.45        55.50         7.76        12.59        12.69 
TCGA-V5-A7RE TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8372 
       16.44         2.66        19.56         6.18         0.26        31.27 
TCGA-BR-8589 TCGA-CG-5721 TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-FP-A4BF TCGA-HJ-7597 
       27.12         6.02        11.44        20.32         5.52        26.47 
TCGA-HU-A4G8 TCGA-MX-A5UJ 
       22.68        19.73 

$`DHX9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 
        2.66        19.96         2.20         7.40        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       13.78        14.76        26.43        11.24        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56        11.08         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DHX9 MUTATED DHX9 WILD-TYPE 
          0.26           0.00 
  DHX9 MUTATED DHX9 WILD-TYPE 
          55.5          122.3 
  DHX9 MUTATED DHX9 WILD-TYPE 
         18.00          13.53 
[1] "0.3 - 55.5 (18.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D991V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHX9 MUTATED         0        0        3        0         4         3
  DHX9 WILD-TYPE      10       20       43       31        80        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX9 MUTATED           0          3          2          2        2         0
  DHX9 WILD-TYPE        29         81         60         37       41         4
D991V3, multiclass
            clus
vv           DHX9 MUTATED DHX9 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DHX9 MUTATED       1   4   9   5
  DHX9 WILD-TYPE    53 131 252  97
D991V4, multiclass
       clus
vv      DHX9 MUTATED DHX9 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               9            252
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DHX9 MUTATED     7   6   3   3
  DHX9 WILD-TYPE 188 167  86  82
D991V5, multiclass
    clus
vv   DHX9 MUTATED DHX9 WILD-TYPE
  N0            7            188
  N1            6            167
  N2            3             86
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V6, binary
                cls
clus               0   1
  DHX9 MUTATED    17   1
  DHX9 WILD-TYPE 465  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED     17    1
  DHX9 WILD-TYPE  465   37
   clus
vv  DHX9 MUTATED DHX9 WILD-TYPE
  0           17            465
  1            1             37
[1] 2 2
[1] FALSE
D991V7, binary
                cls
clus               0   1
  DHX9 MUTATED     7  13
  DHX9 WILD-TYPE 165 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      7   13
  DHX9 WILD-TYPE  165  393
        clus
vv       DHX9 MUTATED DHX9 WILD-TYPE
  FEMALE            7            165
  MALE             13            393
[1] 2 2
[1] FALSE
D991V8, binary
                cls
clus               0   1
  DHX9 MUTATED    19   1
  DHX9 WILD-TYPE 397 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED     19    1
  DHX9 WILD-TYPE  397  101
     clus
vv    DHX9 MUTATED DHX9 WILD-TYPE
  NO            19            397
  YES            1            101
[1] 2 2
[1] FALSE
D991V9, continuous
[1] "Remove cluster labels:" "DHX9 MUTATED"          
clus
  DHX9 MUTATED DHX9 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A2 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-V5-AASW 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
D991V10, continuous
[1] "Remove cluster labels:" "DHX9 MUTATED"          
clus
  DHX9 MUTATED DHX9 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" "DHX9 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DHX9 MUTATED       2                         0
  DHX9 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DHX9 MUTATED                                           0    15
  DHX9 WILD-TYPE                                         1   342
D991V11, multiclass
                                           clus
vv                                          DHX9 MUTATED DHX9 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V12, binary
                cls
clus               0   1
  DHX9 MUTATED     1  14
  DHX9 WILD-TYPE   9 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      1   14
  DHX9 WILD-TYPE    9  384
                        clus
vv                       DHX9 MUTATED DHX9 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(992) Variable = RELB MUTATION ANALYSIS
D992V1, survival
                sevent
clus2              0   1
  RELB MUTATED    11   1
  RELB WILD-TYPE 327 215
  RELB MUTATED RELB WILD-TYPE 
            12            542 
  RELB MUTATED RELB WILD-TYPE 
             1            215 
$`RELB MUTATED`
TCGA-IC-A6RE TCGA-L5-A8NM TCGA-VR-AA4G TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-6452 
        7.69         7.76        18.05        26.70        19.56        34.68 
TCGA-BR-8372 TCGA-CD-8529 TCGA-D7-6524 TCGA-F1-A448 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       31.27        12.30        17.85        21.27        14.07        38.14 

$`RELB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        2.10         1.32         2.66        19.73        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  RELB MUTATED RELB WILD-TYPE 
          7.69           0.00 
  RELB MUTATED RELB WILD-TYPE 
         38.14         122.30 
  RELB MUTATED RELB WILD-TYPE 
        18.805         13.495 
[1] "7.7 - 38.1 (18.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "5.7"
D992V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RELB MUTATED         0        0        2        1         1         3
  RELB WILD-TYPE      10       20       44       30        83        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELB MUTATED           0          2          1          2        1         0
  RELB WILD-TYPE        29         82         61         37       42         4
D992V3, multiclass
            clus
vv           RELB MUTATED RELB WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RELB MUTATED       2   4   2   5
  RELB WILD-TYPE    52 131 259  97
D992V4, multiclass
       clus
vv      RELB MUTATED RELB WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3               2            259
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RELB MUTATED     4   5   1   3
  RELB WILD-TYPE 191 168  88  82
D992V5, multiclass
    clus
vv   RELB MUTATED RELB WILD-TYPE
  N0            4            191
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V6, binary
                cls
clus               0   1
  RELB MUTATED    13   1
  RELB WILD-TYPE 469  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELB MUTATED     13    1
  RELB WILD-TYPE  469   37
   clus
vv  RELB MUTATED RELB WILD-TYPE
  0           13            469
  1            1             37
[1] 2 2
[1] FALSE
D992V7, binary
                cls
clus               0   1
  RELB MUTATED     5   9
  RELB WILD-TYPE 167 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELB MUTATED      5    9
  RELB WILD-TYPE  167  397
        clus
vv       RELB MUTATED RELB WILD-TYPE
  FEMALE            5            167
  MALE              9            397
[1] 2 2
[1] FALSE
D992V8, binary
                cls
clus               0   1
  RELB MUTATED     9   3
  RELB WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELB MUTATED      9    3
  RELB WILD-TYPE  407   99
     clus
vv    RELB MUTATED RELB WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D992V9, continuous
[1] "Remove cluster labels:" "RELB MUTATED"          
clus
  RELB MUTATED RELB WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA7B 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
D992V10, continuous
[1] "Remove cluster labels:" "RELB MUTATED"          
clus
  RELB MUTATED RELB WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IG-A3QL 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" "RELB WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RELB MUTATED       2                         0
  RELB WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RELB MUTATED                                           0    11
  RELB WILD-TYPE                                         1   346
D992V11, multiclass
                                           clus
vv                                          RELB MUTATED RELB WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V12, binary
                cls
clus               0   1
  RELB MUTATED     1   9
  RELB WILD-TYPE   9 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELB MUTATED      1    9
  RELB WILD-TYPE    9  389
                        clus
vv                       RELB MUTATED RELB WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(993) Variable = GPATCH8 MUTATION ANALYSIS
D993V1, survival
                   sevent
clus2                 0   1
  GPATCH8 MUTATED    15  14
  GPATCH8 WILD-TYPE 323 202
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               29               525 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               14               202 
$`GPATCH8 MUTATED`
TCGA-JY-A6FB TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-JY-A6FH TCGA-L5-A43H 
       60.39        58.55         5.92         4.21        47.38         0.30 
TCGA-V5-A7RB TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 
        5.29         6.97         6.61        34.68        44.94        14.43 
TCGA-BR-8081 TCGA-BR-8363 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       32.25         0.26         6.02       105.07        65.10        21.07 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-A4GP TCGA-HU-A4GQ 
       30.51        26.47         5.92        22.32         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-MX-A666 TCGA-VQ-A8PE 
       20.25        12.95        14.07        14.04        22.19 

$`GPATCH8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 
        4.08         9.34         9.67         6.18         9.57        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       37.25        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        37.22        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
              0.1               0.0 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
           105.07            122.30 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            14.43             13.51 
[1] "0.1 - 105.1 (14.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D993V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH8 MUTATED         3        0        4        1         4         3
  GPATCH8 WILD-TYPE       7       20       42       30        80        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH8 MUTATED           5          2          2          4        1
  GPATCH8 WILD-TYPE        24         82         60         35       42
                   vv
clus                STAGE IVA
  GPATCH8 MUTATED           0
  GPATCH8 WILD-TYPE         4
D993V3, multiclass
            clus
vv           GPATCH8 MUTATED GPATCH8 WILD-TYPE
  STAGE I                  3                 7
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 1                30
  STAGE IIA                4                80
  STAGE IIB                3                80
  STAGE III                5                24
  STAGE IIIA               2                82
  STAGE IIIB               2                60
  STAGE IIIC               4                35
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GPATCH8 MUTATED       6   9   9   8
  GPATCH8 WILD-TYPE    48 126 252  94
D993V4, multiclass
       clus
vv      GPATCH8 MUTATED GPATCH8 WILD-TYPE
  T0+T1               6                48
  T2                  9               126
  T3                  9               252
  T4                  8                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GPATCH8 MUTATED     9  13   3   4
  GPATCH8 WILD-TYPE 186 160  86  81
D993V5, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  N0               9               186
  N1              13               160
  N2               3                86
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D993V6, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    26   0
  GPATCH8 WILD-TYPE 456  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     26    0
  GPATCH8 WILD-TYPE  456   38
   clus
vv  GPATCH8 MUTATED GPATCH8 WILD-TYPE
  0              26               456
  1               0                38
[1] 2 2
[1] FALSE
D993V7, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    15  17
  GPATCH8 WILD-TYPE 157 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     15   17
  GPATCH8 WILD-TYPE  157  389
        clus
vv       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  FEMALE              15               157
  MALE                17               389
[1] 2 2
[1] FALSE
D993V8, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    28   1
  GPATCH8 WILD-TYPE 388 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     28    1
  GPATCH8 WILD-TYPE  388  101
     clus
vv    GPATCH8 MUTATED GPATCH8 WILD-TYPE
  NO               28               388
  YES               1               101
[1] 2 2
[1] FALSE
D993V9, continuous
[1] "Remove cluster labels:" "GPATCH8 MUTATED"       
clus
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" "GPATCH8 WILD-TYPE" 
D993V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPATCH8 MUTATED       7                         1
  GPATCH8 WILD-TYPE   126                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPATCH8 MUTATED                                           0    15
  GPATCH8 WILD-TYPE                                         1   342
D993V11, multiclass
                                           clus
vv                                          GPATCH8 MUTATED GPATCH8 WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D993V12, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     1  19
  GPATCH8 WILD-TYPE   9 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      1   19
  GPATCH8 WILD-TYPE    9  379
                        clus
vv                       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              19               379
[1] 2 2
[1] FALSE

Clustering(994) Variable = ZCCHC7 MUTATION ANALYSIS
D994V1, survival
                  sevent
clus2                0   1
  ZCCHC7 MUTATED     5   2
  ZCCHC7 WILD-TYPE 333 214
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
               7              547 
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
               2              214 
$`ZCCHC7 MUTATED`
TCGA-LN-A4A1 TCGA-BR-6566 TCGA-BR-8368 TCGA-BR-8680 TCGA-D7-A6EY TCGA-HJ-7597 
       12.59        32.78         4.31        31.96        11.44        26.47 
TCGA-VQ-A8P2 
       38.14 

$`ZCCHC7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
            4.31             0.00 
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
           38.14           122.30 
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
           26.47            13.55 
[1] "4.3 - 38.1 (26.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D994V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC7 MUTATED         0        0        2        0         2         0
  ZCCHC7 WILD-TYPE      10       20       44       31        82        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC7 MUTATED           0          1          1          0        1
  ZCCHC7 WILD-TYPE        29         83         61         39       42
                  vv
clus               STAGE IVA
  ZCCHC7 MUTATED           0
  ZCCHC7 WILD-TYPE         4
D994V3, multiclass
            clus
vv           ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZCCHC7 MUTATED       0   2   3   2
  ZCCHC7 WILD-TYPE    54 133 258 100
D994V4, multiclass
       clus
vv      ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZCCHC7 MUTATED     4   1   1   1
  ZCCHC7 WILD-TYPE 191 172  88  84
D994V5, multiclass
    clus
vv   ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  N0              4              191
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V6, binary
                  cls
clus                 0   1
  ZCCHC7 MUTATED     5   1
  ZCCHC7 WILD-TYPE 477  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC7 MUTATED      5    1
  ZCCHC7 WILD-TYPE  477   37
   clus
vv  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  0              5              477
  1              1               37
[1] 2 2
[1] FALSE
D994V7, binary
                  cls
clus                 0   1
  ZCCHC7 MUTATED     4   3
  ZCCHC7 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC7 MUTATED      4    3
  ZCCHC7 WILD-TYPE  168  403
        clus
vv       ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D994V8, binary
                  cls
clus                 0   1
  ZCCHC7 MUTATED     6   1
  ZCCHC7 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC7 MUTATED      6    1
  ZCCHC7 WILD-TYPE  410  101
     clus
vv    ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D994V9, continuous
[1] "Remove cluster labels:" "ZCCHC7 MUTATED"        
clus
  ZCCHC7 MUTATED ZCCHC7 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A2 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" "ZCCHC7 WILD-TYPE" 
D994V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC7 MUTATED       2                         0
  ZCCHC7 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC7 MUTATED                                           0     5
  ZCCHC7 WILD-TYPE                                         1   352
D994V11, multiclass
                                           clus
vv                                          ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V12, binary
                  cls
clus                 0   1
  ZCCHC7 MUTATED     0   6
  ZCCHC7 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC7 MUTATED      0    6
  ZCCHC7 WILD-TYPE   10  392
                        clus
vv                       ZCCHC7 MUTATED ZCCHC7 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(995) Variable = VWA3A MUTATION ANALYSIS
D995V1, survival
                 sevent
clus2               0   1
  VWA3A MUTATED    14   1
  VWA3A WILD-TYPE 324 215
  VWA3A MUTATED VWA3A WILD-TYPE 
             15             539 
  VWA3A MUTATED VWA3A WILD-TYPE 
              1             215 
$`VWA3A MUTATED`
TCGA-IG-A97H TCGA-L5-A4OU TCGA-LN-A49M TCGA-LN-A7HV TCGA-R6-A6Y0 TCGA-BR-6802 
       14.50        29.00        12.66        10.52        53.95        30.90 
TCGA-BR-8059 TCGA-BR-8676 TCGA-BR-8680 TCGA-CD-8536 TCGA-F1-6874 TCGA-FP-A4BE 
       14.43         7.53        31.96        12.43        14.47        11.08 
TCGA-HU-A4GU TCGA-VQ-A8P2 TCGA-VQ-A92D 
        6.58        38.14        66.81 

$`VWA3A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
       28.14         6.28        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A94T 
        1.87        15.65        20.81         1.71        42.64        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  VWA3A MUTATED VWA3A WILD-TYPE 
           6.58            0.00 
  VWA3A MUTATED VWA3A WILD-TYPE 
          66.81          122.30 
  VWA3A MUTATED VWA3A WILD-TYPE 
          14.47           13.51 
[1] "6.6 - 66.8 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "7.5"
D995V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VWA3A MUTATED         0        0        2        1         5         1
  VWA3A WILD-TYPE      10       20       44       30        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWA3A MUTATED           1          2          1          0        1         0
  VWA3A WILD-TYPE        28         82         61         39       42         4
D995V3, multiclass
            clus
vv           VWA3A MUTATED VWA3A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  VWA3A MUTATED       0   4   7   3
  VWA3A WILD-TYPE    54 131 254  99
D995V4, multiclass
       clus
vv      VWA3A MUTATED VWA3A WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  VWA3A MUTATED     7   3   2   1
  VWA3A WILD-TYPE 188 170  87  84
D995V5, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  N0             7             188
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V6, binary
                 cls
clus                0   1
  VWA3A MUTATED    13   1
  VWA3A WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED     13    1
  VWA3A WILD-TYPE  469   37
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D995V7, binary
                 cls
clus                0   1
  VWA3A MUTATED     0  15
  VWA3A WILD-TYPE 172 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      0   15
  VWA3A WILD-TYPE  172  391
        clus
vv       VWA3A MUTATED VWA3A WILD-TYPE
  FEMALE             0             172
  MALE              15             391
[1] 2 2
[1] FALSE
D995V8, binary
                 cls
clus                0   1
  VWA3A MUTATED    10   4
  VWA3A WILD-TYPE 406  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED     10    4
  VWA3A WILD-TYPE  406   98
     clus
vv    VWA3A MUTATED VWA3A WILD-TYPE
  NO             10             406
  YES             4              98
[1] 2 2
[1] FALSE
D995V9, continuous
[1] "Remove cluster labels:" "VWA3A MUTATED"         
clus
  VWA3A MUTATED VWA3A WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HW 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
D995V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  VWA3A MUTATED       6                         1
  VWA3A WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VWA3A MUTATED                                           0     8
  VWA3A WILD-TYPE                                         1   349
D995V11, multiclass
                                           clus
vv                                          VWA3A MUTATED VWA3A WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V12, binary
                 cls
clus                0   1
  VWA3A MUTATED     0  12
  VWA3A WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      0   12
  VWA3A WILD-TYPE   10  386
                        clus
vv                       VWA3A MUTATED VWA3A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(996) Variable = SET MUTATION ANALYSIS
D996V1, survival
               sevent
clus2             0   1
  SET MUTATED     5   5
  SET WILD-TYPE 333 211
  SET MUTATED SET WILD-TYPE 
           10           544 
  SET MUTATED SET WILD-TYPE 
            5           211 
$`SET MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-L5-A8NI TCGA-LN-A7HX TCGA-VR-A8EQ TCGA-BR-8382 
       21.99        16.24        13.48        12.23        22.82        25.05 
TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-A74A TCGA-HU-8602 
        1.02        65.10        19.96        22.32 

$`SET WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       20.32        22.29        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SET MUTATED SET WILD-TYPE 
         1.02          0.00 
  SET MUTATED SET WILD-TYPE 
         65.1         122.3 
  SET MUTATED SET WILD-TYPE 
       20.975        13.510 
[1] "1.0 - 65.1 (21.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D996V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SET MUTATED         0        0        1        0         1         1
  SET WILD-TYPE      10       20       45       31        83        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SET MUTATED           2          1          1          1        2         0
  SET WILD-TYPE        27         83         61         38       41         4
D996V3, multiclass
            clus
vv           SET MUTATED SET WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            1            83
  STAGE IIB            1            82
  STAGE III            2            27
  STAGE IIIA           1            83
  STAGE IIIB           1            61
  STAGE IIIC           1            38
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  SET MUTATED       0   2   4   4
  SET WILD-TYPE    54 133 257  98
D996V4, multiclass
       clus
vv      SET MUTATED SET WILD-TYPE
  T0+T1           0            54
  T2              2           133
  T3              4           257
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SET MUTATED     3   4   2   1
  SET WILD-TYPE 192 169  87  84
D996V5, multiclass
    clus
vv   SET MUTATED SET WILD-TYPE
  N0           3           192
  N1           4           169
  N2           2            87
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V6, binary
               cls
clus              0   1
  SET MUTATED     7   2
  SET WILD-TYPE 475  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      7    2
  SET WILD-TYPE  475   36
   clus
vv  SET MUTATED SET WILD-TYPE
  0           7           475
  1           2            36
[1] 2 2
[1] FALSE
D996V7, binary
               cls
clus              0   1
  SET MUTATED     5   5
  SET WILD-TYPE 167 401
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      5    5
  SET WILD-TYPE  167  401
        clus
vv       SET MUTATED SET WILD-TYPE
  FEMALE           5           167
  MALE             5           401
[1] 2 2
[1] FALSE
D996V8, binary
               cls
clus              0   1
  SET MUTATED     5   3
  SET WILD-TYPE 411  99
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      5    3
  SET WILD-TYPE  411   99
     clus
vv    SET MUTATED SET WILD-TYPE
  NO            5           411
  YES           3            99
[1] 2 2
[1] FALSE
D996V9, continuous
[1] "Remove cluster labels:" "SET MUTATED"           
clus
  SET MUTATED SET WILD-TYPE 
            2            66 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HY    TCGA-LN-A7HZ 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV    TCGA-V5-AASW 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8ET 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY    TCGA-VR-A8EZ 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B    TCGA-VR-AA7D 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8    TCGA-Z6-A8JD 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-Z6-A8JE 
"SET WILD-TYPE" 
D996V10, continuous
[1] "Remove cluster labels:" "SET MUTATED"           
clus
  SET MUTATED SET WILD-TYPE 
            1            97 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A4OI    TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-Q9-A6FU    TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-IG-A6QS    TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-JY-A6FG    TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A43H    TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A4OP    TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A4OX    TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A8NF    TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-L5-A8NS    TCGA-L5-A8NW    TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A4A6    TCGA-LN-A4A9    TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-LN-A7HW    TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-Q9-A6FW    TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-R6-A8W5    TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-V5-A7RC    TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7 
"SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" "SET WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-AAPN 
"SET WILD-TYPE" "SET WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  SET MUTATED       2                         0
  SET WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SET MUTATED                                           0     5
  SET WILD-TYPE                                         1   352
D996V11, multiclass
                                           clus
vv                                          SET MUTATED SET WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V12, binary
               cls
clus              0   1
  SET MUTATED     0   5
  SET WILD-TYPE  10 393
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      0    5
  SET WILD-TYPE   10  393
                        clus
vv                       SET MUTATED SET WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           5           393
[1] 2 2
[1] FALSE

Clustering(997) Variable = RAVER1 MUTATION ANALYSIS
D997V1, survival
                  sevent
clus2                0   1
  RAVER1 MUTATED     7   2
  RAVER1 WILD-TYPE 331 214
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               9              545 
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               2              214 
$`RAVER1 MUTATED`
TCGA-L5-A4OI TCGA-LN-A4A1 TCGA-R6-A6DN TCGA-BR-8487 TCGA-CD-A4MG TCGA-FP-A4BE 
       19.99        12.59         8.02         1.12         6.58        11.08 
TCGA-HU-A4GT TCGA-IP-7968 TCGA-SW-A7EA 
        6.51         2.53        19.04 

$`RAVER1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RAVER1 MUTATED RAVER1 WILD-TYPE 
            1.12             0.00 
  RAVER1 MUTATED RAVER1 WILD-TYPE 
           19.99           122.30 
  RAVER1 MUTATED RAVER1 WILD-TYPE 
            8.02            13.78 
[1] "1.1 - 20.0 (8.0)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D997V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAVER1 MUTATED         0        0        1        0         5         0
  RAVER1 WILD-TYPE      10       20       45       31        79        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAVER1 MUTATED           0          0          1          1        0
  RAVER1 WILD-TYPE        29         84         61         38       43
                  vv
clus               STAGE IVA
  RAVER1 MUTATED           0
  RAVER1 WILD-TYPE         4
D997V3, multiclass
            clus
vv           RAVER1 MUTATED RAVER1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               5               79
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RAVER1 MUTATED       0   1   7   0
  RAVER1 WILD-TYPE    54 134 254 102
D997V4, multiclass
       clus
vv      RAVER1 MUTATED RAVER1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 7              254
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RAVER1 MUTATED     6   0   1   1
  RAVER1 WILD-TYPE 189 173  88  84
D997V5, multiclass
    clus
vv   RAVER1 MUTATED RAVER1 WILD-TYPE
  N0              6              189
  N1              0              173
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V6, binary
                  cls
clus                 0   1
  RAVER1 MUTATED     6   0
  RAVER1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAVER1 MUTATED      6    0
  RAVER1 WILD-TYPE  476   38
   clus
vv  RAVER1 MUTATED RAVER1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D997V7, binary
                  cls
clus                 0   1
  RAVER1 MUTATED     3   6
  RAVER1 WILD-TYPE 169 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAVER1 MUTATED      3    6
  RAVER1 WILD-TYPE  169  400
        clus
vv       RAVER1 MUTATED RAVER1 WILD-TYPE
  FEMALE              3              169
  MALE                6              400
[1] 2 2
[1] FALSE
D997V8, binary
                  cls
clus                 0   1
  RAVER1 MUTATED     6   1
  RAVER1 WILD-TYPE 410 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAVER1 MUTATED      6    1
  RAVER1 WILD-TYPE  410  101
     clus
vv    RAVER1 MUTATED RAVER1 WILD-TYPE
  NO               6              410
  YES              1              101
[1] 2 2
[1] FALSE
D997V9, continuous
[1] "Remove cluster labels:" "RAVER1 MUTATED"        
clus
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A2 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
D997V10, continuous
[1] "Remove cluster labels:" "RAVER1 MUTATED"        
clus
  RAVER1 MUTATED RAVER1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6L4 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" "RAVER1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RAVER1 MUTATED       3                         1
  RAVER1 WILD-TYPE   130                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAVER1 MUTATED                                           0     5
  RAVER1 WILD-TYPE                                         1   352
D997V11, multiclass
                                           clus
vv                                          RAVER1 MUTATED RAVER1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V12, binary
                  cls
clus                 0   1
  RAVER1 MUTATED     0   8
  RAVER1 WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAVER1 MUTATED      0    8
  RAVER1 WILD-TYPE   10  390
                        clus
vv                       RAVER1 MUTATED RAVER1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(998) Variable = PTPRU MUTATION ANALYSIS
D998V1, survival
                 sevent
clus2               0   1
  PTPRU MUTATED    18  10
  PTPRU WILD-TYPE 320 206
  PTPRU MUTATED PTPRU WILD-TYPE 
             28             526 
  PTPRU MUTATED PTPRU WILD-TYPE 
             10             206 
$`PTPRU MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-IG-A97I TCGA-LN-A49M TCGA-LN-A4A4 TCGA-LN-A4A5 
        4.31        19.99        12.16        12.66        12.59        22.39 
TCGA-R6-A6L4 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8487 TCGA-BR-8680 
       16.31        34.68        29.59         2.20         1.12        31.96 
TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5726 
        1.48        16.14        20.02        15.95       105.07        28.96 
TCGA-CG-5728 TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 
       65.10        77.29        24.20         6.58        20.25        14.07 
TCGA-IN-8663 TCGA-R5-A7ZF TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        3.39         8.52        37.41        38.14 

$`PTPRU WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       12.62        12.46        12.59        12.49        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
       12.20        11.77        12.62         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
        0.99        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PTPRU MUTATED PTPRU WILD-TYPE 
           1.12            0.00 
  PTPRU MUTATED PTPRU WILD-TYPE 
         105.07          122.30 
  PTPRU MUTATED PTPRU WILD-TYPE 
         18.150          13.445 
[1] "1.1 - 105.1 (18.1)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D998V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPRU MUTATED         0        2        2        3         5         6
  PTPRU WILD-TYPE      10       18       44       28        79        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRU MUTATED           1          1          2          3        3         0
  PTPRU WILD-TYPE        28         83         60         36       40         4
D998V3, multiclass
            clus
vv           PTPRU MUTATED PTPRU WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              5              79
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPRU MUTATED       3   8  10   8
  PTPRU WILD-TYPE    51 127 251  94
D998V4, multiclass
       clus
vv      PTPRU MUTATED PTPRU WILD-TYPE
  T0+T1             3              51
  T2                8             127
  T3               10             251
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPRU MUTATED    12   9   4   3
  PTPRU WILD-TYPE 183 164  85  82
D998V5, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  N0            12             183
  N1             9             164
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V6, binary
                 cls
clus                0   1
  PTPRU MUTATED    23   3
  PTPRU WILD-TYPE 459  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     23    3
  PTPRU WILD-TYPE  459   35
   clus
vv  PTPRU MUTATED PTPRU WILD-TYPE
  0            23             459
  1             3              35
[1] 2 2
[1] FALSE
D998V7, binary
                 cls
clus                0   1
  PTPRU MUTATED    10  20
  PTPRU WILD-TYPE 162 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     10   20
  PTPRU WILD-TYPE  162  386
        clus
vv       PTPRU MUTATED PTPRU WILD-TYPE
  FEMALE            10             162
  MALE              20             386
[1] 2 2
[1] FALSE
D998V8, binary
                 cls
clus                0   1
  PTPRU MUTATED    20   5
  PTPRU WILD-TYPE 396  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     20    5
  PTPRU WILD-TYPE  396   97
     clus
vv    PTPRU MUTATED PTPRU WILD-TYPE
  NO             20             396
  YES             5              97
[1] 2 2
[1] FALSE
D998V9, continuous
D998V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPRU MUTATED       8                         1
  PTPRU WILD-TYPE   125                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPRU MUTATED                                           0    15
  PTPRU WILD-TYPE                                         1   342
D998V11, multiclass
                                           clus
vv                                          PTPRU MUTATED PTPRU WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V12, binary
                 cls
clus                0   1
  PTPRU MUTATED     0  20
  PTPRU WILD-TYPE  10 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED      0   20
  PTPRU WILD-TYPE   10  378
                        clus
vv                       PTPRU MUTATED PTPRU WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(999) Variable = SOS2 MUTATION ANALYSIS
D999V1, survival
                sevent
clus2              0   1
  SOS2 MUTATED    15   3
  SOS2 WILD-TYPE 323 213
  SOS2 MUTATED SOS2 WILD-TYPE 
            18            536 
  SOS2 MUTATED SOS2 WILD-TYPE 
             3            213 
$`SOS2 MUTATED`
TCGA-LN-A8I1 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-7707 TCGA-BR-8078 
       13.18         9.34        34.68         9.17        35.84        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4PE 
        9.60        32.25        31.27         1.12        28.14        20.42 
TCGA-CD-8536 TCGA-CG-4305 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4HD 
       12.43        15.95        14.47        22.32         0.76        33.40 

$`SOS2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 
       37.25        14.43        11.44         0.69         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        5.92        24.39        28.96        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SOS2 MUTATED SOS2 WILD-TYPE 
          0.76           0.00 
  SOS2 MUTATED SOS2 WILD-TYPE 
         35.84         122.30 
  SOS2 MUTATED SOS2 WILD-TYPE 
        18.185         13.510 
[1] "0.8 - 35.8 (18.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D999V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOS2 MUTATED         0        1        3        2         3         4
  SOS2 WILD-TYPE      10       19       43       29        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOS2 MUTATED           0          1          0          3        0         0
  SOS2 WILD-TYPE        29         83         62         36       43         4
D999V3, multiclass
            clus
vv           SOS2 MUTATED SOS2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              3             43
  STAGE II              2             29
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SOS2 MUTATED       2   5   4   7
  SOS2 WILD-TYPE    52 130 257  95
D999V4, multiclass
       clus
vv      SOS2 MUTATED SOS2 WILD-TYPE
  T0+T1            2             52
  T2               5            130
  T3               4            257
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SOS2 MUTATED    12   2   1   3
  SOS2 WILD-TYPE 183 171  88  82
D999V5, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  N0           12            183
  N1            2            171
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V6, binary
                cls
clus               0   1
  SOS2 MUTATED    19   0
  SOS2 WILD-TYPE 463  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     19    0
  SOS2 WILD-TYPE  463   38
   clus
vv  SOS2 MUTATED SOS2 WILD-TYPE
  0           19            463
  1            0             38
[1] 2 2
[1] FALSE
D999V7, binary
                cls
clus               0   1
  SOS2 MUTATED    10   9
  SOS2 WILD-TYPE 162 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     10    9
  SOS2 WILD-TYPE  162  397
        clus
vv       SOS2 MUTATED SOS2 WILD-TYPE
  FEMALE           10            162
  MALE              9            397
[1] 2 2
[1] FALSE
D999V8, binary
                cls
clus               0   1
  SOS2 MUTATED    17   1
  SOS2 WILD-TYPE 399 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     17    1
  SOS2 WILD-TYPE  399  101
     clus
vv    SOS2 MUTATED SOS2 WILD-TYPE
  NO            17            399
  YES            1            101
[1] 2 2
[1] FALSE
D999V9, continuous
D999V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SOS2 MUTATED       5                         0
  SOS2 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOS2 MUTATED                                           0    13
  SOS2 WILD-TYPE                                         1   344
D999V11, multiclass
                                           clus
vv                                          SOS2 MUTATED SOS2 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V12, binary
                cls
clus               0   1
  SOS2 MUTATED     0  18
  SOS2 WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      0   18
  SOS2 WILD-TYPE   10  380
                        clus
vv                       SOS2 MUTATED SOS2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(1000) Variable = HSF4 MUTATION ANALYSIS
D1000V1, survival
                sevent
clus2              0   1
  HSF4 MUTATED     6   4
  HSF4 WILD-TYPE 332 212
  HSF4 MUTATED HSF4 WILD-TYPE 
            10            544 
  HSF4 MUTATED HSF4 WILD-TYPE 
             4            212 
$`HSF4 MUTATED`
TCGA-LN-A4A1 TCGA-Q9-A6FW TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 
       12.59         7.82        44.94         0.26        31.27        25.05 
TCGA-CD-8536 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-HU-A4GT 
       12.43        21.07         0.10         6.51 

$`HSF4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HSF4 MUTATED HSF4 WILD-TYPE 
           0.1            0.0 
  HSF4 MUTATED HSF4 WILD-TYPE 
         44.94         122.30 
  HSF4 MUTATED HSF4 WILD-TYPE 
         12.51          13.63 
[1] "0.1 - 44.9 (12.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1000V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSF4 MUTATED         0        0        1        1         3         0
  HSF4 WILD-TYPE      10       20       45       30        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HSF4 MUTATED           0          1          1          3        0         0
  HSF4 WILD-TYPE        29         83         61         36       43         4
D1000V3, multiclass
            clus
vv           HSF4 MUTATED HSF4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HSF4 MUTATED       0   2   5   3
  HSF4 WILD-TYPE    54 133 256  99
D1000V4, multiclass
       clus
vv      HSF4 MUTATED HSF4 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               5            256
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HSF4 MUTATED     5   0   3   2
  HSF4 WILD-TYPE 190 173  86  83
D1000V5, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  N0            5            190
  N1            0            173
  N2            3             86
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V6, binary
                cls
clus               0   1
  HSF4 MUTATED    10   0
  HSF4 WILD-TYPE 472  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED     10    0
  HSF4 WILD-TYPE  472   38
   clus
vv  HSF4 MUTATED HSF4 WILD-TYPE
  0           10            472
  1            0             38
[1] 2 2
[1] FALSE
D1000V7, binary
                cls
clus               0   1
  HSF4 MUTATED     5   5
  HSF4 WILD-TYPE 167 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      5    5
  HSF4 WILD-TYPE  167  401
        clus
vv       HSF4 MUTATED HSF4 WILD-TYPE
  FEMALE            5            167
  MALE              5            401
[1] 2 2
[1] FALSE
D1000V8, binary
                cls
clus               0   1
  HSF4 MUTATED    10   0
  HSF4 WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED     10    0
  HSF4 WILD-TYPE  406  102
     clus
vv    HSF4 MUTATED HSF4 WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D1000V9, continuous
[1] "Remove cluster labels:" "HSF4 MUTATED"          
clus
  HSF4 MUTATED HSF4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A2 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
D1000V10, continuous
[1] "Remove cluster labels:" "HSF4 MUTATED"          
clus
  HSF4 MUTATED HSF4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-R6-A6DN 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" "HSF4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"HSF4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HSF4 MUTATED       4                         0
  HSF4 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSF4 MUTATED                                           0     5
  HSF4 WILD-TYPE                                         1   352
D1000V11, multiclass
                                           clus
vv                                          HSF4 MUTATED HSF4 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V12, binary
                cls
clus               0   1
  HSF4 MUTATED     0   9
  HSF4 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      0    9
  HSF4 WILD-TYPE   10  389
                        clus
vv                       HSF4 MUTATED HSF4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(1001) Variable = OR51F1 MUTATION ANALYSIS
D1001V1, survival
                  sevent
clus2                0   1
  OR51F1 MUTATED     7   4
  OR51F1 WILD-TYPE 331 212
  OR51F1 MUTATED OR51F1 WILD-TYPE 
              11              543 
  OR51F1 MUTATED OR51F1 WILD-TYPE 
               4              212 
$`OR51F1 MUTATED`
TCGA-JY-A938 TCGA-2H-A9GI TCGA-2H-A9GL TCGA-B7-5816 TCGA-BR-8680 TCGA-CD-8535 
       34.85        14.30         5.92        26.70        31.96        12.82 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-8608 TCGA-RD-A7BT TCGA-VQ-A8P2 
        6.58         6.02        21.07         8.61        38.14 

$`OR51F1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  OR51F1 MUTATED OR51F1 WILD-TYPE 
            5.92             0.00 
  OR51F1 MUTATED OR51F1 WILD-TYPE 
           38.14           122.30 
  OR51F1 MUTATED OR51F1 WILD-TYPE 
           14.30            13.55 
[1] "5.9 - 38.1 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1001V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR51F1 MUTATED         0        0        0        0         1         2
  OR51F1 WILD-TYPE      10       20       46       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51F1 MUTATED           2          2          1          0        3
  OR51F1 WILD-TYPE        27         82         61         39       40
                  vv
clus               STAGE IVA
  OR51F1 MUTATED           0
  OR51F1 WILD-TYPE         4
D1001V3, multiclass
            clus
vv           OR51F1 MUTATED OR51F1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OR51F1 MUTATED       1   0   6   5
  OR51F1 WILD-TYPE    53 135 255  97
D1001V4, multiclass
       clus
vv      OR51F1 MUTATED OR51F1 WILD-TYPE
  T0+T1              1               53
  T2                 0              135
  T3                 6              255
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR51F1 MUTATED     3   5   2   1
  OR51F1 WILD-TYPE 192 168  87  84
D1001V5, multiclass
    clus
vv   OR51F1 MUTATED OR51F1 WILD-TYPE
  N0              3              192
  N1              5              168
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V6, binary
                  cls
clus                 0   1
  OR51F1 MUTATED    11   1
  OR51F1 WILD-TYPE 471  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51F1 MUTATED     11    1
  OR51F1 WILD-TYPE  471   37
   clus
vv  OR51F1 MUTATED OR51F1 WILD-TYPE
  0             11              471
  1              1               37
[1] 2 2
[1] FALSE
D1001V7, binary
                  cls
clus                 0   1
  OR51F1 MUTATED     2  10
  OR51F1 WILD-TYPE 170 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51F1 MUTATED      2   10
  OR51F1 WILD-TYPE  170  396
        clus
vv       OR51F1 MUTATED OR51F1 WILD-TYPE
  FEMALE              2              170
  MALE               10              396
[1] 2 2
[1] FALSE
D1001V8, binary
                  cls
clus                 0   1
  OR51F1 MUTATED     9   2
  OR51F1 WILD-TYPE 407 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51F1 MUTATED      9    2
  OR51F1 WILD-TYPE  407  100
     clus
vv    OR51F1 MUTATED OR51F1 WILD-TYPE
  NO               9              407
  YES              2              100
[1] 2 2
[1] FALSE
D1001V9, continuous
D1001V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OR51F1 MUTATED       4                         0
  OR51F1 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR51F1 MUTATED                                           1     4
  OR51F1 WILD-TYPE                                         0   353
D1001V11, multiclass
                                           clus
vv                                          OR51F1 MUTATED OR51F1 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V12, binary
                  cls
clus                 0   1
  OR51F1 MUTATED     0   7
  OR51F1 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51F1 MUTATED      0    7
  OR51F1 WILD-TYPE   10  391
                        clus
vv                       OR51F1 MUTATED OR51F1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(1002) Variable = DNAH10 MUTATION ANALYSIS
D1002V1, survival
                  sevent
clus2                0   1
  DNAH10 MUTATED    32  22
  DNAH10 WILD-TYPE 306 194
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              54              500 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
              22              194 
$`DNAH10 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NT TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4P3 
        4.31        19.99        27.12         7.69         2.63        18.64 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-L5-A43E 
        0.79         9.96       122.10        44.75        47.38        30.25 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NM TCGA-L5-A8NS 
       26.33        21.01         2.60        55.50         7.76        13.41 
TCGA-LN-A8I0 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4280 
       13.38        26.70         6.97        30.90         9.34         6.61 
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8382 
       34.68        19.33        32.78        44.94         0.26        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CD-8536 
        1.12        27.12        28.14        31.96         1.48        12.43 
TCGA-CD-A4MI TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YY 
       11.77         8.05         9.01         6.02        21.07        13.78 
TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       14.47        26.47        22.68         6.51         6.58        20.25 
TCGA-IN-A6RL TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-VQ-A8DV TCGA-VQ-A8P2 
       13.35        74.53        16.67       115.69        13.25        38.14 

$`DNAH10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82         0.36        35.97         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.12         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
       12.82        14.86         4.67        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM 
       24.03         6.28         3.16         0.30        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
        4.90        29.00         7.13         7.43        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        4.64         7.43        18.35         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        15.95        13.87        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
       25.18         9.21        20.22        12.79         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79         5.46        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DNAH10 MUTATED DNAH10 WILD-TYPE 
            0.26             0.00 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
           122.1            122.3 
  DNAH10 MUTATED DNAH10 WILD-TYPE 
          17.655           13.495 
[1] "0.3 - 122.1 (17.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1002V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH10 MUTATED         4        1        6        2         6        16
  DNAH10 WILD-TYPE       6       19       40       29        78        67
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH10 MUTATED           2          8          3          6        5
  DNAH10 WILD-TYPE        27         76         59         33       38
                  vv
clus               STAGE IVA
  DNAH10 MUTATED           0
  DNAH10 WILD-TYPE         4
D1002V3, multiclass
            clus
vv           DNAH10 MUTATED DNAH10 WILD-TYPE
  STAGE I                 4                6
  STAGE IA                1               19
  STAGE IB                6               40
  STAGE II                2               29
  STAGE IIA               6               78
  STAGE IIB              16               67
  STAGE III               2               27
  STAGE IIIA              8               76
  STAGE IIIB              3               59
  STAGE IIIC              6               33
  STAGE IV                5               38
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DNAH10 MUTATED       7  18  21  15
  DNAH10 WILD-TYPE    47 117 240  87
D1002V4, multiclass
       clus
vv      DNAH10 MUTATED DNAH10 WILD-TYPE
  T0+T1              7               47
  T2                18              117
  T3                21              240
  T4                15               87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DNAH10 MUTATED    23  26   5   7
  DNAH10 WILD-TYPE 172 147  84  78
D1002V5, multiclass
    clus
vv   DNAH10 MUTATED DNAH10 WILD-TYPE
  N0             23              172
  N1             26              147
  N2              5               84
  N3              7               78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V6, binary
                  cls
clus                 0   1
  DNAH10 MUTATED    53   3
  DNAH10 WILD-TYPE 429  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     53    3
  DNAH10 WILD-TYPE  429   35
   clus
vv  DNAH10 MUTATED DNAH10 WILD-TYPE
  0             53              429
  1              3               35
[1] 2 2
[1] FALSE
D1002V7, binary
                  cls
clus                 0   1
  DNAH10 MUTATED    23  40
  DNAH10 WILD-TYPE 149 366
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     23   40
  DNAH10 WILD-TYPE  149  366
        clus
vv       DNAH10 MUTATED DNAH10 WILD-TYPE
  FEMALE             23              149
  MALE               40              366
[1] 2 2
[1] FALSE
D1002V8, binary
                  cls
clus                 0   1
  DNAH10 MUTATED    47   9
  DNAH10 WILD-TYPE 369  93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED     47    9
  DNAH10 WILD-TYPE  369   93
     clus
vv    DNAH10 MUTATED DNAH10 WILD-TYPE
  NO              47              369
  YES              9               93
[1] 2 2
[1] FALSE
D1002V9, continuous
[1] "Remove cluster labels:" "DNAH10 MUTATED"        
clus
  DNAH10 MUTATED DNAH10 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3       TCGA-IG-A7DP 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" "DNAH10 WILD-TYPE" 
D1002V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DNAH10 MUTATED      10                         1
  DNAH10 WILD-TYPE   123                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAH10 MUTATED                                           0    46
  DNAH10 WILD-TYPE                                         1   311
D1002V11, multiclass
                                           clus
vv                                          DNAH10 MUTATED DNAH10 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 46              311
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V12, binary
                  cls
clus                 0   1
  DNAH10 MUTATED     1  41
  DNAH10 WILD-TYPE   9 357
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH10 MUTATED      1   41
  DNAH10 WILD-TYPE    9  357
                        clus
vv                       DNAH10 MUTATED DNAH10 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             41              357
[1] 2 2
[1] FALSE

Clustering(1003) Variable = PTX4 MUTATION ANALYSIS
D1003V1, survival
                sevent
clus2              0   1
  PTX4 MUTATED     9   5
  PTX4 WILD-TYPE 329 211
  PTX4 MUTATED PTX4 WILD-TYPE 
            14            540 
  PTX4 MUTATED PTX4 WILD-TYPE 
             5            211 
$`PTX4 MUTATED`
TCGA-S8-A6BV TCGA-L5-A8NN TCGA-LN-A8HZ TCGA-VR-AA4G TCGA-BR-8372 TCGA-BR-8591 
       20.02         5.49        12.33        18.05        31.27        28.14 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-D7-A4YV TCGA-D7-A6EZ TCGA-FP-A4BE TCGA-HF-A5NB 
        6.58        11.77         5.92        20.32        11.08        30.51 
TCGA-HJ-7597 TCGA-HU-A4GN 
       26.47        29.98 

$`PTX4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        11.44        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PTX4 MUTATED PTX4 WILD-TYPE 
          5.49           0.00 
  PTX4 MUTATED PTX4 WILD-TYPE 
         31.27         122.30 
  PTX4 MUTATED PTX4 WILD-TYPE 
        19.035         13.530 
[1] "5.5 - 31.3 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1003V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTX4 MUTATED         0        0        1        0         4         2
  PTX4 WILD-TYPE      10       20       45       31        80        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTX4 MUTATED           1          4          0          3        0         0
  PTX4 WILD-TYPE        28         80         62         36       43         4
D1003V3, multiclass
            clus
vv           PTX4 MUTATED PTX4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             4             80
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            4             80
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PTX4 MUTATED       0   4   8   4
  PTX4 WILD-TYPE    54 131 253  98
D1003V4, multiclass
       clus
vv      PTX4 MUTATED PTX4 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               8            253
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PTX4 MUTATED     5   5   2   3
  PTX4 WILD-TYPE 190 168  87  82
D1003V5, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  N0            5            190
  N1            5            168
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V6, binary
                cls
clus               0   1
  PTX4 MUTATED    13   0
  PTX4 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED     13    0
  PTX4 WILD-TYPE  469   38
   clus
vv  PTX4 MUTATED PTX4 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D1003V7, binary
                cls
clus               0   1
  PTX4 MUTATED     5  11
  PTX4 WILD-TYPE 167 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      5   11
  PTX4 WILD-TYPE  167  395
        clus
vv       PTX4 MUTATED PTX4 WILD-TYPE
  FEMALE            5            167
  MALE             11            395
[1] 2 2
[1] FALSE
D1003V8, binary
                cls
clus               0   1
  PTX4 MUTATED    12   3
  PTX4 WILD-TYPE 404  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED     12    3
  PTX4 WILD-TYPE  404   99
     clus
vv    PTX4 MUTATED PTX4 WILD-TYPE
  NO            12            404
  YES            3             99
[1] 2 2
[1] FALSE
D1003V9, continuous
[1] "Remove cluster labels:" "PTX4 MUTATED"          
clus
  PTX4 MUTATED PTX4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA7B 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PTX4 WILD-TYPE" "PTX4 WILD-TYPE" "PTX4 WILD-TYPE" 
D1003V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PTX4 MUTATED       4                         1
  PTX4 WILD-TYPE   129                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTX4 MUTATED                                           0    10
  PTX4 WILD-TYPE                                         1   347
D1003V11, multiclass
                                           clus
vv                                          PTX4 MUTATED PTX4 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V12, binary
                cls
clus               0   1
  PTX4 MUTATED     0  13
  PTX4 WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      0   13
  PTX4 WILD-TYPE   10  385
                        clus
vv                       PTX4 MUTATED PTX4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(1004) Variable = AMELX MUTATION ANALYSIS
D1004V1, survival
                 sevent
clus2               0   1
  AMELX MUTATED     4   1
  AMELX WILD-TYPE 334 215
  AMELX MUTATED AMELX WILD-TYPE 
              5             549 
  AMELX MUTATED AMELX WILD-TYPE 
              1             215 
$`AMELX MUTATED`
TCGA-IC-A6RE TCGA-BR-6452 TCGA-D7-6528 TCGA-D7-A6EY TCGA-HF-A5NB 
        7.69        34.68        15.22        11.44        30.51 

$`AMELX WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMELX MUTATED AMELX WILD-TYPE 
           7.69            0.00 
  AMELX MUTATED AMELX WILD-TYPE 
          34.68          122.30 
  AMELX MUTATED AMELX WILD-TYPE 
          15.22           13.55 
[1] "7.7 - 34.7 (15.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D1004V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMELX MUTATED         0        1        1        0         1         1
  AMELX WILD-TYPE      10       19       45       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMELX MUTATED           0          0          1          1        0         0
  AMELX WILD-TYPE        29         84         61         38       43         4
D1004V3, multiclass
            clus
vv           AMELX MUTATED AMELX WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AMELX MUTATED       2   1   2   1
  AMELX WILD-TYPE    52 134 259 101
D1004V4, multiclass
       clus
vv      AMELX MUTATED AMELX WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AMELX MUTATED     3   1   0   2
  AMELX WILD-TYPE 192 172  89  83
D1004V5, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  N0             3             192
  N1             1             172
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V6, binary
                 cls
clus                0   1
  AMELX MUTATED     6   0
  AMELX WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      6    0
  AMELX WILD-TYPE  476   38
   clus
vv  AMELX MUTATED AMELX WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1004V7, binary
                 cls
clus                0   1
  AMELX MUTATED     4   2
  AMELX WILD-TYPE 168 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      4    2
  AMELX WILD-TYPE  168  404
        clus
vv       AMELX MUTATED AMELX WILD-TYPE
  FEMALE             4             168
  MALE               2             404
[1] 2 2
[1] FALSE
D1004V8, binary
                 cls
clus                0   1
  AMELX MUTATED     4   2
  AMELX WILD-TYPE 412 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      4    2
  AMELX WILD-TYPE  412  100
     clus
vv    AMELX MUTATED AMELX WILD-TYPE
  NO              4             412
  YES             2             100
[1] 2 2
[1] FALSE
D1004V9, continuous
D1004V10, continuous
[1] "Remove cluster labels:" "AMELX MUTATED"         
clus
  AMELX MUTATED AMELX WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" "AMELX WILD-TYPE" 
     TCGA-Z6-AAPN 
"AMELX WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AMELX MUTATED       1                         0
  AMELX WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMELX MUTATED                                           0     4
  AMELX WILD-TYPE                                         1   353
D1004V11, multiclass
                                           clus
vv                                          AMELX MUTATED AMELX WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V12, binary
                 cls
clus                0   1
  AMELX MUTATED     0   5
  AMELX WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      0    5
  AMELX WILD-TYPE   10  393
                        clus
vv                       AMELX MUTATED AMELX WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1005) Variable = CHD3 MUTATION ANALYSIS
D1005V1, survival
                sevent
clus2              0   1
  CHD3 MUTATED    23  12
  CHD3 WILD-TYPE 315 204
  CHD3 MUTATED CHD3 WILD-TYPE 
            35            519 
  CHD3 MUTATED CHD3 WILD-TYPE 
            12            204 
$`CHD3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A8NG TCGA-S8-A6BV TCGA-L5-A4OU TCGA-L5-A8NM 
        4.31        19.99        35.97        20.02        29.00         7.76 
TCGA-L5-A8NV TCGA-LN-A49X TCGA-LN-A5U7 TCGA-R6-A6L4 TCGA-BR-4257 TCGA-BR-6452 
       52.57        12.62        25.25        16.31         9.67        34.68 
TCGA-BR-7707 TCGA-BR-8289 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-5804 
       35.84         2.66        25.05         1.12        31.96        12.10 
TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6817 
       12.43        15.95        36.00       105.07        65.10        12.79 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G8 
        7.13         0.62        21.27        77.29        30.51        22.68 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-RD-A7BT TCGA-VQ-A8P2 
        0.10        20.25        14.07         8.61        38.14 

$`CHD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 
        4.70        22.82         0.36        27.12         5.16        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        6.02         0.99        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        4.34        19.96         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CHD3 MUTATED CHD3 WILD-TYPE 
           0.1            0.0 
  CHD3 MUTATED CHD3 WILD-TYPE 
        105.07         122.30 
  CHD3 MUTATED CHD3 WILD-TYPE 
         20.02          13.41 
[1] "0.1 - 105.1 (20.0)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.5"
D1005V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHD3 MUTATED         1        0        3        5         6         4
  CHD3 WILD-TYPE       9       20       43       26        78        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD3 MUTATED           1          3          2          5        4         0
  CHD3 WILD-TYPE        28         81         60         34       39         4
D1005V3, multiclass
            clus
vv           CHD3 MUTATED CHD3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              5             26
  STAGE IIA             6             78
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            5             34
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CHD3 MUTATED       3   9  15   9
  CHD3 WILD-TYPE    51 126 246  93
D1005V4, multiclass
       clus
vv      CHD3 MUTATED CHD3 WILD-TYPE
  T0+T1            3             51
  T2               9            126
  T3              15            246
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CHD3 MUTATED    11  12   3   9
  CHD3 WILD-TYPE 184 161  86  76
D1005V5, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  N0           11            184
  N1           12            161
  N2            3             86
  N3            9             76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V6, binary
                cls
clus               0   1
  CHD3 MUTATED    30   3
  CHD3 WILD-TYPE 452  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     30    3
  CHD3 WILD-TYPE  452   35
   clus
vv  CHD3 MUTATED CHD3 WILD-TYPE
  0           30            452
  1            3             35
[1] 2 2
[1] FALSE
D1005V7, binary
                cls
clus               0   1
  CHD3 MUTATED    14  24
  CHD3 WILD-TYPE 158 382
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     14   24
  CHD3 WILD-TYPE  158  382
        clus
vv       CHD3 MUTATED CHD3 WILD-TYPE
  FEMALE           14            158
  MALE             24            382
[1] 2 2
[1] FALSE
D1005V8, binary
                cls
clus               0   1
  CHD3 MUTATED    29   6
  CHD3 WILD-TYPE 387  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     29    6
  CHD3 WILD-TYPE  387   96
     clus
vv    CHD3 MUTATED CHD3 WILD-TYPE
  NO            29            387
  YES            6             96
[1] 2 2
[1] FALSE
D1005V9, continuous
[1] "Remove cluster labels:" "CHD3 MUTATED"          
clus
  CHD3 MUTATED CHD3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A7HV     TCGA-LN-A7HW 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CHD3 WILD-TYPE" "CHD3 WILD-TYPE" 
D1005V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CHD3 MUTATED       9                         1
  CHD3 WILD-TYPE   124                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHD3 MUTATED                                           1    21
  CHD3 WILD-TYPE                                         0   336
D1005V11, multiclass
                                           clus
vv                                          CHD3 MUTATED CHD3 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               21            336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V12, binary
                cls
clus               0   1
  CHD3 MUTATED     1  24
  CHD3 WILD-TYPE   9 374
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED      1   24
  CHD3 WILD-TYPE    9  374
                        clus
vv                       CHD3 MUTATED CHD3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           24            374
[1] 2 2
[1] FALSE

Clustering(1006) Variable = PCDH15 MUTATION ANALYSIS
D1006V1, survival
                  sevent
clus2                0   1
  PCDH15 MUTATED    43  33
  PCDH15 WILD-TYPE 295 183
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              76              478 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              33              183 
$`PCDH15 MUTATED`
TCGA-JY-A938 TCGA-L5-A4OI TCGA-CG-4460 TCGA-CG-5727 TCGA-2H-A9GL TCGA-2H-A9GN 
       34.85        19.99        21.99        79.07         5.92         8.94 
TCGA-IG-A4P3 TCGA-IG-A51D TCGA-JY-A6FG TCGA-JY-A93D TCGA-L5-A43E TCGA-L5-A4OH 
       18.64        17.03        41.52        31.56        30.25        32.61 
TCGA-L5-A4OQ TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A8 TCGA-Q9-A6FW 
        1.38        10.36        13.41        12.46        15.52         7.82 
TCGA-R6-A6XG TCGA-RE-A7BO TCGA-VR-A8EX TCGA-XP-A8T8 TCGA-ZR-A9CJ TCGA-B7-5818 
       38.40         7.00        28.11        14.37        19.73        11.70 
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6706 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8081 
        6.97         6.61        18.05        44.94        14.43        32.25 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8680 
        0.26        31.27        25.18         1.12         9.34        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4PE TCGA-BR-A4QL 
        9.86        20.88         8.22        13.87        20.42        16.14 
TCGA-CD-5813 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 
       12.39        12.30        12.59        12.30        11.61         7.99 
TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5720 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6818 
       18.97         1.02         0.99        17.85        17.19        12.36 
TCGA-D7-8572 TCGA-D7-A4Z0 TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-8604 TCGA-HU-A4G8 
       16.80        14.76        14.47        11.08        22.82        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A7NT 
       29.98         0.10        20.25        33.40        12.46        10.62 
TCGA-MX-A5UG TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DV 
        3.72        18.21        74.53        19.04        48.79        13.25 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A91U 
       37.22        22.19        17.85         1.71 

$`PCDH15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        47.05        22.98        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63        13.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.85        12.26        33.11         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        25.08        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32         2.66        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        25.61        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       24.79        32.58        10.68        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01         7.07        30.97         6.97        36.00 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       18.61        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        21.37         8.98         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       63.62        36.95        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PM 
        5.46        13.02        43.36        37.41        38.14         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PCDH15 MUTATED PCDH15 WILD-TYPE 
             0.1              0.0 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
           79.07           122.30 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
          15.830           13.395 
[1] "0.1 - 79.1 (15.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D1006V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCDH15 MUTATED         2        2        9        3         8        13
  PCDH15 WILD-TYPE       8       18       37       28        76        70
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH15 MUTATED           5         12          8          9        6
  PCDH15 WILD-TYPE        24         72         54         30       37
                  vv
clus               STAGE IVA
  PCDH15 MUTATED           1
  PCDH15 WILD-TYPE         3
D1006V3, multiclass
            clus
vv           PCDH15 MUTATED PCDH15 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                2               18
  STAGE IB                9               37
  STAGE II                3               28
  STAGE IIA               8               76
  STAGE IIB              13               70
  STAGE III               5               24
  STAGE IIIA             12               72
  STAGE IIIB              8               54
  STAGE IIIC              9               30
  STAGE IV                6               37
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PCDH15 MUTATED       9  19  33  18
  PCDH15 WILD-TYPE    45 116 228  84
D1006V4, multiclass
       clus
vv      PCDH15 MUTATED PCDH15 WILD-TYPE
  T0+T1              9               45
  T2                19              116
  T3                33              228
  T4                18               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PCDH15 MUTATED    27  27  14  11
  PCDH15 WILD-TYPE 168 146  75  74
D1006V5, multiclass
    clus
vv   PCDH15 MUTATED PCDH15 WILD-TYPE
  N0             27              168
  N1             27              146
  N2             14               75
  N3             11               74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V6, binary
                  cls
clus                 0   1
  PCDH15 MUTATED    69   6
  PCDH15 WILD-TYPE 413  32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     69    6
  PCDH15 WILD-TYPE  413   32
   clus
vv  PCDH15 MUTATED PCDH15 WILD-TYPE
  0             69              413
  1              6               32
[1] 2 2
[1] FALSE
D1006V7, binary
                  cls
clus                 0   1
  PCDH15 MUTATED    26  55
  PCDH15 WILD-TYPE 146 351
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     26   55
  PCDH15 WILD-TYPE  146  351
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  FEMALE             26              146
  MALE               55              351
[1] 2 2
[1] FALSE
D1006V8, binary
                  cls
clus                 0   1
  PCDH15 MUTATED    63  13
  PCDH15 WILD-TYPE 353  89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED     63   13
  PCDH15 WILD-TYPE  353   89
     clus
vv    PCDH15 MUTATED PCDH15 WILD-TYPE
  NO              63              353
  YES             13               89
[1] 2 2
[1] FALSE
D1006V9, continuous
D1006V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PCDH15 MUTATED      20                         2
  PCDH15 WILD-TYPE   113                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCDH15 MUTATED                                           0    49
  PCDH15 WILD-TYPE                                         1   308
D1006V11, multiclass
                                           clus
vv                                          PCDH15 MUTATED PCDH15 WILD-TYPE
  ASIAN                                                 20              113
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 49              308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V12, binary
                  cls
clus                 0   1
  PCDH15 MUTATED     2  57
  PCDH15 WILD-TYPE   8 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED      2   57
  PCDH15 WILD-TYPE    8  341
                        clus
vv                       PCDH15 MUTATED PCDH15 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             57              341
[1] 2 2
[1] FALSE

Clustering(1007) Variable = NKD2 MUTATION ANALYSIS
D1007V1, survival
                sevent
clus2              0   1
  NKD2 MUTATED     3   2
  NKD2 WILD-TYPE 335 214
  NKD2 MUTATED NKD2 WILD-TYPE 
             5            549 
  NKD2 MUTATED NKD2 WILD-TYPE 
             2            214 
$`NKD2 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FA TCGA-LN-A5U7 TCGA-V5-A7RB TCGA-MX-A5UJ 
       19.99        44.75        25.25         5.29        19.73 

$`NKD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  NKD2 MUTATED NKD2 WILD-TYPE 
          5.29           0.00 
  NKD2 MUTATED NKD2 WILD-TYPE 
         44.75         122.30 
  NKD2 MUTATED NKD2 WILD-TYPE 
         19.99          13.51 
[1] "5.3 - 44.8 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1007V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NKD2 MUTATED         0        0        0        0         1         1
  NKD2 WILD-TYPE      10       20       46       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NKD2 MUTATED           0          1          0          1        0         0
  NKD2 WILD-TYPE        29         83         62         38       43         4
D1007V3, multiclass
            clus
vv           NKD2 MUTATED NKD2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NKD2 MUTATED       1   2   2   0
  NKD2 WILD-TYPE    53 133 259 102
D1007V4, multiclass
       clus
vv      NKD2 MUTATED NKD2 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               2            259
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NKD2 MUTATED     1   3   1   1
  NKD2 WILD-TYPE 194 170  88  84
D1007V5, multiclass
    clus
vv   NKD2 MUTATED NKD2 WILD-TYPE
  N0            1            194
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V6, binary
                cls
clus               0   1
  NKD2 MUTATED     4   0
  NKD2 WILD-TYPE 478  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      4    0
  NKD2 WILD-TYPE  478   38
   clus
vv  NKD2 MUTATED NKD2 WILD-TYPE
  0            4            478
  1            0             38
[1] 2 2
[1] FALSE
D1007V7, binary
                cls
clus               0   1
  NKD2 MUTATED     2   4
  NKD2 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      2    4
  NKD2 WILD-TYPE  170  402
        clus
vv       NKD2 MUTATED NKD2 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D1007V8, binary
                cls
clus               0   1
  NKD2 MUTATED     5   0
  NKD2 WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      5    0
  NKD2 WILD-TYPE  411  102
     clus
vv    NKD2 MUTATED NKD2 WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D1007V9, continuous
[1] "Remove cluster labels:" "NKD2 MUTATED"          
clus
  NKD2 MUTATED NKD2 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A7HV 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"NKD2 WILD-TYPE" "NKD2 WILD-TYPE" 
D1007V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NKD2 MUTATED       2                         0
  NKD2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NKD2 MUTATED                                           0     3
  NKD2 WILD-TYPE                                         1   354
D1007V11, multiclass
                                           clus
vv                                          NKD2 MUTATED NKD2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V12, binary
                cls
clus               0   1
  NKD2 MUTATED     1   3
  NKD2 WILD-TYPE   9 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKD2 MUTATED      1    3
  NKD2 WILD-TYPE    9  395
                        clus
vv                       NKD2 MUTATED NKD2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(1008) Variable = BUB1B MUTATION ANALYSIS
D1008V1, survival
                 sevent
clus2               0   1
  BUB1B MUTATED    12   2
  BUB1B WILD-TYPE 326 214
  BUB1B MUTATED BUB1B WILD-TYPE 
             14             540 
  BUB1B MUTATED BUB1B WILD-TYPE 
              2             214 
$`BUB1B MUTATED`
TCGA-JY-A6FB TCGA-LN-A7HY TCGA-VR-A8EP TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 
       60.39        12.03        27.09         6.61        29.59         6.18 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-D7-5577 TCGA-HF-7132 
        4.31         1.12        27.12        31.96        25.71        77.29 
TCGA-HU-A4GN TCGA-KB-A6F5 
       29.98         5.56 

$`BUB1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  BUB1B MUTATED BUB1B WILD-TYPE 
           1.12            0.00 
  BUB1B MUTATED BUB1B WILD-TYPE 
          77.29          122.30 
  BUB1B MUTATED BUB1B WILD-TYPE 
          26.40           13.53 
[1] "1.1 - 77.3 (26.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.6"
D1008V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BUB1B MUTATED         1        0        1        1         3         2
  BUB1B WILD-TYPE       9       20       45       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BUB1B MUTATED           2          2          2          0        1         0
  BUB1B WILD-TYPE        27         82         60         39       42         4
D1008V3, multiclass
            clus
vv           BUB1B MUTATED BUB1B WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BUB1B MUTATED       1   5   5   4
  BUB1B WILD-TYPE    53 130 256  98
D1008V4, multiclass
       clus
vv      BUB1B MUTATED BUB1B WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BUB1B MUTATED     6   5   3   1
  BUB1B WILD-TYPE 189 168  86  84
D1008V5, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  N0             6             189
  N1             5             168
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V6, binary
                 cls
clus                0   1
  BUB1B MUTATED    14   1
  BUB1B WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED     14    1
  BUB1B WILD-TYPE  468   37
   clus
vv  BUB1B MUTATED BUB1B WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D1008V7, binary
                 cls
clus                0   1
  BUB1B MUTATED     5  10
  BUB1B WILD-TYPE 167 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      5   10
  BUB1B WILD-TYPE  167  396
        clus
vv       BUB1B MUTATED BUB1B WILD-TYPE
  FEMALE             5             167
  MALE              10             396
[1] 2 2
[1] FALSE
D1008V8, binary
                 cls
clus                0   1
  BUB1B MUTATED    14   1
  BUB1B WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED     14    1
  BUB1B WILD-TYPE  402  101
     clus
vv    BUB1B MUTATED BUB1B WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D1008V9, continuous
[1] "Remove cluster labels:" "BUB1B MUTATED"         
clus
  BUB1B MUTATED BUB1B WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EQ 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
D1008V10, continuous
[1] "Remove cluster labels:" "BUB1B MUTATED"         
clus
  BUB1B MUTATED BUB1B WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8ER 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" "BUB1B WILD-TYPE" 
     TCGA-Z6-AAPN 
"BUB1B WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BUB1B MUTATED       3                         0
  BUB1B WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BUB1B MUTATED                                           0    10
  BUB1B WILD-TYPE                                         1   347
D1008V11, multiclass
                                           clus
vv                                          BUB1B MUTATED BUB1B WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V12, binary
                 cls
clus                0   1
  BUB1B MUTATED     0  11
  BUB1B WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      0   11
  BUB1B WILD-TYPE   10  387
                        clus
vv                       BUB1B MUTATED BUB1B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1009) Variable = EXOSC10 MUTATION ANALYSIS
D1009V1, survival
                   sevent
clus2                 0   1
  EXOSC10 MUTATED     9   4
  EXOSC10 WILD-TYPE 329 212
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               13               541 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                4               212 
$`EXOSC10 MUTATED`
TCGA-L5-A4OI TCGA-L5-A88S TCGA-L5-A893 TCGA-BR-4201 TCGA-BR-8059 TCGA-BR-8078 
       19.99        15.48         3.02        30.90        14.43        29.59 
TCGA-CG-5721 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4H8 
        6.02        13.78        11.44        11.08        26.47        14.07 
TCGA-VQ-A8P2 
       38.14 

$`EXOSC10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
             3.02              0.00 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            38.14            122.30 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            14.43             13.51 
[1] "3.0 - 38.1 (14.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1009V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXOSC10 MUTATED         1        0        4        0         1         1
  EXOSC10 WILD-TYPE       9       20       42       31        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXOSC10 MUTATED           1          1          2          1        1
  EXOSC10 WILD-TYPE        28         83         60         38       42
                   vv
clus                STAGE IVA
  EXOSC10 MUTATED           0
  EXOSC10 WILD-TYPE         4
D1009V3, multiclass
            clus
vv           EXOSC10 MUTATED EXOSC10 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  EXOSC10 MUTATED       2   3   5   4
  EXOSC10 WILD-TYPE    52 132 256  98
D1009V4, multiclass
       clus
vv      EXOSC10 MUTATED EXOSC10 WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  5               256
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  EXOSC10 MUTATED     6   4   0   3
  EXOSC10 WILD-TYPE 189 169  89  82
D1009V5, multiclass
    clus
vv   EXOSC10 MUTATED EXOSC10 WILD-TYPE
  N0               6               189
  N1               4               169
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V6, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED    12   0
  EXOSC10 WILD-TYPE 470  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED     12    0
  EXOSC10 WILD-TYPE  470   38
   clus
vv  EXOSC10 MUTATED EXOSC10 WILD-TYPE
  0              12               470
  1               0                38
[1] 2 2
[1] FALSE
D1009V7, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED     7   8
  EXOSC10 WILD-TYPE 165 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      7    8
  EXOSC10 WILD-TYPE  165  398
        clus
vv       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  FEMALE               7               165
  MALE                 8               398
[1] 2 2
[1] FALSE
D1009V8, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED    11   3
  EXOSC10 WILD-TYPE 405  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED     11    3
  EXOSC10 WILD-TYPE  405   99
     clus
vv    EXOSC10 MUTATED EXOSC10 WILD-TYPE
  NO               11               405
  YES               3                99
[1] 2 2
[1] FALSE
D1009V9, continuous
D1009V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EXOSC10 MUTATED       1                         1
  EXOSC10 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXOSC10 MUTATED                                           0    12
  EXOSC10 WILD-TYPE                                         1   345
D1009V11, multiclass
                                           clus
vv                                          EXOSC10 MUTATED EXOSC10 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V12, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED     0  10
  EXOSC10 WILD-TYPE  10 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      0   10
  EXOSC10 WILD-TYPE   10  388
                        clus
vv                       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(1010) Variable = KCNN3 MUTATION ANALYSIS
D1010V1, survival
                 sevent
clus2               0   1
  KCNN3 MUTATED     8   7
  KCNN3 WILD-TYPE 330 209
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             15             539 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7             209 
$`KCNN3 MUTATED`
TCGA-S8-A6BV TCGA-L5-A8NM TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-VR-A8EP TCGA-BR-4184 
       20.02         7.76        16.31        38.40        27.09         6.97 
TCGA-BR-4280 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4306 
        6.61        36.16        35.84        31.96        11.77         1.02 
TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4GU 
       11.44        30.51         6.58 

$`KCNN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        7.82         8.02         7.59         5.06         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       31.20        44.94        21.90         9.21        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  KCNN3 MUTATED KCNN3 WILD-TYPE 
           1.02            0.00 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
           38.4           122.3 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
          16.31           13.55 
[1] "1.0 - 38.4 (16.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1010V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNN3 MUTATED         0        1        1        0         0         2
  KCNN3 WILD-TYPE      10       19       45       31        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNN3 MUTATED           1          3          2          1        2         0
  KCNN3 WILD-TYPE        28         81         60         38       41         4
D1010V3, multiclass
            clus
vv           KCNN3 MUTATED KCNN3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNN3 MUTATED       1   3   7   2
  KCNN3 WILD-TYPE    53 132 254 100
D1010V4, multiclass
       clus
vv      KCNN3 MUTATED KCNN3 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNN3 MUTATED     2   6   3   2
  KCNN3 WILD-TYPE 193 167  86  83
D1010V5, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  N0             2             193
  N1             6             167
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V6, binary
                 cls
clus                0   1
  KCNN3 MUTATED     9   2
  KCNN3 WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      9    2
  KCNN3 WILD-TYPE  473   36
   clus
vv  KCNN3 MUTATED KCNN3 WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D1010V7, binary
                 cls
clus                0   1
  KCNN3 MUTATED     5  10
  KCNN3 WILD-TYPE 167 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      5   10
  KCNN3 WILD-TYPE  167  396
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  FEMALE             5             167
  MALE              10             396
[1] 2 2
[1] FALSE
D1010V8, binary
                 cls
clus                0   1
  KCNN3 MUTATED    13   1
  KCNN3 WILD-TYPE 403 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED     13    1
  KCNN3 WILD-TYPE  403  101
     clus
vv    KCNN3 MUTATED KCNN3 WILD-TYPE
  NO             13             403
  YES             1             101
[1] 2 2
[1] FALSE
D1010V9, continuous
[1] "Remove cluster labels:" "KCNN3 MUTATED"         
clus
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
D1010V10, continuous
[1] "Remove cluster labels:" "KCNN3 MUTATED"         
clus
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8ER      TCGA-VR-A8EU 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" "KCNN3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNN3 MUTATED       3                         0
  KCNN3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNN3 MUTATED                                           0    10
  KCNN3 WILD-TYPE                                         1   347
D1010V11, multiclass
                                           clus
vv                                          KCNN3 MUTATED KCNN3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V12, binary
                 cls
clus                0   1
  KCNN3 MUTATED     0  11
  KCNN3 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      0   11
  KCNN3 WILD-TYPE   10  387
                        clus
vv                       KCNN3 MUTATED KCNN3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1011) Variable = TIE1 MUTATION ANALYSIS
D1011V1, survival
                sevent
clus2              0   1
  TIE1 MUTATED    15  11
  TIE1 WILD-TYPE 323 205
  TIE1 MUTATED TIE1 WILD-TYPE 
            26            528 
  TIE1 MUTATED TIE1 WILD-TYPE 
            11            205 
$`TIE1 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-JY-A93D TCGA-L5-A8NQ TCGA-BR-4280 TCGA-BR-6452 
       19.99        21.99        31.56        21.37         6.61        34.68 
TCGA-BR-8059 TCGA-BR-8285 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MI TCGA-CG-5721 
       14.43         0.56        31.96        12.30        11.77         6.02 
TCGA-D7-6822 TCGA-D7-A6EY TCGA-F1-6874 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HU-A4G8 
       12.33        11.44        14.47        19.53        30.51        22.68 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IN-8462 TCGA-IN-8663 
       29.98         6.51         6.58        20.25        18.81         3.39 
TCGA-VQ-A8DL TCGA-VQ-A8DV 
        0.92        13.25 

$`TIE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       11.77        21.37         8.98         0.10         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        33.40        36.36         3.45        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        19.04         5.79        48.79         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TIE1 MUTATED TIE1 WILD-TYPE 
          0.56           0.00 
  TIE1 MUTATED TIE1 WILD-TYPE 
         34.68         122.30 
  TIE1 MUTATED TIE1 WILD-TYPE 
         14.45          13.53 
[1] "0.6 - 34.7 (14.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1011V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIE1 MUTATED         0        0        3        0         5         6
  TIE1 WILD-TYPE      10       20       43       31        79        77
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIE1 MUTATED           2          1          1          5        5         0
  TIE1 WILD-TYPE        27         83         61         34       38         4
D1011V3, multiclass
            clus
vv           TIE1 MUTATED TIE1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             6             77
  STAGE III             2             27
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            5             34
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TIE1 MUTATED       0   9   9  10
  TIE1 WILD-TYPE    54 126 252  92
D1011V4, multiclass
       clus
vv      TIE1 MUTATED TIE1 WILD-TYPE
  T0+T1            0             54
  T2               9            126
  T3               9            252
  T4              10             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TIE1 MUTATED     9  10   4   5
  TIE1 WILD-TYPE 186 163  85  80
D1011V5, multiclass
    clus
vv   TIE1 MUTATED TIE1 WILD-TYPE
  N0            9            186
  N1           10            163
  N2            4             85
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V6, binary
                cls
clus               0   1
  TIE1 MUTATED    24   3
  TIE1 WILD-TYPE 458  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIE1 MUTATED     24    3
  TIE1 WILD-TYPE  458   35
   clus
vv  TIE1 MUTATED TIE1 WILD-TYPE
  0           24            458
  1            3             35
[1] 2 2
[1] FALSE
D1011V7, binary
                cls
clus               0   1
  TIE1 MUTATED    11  17
  TIE1 WILD-TYPE 161 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIE1 MUTATED     11   17
  TIE1 WILD-TYPE  161  389
        clus
vv       TIE1 MUTATED TIE1 WILD-TYPE
  FEMALE           11            161
  MALE             17            389
[1] 2 2
[1] FALSE
D1011V8, binary
                cls
clus               0   1
  TIE1 MUTATED    23   4
  TIE1 WILD-TYPE 393  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIE1 MUTATED     23    4
  TIE1 WILD-TYPE  393   98
     clus
vv    TIE1 MUTATED TIE1 WILD-TYPE
  NO            23            393
  YES            4             98
[1] 2 2
[1] FALSE
D1011V9, continuous
D1011V10, continuous
[1] "Remove cluster labels:" "TIE1 MUTATED"          
clus
  TIE1 MUTATED TIE1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NR 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" "TIE1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TIE1 MUTATED       8                         0
  TIE1 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIE1 MUTATED                                           0    17
  TIE1 WILD-TYPE                                         1   340
D1011V11, multiclass
                                           clus
vv                                          TIE1 MUTATED TIE1 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V12, binary
                cls
clus               0   1
  TIE1 MUTATED     0  20
  TIE1 WILD-TYPE  10 378
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIE1 MUTATED      0   20
  TIE1 WILD-TYPE   10  378
                        clus
vv                       TIE1 MUTATED TIE1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           20            378
[1] 2 2
[1] FALSE

Clustering(1012) Variable = MBOAT2 MUTATION ANALYSIS
D1012V1, survival
                  sevent
clus2                0   1
  MBOAT2 MUTATED     2   1
  MBOAT2 WILD-TYPE 336 215
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               3              551 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               1              215 
$`MBOAT2 MUTATED`
TCGA-R6-A8W8 TCGA-HF-7132 TCGA-HU-A4GT 
        2.89        77.29         6.51 

$`MBOAT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
            2.89             0.00 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
           77.29           122.30 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
            6.51            13.58 
[1] "2.9 - 77.3 (6.5)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1012V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBOAT2 MUTATED         0        0        0        1         1         0
  MBOAT2 WILD-TYPE      10       20       46       30        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBOAT2 MUTATED           0          0          0          0        0
  MBOAT2 WILD-TYPE        29         84         62         39       43
                  vv
clus               STAGE IVA
  MBOAT2 MUTATED           0
  MBOAT2 WILD-TYPE         4
D1012V3, multiclass
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              533 
      TCGA-IC-A6RF       TCGA-JY-A6FB       TCGA-JY-A938       TCGA-L5-A43I 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A43J       TCGA-L5-A4OE       TCGA-L5-A4OG       TCGA-L5-A4OI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A88T       TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-S8-A6BV       TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4476       TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-F1-6177       TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A663       TCGA-2H-A9GF       TCGA-2H-A9GG       TCGA-2H-A9GH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GI       TCGA-2H-A9GJ       TCGA-2H-A9GK       TCGA-2H-A9GL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GM       TCGA-2H-A9GN       TCGA-2H-A9GO       TCGA-2H-A9GQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GR       TCGA-IC-A6RE       TCGA-IG-A3I8       TCGA-IG-A3QL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YB       TCGA-IG-A3YC 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QS       TCGA-IG-A4QT       TCGA-IG-A50L 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A51D       TCGA-IG-A5B8       TCGA-IG-A5S3       TCGA-IG-A625 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A7DP       TCGA-IG-A8O2       TCGA-IG-A97H 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A97I       TCGA-JY-A6F8       TCGA-JY-A6FA       TCGA-JY-A6FD 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-JY-A939 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-JY-A93C       TCGA-JY-A93D       TCGA-JY-A93E       TCGA-JY-A93F 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OH       TCGA-L5-A4OJ       TCGA-L5-A4OM       TCGA-L5-A4ON 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OS       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A88W 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A88Z       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NH       TCGA-L5-A8NI       TCGA-L5-A8NJ       TCGA-L5-A8NK 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NL       TCGA-L5-A8NM       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NU       TCGA-L5-A8NV 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NW       TCGA-L7-A6VZ       TCGA-LN-A49K       TCGA-LN-A49L 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-LN-A8I1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A9FO       TCGA-LN-A9FP       TCGA-LN-A9FQ       TCGA-LN-A9FR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A8W5       TCGA-RE-A7BO 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-S8-A6BW       TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-VR-A8EO 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-Z6-A9VB       TCGA-Z6-AAPN       TCGA-ZR-A9CJ       TCGA-B7-5816 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-5818       TCGA-B7-A5TI       TCGA-B7-A5TJ       TCGA-B7-A5TK 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-A5TN       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4253 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4361       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5813       TCGA-CD-8524 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7133       TCGA-HF-7134 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597       TCGA-HU-8243 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A5UJ       TCGA-MX-A666       TCGA-R5-A7O7       TCGA-R5-A7ZE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR       TCGA-R5-A804 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT       TCGA-RD-A7BW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW       TCGA-RD-A8N0 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4       TCGA-RD-A8N5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA       TCGA-SW-A7EB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU       TCGA-VQ-A8DV 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U       TCGA-VQ-A91V 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64       TCGA-VQ-AA68 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B       TCGA-VQ-AA6F 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J       TCGA-VQ-AA6K 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-ZA-A8F6 
"MBOAT2 WILD-TYPE" 
                  vv
clus               T0+T1  T2  T3  T4
  MBOAT2 MUTATED       1   1   1   0
  MBOAT2 WILD-TYPE    53 134 260 102
D1012V4, multiclass
       clus
vv      MBOAT2 MUTATED MBOAT2 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 1              260
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MBOAT2 MUTATED     1   1   0   0
  MBOAT2 WILD-TYPE 194 172  89  85
D1012V5, multiclass
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              540 
      TCGA-IC-A6RF       TCGA-JY-A6FB       TCGA-JY-A938       TCGA-L5-A43I 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A43J       TCGA-L5-A43M       TCGA-L5-A4OE       TCGA-L5-A4OG 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-S8-A6BV       TCGA-CG-4444 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476       TCGA-CG-5716 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663       TCGA-2H-A9GF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GG       TCGA-2H-A9GH       TCGA-2H-A9GI       TCGA-2H-A9GJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GK       TCGA-2H-A9GL       TCGA-2H-A9GM       TCGA-2H-A9GN 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-2H-A9GO       TCGA-2H-A9GQ       TCGA-2H-A9GR       TCGA-IC-A6RE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A4P3       TCGA-IG-A4QS 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A51D       TCGA-IG-A5B8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A5S3       TCGA-IG-A625       TCGA-IG-A6QS       TCGA-IG-A8O2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A97I       TCGA-JY-A6F8       TCGA-JY-A6FA       TCGA-JY-A6FD 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-JY-A939 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-JY-A93C       TCGA-JY-A93D       TCGA-JY-A93E       TCGA-JY-A93F 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OH       TCGA-L5-A4OJ       TCGA-L5-A4OM       TCGA-L5-A4ON 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OS       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A88W 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A88Z       TCGA-L5-A891       TCGA-L5-A893       TCGA-L5-A8NE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NH       TCGA-L5-A8NI       TCGA-L5-A8NJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NL       TCGA-L5-A8NM       TCGA-L5-A8NN 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NV       TCGA-L5-A8NW       TCGA-L7-A6VZ       TCGA-LN-A49K 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49L       TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4A1       TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4A5       TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4MQ       TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A7HY       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A8I1       TCGA-LN-A9FO       TCGA-LN-A9FP       TCGA-LN-A9FQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A9FR       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A8W5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RE-A7BO       TCGA-S8-A6BW       TCGA-V5-A7RB       TCGA-V5-A7RE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE       TCGA-Z6-A9VB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-Z6-AAPN       TCGA-ZR-A9CJ       TCGA-B7-5816       TCGA-B7-5818 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-A5TI       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6ET       TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6EZ       TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A748       TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-EQ-8122       TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-F1-A72C       TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A9TM       TCGA-HF-7133       TCGA-HF-7134       TCGA-HF-7136 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-A5NB       TCGA-HJ-7597       TCGA-HU-8238       TCGA-HU-8243 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-7808       TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RJ       TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RP       TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A7NT       TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IP-7968       TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-R5-A7O7       TCGA-R5-A7ZE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A804       TCGA-R5-A805 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A7BS       TCGA-RD-A7BT       TCGA-RD-A7BW       TCGA-RD-A7C1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8MV       TCGA-RD-A8MW       TCGA-RD-A8N0       TCGA-RD-A8N1 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N2       TCGA-RD-A8N4       TCGA-RD-A8N5       TCGA-RD-A8N6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N9       TCGA-SW-A7EA       TCGA-SW-A7EB       TCGA-VQ-A8DL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8DT       TCGA-VQ-A8DU       TCGA-VQ-A8DV       TCGA-VQ-A8DZ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2       TCGA-VQ-A8P3 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM       TCGA-VQ-A8PQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A91Q       TCGA-VQ-A91U       TCGA-VQ-A91V       TCGA-VQ-A92D 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A94T       TCGA-VQ-AA64       TCGA-VQ-AA68       TCGA-VQ-AA69 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6A       TCGA-VQ-AA6B       TCGA-VQ-AA6F       TCGA-VQ-AA6G 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6I       TCGA-VQ-AA6J       TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
D1012V6, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     3   0
  MBOAT2 WILD-TYPE 479  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      3    0
  MBOAT2 WILD-TYPE  479   38
   clus
vv  MBOAT2 MUTATED MBOAT2 WILD-TYPE
  0              3              479
  1              0               38
[1] 2 2
[1] FALSE
D1012V7, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     2   2
  MBOAT2 WILD-TYPE 170 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      2    2
  MBOAT2 WILD-TYPE  170  404
        clus
vv       MBOAT2 MUTATED MBOAT2 WILD-TYPE
  FEMALE              2              170
  MALE                2              404
[1] 2 2
[1] FALSE
D1012V8, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     2   1
  MBOAT2 WILD-TYPE 414 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      2    1
  MBOAT2 WILD-TYPE  414  101
     clus
vv    MBOAT2 MUTATED MBOAT2 WILD-TYPE
  NO               2              414
  YES              1              101
[1] 2 2
[1] FALSE
D1012V9, continuous
D1012V10, continuous
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"MBOAT2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MBOAT2 MUTATED       1                         0
  MBOAT2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBOAT2 MUTATED                                           0     2
  MBOAT2 WILD-TYPE                                         1   355
D1012V11, multiclass
                                           clus
vv                                          MBOAT2 MUTATED MBOAT2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V12, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     0   3
  MBOAT2 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      0    3
  MBOAT2 WILD-TYPE   10  395
                        clus
vv                       MBOAT2 MUTATED MBOAT2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(1013) Variable = HORMAD1 MUTATION ANALYSIS
D1013V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED     6   3
  HORMAD1 WILD-TYPE 332 213
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                9               545 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                3               213 
$`HORMAD1 MUTATED`
TCGA-CG-4460 TCGA-IC-A6RE TCGA-IG-A97I TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-8361 
       21.99         7.69        12.16        11.70         6.97        31.10 
TCGA-CD-A4MJ TCGA-D7-A6EY TCGA-HF-7132 
       12.62        11.44        77.29 

$`HORMAD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             6.97              0.00 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            77.29            122.30 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            12.16             13.68 
[1] "7.0 - 77.3 (12.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.3"
D1013V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HORMAD1 MUTATED         0        0        2        1         1         1
  HORMAD1 WILD-TYPE      10       20       44       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HORMAD1 MUTATED           0          1          1          1        1
  HORMAD1 WILD-TYPE        29         83         61         38       42
                   vv
clus                STAGE IVA
  HORMAD1 MUTATED           0
  HORMAD1 WILD-TYPE         4
D1013V3, multiclass
            clus
vv           HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  HORMAD1 MUTATED       1   4   2   2
  HORMAD1 WILD-TYPE    53 131 259 100
D1013V4, multiclass
       clus
vv      HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  HORMAD1 MUTATED     3   4   1   1
  HORMAD1 WILD-TYPE 192 169  88  84
D1013V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               3               192
  N1               4               169
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V6, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     7   1
  HORMAD1 WILD-TYPE 475  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      7    1
  HORMAD1 WILD-TYPE  475   37
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0               7               475
  1               1                37
[1] 2 2
[1] FALSE
D1013V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     3   6
  HORMAD1 WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      3    6
  HORMAD1 WILD-TYPE  169  400
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D1013V8, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     7   2
  HORMAD1 WILD-TYPE 409 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      7    2
  HORMAD1 WILD-TYPE  409  100
     clus
vv    HORMAD1 MUTATED HORMAD1 WILD-TYPE
  NO                7               409
  YES               2               100
[1] 2 2
[1] FALSE
D1013V9, continuous
D1013V10, continuous
[1] "Remove cluster labels:" "HORMAD1 MUTATED"       
clus
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IG-A3QL 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" "HORMAD1 WILD-TYPE" 
       TCGA-Z6-AAPN 
"HORMAD1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HORMAD1 MUTATED       1                         0
  HORMAD1 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HORMAD1 MUTATED                                           0     6
  HORMAD1 WILD-TYPE                                         1   351
D1013V11, multiclass
                                           clus
vv                                          HORMAD1 MUTATED HORMAD1 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V12, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     0   7
  HORMAD1 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      0    7
  HORMAD1 WILD-TYPE   10  391
                        clus
vv                       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(1014) Variable = KIAA1549 MUTATION ANALYSIS
D1014V1, survival
                    sevent
clus2                  0   1
  KIAA1549 MUTATED    21   9
  KIAA1549 WILD-TYPE 317 207
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                30                524 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 9                207 
$`KIAA1549 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3QL TCGA-JY-A6FE TCGA-JY-A93F TCGA-L5-A8NM TCGA-L5-A8NU 
       19.99        35.21         3.68        24.03         7.76        83.24 
TCGA-LN-A7HX TCGA-R6-A6Y2 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8081 
       12.23         9.30         6.97        34.68        29.59        32.25 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-8531 
       31.27        25.05        28.14        31.96        20.42        12.59 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4GH TCGA-HU-A4GN 
        6.58         6.02        11.44        14.47        11.77        29.98 
TCGA-HU-A4GT TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-AB1V TCGA-VQ-A8P2 TCGA-VQ-A91Q 
        6.51        23.80        14.07        15.75        38.14        20.81 

$`KIAA1549 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35        53.95        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.39        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        25.81        21.37         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U 
       37.22        22.19        17.85         1.87        15.65         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
              3.68               0.00 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
             83.24             122.30 
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
            20.205             13.445 
[1] "3.7 - 83.2 (20.2)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.6"
D1014V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1549 MUTATED         0        2        5        0         7         4
  KIAA1549 WILD-TYPE      10       18       41       31        77        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1549 MUTATED           1          4          1          4        3
  KIAA1549 WILD-TYPE        28         80         61         35       40
                    vv
clus                 STAGE IVA
  KIAA1549 MUTATED           0
  KIAA1549 WILD-TYPE         4
D1014V3, multiclass
            clus
vv           KIAA1549 MUTATED KIAA1549 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  2                 18
  STAGE IB                  5                 41
  STAGE II                  0                 31
  STAGE IIA                 7                 77
  STAGE IIB                 4                 79
  STAGE III                 1                 28
  STAGE IIIA                4                 80
  STAGE IIIB                1                 61
  STAGE IIIC                4                 35
  STAGE IV                  3                 40
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA1549 MUTATED       4   9   9  10
  KIAA1549 WILD-TYPE    50 126 252  92
D1014V4, multiclass
       clus
vv      KIAA1549 MUTATED KIAA1549 WILD-TYPE
  T0+T1                4                 50
  T2                   9                126
  T3                   9                252
  T4                  10                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA1549 MUTATED    16   8   1   6
  KIAA1549 WILD-TYPE 179 165  88  79
D1014V5, multiclass
    clus
vv   KIAA1549 MUTATED KIAA1549 WILD-TYPE
  N0               16                179
  N1                8                165
  N2                1                 88
  N3                6                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V6, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED    29   1
  KIAA1549 WILD-TYPE 453  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED     29    1
  KIAA1549 WILD-TYPE  453   37
   clus
vv  KIAA1549 MUTATED KIAA1549 WILD-TYPE
  0               29                453
  1                1                 37
[1] 2 2
[1] FALSE
D1014V7, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED    12  21
  KIAA1549 WILD-TYPE 160 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED     12   21
  KIAA1549 WILD-TYPE  160  385
        clus
vv       KIAA1549 MUTATED KIAA1549 WILD-TYPE
  FEMALE               12                160
  MALE                 21                385
[1] 2 2
[1] FALSE
D1014V8, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED    26   4
  KIAA1549 WILD-TYPE 390  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED     26    4
  KIAA1549 WILD-TYPE  390   98
     clus
vv    KIAA1549 MUTATED KIAA1549 WILD-TYPE
  NO                26                390
  YES                4                 98
[1] 2 2
[1] FALSE
D1014V9, continuous
[1] "Remove cluster labels:" "KIAA1549 MUTATED"      
clus
  KIAA1549 MUTATED KIAA1549 WILD-TYPE 
                 2                 66 
        TCGA-IG-A3I8         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-IG-A3YB         TCGA-IG-A3YC         TCGA-IG-A51D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-IG-A5S3         TCGA-IG-A7DP         TCGA-KH-A6WC 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49K         TCGA-LN-A49L         TCGA-LN-A49M 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49N         TCGA-LN-A49O         TCGA-LN-A49P 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A49X 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A49Y         TCGA-LN-A4A1         TCGA-LN-A4A2 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A4         TCGA-LN-A4A5 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A8         TCGA-LN-A4A9 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A4MQ         TCGA-LN-A4MR         TCGA-LN-A5U5 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HY         TCGA-LN-A7HZ 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-A7RE 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-V5-AASW         TCGA-V5-AASX 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EO         TCGA-VR-A8EP         TCGA-VR-A8EQ 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8ET         TCGA-VR-A8EU 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EY 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7B         TCGA-VR-AA7D 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-XP-A8T6         TCGA-XP-A8T7 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
        TCGA-XP-A8T8         TCGA-Z6-A8JD         TCGA-Z6-A8JE 
"KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" "KIAA1549 WILD-TYPE" 
D1014V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1549 MUTATED       9                         0
  KIAA1549 WILD-TYPE   124                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1549 MUTATED                                           0    22
  KIAA1549 WILD-TYPE                                         1   335
D1014V11, multiclass
                                           clus
vv                                          KIAA1549 MUTATED KIAA1549 WILD-TYPE
  ASIAN                                                    9                124
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V12, binary
                    cls
clus                   0   1
  KIAA1549 MUTATED     1  24
  KIAA1549 WILD-TYPE   9 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1549 MUTATED      1   24
  KIAA1549 WILD-TYPE    9  374
                        clus
vv                       KIAA1549 MUTATED KIAA1549 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               24                374
[1] 2 2
[1] FALSE

Clustering(1015) Variable = COL4A3BP MUTATION ANALYSIS
D1015V1, survival
                    sevent
clus2                  0   1
  COL4A3BP MUTATED     3   3
  COL4A3BP WILD-TYPE 335 213
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
                 6                548 
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
                 3                213 
$`COL4A3BP MUTATED`
TCGA-L5-A8NF TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-CG-4300 TCGA-R5-A7ZR 
        2.66        32.25        31.27         1.12        20.02         6.08 

$`COL4A3BP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
              1.12               0.00 
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
             32.25             122.30 
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
            13.050             13.565 
[1] "1.1 - 32.2 (13.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1015V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL4A3BP MUTATED         0        0        0        0         1         1
  COL4A3BP WILD-TYPE      10       20       46       31        83        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL4A3BP MUTATED           1          0          1          1        0
  COL4A3BP WILD-TYPE        28         84         61         38       43
                    vv
clus                 STAGE IVA
  COL4A3BP MUTATED           1
  COL4A3BP WILD-TYPE         3
D1015V3, multiclass
            clus
vv           COL4A3BP MUTATED COL4A3BP WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 1                 82
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                1                 61
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  COL4A3BP MUTATED       1   0   3   2
  COL4A3BP WILD-TYPE    53 135 258 100
D1015V4, multiclass
       clus
vv      COL4A3BP MUTATED COL4A3BP WILD-TYPE
  T0+T1                1                 53
  T2                   0                135
  T3                   3                258
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  COL4A3BP MUTATED     3   0   1   1
  COL4A3BP WILD-TYPE 192 173  88  84
D1015V5, multiclass
    clus
vv   COL4A3BP MUTATED COL4A3BP WILD-TYPE
  N0                3                192
  N1                0                173
  N2                1                 88
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V6, binary
                    cls
clus                   0   1
  COL4A3BP MUTATED     5   1
  COL4A3BP WILD-TYPE 477  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  COL4A3BP MUTATED      5    1
  COL4A3BP WILD-TYPE  477   37
   clus
vv  COL4A3BP MUTATED COL4A3BP WILD-TYPE
  0                5                477
  1                1                 37
[1] 2 2
[1] FALSE
D1015V7, binary
                    cls
clus                   0   1
  COL4A3BP MUTATED     3   3
  COL4A3BP WILD-TYPE 169 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  COL4A3BP MUTATED      3    3
  COL4A3BP WILD-TYPE  169  403
        clus
vv       COL4A3BP MUTATED COL4A3BP WILD-TYPE
  FEMALE                3                169
  MALE                  3                403
[1] 2 2
[1] FALSE
D1015V8, binary
                    cls
clus                   0   1
  COL4A3BP MUTATED     5   0
  COL4A3BP WILD-TYPE 411 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  COL4A3BP MUTATED      5    0
  COL4A3BP WILD-TYPE  411  102
     clus
vv    COL4A3BP MUTATED COL4A3BP WILD-TYPE
  NO                 5                411
  YES                0                102
[1] 2 2
[1] FALSE
D1015V9, continuous
D1015V10, continuous
[1] "Remove cluster labels:" "COL4A3BP MUTATED"      
clus
  COL4A3BP MUTATED COL4A3BP WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" "COL4A3BP WILD-TYPE" 
        TCGA-Z6-AAPN 
"COL4A3BP WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  COL4A3BP MUTATED       0                         1
  COL4A3BP WILD-TYPE   133                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL4A3BP MUTATED                                           0     4
  COL4A3BP WILD-TYPE                                         1   353
D1015V11, multiclass
                                           clus
vv                                          COL4A3BP MUTATED COL4A3BP WILD-TYPE
  ASIAN                                                    0                133
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V12, binary
                    cls
clus                   0   1
  COL4A3BP MUTATED     0   4
  COL4A3BP WILD-TYPE  10 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  COL4A3BP MUTATED      0    4
  COL4A3BP WILD-TYPE   10  394
                        clus
vv                       COL4A3BP MUTATED COL4A3BP WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                4                394
[1] 2 2
[1] FALSE

Clustering(1016) Variable = HCRTR1 MUTATION ANALYSIS
D1016V1, survival
                  sevent
clus2                0   1
  HCRTR1 MUTATED     4   1
  HCRTR1 WILD-TYPE 334 215
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               5              549 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               1              215 
$`HCRTR1 MUTATED`
TCGA-BR-4201 TCGA-BR-8297 TCGA-CG-5723 TCGA-HU-A4GN TCGA-MX-A5UJ 
       30.90         7.40       105.07        29.98        19.73 

$`HCRTR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
             7.4              0.0 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
          105.07           122.30 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
           29.98            13.51 
[1] "7.4 - 105.1 (30.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "3.5"
D1016V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HCRTR1 MUTATED         0        0        0        1         1         0
  HCRTR1 WILD-TYPE      10       20       46       30        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR1 MUTATED           0          2          0          1        0
  HCRTR1 WILD-TYPE        29         82         62         38       43
                  vv
clus               STAGE IVA
  HCRTR1 MUTATED           0
  HCRTR1 WILD-TYPE         4
D1016V3, multiclass
            clus
vv           HCRTR1 MUTATED HCRTR1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HCRTR1 MUTATED       0   3   1   2
  HCRTR1 WILD-TYPE    54 132 260 100
D1016V4, multiclass
       clus
vv      HCRTR1 MUTATED HCRTR1 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 1              260
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HCRTR1 MUTATED     1   2   1   1
  HCRTR1 WILD-TYPE 194 171  88  84
D1016V5, multiclass
    clus
vv   HCRTR1 MUTATED HCRTR1 WILD-TYPE
  N0              1              194
  N1              2              171
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V6, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     6   0
  HCRTR1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      6    0
  HCRTR1 WILD-TYPE  476   38
   clus
vv  HCRTR1 MUTATED HCRTR1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D1016V7, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     3   3
  HCRTR1 WILD-TYPE 169 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      3    3
  HCRTR1 WILD-TYPE  169  403
        clus
vv       HCRTR1 MUTATED HCRTR1 WILD-TYPE
  FEMALE              3              169
  MALE                3              403
[1] 2 2
[1] FALSE
D1016V8, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     5   0
  HCRTR1 WILD-TYPE 411 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      5    0
  HCRTR1 WILD-TYPE  411  102
     clus
vv    HCRTR1 MUTATED HCRTR1 WILD-TYPE
  NO               5              411
  YES              0              102
[1] 2 2
[1] FALSE
D1016V9, continuous
D1016V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HCRTR1 MUTATED       1                         0
  HCRTR1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HCRTR1 MUTATED                                           0     4
  HCRTR1 WILD-TYPE                                         1   353
D1016V11, multiclass
                                           clus
vv                                          HCRTR1 MUTATED HCRTR1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V12, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     0   5
  HCRTR1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      0    5
  HCRTR1 WILD-TYPE   10  393
                        clus
vv                       HCRTR1 MUTATED HCRTR1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1017) Variable = DHRS9 MUTATION ANALYSIS
D1017V1, survival
                 sevent
clus2               0   1
  DHRS9 MUTATED     6   3
  DHRS9 WILD-TYPE 332 213
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              9             545 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              3             213 
$`DHRS9 MUTATED`
TCGA-CG-4444 TCGA-L5-A4OP TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8291 
       47.05         7.17        30.90         9.67        34.68        19.96 
TCGA-D7-6528 TCGA-HU-A4H0 TCGA-VQ-A8P2 
       15.22         2.10        38.14 

$`DHRS9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DHRS9 MUTATED DHRS9 WILD-TYPE 
            2.1             0.0 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
          47.05          122.30 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
          19.96           13.51 
[1] "2.1 - 47.0 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1017V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHRS9 MUTATED         0        1        1        0         1         1
  DHRS9 WILD-TYPE      10       19       45       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHRS9 MUTATED           0          3          0          1        0         0
  DHRS9 WILD-TYPE        29         81         62         38       43         4
D1017V3, multiclass
            clus
vv           DHRS9 MUTATED DHRS9 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DHRS9 MUTATED       1   3   2   3
  DHRS9 WILD-TYPE    53 132 259  99
D1017V4, multiclass
       clus
vv      DHRS9 MUTATED DHRS9 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DHRS9 MUTATED     4   2   1   1
  DHRS9 WILD-TYPE 191 171  88  84
D1017V5, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  N0             4             191
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V6, binary
                 cls
clus                0   1
  DHRS9 MUTATED     9   0
  DHRS9 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      9    0
  DHRS9 WILD-TYPE  473   38
   clus
vv  DHRS9 MUTATED DHRS9 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D1017V7, binary
                 cls
clus                0   1
  DHRS9 MUTATED     6   4
  DHRS9 WILD-TYPE 166 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      6    4
  DHRS9 WILD-TYPE  166  402
        clus
vv       DHRS9 MUTATED DHRS9 WILD-TYPE
  FEMALE             6             166
  MALE               4             402
[1] 2 2
[1] FALSE
D1017V8, binary
                 cls
clus                0   1
  DHRS9 MUTATED     6   2
  DHRS9 WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      6    2
  DHRS9 WILD-TYPE  410  100
     clus
vv    DHRS9 MUTATED DHRS9 WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D1017V9, continuous
D1017V10, continuous
[1] "Remove cluster labels:" "DHRS9 MUTATED"         
clus
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OQ 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" "DHRS9 WILD-TYPE" 
     TCGA-Z6-AAPN 
"DHRS9 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DHRS9 MUTATED       1                         0
  DHRS9 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DHRS9 MUTATED                                           0     8
  DHRS9 WILD-TYPE                                         1   349
D1017V11, multiclass
                                           clus
vv                                          DHRS9 MUTATED DHRS9 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V12, binary
                 cls
clus                0   1
  DHRS9 MUTATED     0   7
  DHRS9 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      0    7
  DHRS9 WILD-TYPE   10  391
                        clus
vv                       DHRS9 MUTATED DHRS9 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1018) Variable = MBD3 MUTATION ANALYSIS
D1018V1, survival
                sevent
clus2              0   1
  MBD3 MUTATED     9   3
  MBD3 WILD-TYPE 329 213
  MBD3 MUTATED MBD3 WILD-TYPE 
            12            542 
  MBD3 MUTATED MBD3 WILD-TYPE 
             3            213 
$`MBD3 MUTATED`
TCGA-JY-A6FH TCGA-R6-A6DN TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 
       47.38         8.02        34.68        36.16        35.84        29.59 
TCGA-BR-8081 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4G9 
       32.25         6.58         6.02         5.92        11.08        24.20 

$`MBD3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44         0.69         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MBD3 MUTATED MBD3 WILD-TYPE 
          5.92           0.00 
  MBD3 MUTATED MBD3 WILD-TYPE 
         47.38         122.30 
  MBD3 MUTATED MBD3 WILD-TYPE 
        26.895         13.530 
[1] "5.9 - 47.4 (26.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D1018V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD3 MUTATED         0        2        1        0         3         4
  MBD3 WILD-TYPE      10       18       45       31        81        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBD3 MUTATED           0          1          0          0        2         0
  MBD3 WILD-TYPE        29         83         62         39       41         4
D1018V3, multiclass
            clus
vv           MBD3 MUTATED MBD3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MBD3 MUTATED       2   2   4   5
  MBD3 WILD-TYPE    52 133 257  97
D1018V4, multiclass
       clus
vv      MBD3 MUTATED MBD3 WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               4            257
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MBD3 MUTATED     9   3   1   0
  MBD3 WILD-TYPE 186 170  88  85
D1018V5, multiclass
    clus
vv   MBD3 MUTATED MBD3 WILD-TYPE
  N0            9            186
  N1            3            170
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V6, binary
                cls
clus               0   1
  MBD3 MUTATED    13   0
  MBD3 WILD-TYPE 469  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED     13    0
  MBD3 WILD-TYPE  469   38
   clus
vv  MBD3 MUTATED MBD3 WILD-TYPE
  0           13            469
  1            0             38
[1] 2 2
[1] FALSE
D1018V7, binary
                cls
clus               0   1
  MBD3 MUTATED     8   6
  MBD3 WILD-TYPE 164 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      8    6
  MBD3 WILD-TYPE  164  400
        clus
vv       MBD3 MUTATED MBD3 WILD-TYPE
  FEMALE            8            164
  MALE              6            400
[1] 2 2
[1] FALSE
D1018V8, binary
                cls
clus               0   1
  MBD3 MUTATED    10   1
  MBD3 WILD-TYPE 406 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED     10    1
  MBD3 WILD-TYPE  406  101
     clus
vv    MBD3 MUTATED MBD3 WILD-TYPE
  NO            10            406
  YES            1            101
[1] 2 2
[1] FALSE
D1018V9, continuous
D1018V10, continuous
[1] "Remove cluster labels:" "MBD3 MUTATED"          
clus
  MBD3 MUTATED MBD3 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-KH-A6WC     TCGA-L5-A43C 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6L4 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MBD3 MUTATED       2                         1
  MBD3 WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBD3 MUTATED                                           0    10
  MBD3 WILD-TYPE                                         1   347
D1018V11, multiclass
                                           clus
vv                                          MBD3 MUTATED MBD3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V12, binary
                cls
clus               0   1
  MBD3 MUTATED     0  12
  MBD3 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      0   12
  MBD3 WILD-TYPE   10  386
                        clus
vv                       MBD3 MUTATED MBD3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1019) Variable = ERI1 MUTATION ANALYSIS
D1019V1, survival
                sevent
clus2              0   1
  ERI1 MUTATED     2   2
  ERI1 WILD-TYPE 336 214
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            550 
  ERI1 MUTATED ERI1 WILD-TYPE 
             2            214 
$`ERI1 MUTATED`
TCGA-BR-4257 TCGA-CG-4477 TCGA-VQ-A8DL TCGA-ZA-A8F6 
        9.67        30.97         0.92        17.26 

$`ERI1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97         7.07         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        27.55        12.43 

  ERI1 MUTATED ERI1 WILD-TYPE 
          0.92           0.00 
  ERI1 MUTATED ERI1 WILD-TYPE 
         30.97         122.30 
  ERI1 MUTATED ERI1 WILD-TYPE 
        13.465         13.565 
[1] "0.9 - 31.0 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1019V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERI1 MUTATED         0        0        2        0         1         0
  ERI1 WILD-TYPE      10       20       44       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERI1 MUTATED           0          0          0          0        0         0
  ERI1 WILD-TYPE        29         84         62         39       43         4
D1019V3, multiclass
            clus
vv           ERI1 MUTATED ERI1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ERI1 MUTATED       0   2   1   0
  ERI1 WILD-TYPE    54 133 260 102
D1019V4, multiclass
       clus
vv      ERI1 MUTATED ERI1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               1            260
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ERI1 MUTATED     3   0   0   0
  ERI1 WILD-TYPE 192 173  89  85
D1019V5, multiclass
    clus
vv   ERI1 MUTATED ERI1 WILD-TYPE
  N0            3            192
  N1            0            173
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V6, binary
                cls
clus               0   1
  ERI1 MUTATED     3   0
  ERI1 WILD-TYPE 479  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    0
  ERI1 WILD-TYPE  479   38
   clus
vv  ERI1 MUTATED ERI1 WILD-TYPE
  0            3            479
  1            0             38
[1] 2 2
[1] FALSE
D1019V7, binary
                cls
clus               0   1
  ERI1 MUTATED     3   1
  ERI1 WILD-TYPE 169 405
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    1
  ERI1 WILD-TYPE  169  405
        clus
vv       ERI1 MUTATED ERI1 WILD-TYPE
  FEMALE            3            169
  MALE              1            405
[1] 2 2
[1] FALSE
D1019V8, binary
                cls
clus               0   1
  ERI1 MUTATED     3   1
  ERI1 WILD-TYPE 413 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    1
  ERI1 WILD-TYPE  413  101
     clus
vv    ERI1 MUTATED ERI1 WILD-TYPE
  NO             3            413
  YES            1            101
[1] 2 2
[1] FALSE
D1019V9, continuous
D1019V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ERI1 MUTATED       0                         0
  ERI1 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERI1 MUTATED                                           0     3
  ERI1 WILD-TYPE                                         1   354
D1019V11, multiclass
                                           clus
vv                                          ERI1 MUTATED ERI1 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V12, binary
                cls
clus               0   1
  ERI1 MUTATED     0   2
  ERI1 WILD-TYPE  10 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      0    2
  ERI1 WILD-TYPE   10  396
                        clus
vv                       ERI1 MUTATED ERI1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            2            396
[1] 2 2
[1] FALSE

Clustering(1020) Variable = POU5F1B MUTATION ANALYSIS
D1020V1, survival
                   sevent
clus2                 0   1
  POU5F1B MUTATED     4   5
  POU5F1B WILD-TYPE 334 211
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                9               545 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                5               211 
$`POU5F1B MUTATED`
TCGA-L5-A8NI TCGA-BR-6452 TCGA-BR-7959 TCGA-BR-8382 TCGA-CD-A4MJ TCGA-CG-5725 
       13.48        34.68        33.21        25.05        12.62        15.02 
TCGA-HJ-7597 TCGA-HU-A4GT TCGA-VQ-A91Q 
       26.47         6.51        20.81 

$`POU5F1B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        15.65         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  POU5F1B MUTATED POU5F1B WILD-TYPE 
             6.51              0.00 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
            34.68            122.30 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
            20.81             13.51 
[1] "6.5 - 34.7 (20.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1020V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POU5F1B MUTATED         0        0        3        0         2         0
  POU5F1B WILD-TYPE      10       20       43       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POU5F1B MUTATED           1          1          0          1        1
  POU5F1B WILD-TYPE        28         83         62         38       42
                   vv
clus                STAGE IVA
  POU5F1B MUTATED           0
  POU5F1B WILD-TYPE         4
D1020V3, multiclass
            clus
vv           POU5F1B MUTATED POU5F1B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 3                43
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  POU5F1B MUTATED       0   3   4   2
  POU5F1B WILD-TYPE    54 132 257 100
D1020V4, multiclass
       clus
vv      POU5F1B MUTATED POU5F1B WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  POU5F1B MUTATED     5   2   0   2
  POU5F1B WILD-TYPE 190 171  89  83
D1020V5, multiclass
    clus
vv   POU5F1B MUTATED POU5F1B WILD-TYPE
  N0               5               190
  N1               2               171
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V6, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     8   0
  POU5F1B WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      8    0
  POU5F1B WILD-TYPE  474   38
   clus
vv  POU5F1B MUTATED POU5F1B WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D1020V7, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     4   5
  POU5F1B WILD-TYPE 168 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      4    5
  POU5F1B WILD-TYPE  168  401
        clus
vv       POU5F1B MUTATED POU5F1B WILD-TYPE
  FEMALE               4               168
  MALE                 5               401
[1] 2 2
[1] FALSE
D1020V8, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     8   1
  POU5F1B WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      8    1
  POU5F1B WILD-TYPE  408  101
     clus
vv    POU5F1B MUTATED POU5F1B WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D1020V9, continuous
D1020V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  POU5F1B MUTATED       2                         0
  POU5F1B WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POU5F1B MUTATED                                           0     5
  POU5F1B WILD-TYPE                                         1   352
D1020V11, multiclass
                                           clus
vv                                          POU5F1B MUTATED POU5F1B WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V12, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     0   6
  POU5F1B WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      0    6
  POU5F1B WILD-TYPE   10  392
                        clus
vv                       POU5F1B MUTATED POU5F1B WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1021) Variable = MYCN MUTATION ANALYSIS
D1021V1, survival
                sevent
clus2              0   1
  MYCN MUTATED     5   2
  MYCN WILD-TYPE 333 214
  MYCN MUTATED MYCN WILD-TYPE 
             7            547 
  MYCN MUTATED MYCN WILD-TYPE 
             2            214 
$`MYCN MUTATED`
TCGA-LN-A49W TCGA-BR-7703 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-5723 TCGA-HU-A4GT 
       13.25        36.16         0.26        16.14       105.07         6.51 
TCGA-VQ-A91V 
       42.64 

$`MYCN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        12.59        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  MYCN MUTATED MYCN WILD-TYPE 
          0.26           0.00 
  MYCN MUTATED MYCN WILD-TYPE 
        105.07         122.30 
  MYCN MUTATED MYCN WILD-TYPE 
         16.14          13.55 
[1] "0.3 - 105.1 (16.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D1021V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYCN MUTATED         1        1        1        1         1         0
  MYCN WILD-TYPE       9       19       45       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYCN MUTATED           1          1          1          0        0         0
  MYCN WILD-TYPE        28         83         61         39       43         4
D1021V3, multiclass
            clus
vv           MYCN MUTATED MYCN WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MYCN MUTATED       2   2   4   0
  MYCN WILD-TYPE    52 133 257 102
D1021V4, multiclass
       clus
vv      MYCN MUTATED MYCN WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               4            257
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MYCN MUTATED     3   3   1   1
  MYCN WILD-TYPE 192 170  88  84
D1021V5, multiclass
    clus
vv   MYCN MUTATED MYCN WILD-TYPE
  N0            3            192
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V6, binary
                cls
clus               0   1
  MYCN MUTATED     7   0
  MYCN WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      7    0
  MYCN WILD-TYPE  475   38
   clus
vv  MYCN MUTATED MYCN WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D1021V7, binary
                cls
clus               0   1
  MYCN MUTATED     3   5
  MYCN WILD-TYPE 169 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      3    5
  MYCN WILD-TYPE  169  401
        clus
vv       MYCN MUTATED MYCN WILD-TYPE
  FEMALE            3            169
  MALE              5            401
[1] 2 2
[1] FALSE
D1021V8, binary
                cls
clus               0   1
  MYCN MUTATED     6   2
  MYCN WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      6    2
  MYCN WILD-TYPE  410  100
     clus
vv    MYCN MUTATED MYCN WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D1021V9, continuous
[1] "Remove cluster labels:" "MYCN MUTATED"          
clus
  MYCN MUTATED MYCN WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
D1021V10, continuous
[1] "Remove cluster labels:" "MYCN MUTATED"          
clus
  MYCN MUTATED MYCN WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A4A3     TCGA-LN-A4A6 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" "MYCN WILD-TYPE" 
    TCGA-Z6-AAPN 
"MYCN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MYCN MUTATED       2                         1
  MYCN WILD-TYPE   131                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYCN MUTATED                                           0     3
  MYCN WILD-TYPE                                         1   354
D1021V11, multiclass
                                           clus
vv                                          MYCN MUTATED MYCN WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V12, binary
                cls
clus               0   1
  MYCN MUTATED     0   5
  MYCN WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      0    5
  MYCN WILD-TYPE   10  393
                        clus
vv                       MYCN MUTATED MYCN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1022) Variable = TCN2 MUTATION ANALYSIS
D1022V1, survival
                sevent
clus2              0   1
  TCN2 MUTATED     8   4
  TCN2 WILD-TYPE 330 212
  TCN2 MUTATED TCN2 WILD-TYPE 
            12            542 
  TCN2 MUTATED TCN2 WILD-TYPE 
             4            212 
$`TCN2 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-VR-AA7B TCGA-ZR-A9CJ TCGA-BR-7704 
        4.31         7.76        21.37        11.24        19.73        35.24 
TCGA-BR-A4IY TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4H8 
       12.89        21.27        11.08        77.29        22.68        14.07 

$`TCN2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TCN2 MUTATED TCN2 WILD-TYPE 
          4.31           0.00 
  TCN2 MUTATED TCN2 WILD-TYPE 
         77.29         122.30 
  TCN2 MUTATED TCN2 WILD-TYPE 
         16.90          13.53 
[1] "4.3 - 77.3 (16.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1022V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCN2 MUTATED         0        0        1        2         2         4
  TCN2 WILD-TYPE      10       20       45       29        82        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCN2 MUTATED           0          0          1          1        1         0
  TCN2 WILD-TYPE        29         84         61         38       42         4
D1022V3, multiclass
            clus
vv           TCN2 MUTATED TCN2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TCN2 MUTATED       1   3   7   1
  TCN2 WILD-TYPE    53 132 254 101
D1022V4, multiclass
       clus
vv      TCN2 MUTATED TCN2 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               7            254
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TCN2 MUTATED     5   4   0   3
  TCN2 WILD-TYPE 190 169  89  82
D1022V5, multiclass
    clus
vv   TCN2 MUTATED TCN2 WILD-TYPE
  N0            5            190
  N1            4            169
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V6, binary
                cls
clus               0   1
  TCN2 MUTATED     9   1
  TCN2 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCN2 MUTATED      9    1
  TCN2 WILD-TYPE  473   37
   clus
vv  TCN2 MUTATED TCN2 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D1022V7, binary
                cls
clus               0   1
  TCN2 MUTATED     4   8
  TCN2 WILD-TYPE 168 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCN2 MUTATED      4    8
  TCN2 WILD-TYPE  168  398
        clus
vv       TCN2 MUTATED TCN2 WILD-TYPE
  FEMALE            4            168
  MALE              8            398
[1] 2 2
[1] FALSE
D1022V8, binary
                cls
clus               0   1
  TCN2 MUTATED     8   3
  TCN2 WILD-TYPE 408  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCN2 MUTATED      8    3
  TCN2 WILD-TYPE  408   99
     clus
vv    TCN2 MUTATED TCN2 WILD-TYPE
  NO             8            408
  YES            3             99
[1] 2 2
[1] FALSE
D1022V9, continuous
[1] "Remove cluster labels:" "TCN2 MUTATED"          
clus
  TCN2 MUTATED TCN2 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
D1022V10, continuous
[1] "Remove cluster labels:" "TCN2 MUTATED"          
clus
  TCN2 MUTATED TCN2 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NR 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O     TCGA-LN-A49P 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6     TCGA-LN-A4A9 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" "TCN2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TCN2 MUTATED       3                         1
  TCN2 WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCN2 MUTATED                                           0     7
  TCN2 WILD-TYPE                                         1   350
D1022V11, multiclass
                                           clus
vv                                          TCN2 MUTATED TCN2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V12, binary
                cls
clus               0   1
  TCN2 MUTATED     1   6
  TCN2 WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCN2 MUTATED      1    6
  TCN2 WILD-TYPE    9  392
                        clus
vv                       TCN2 MUTATED TCN2 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1023) Variable = IFT74 MUTATION ANALYSIS
D1023V1, survival
                 sevent
clus2               0   1
  IFT74 MUTATED     6   6
  IFT74 WILD-TYPE 332 210
  IFT74 MUTATED IFT74 WILD-TYPE 
             12             542 
  IFT74 MUTATED IFT74 WILD-TYPE 
              6             210 
$`IFT74 MUTATED`
TCGA-2H-A9GF TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-VR-A8EQ TCGA-BR-4280 TCGA-BR-8591 
       25.78        53.95         2.89        22.82         6.61        28.14 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-8602 TCGA-RD-A7BW 
       31.96         6.58         6.02        30.51        22.32         5.13 

$`IFT74 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        7.04        38.40         6.35         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  IFT74 MUTATED IFT74 WILD-TYPE 
           2.89            0.00 
  IFT74 MUTATED IFT74 WILD-TYPE 
          53.95          122.30 
  IFT74 MUTATED IFT74 WILD-TYPE 
          22.57           13.53 
[1] "2.9 - 54.0 (22.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1023V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFT74 MUTATED         0        0        1        0         1         1
  IFT74 WILD-TYPE      10       20       45       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFT74 MUTATED           3          0          0          2        2         0
  IFT74 WILD-TYPE        26         84         62         37       41         4
D1023V3, multiclass
            clus
vv           IFT74 MUTATED IFT74 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              3              26
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IFT74 MUTATED       0   2   3   5
  IFT74 WILD-TYPE    54 133 258  97
D1023V4, multiclass
       clus
vv      IFT74 MUTATED IFT74 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                3             258
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IFT74 MUTATED     3   4   1   2
  IFT74 WILD-TYPE 192 169  88  83
D1023V5, multiclass
    clus
vv   IFT74 MUTATED IFT74 WILD-TYPE
  N0             3             192
  N1             4             169
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V6, binary
                 cls
clus                0   1
  IFT74 MUTATED     9   1
  IFT74 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT74 MUTATED      9    1
  IFT74 WILD-TYPE  473   37
   clus
vv  IFT74 MUTATED IFT74 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D1023V7, binary
                 cls
clus                0   1
  IFT74 MUTATED     4   8
  IFT74 WILD-TYPE 168 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT74 MUTATED      4    8
  IFT74 WILD-TYPE  168  398
        clus
vv       IFT74 MUTATED IFT74 WILD-TYPE
  FEMALE             4             168
  MALE               8             398
[1] 2 2
[1] FALSE
D1023V8, binary
                 cls
clus                0   1
  IFT74 MUTATED     9   3
  IFT74 WILD-TYPE 407  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT74 MUTATED      9    3
  IFT74 WILD-TYPE  407   99
     clus
vv    IFT74 MUTATED IFT74 WILD-TYPE
  NO              9             407
  YES             3              99
[1] 2 2
[1] FALSE
D1023V9, continuous
[1] "Remove cluster labels:" "IFT74 MUTATED"         
clus
  IFT74 MUTATED IFT74 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
D1023V10, continuous
[1] "Remove cluster labels:" "IFT74 MUTATED"         
clus
  IFT74 MUTATED IFT74 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" "IFT74 WILD-TYPE" 
     TCGA-Z6-AAPN 
"IFT74 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IFT74 MUTATED       3                         0
  IFT74 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFT74 MUTATED                                           0     6
  IFT74 WILD-TYPE                                         1   351
D1023V11, multiclass
                                           clus
vv                                          IFT74 MUTATED IFT74 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V12, binary
                 cls
clus                0   1
  IFT74 MUTATED     0   8
  IFT74 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT74 MUTATED      0    8
  IFT74 WILD-TYPE   10  390
                        clus
vv                       IFT74 MUTATED IFT74 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1024) Variable = EVI2B MUTATION ANALYSIS
D1024V1, survival
                 sevent
clus2               0   1
  EVI2B MUTATED     8   1
  EVI2B WILD-TYPE 330 215
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             545 
  EVI2B MUTATED EVI2B WILD-TYPE 
              1             215 
$`EVI2B MUTATED`
TCGA-BR-8081 TCGA-BR-A4CQ TCGA-CD-8529 TCGA-CG-4440 TCGA-D7-6817 TCGA-FP-8631 
       32.25        34.98        12.30         4.01        12.79         0.56 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-VQ-A8P2 
        6.58        14.07        38.14 

$`EVI2B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       14.43        11.44         0.69        29.59         9.60         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  EVI2B MUTATED EVI2B WILD-TYPE 
           0.56            0.00 
  EVI2B MUTATED EVI2B WILD-TYPE 
          38.14          122.30 
  EVI2B MUTATED EVI2B WILD-TYPE 
          12.79           13.58 
[1] "0.6 - 38.1 (12.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "3.3"
D1024V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EVI2B MUTATED         0        0        1        0         0         2
  EVI2B WILD-TYPE      10       20       45       31        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EVI2B MUTATED           0          4          0          0        2         0
  EVI2B WILD-TYPE        29         80         62         39       41         4
D1024V3, multiclass
            clus
vv           EVI2B MUTATED EVI2B WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EVI2B MUTATED       1   1   3   4
  EVI2B WILD-TYPE    53 134 258  98
D1024V4, multiclass
       clus
vv      EVI2B MUTATED EVI2B WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EVI2B MUTATED     2   4   1   2
  EVI2B WILD-TYPE 193 169  88  83
D1024V5, multiclass
    clus
vv   EVI2B MUTATED EVI2B WILD-TYPE
  N0             2             193
  N1             4             169
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V6, binary
                 cls
clus                0   1
  EVI2B MUTATED     6   2
  EVI2B WILD-TYPE 476  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      6    2
  EVI2B WILD-TYPE  476   36
   clus
vv  EVI2B MUTATED EVI2B WILD-TYPE
  0             6             476
  1             2              36
[1] 2 2
[1] FALSE
D1024V7, binary
                 cls
clus                0   1
  EVI2B MUTATED     2   7
  EVI2B WILD-TYPE 170 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      2    7
  EVI2B WILD-TYPE  170  399
        clus
vv       EVI2B MUTATED EVI2B WILD-TYPE
  FEMALE             2             170
  MALE               7             399
[1] 2 2
[1] FALSE
D1024V8, binary
                 cls
clus                0   1
  EVI2B MUTATED     4   3
  EVI2B WILD-TYPE 412  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      4    3
  EVI2B WILD-TYPE  412   99
     clus
vv    EVI2B MUTATED EVI2B WILD-TYPE
  NO              4             412
  YES             3              99
[1] 2 2
[1] FALSE
D1024V9, continuous
D1024V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EVI2B MUTATED       3                         0
  EVI2B WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EVI2B MUTATED                                           0     5
  EVI2B WILD-TYPE                                         1   352
D1024V11, multiclass
                                           clus
vv                                          EVI2B MUTATED EVI2B WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V12, binary
                 cls
clus                0   1
  EVI2B MUTATED     0   7
  EVI2B WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      0    7
  EVI2B WILD-TYPE   10  391
                        clus
vv                       EVI2B MUTATED EVI2B WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1025) Variable = PTPRJ MUTATION ANALYSIS
D1025V1, survival
                 sevent
clus2               0   1
  PTPRJ MUTATED    21   9
  PTPRJ WILD-TYPE 317 207
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             30             524 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
              9             207 
$`PTPRJ MUTATED`
TCGA-CG-5727 TCGA-2H-A9GG TCGA-IC-A6RE TCGA-L5-A88Z TCGA-L5-A8NN TCGA-R6-A6XG 
       79.07        20.05         7.69         7.40         5.49        38.40 
TCGA-R6-A6Y0 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 
       53.95        26.70        11.70         6.97        30.90         9.67 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 
       34.68        30.90        31.27         6.58         6.02       105.07 
TCGA-D7-8570 TCGA-D7-A6F2 TCGA-F1-A448 TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GN 
       24.72        15.65        21.27        77.29        24.20        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-IN-8462 TCGA-IN-A6RR TCGA-R5-A805 TCGA-VQ-A8PK 
        0.10         6.58        18.81         6.74         9.24        17.85 

$`PTPRJ WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31         7.04         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        11.77        21.37         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        22.19         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PTPRJ MUTATED PTPRJ WILD-TYPE 
            0.1             0.0 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
         105.07          122.30 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
         19.430          13.495 
[1] "0.1 - 105.1 (19.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1025V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPRJ MUTATED         1        1        2        3         4         5
  PTPRJ WILD-TYPE       9       19       44       28        80        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRJ MUTATED           2          4          4          2        1         0
  PTPRJ WILD-TYPE        27         80         58         37       42         4
D1025V3, multiclass
            clus
vv           PTPRJ MUTATED PTPRJ WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              4              80
  STAGE IIB              5              78
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             4              58
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPRJ MUTATED       4   8  13   6
  PTPRJ WILD-TYPE    50 127 248  96
D1025V4, multiclass
       clus
vv      PTPRJ MUTATED PTPRJ WILD-TYPE
  T0+T1             4              50
  T2                8             127
  T3               13             248
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPRJ MUTATED     9  13   3   4
  PTPRJ WILD-TYPE 186 160  86  81
D1025V5, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  N0             9             186
  N1            13             160
  N2             3              86
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V6, binary
                 cls
clus                0   1
  PTPRJ MUTATED    30   0
  PTPRJ WILD-TYPE 452  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     30    0
  PTPRJ WILD-TYPE  452   38
   clus
vv  PTPRJ MUTATED PTPRJ WILD-TYPE
  0            30             452
  1             0              38
[1] 2 2
[1] FALSE
D1025V7, binary
                 cls
clus                0   1
  PTPRJ MUTATED     8  26
  PTPRJ WILD-TYPE 164 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      8   26
  PTPRJ WILD-TYPE  164  380
        clus
vv       PTPRJ MUTATED PTPRJ WILD-TYPE
  FEMALE             8             164
  MALE              26             380
[1] 2 2
[1] FALSE
D1025V8, binary
                 cls
clus                0   1
  PTPRJ MUTATED    29   2
  PTPRJ WILD-TYPE 387 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     29    2
  PTPRJ WILD-TYPE  387  100
     clus
vv    PTPRJ MUTATED PTPRJ WILD-TYPE
  NO             29             387
  YES             2             100
[1] 2 2
[1] FALSE
D1025V9, continuous
D1025V10, continuous
[1] "Remove cluster labels:" "PTPRJ MUTATED"         
clus
  PTPRJ MUTATED PTPRJ WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IG-A3QL 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" "PTPRJ WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPRJ MUTATED       5                         1
  PTPRJ WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPRJ MUTATED                                           0    23
  PTPRJ WILD-TYPE                                         1   334
D1025V11, multiclass
                                           clus
vv                                          PTPRJ MUTATED PTPRJ WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V12, binary
                 cls
clus                0   1
  PTPRJ MUTATED     1  25
  PTPRJ WILD-TYPE   9 373
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      1   25
  PTPRJ WILD-TYPE    9  373
                        clus
vv                       PTPRJ MUTATED PTPRJ WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            25             373
[1] 2 2
[1] FALSE

Clustering(1026) Variable = GPR114 MUTATION ANALYSIS
D1026V1, survival
                  sevent
clus2                0   1
  GPR114 MUTATED     8   2
  GPR114 WILD-TYPE 330 214
  GPR114 MUTATED GPR114 WILD-TYPE 
              10              544 
  GPR114 MUTATED GPR114 WILD-TYPE 
               2              214 
$`GPR114 MUTATED`
TCGA-L5-A4OI TCGA-BR-6706 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8536 
       19.99        18.05         4.31        25.05        31.96        12.43 
TCGA-D7-8578 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GU 
       21.14        14.47        22.68         6.58 

$`GPR114 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GPR114 MUTATED GPR114 WILD-TYPE 
            4.31             0.00 
  GPR114 MUTATED GPR114 WILD-TYPE 
           31.96           122.30 
  GPR114 MUTATED GPR114 WILD-TYPE 
           19.02            13.51 
[1] "4.3 - 32.0 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D1026V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR114 MUTATED         0        0        3        1         0         2
  GPR114 WILD-TYPE      10       20       43       30        84        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR114 MUTATED           0          1          0          2        1
  GPR114 WILD-TYPE        29         83         62         37       42
                  vv
clus               STAGE IVA
  GPR114 MUTATED           0
  GPR114 WILD-TYPE         4
D1026V3, multiclass
            clus
vv           GPR114 MUTATED GPR114 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR114 MUTATED       0   3   5   2
  GPR114 WILD-TYPE    54 132 256 100
D1026V4, multiclass
       clus
vv      GPR114 MUTATED GPR114 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 5              256
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR114 MUTATED     4   3   1   2
  GPR114 WILD-TYPE 191 170  88  83
D1026V5, multiclass
    clus
vv   GPR114 MUTATED GPR114 WILD-TYPE
  N0              4              191
  N1              3              170
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V6, binary
                  cls
clus                 0   1
  GPR114 MUTATED     8   1
  GPR114 WILD-TYPE 474  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      8    1
  GPR114 WILD-TYPE  474   37
   clus
vv  GPR114 MUTATED GPR114 WILD-TYPE
  0              8              474
  1              1               37
[1] 2 2
[1] FALSE
D1026V7, binary
                  cls
clus                 0   1
  GPR114 MUTATED     3   7
  GPR114 WILD-TYPE 169 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      3    7
  GPR114 WILD-TYPE  169  399
        clus
vv       GPR114 MUTATED GPR114 WILD-TYPE
  FEMALE              3              169
  MALE                7              399
[1] 2 2
[1] FALSE
D1026V8, binary
                  cls
clus                 0   1
  GPR114 MUTATED    10   0
  GPR114 WILD-TYPE 406 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED     10    0
  GPR114 WILD-TYPE  406  102
     clus
vv    GPR114 MUTATED GPR114 WILD-TYPE
  NO              10              406
  YES              0              102
[1] 2 2
[1] FALSE
D1026V9, continuous
D1026V10, continuous
[1] "Remove cluster labels:" "GPR114 MUTATED"        
clus
  GPR114 MUTATED GPR114 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" "GPR114 WILD-TYPE" 
      TCGA-Z6-AAPN 
"GPR114 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR114 MUTATED       4                         0
  GPR114 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR114 MUTATED                                           0     6
  GPR114 WILD-TYPE                                         1   351
D1026V11, multiclass
                                           clus
vv                                          GPR114 MUTATED GPR114 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V12, binary
                  cls
clus                 0   1
  GPR114 MUTATED     0   9
  GPR114 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      0    9
  GPR114 WILD-TYPE   10  389
                        clus
vv                       GPR114 MUTATED GPR114 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1027) Variable = TUBGCP4 MUTATION ANALYSIS
D1027V1, survival
                   sevent
clus2                 0   1
  TUBGCP4 MUTATED     4   3
  TUBGCP4 WILD-TYPE 334 213
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
                7               547 
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
                3               213 
$`TUBGCP4 MUTATED`
TCGA-R6-A6XG TCGA-BR-4201 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-KB-A93J 
       38.40        30.90        31.27        16.14        11.77        36.95 
TCGA-VQ-A8P2 
       38.14 

$`TUBGCP4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
            11.77              0.00 
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
             38.4             122.3 
  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE 
            31.27             13.51 
[1] "11.8 - 38.4 (31.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D1027V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TUBGCP4 MUTATED         0        0        0        1         0         0
  TUBGCP4 WILD-TYPE      10       20       46       30        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBGCP4 MUTATED           0          3          1          1        0
  TUBGCP4 WILD-TYPE        29         81         61         38       43
                   vv
clus                STAGE IVA
  TUBGCP4 MUTATED           0
  TUBGCP4 WILD-TYPE         4
D1027V3, multiclass
            clus
vv           TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                0                84
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TUBGCP4 MUTATED       0   2   2   3
  TUBGCP4 WILD-TYPE    54 133 259  99
D1027V4, multiclass
       clus
vv      TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  2               259
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TUBGCP4 MUTATED     1   3   0   2
  TUBGCP4 WILD-TYPE 194 170  89  83
D1027V5, multiclass
    clus
vv   TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  N0               1               194
  N1               3               170
  N2               0                89
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V6, binary
                   cls
clus                  0   1
  TUBGCP4 MUTATED     7   0
  TUBGCP4 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TUBGCP4 MUTATED      7    0
  TUBGCP4 WILD-TYPE  475   38
   clus
vv  TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D1027V7, binary
                   cls
clus                  0   1
  TUBGCP4 MUTATED     3   5
  TUBGCP4 WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TUBGCP4 MUTATED      3    5
  TUBGCP4 WILD-TYPE  169  401
        clus
vv       TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D1027V8, binary
                   cls
clus                  0   1
  TUBGCP4 MUTATED     5   2
  TUBGCP4 WILD-TYPE 411 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TUBGCP4 MUTATED      5    2
  TUBGCP4 WILD-TYPE  411  100
     clus
vv    TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  NO                5               411
  YES               2               100
[1] 2 2
[1] FALSE
D1027V9, continuous
D1027V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TUBGCP4 MUTATED       1                         0
  TUBGCP4 WILD-TYPE   132                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TUBGCP4 MUTATED                                           0     7
  TUBGCP4 WILD-TYPE                                         1   350
D1027V11, multiclass
                                           clus
vv                                          TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V12, binary
                   cls
clus                  0   1
  TUBGCP4 MUTATED     0   6
  TUBGCP4 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TUBGCP4 MUTATED      0    6
  TUBGCP4 WILD-TYPE   10  392
                        clus
vv                       TUBGCP4 MUTATED TUBGCP4 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1028) Variable = F13A1 MUTATION ANALYSIS
D1028V1, survival
                 sevent
clus2               0   1
  F13A1 MUTATED    13   6
  F13A1 WILD-TYPE 325 210
  F13A1 MUTATED F13A1 WILD-TYPE 
             19             535 
  F13A1 MUTATED F13A1 WILD-TYPE 
              6             210 
$`F13A1 MUTATED`
TCGA-CG-4460 TCGA-KH-A6WC TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6802 
       21.99         6.28        11.70        30.90         6.61        30.90 
TCGA-BR-7197 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CG-4305 
        9.21        31.10         1.12        31.96         1.48        15.95 
TCGA-D7-6528 TCGA-D7-A4Z0 TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-MX-A5UJ TCGA-RD-A7BW 
       15.22        14.76         6.51        21.17        19.73         5.13 
TCGA-VQ-A8PK 
       17.85 

$`F13A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        44.94        21.90        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  F13A1 MUTATED F13A1 WILD-TYPE 
           1.12            0.00 
  F13A1 MUTATED F13A1 WILD-TYPE 
          31.96          122.30 
  F13A1 MUTATED F13A1 WILD-TYPE 
          15.22           13.51 
[1] "1.1 - 32.0 (15.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1028V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  F13A1 MUTATED         0        1        3        2         2         1
  F13A1 WILD-TYPE      10       19       43       29        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F13A1 MUTATED           1          3          1          2        2         0
  F13A1 WILD-TYPE        28         81         61         37       41         4
D1028V3, multiclass
            clus
vv           F13A1 MUTATED F13A1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               2              29
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  F13A1 MUTATED       1   7   7   4
  F13A1 WILD-TYPE    53 128 254  98
D1028V4, multiclass
       clus
vv      F13A1 MUTATED F13A1 WILD-TYPE
  T0+T1             1              53
  T2                7             128
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  F13A1 MUTATED     7   3   6   2
  F13A1 WILD-TYPE 188 170  83  83
D1028V5, multiclass
    clus
vv   F13A1 MUTATED F13A1 WILD-TYPE
  N0             7             188
  N1             3             170
  N2             6              83
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V6, binary
                 cls
clus                0   1
  F13A1 MUTATED    17   2
  F13A1 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F13A1 MUTATED     17    2
  F13A1 WILD-TYPE  465   36
   clus
vv  F13A1 MUTATED F13A1 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D1028V7, binary
                 cls
clus                0   1
  F13A1 MUTATED    11   8
  F13A1 WILD-TYPE 161 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F13A1 MUTATED     11    8
  F13A1 WILD-TYPE  161  398
        clus
vv       F13A1 MUTATED F13A1 WILD-TYPE
  FEMALE            11             161
  MALE               8             398
[1] 2 2
[1] FALSE
D1028V8, binary
                 cls
clus                0   1
  F13A1 MUTATED    16   3
  F13A1 WILD-TYPE 400  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F13A1 MUTATED     16    3
  F13A1 WILD-TYPE  400   99
     clus
vv    F13A1 MUTATED F13A1 WILD-TYPE
  NO             16             400
  YES             3              99
[1] 2 2
[1] FALSE
D1028V9, continuous
[1] "Remove cluster labels:" "F13A1 MUTATED"         
clus
  F13A1 MUTATED F13A1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
D1028V10, continuous
[1] "Remove cluster labels:" "F13A1 MUTATED"         
clus
  F13A1 MUTATED F13A1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-L5-A43C 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" "F13A1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"F13A1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  F13A1 MUTATED       3                         0
  F13A1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  F13A1 MUTATED                                           0    14
  F13A1 WILD-TYPE                                         1   343
D1028V11, multiclass
                                           clus
vv                                          F13A1 MUTATED F13A1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V12, binary
                 cls
clus                0   1
  F13A1 MUTATED     0  16
  F13A1 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F13A1 MUTATED      0   16
  F13A1 WILD-TYPE   10  382
                        clus
vv                       F13A1 MUTATED F13A1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(1029) Variable = ZBTB49 MUTATION ANALYSIS
D1029V1, survival
                  sevent
clus2                0   1
  ZBTB49 MUTATED    10   1
  ZBTB49 WILD-TYPE 328 215
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
              11              543 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               1              215 
$`ZBTB49 MUTATED`
TCGA-JY-A93E TCGA-R6-A6Y0 TCGA-VR-A8EO TCGA-BR-6802 TCGA-BR-7901 TCGA-BR-8368 
       25.22        53.95        25.81        30.90         3.45         4.31 
TCGA-CD-8530 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4GN TCGA-RD-A8N1 
       12.39        14.47        22.32        29.98       115.69 

$`ZBTB49 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
            3.45             0.00 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
          115.69           122.30 
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
           25.22            13.51 
[1] "3.5 - 115.7 (25.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "6.4"
D1029V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB49 MUTATED         0        0        2        1         2         2
  ZBTB49 WILD-TYPE      10       20       44       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB49 MUTATED           0          2          1          0        0
  ZBTB49 WILD-TYPE        29         82         61         39       43
                  vv
clus               STAGE IVA
  ZBTB49 MUTATED           0
  ZBTB49 WILD-TYPE         4
D1029V3, multiclass
            clus
vv           ZBTB49 MUTATED ZBTB49 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZBTB49 MUTATED       0   3   6   1
  ZBTB49 WILD-TYPE    54 132 255 101
D1029V4, multiclass
       clus
vv      ZBTB49 MUTATED ZBTB49 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 6              255
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZBTB49 MUTATED     5   3   2   0
  ZBTB49 WILD-TYPE 190 170  87  85
D1029V5, multiclass
    clus
vv   ZBTB49 MUTATED ZBTB49 WILD-TYPE
  N0              5              190
  N1              3              170
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V6, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED    10   0
  ZBTB49 WILD-TYPE 472  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED     10    0
  ZBTB49 WILD-TYPE  472   38
   clus
vv  ZBTB49 MUTATED ZBTB49 WILD-TYPE
  0             10              472
  1              0               38
[1] 2 2
[1] FALSE
D1029V7, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     2   9
  ZBTB49 WILD-TYPE 170 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      2    9
  ZBTB49 WILD-TYPE  170  397
        clus
vv       ZBTB49 MUTATED ZBTB49 WILD-TYPE
  FEMALE              2              170
  MALE                9              397
[1] 2 2
[1] FALSE
D1029V8, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     8   3
  ZBTB49 WILD-TYPE 408  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      8    3
  ZBTB49 WILD-TYPE  408   99
     clus
vv    ZBTB49 MUTATED ZBTB49 WILD-TYPE
  NO               8              408
  YES              3               99
[1] 2 2
[1] FALSE
D1029V9, continuous
[1] "Remove cluster labels:" "ZBTB49 MUTATED"        
clus
  ZBTB49 MUTATED ZBTB49 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EP 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" "ZBTB49 WILD-TYPE" 
D1029V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB49 MUTATED       3                         0
  ZBTB49 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB49 MUTATED                                           0     8
  ZBTB49 WILD-TYPE                                         1   349
D1029V11, multiclass
                                           clus
vv                                          ZBTB49 MUTATED ZBTB49 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V12, binary
                  cls
clus                 0   1
  ZBTB49 MUTATED     0   9
  ZBTB49 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB49 MUTATED      0    9
  ZBTB49 WILD-TYPE   10  389
                        clus
vv                       ZBTB49 MUTATED ZBTB49 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1030) Variable = NUPL2 MUTATION ANALYSIS
D1030V1, survival
                 sevent
clus2               0   1
  NUPL2 MUTATED     5   3
  NUPL2 WILD-TYPE 333 213
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              8             546 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              3             213 
$`NUPL2 MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-8591 TCGA-CD-8527 TCGA-CD-A4MG TCGA-D7-8570 
       19.99         6.97        28.14         7.17         6.58        24.72 
TCGA-FP-8211 TCGA-VQ-A8P2 
       13.58        38.14 

$`NUPL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        17.06        59.54         5.03         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NUPL2 MUTATED NUPL2 WILD-TYPE 
           6.58            0.00 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          38.14          122.30 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
         16.785          13.530 
[1] "6.6 - 38.1 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1030V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUPL2 MUTATED         0        0        0        1         1         1
  NUPL2 WILD-TYPE      10       20       46       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUPL2 MUTATED           0          3          1          2        0         0
  NUPL2 WILD-TYPE        29         81         61         37       43         4
D1030V3, multiclass
            clus
vv           NUPL2 MUTATED NUPL2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NUPL2 MUTATED       0   1   5   3
  NUPL2 WILD-TYPE    54 134 256  99
D1030V4, multiclass
       clus
vv      NUPL2 MUTATED NUPL2 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NUPL2 MUTATED     2   4   0   3
  NUPL2 WILD-TYPE 193 169  89  82
D1030V5, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V6, binary
                 cls
clus                0   1
  NUPL2 MUTATED     6   0
  NUPL2 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      6    0
  NUPL2 WILD-TYPE  476   38
   clus
vv  NUPL2 MUTATED NUPL2 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1030V7, binary
                 cls
clus                0   1
  NUPL2 MUTATED     2   7
  NUPL2 WILD-TYPE 170 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      2    7
  NUPL2 WILD-TYPE  170  399
        clus
vv       NUPL2 MUTATED NUPL2 WILD-TYPE
  FEMALE             2             170
  MALE               7             399
[1] 2 2
[1] FALSE
D1030V8, binary
                 cls
clus                0   1
  NUPL2 MUTATED     6   2
  NUPL2 WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      6    2
  NUPL2 WILD-TYPE  410  100
     clus
vv    NUPL2 MUTATED NUPL2 WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D1030V9, continuous
D1030V10, continuous
[1] "Remove cluster labels:" "NUPL2 MUTATED"         
clus
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" "NUPL2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"NUPL2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NUPL2 MUTATED       2                         0
  NUPL2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUPL2 MUTATED                                           0     7
  NUPL2 WILD-TYPE                                         1   350
D1030V11, multiclass
                                           clus
vv                                          NUPL2 MUTATED NUPL2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V12, binary
                 cls
clus                0   1
  NUPL2 MUTATED     0   7
  NUPL2 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      0    7
  NUPL2 WILD-TYPE   10  391
                        clus
vv                       NUPL2 MUTATED NUPL2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1031) Variable = RAI2 MUTATION ANALYSIS
D1031V1, survival
                sevent
clus2              0   1
  RAI2 MUTATED     5   3
  RAI2 WILD-TYPE 333 213
  RAI2 MUTATED RAI2 WILD-TYPE 
             8            546 
  RAI2 MUTATED RAI2 WILD-TYPE 
             3            213 
$`RAI2 MUTATED`
TCGA-CG-4460 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-A4QL TCGA-CG-5721 TCGA-HF-7134 
       21.99        35.24        28.73        16.14         6.02        52.21 
TCGA-HU-A4GU TCGA-VQ-AA6J 
        6.58        27.55 

$`RAI2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        12.43        17.26 

  RAI2 MUTATED RAI2 WILD-TYPE 
          6.02           0.00 
  RAI2 MUTATED RAI2 WILD-TYPE 
         52.21         122.30 
  RAI2 MUTATED RAI2 WILD-TYPE 
         24.77          13.51 
[1] "6.0 - 52.2 (24.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1031V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAI2 MUTATED         0        1        1        1         0         1
  RAI2 WILD-TYPE      10       19       45       30        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAI2 MUTATED           0          0          3          0        2         0
  RAI2 WILD-TYPE        29         84         59         39       41         4
D1031V3, multiclass
            clus
vv           RAI2 MUTATED RAI2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            3             59
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  RAI2 MUTATED       1   1   4   3
  RAI2 WILD-TYPE    53 134 257  99
D1031V4, multiclass
       clus
vv      RAI2 MUTATED RAI2 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               4            257
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  RAI2 MUTATED     3   3   1   2
  RAI2 WILD-TYPE 192 170  88  83
D1031V5, multiclass
    clus
vv   RAI2 MUTATED RAI2 WILD-TYPE
  N0            3            192
  N1            3            170
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V6, binary
                cls
clus               0   1
  RAI2 MUTATED     8   1
  RAI2 WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      8    1
  RAI2 WILD-TYPE  474   37
   clus
vv  RAI2 MUTATED RAI2 WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D1031V7, binary
                cls
clus               0   1
  RAI2 MUTATED     3   6
  RAI2 WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      3    6
  RAI2 WILD-TYPE  169  400
        clus
vv       RAI2 MUTATED RAI2 WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D1031V8, binary
                cls
clus               0   1
  RAI2 MUTATED     8   0
  RAI2 WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      8    0
  RAI2 WILD-TYPE  408  102
     clus
vv    RAI2 MUTATED RAI2 WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D1031V9, continuous
D1031V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RAI2 MUTATED       1                         1
  RAI2 WILD-TYPE   132                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAI2 MUTATED                                           0     3
  RAI2 WILD-TYPE                                         1   354
D1031V11, multiclass
                                           clus
vv                                          RAI2 MUTATED RAI2 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V12, binary
                cls
clus               0   1
  RAI2 MUTATED     0   4
  RAI2 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      0    4
  RAI2 WILD-TYPE   10  394
                        clus
vv                       RAI2 MUTATED RAI2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(1032) Variable = LEFTY1 MUTATION ANALYSIS
D1032V1, survival
                  sevent
clus2                0   1
  LEFTY1 MUTATED     2   1
  LEFTY1 WILD-TYPE 336 215
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              551 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               1              215 
$`LEFTY1 MUTATED`
TCGA-CD-A48A TCGA-IN-8663 TCGA-VQ-A8P2 
       12.43         3.39        38.14 

$`LEFTY1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.82        12.43         6.31        12.30        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
            3.39             0.00 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
           38.14           122.30 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
           12.43            13.58 
[1] "3.4 - 38.1 (12.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1032V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LEFTY1 MUTATED         0        0        0        0         1         1
  LEFTY1 WILD-TYPE      10       20       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEFTY1 MUTATED           0          1          0          0        0
  LEFTY1 WILD-TYPE        29         83         62         39       43
                  vv
clus               STAGE IVA
  LEFTY1 MUTATED           0
  LEFTY1 WILD-TYPE         4
D1032V3, multiclass
            clus
vv           LEFTY1 MUTATED LEFTY1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  LEFTY1 MUTATED       0   1   1   1
  LEFTY1 WILD-TYPE    54 134 260 101
D1032V4, multiclass
       clus
vv      LEFTY1 MUTATED LEFTY1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 1              260
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  LEFTY1 MUTATED     1   1   1   0
  LEFTY1 WILD-TYPE 194 172  88  85
D1032V5, multiclass
    clus
vv   LEFTY1 MUTATED LEFTY1 WILD-TYPE
  N0              1              194
  N1              1              172
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V6, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     3   0
  LEFTY1 WILD-TYPE 479  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      3    0
  LEFTY1 WILD-TYPE  479   38
   clus
vv  LEFTY1 MUTATED LEFTY1 WILD-TYPE
  0              3              479
  1              0               38
[1] 2 2
[1] FALSE
D1032V7, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     0   3
  LEFTY1 WILD-TYPE 172 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      0    3
  LEFTY1 WILD-TYPE  172  403
        clus
vv       LEFTY1 MUTATED LEFTY1 WILD-TYPE
  FEMALE              0              172
  MALE                3              403
[1] 2 2
[1] FALSE
D1032V8, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     1   2
  LEFTY1 WILD-TYPE 415 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      1    2
  LEFTY1 WILD-TYPE  415  100
     clus
vv    LEFTY1 MUTATED LEFTY1 WILD-TYPE
  NO               1              415
  YES              2              100
[1] 2 2
[1] FALSE
D1032V9, continuous
D1032V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LEFTY1 MUTATED       1                         0
  LEFTY1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LEFTY1 MUTATED                                           0     2
  LEFTY1 WILD-TYPE                                         1   355
D1032V11, multiclass
                                           clus
vv                                          LEFTY1 MUTATED LEFTY1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V12, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     0   2
  LEFTY1 WILD-TYPE  10 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      0    2
  LEFTY1 WILD-TYPE   10  396
                        clus
vv                       LEFTY1 MUTATED LEFTY1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              2              396
[1] 2 2
[1] FALSE

Clustering(1033) Variable = IKBIP MUTATION ANALYSIS
D1033V1, survival
                 sevent
clus2               0   1
  IKBIP MUTATED     2   1
  IKBIP WILD-TYPE 336 215
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             551 
  IKBIP MUTATED IKBIP WILD-TYPE 
              1             215 
$`IKBIP MUTATED`
TCGA-D7-6525 TCGA-HF-7132 TCGA-VQ-A8P2 
       13.35        77.29        38.14 

$`IKBIP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  IKBIP MUTATED IKBIP WILD-TYPE 
          13.35            0.00 
  IKBIP MUTATED IKBIP WILD-TYPE 
          77.29          122.30 
  IKBIP MUTATED IKBIP WILD-TYPE 
          38.14           13.55 
[1] "13.3 - 77.3 (38.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D1033V2, continuous
[1] "Remove cluster labels:" "IKBIP MUTATED"         
clus
  IKBIP MUTATED IKBIP WILD-TYPE 
              2             569 
     TCGA-IC-A6RF      TCGA-JY-A6FB      TCGA-JY-A938      TCGA-L5-A43I 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A43J      TCGA-L5-A43M      TCGA-L5-A4OE      TCGA-L5-A4OG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-S8-A6BV      TCGA-CG-4444 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-5716 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-KB-A93G      TCGA-MX-A663      TCGA-2H-A9GF      TCGA-2H-A9GG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-2H-A9GH      TCGA-2H-A9GI      TCGA-2H-A9GJ      TCGA-2H-A9GK 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-2H-A9GL      TCGA-2H-A9GM      TCGA-2H-A9GN      TCGA-2H-A9GO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-2H-A9GQ      TCGA-2H-A9GR      TCGA-IC-A6RE      TCGA-IG-A3I8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QS      TCGA-IG-A4QT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A51D      TCGA-IG-A5B8      TCGA-IG-A5S3 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A625      TCGA-IG-A6QS      TCGA-IG-A7DP      TCGA-IG-A8O2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A97H      TCGA-IG-A97I      TCGA-JY-A6F8      TCGA-JY-A6FA 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A6FD      TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A939      TCGA-JY-A93C      TCGA-JY-A93D      TCGA-JY-A93E 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A93F      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OF      TCGA-L5-A4OH      TCGA-L5-A4OJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OR      TCGA-L5-A4OS      TCGA-L5-A4OT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A88W      TCGA-L5-A88Z      TCGA-L5-A891 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NH 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NI      TCGA-L5-A8NJ      TCGA-L5-A8NK      TCGA-L5-A8NL 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NM      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NU      TCGA-L5-A8NV      TCGA-L5-A8NW 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L7-A56G      TCGA-L7-A6VZ      TCGA-LN-A49K      TCGA-LN-A49L 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-LN-A8I1 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A9FO      TCGA-LN-A9FP      TCGA-LN-A9FQ      TCGA-LN-A9FR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6DQ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A6KZ      TCGA-R6-A6L4      TCGA-R6-A6L6      TCGA-R6-A6XG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y0      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-R6-A8WG      TCGA-RE-A7BO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-S8-A6BW      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-A8JD 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-Z6-A8JE      TCGA-Z6-A9VB      TCGA-Z6-AAPN      TCGA-ZR-A9CJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI      TCGA-B7-A5TJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183      TCGA-BR-4184 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5802      TCGA-CD-5803 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4300      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4477 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5728      TCGA-CG-5730 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HF-A5NB 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RJ      TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RP      TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A7NT      TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IP-7968      TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-ZA-A8F6 
"IKBIP WILD-TYPE" 
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IKBIP MUTATED         0        0        0        1         0         0
  IKBIP WILD-TYPE      10       20       46       30        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IKBIP MUTATED           0          2          0          0        0         0
  IKBIP WILD-TYPE        29         82         62         39       43         4
D1033V3, multiclass
            clus
vv           IKBIP MUTATED IKBIP WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IKBIP MUTATED       0   2   0   1
  IKBIP WILD-TYPE    54 133 261 101
D1033V4, multiclass
       clus
vv      IKBIP MUTATED IKBIP WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                0             261
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IKBIP MUTATED     0   2   1   0
  IKBIP WILD-TYPE 195 171  88  85
D1033V5, multiclass
    clus
vv   IKBIP MUTATED IKBIP WILD-TYPE
  N0             0             195
  N1             2             171
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V6, binary
                 cls
clus                0   1
  IKBIP MUTATED     3   0
  IKBIP WILD-TYPE 479  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      3    0
  IKBIP WILD-TYPE  479   38
   clus
vv  IKBIP MUTATED IKBIP WILD-TYPE
  0             3             479
  1             0              38
[1] 2 2
[1] FALSE
D1033V7, binary
                 cls
clus                0   1
  IKBIP MUTATED     0   3
  IKBIP WILD-TYPE 172 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      0    3
  IKBIP WILD-TYPE  172  403
        clus
vv       IKBIP MUTATED IKBIP WILD-TYPE
  FEMALE             0             172
  MALE               3             403
[1] 2 2
[1] FALSE
D1033V8, binary
                 cls
clus                0   1
  IKBIP MUTATED     1   2
  IKBIP WILD-TYPE 415 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      1    2
  IKBIP WILD-TYPE  415  100
     clus
vv    IKBIP MUTATED IKBIP WILD-TYPE
  NO              1             415
  YES             2             100
[1] 2 2
[1] FALSE
D1033V9, continuous
D1033V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IKBIP MUTATED       0                         0
  IKBIP WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IKBIP MUTATED                                           0     2
  IKBIP WILD-TYPE                                         1   355
D1033V11, multiclass
[1] "Remove cluster labels:" "IKBIP MUTATED"         
clus
  IKBIP MUTATED IKBIP WILD-TYPE 
              2             503 
     TCGA-IC-A6RF      TCGA-JY-A6FB      TCGA-JY-A938      TCGA-L5-A43I 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG      TCGA-L5-A4OI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-S8-A6BV      TCGA-EQ-A4SO      TCGA-F1-6177 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-KB-A93G      TCGA-MX-A663      TCGA-IC-A6RE 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QS 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A51D      TCGA-IG-A5B8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A5S3      TCGA-IG-A625      TCGA-IG-A6QS      TCGA-IG-A7DP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-IG-A97I      TCGA-JY-A6F8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A6FA      TCGA-JY-A6FD      TCGA-JY-A6FE      TCGA-JY-A6FG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-JY-A939      TCGA-JY-A93C      TCGA-JY-A93D 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-JY-A93E      TCGA-JY-A93F      TCGA-KH-A6WC      TCGA-L5-A43C 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OF      TCGA-L5-A4OH 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OJ      TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OR      TCGA-L5-A4OS 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX      TCGA-L5-A88S 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A88W      TCGA-L5-A88Z      TCGA-L5-A891 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NH 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NI      TCGA-L5-A8NJ      TCGA-L5-A8NK      TCGA-L5-A8NL 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NM      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NS 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L5-A8NU      TCGA-L5-A8NV      TCGA-L5-A8NW      TCGA-L7-A56G 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-L7-A6VZ      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-LN-A8I1      TCGA-LN-A9FO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-LN-A9FP      TCGA-LN-A9FQ      TCGA-LN-A9FR      TCGA-Q9-A6FW 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6DQ      TCGA-R6-A6KZ      TCGA-R6-A6L4 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A6L6      TCGA-R6-A6XG      TCGA-R6-A6XQ      TCGA-R6-A6Y0 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R6-A8WG      TCGA-RE-A7BO      TCGA-S8-A6BW      TCGA-V5-A7RC 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE      TCGA-Z6-A9VB 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-Z6-AAPN      TCGA-ZR-A9CJ      TCGA-B7-5816      TCGA-B7-5818 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4256      TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4361      TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8078 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A6EV      TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A6F0      TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A74A      TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RJ      TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RP      TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A7NT      TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IP-7968      TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-MX-A666      TCGA-R5-A7O7      TCGA-R5-A7ZE      TCGA-R5-A7ZF 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A7ZI      TCGA-R5-A7ZR      TCGA-R5-A804      TCGA-R5-A805 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A7BS      TCGA-RD-A7BT      TCGA-RD-A7BW      TCGA-RD-A7C1 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8MV      TCGA-RD-A8MW      TCGA-RD-A8N0      TCGA-RD-A8N1 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N2      TCGA-RD-A8N4      TCGA-RD-A8N5      TCGA-RD-A8N6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N9      TCGA-SW-A7EA      TCGA-SW-A7EB      TCGA-VQ-A8DL 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8DU      TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8E7      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA64      TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6B      TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6J      TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
D1033V12, binary
                 cls
clus                0   1
  IKBIP MUTATED     0   1
  IKBIP WILD-TYPE  10 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      0    1
  IKBIP WILD-TYPE   10  397
                        clus
vv                       IKBIP MUTATED IKBIP WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             1             397
[1] 2 2
[1] FALSE

Clustering(1034) Variable = SLC12A1 MUTATION ANALYSIS
D1034V1, survival
                   sevent
clus2                 0   1
  SLC12A1 MUTATED    16  10
  SLC12A1 WILD-TYPE 322 206
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
               26               528 
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
               10               206 
$`SLC12A1 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A893 TCGA-L5-A8NU TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 
       21.01         3.02        83.24        12.59        11.54        12.33 
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6456 TCGA-BR-8297 TCGA-BR-8367 TCGA-BR-8368 
        6.97         9.34        17.29         7.40        26.33         4.31 
TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-A4QI TCGA-CD-5804 TCGA-CD-A4MG 
       31.27         9.21        31.96        21.44        12.10         6.58 
TCGA-CG-5721 TCGA-F1-6874 TCGA-F1-6875 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
        6.02        14.47        72.23        22.68        29.98         0.10 
TCGA-VQ-A8P2 TCGA-VQ-A91V 
       38.14        42.64 

$`SLC12A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19        17.52         0.95        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       32.52        13.51        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         7.13         0.62         7.99        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       17.85         1.87        15.65        20.81         1.71        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
              0.1               0.0 
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
            83.24            122.30 
  SLC12A1 MUTATED SLC12A1 WILD-TYPE 
           13.530            13.565 
[1] "0.1 - 83.2 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1034V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC12A1 MUTATED         2        1        2        0         5         4
  SLC12A1 WILD-TYPE       8       19       44       31        79        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A1 MUTATED           1          4          1          4        2
  SLC12A1 WILD-TYPE        28         80         61         35       41
                   vv
clus                STAGE IVA
  SLC12A1 MUTATED           0
  SLC12A1 WILD-TYPE         4
D1034V3, multiclass
            clus
vv           SLC12A1 MUTATED SLC12A1 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 1                19
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                5                79
  STAGE IIB                4                79
  STAGE III                1                28
  STAGE IIIA               4                80
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC12A1 MUTATED       2   7   9   9
  SLC12A1 WILD-TYPE    52 128 252  93
D1034V4, multiclass
       clus
vv      SLC12A1 MUTATED SLC12A1 WILD-TYPE
  T0+T1               2                52
  T2                  7               128
  T3                  9               252
  T4                  9                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC12A1 MUTATED    11  11   3   4
  SLC12A1 WILD-TYPE 184 162  86  81
D1034V5, multiclass
    clus
vv   SLC12A1 MUTATED SLC12A1 WILD-TYPE
  N0              11               184
  N1              11               162
  N2               3                86
  N3               4                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V6, binary
                   cls
clus                  0   1
  SLC12A1 MUTATED    27   1
  SLC12A1 WILD-TYPE 455  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A1 MUTATED     27    1
  SLC12A1 WILD-TYPE  455   37
   clus
vv  SLC12A1 MUTATED SLC12A1 WILD-TYPE
  0              27               455
  1               1                37
[1] 2 2
[1] FALSE
D1034V7, binary
                   cls
clus                  0   1
  SLC12A1 MUTATED     9  20
  SLC12A1 WILD-TYPE 163 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A1 MUTATED      9   20
  SLC12A1 WILD-TYPE  163  386
        clus
vv       SLC12A1 MUTATED SLC12A1 WILD-TYPE
  FEMALE               9               163
  MALE                20               386
[1] 2 2
[1] FALSE
D1034V8, binary
                   cls
clus                  0   1
  SLC12A1 MUTATED    22   4
  SLC12A1 WILD-TYPE 394  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A1 MUTATED     22    4
  SLC12A1 WILD-TYPE  394   98
     clus
vv    SLC12A1 MUTATED SLC12A1 WILD-TYPE
  NO               22               394
  YES               4                98
[1] 2 2
[1] FALSE
D1034V9, continuous
D1034V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC12A1 MUTATED       9                         1
  SLC12A1 WILD-TYPE   124                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC12A1 MUTATED                                           0    17
  SLC12A1 WILD-TYPE                                         1   340
D1034V11, multiclass
                                           clus
vv                                          SLC12A1 MUTATED SLC12A1 WILD-TYPE
  ASIAN                                                   9               124
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V12, binary
                   cls
clus                  0   1
  SLC12A1 MUTATED     0  23
  SLC12A1 WILD-TYPE  10 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A1 MUTATED      0   23
  SLC12A1 WILD-TYPE   10  375
                        clus
vv                       SLC12A1 MUTATED SLC12A1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              23               375
[1] 2 2
[1] FALSE

Clustering(1035) Variable = CARD11 MUTATION ANALYSIS
D1035V1, survival
                  sevent
clus2                0   1
  CARD11 MUTATED    19   7
  CARD11 WILD-TYPE 319 209
  CARD11 MUTATED CARD11 WILD-TYPE 
              26              528 
  CARD11 MUTATED CARD11 WILD-TYPE 
               7              209 
$`CARD11 MUTATED`
TCGA-JY-A6FA TCGA-L5-A8NS TCGA-LN-A4A4 TCGA-LN-A5U7 TCGA-V5-AASV TCGA-BR-4184 
       44.75        13.41        12.59        25.25        15.35         6.97 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8297 
       34.68        32.78        19.89        44.94        35.84         7.40 
TCGA-BR-8486 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 
       20.22        28.14        31.96         6.58         1.02         6.02 
TCGA-D7-A74A TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H5 
       19.96        52.21        30.51        22.32         0.10        23.80 
TCGA-VQ-A8P2 TCGA-VQ-A94T 
       38.14        11.24 

$`CARD11 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 
        5.52         6.21        77.29        63.06        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CARD11 MUTATED CARD11 WILD-TYPE 
             0.1              0.0 
  CARD11 MUTATED CARD11 WILD-TYPE 
           52.21           122.30 
  CARD11 MUTATED CARD11 WILD-TYPE 
          21.270           13.445 
[1] "0.1 - 52.2 (21.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D1035V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CARD11 MUTATED         0        2        2        0         6         5
  CARD11 WILD-TYPE      10       18       44       31        78        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CARD11 MUTATED           1          3          1          4        3
  CARD11 WILD-TYPE        28         81         61         35       40
                  vv
clus               STAGE IVA
  CARD11 MUTATED           0
  CARD11 WILD-TYPE         4
D1035V3, multiclass
            clus
vv           CARD11 MUTATED CARD11 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               6               78
  STAGE IIB               5               78
  STAGE III               1               28
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              4               35
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CARD11 MUTATED       3   4  12   9
  CARD11 WILD-TYPE    51 131 249  93
D1035V4, multiclass
       clus
vv      CARD11 MUTATED CARD11 WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                12              249
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CARD11 MUTATED    14   6   5   3
  CARD11 WILD-TYPE 181 167  84  82
D1035V5, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  N0             14              181
  N1              6              167
  N2              5               84
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V6, binary
                  cls
clus                 0   1
  CARD11 MUTATED    25   2
  CARD11 WILD-TYPE 457  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     25    2
  CARD11 WILD-TYPE  457   36
   clus
vv  CARD11 MUTATED CARD11 WILD-TYPE
  0             25              457
  1              2               36
[1] 2 2
[1] FALSE
D1035V7, binary
                  cls
clus                 0   1
  CARD11 MUTATED    10  19
  CARD11 WILD-TYPE 162 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     10   19
  CARD11 WILD-TYPE  162  387
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  FEMALE             10              162
  MALE               19              387
[1] 2 2
[1] FALSE
D1035V8, binary
                  cls
clus                 0   1
  CARD11 MUTATED    21   5
  CARD11 WILD-TYPE 395  97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     21    5
  CARD11 WILD-TYPE  395   97
     clus
vv    CARD11 MUTATED CARD11 WILD-TYPE
  NO              21              395
  YES              5               97
[1] 2 2
[1] FALSE
D1035V9, continuous
D1035V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CARD11 MUTATED       8                         1
  CARD11 WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CARD11 MUTATED                                           0    15
  CARD11 WILD-TYPE                                         1   342
D1035V11, multiclass
                                           clus
vv                                          CARD11 MUTATED CARD11 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V12, binary
                  cls
clus                 0   1
  CARD11 MUTATED     0  21
  CARD11 WILD-TYPE  10 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED      0   21
  CARD11 WILD-TYPE   10  377
                        clus
vv                       CARD11 MUTATED CARD11 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(1036) Variable = OLFM1 MUTATION ANALYSIS
D1036V1, survival
                 sevent
clus2               0   1
  OLFM1 MUTATED     9   5
  OLFM1 WILD-TYPE 329 211
  OLFM1 MUTATED OLFM1 WILD-TYPE 
             14             540 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
              5             211 
$`OLFM1 MUTATED`
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-L7-A6VZ TCGA-LN-A49M TCGA-R6-A8W8 TCGA-VR-A8EU 
       16.24         7.69        10.36        12.66         2.89        18.31 
TCGA-BR-7707 TCGA-BR-8682 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-A4YY 
       35.84        32.58        16.14         1.02       105.07        13.78 
TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.51        38.14 

$`OLFM1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94         8.94         4.21        32.45        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30        15.78         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  OLFM1 MUTATED OLFM1 WILD-TYPE 
           1.02            0.00 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
         105.07          122.30 
  OLFM1 MUTATED OLFM1 WILD-TYPE 
          14.96           13.53 
[1] "1.0 - 105.1 (15.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1036V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OLFM1 MUTATED         0        0        1        1         2         2
  OLFM1 WILD-TYPE      10       20       45       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OLFM1 MUTATED           0          1          2          1        2         1
  OLFM1 WILD-TYPE        29         83         60         38       41         3
D1036V3, multiclass
            clus
vv           OLFM1 MUTATED OLFM1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OLFM1 MUTATED       2   3   6   2
  OLFM1 WILD-TYPE    52 132 255 100
D1036V4, multiclass
       clus
vv      OLFM1 MUTATED OLFM1 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OLFM1 MUTATED     4   5   1   3
  OLFM1 WILD-TYPE 191 168  88  82
D1036V5, multiclass
    clus
vv   OLFM1 MUTATED OLFM1 WILD-TYPE
  N0             4             191
  N1             5             168
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V6, binary
                 cls
clus                0   1
  OLFM1 MUTATED    10   3
  OLFM1 WILD-TYPE 472  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED     10    3
  OLFM1 WILD-TYPE  472   35
   clus
vv  OLFM1 MUTATED OLFM1 WILD-TYPE
  0            10             472
  1             3              35
[1] 2 2
[1] FALSE
D1036V7, binary
                 cls
clus                0   1
  OLFM1 MUTATED     4  11
  OLFM1 WILD-TYPE 168 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      4   11
  OLFM1 WILD-TYPE  168  395
        clus
vv       OLFM1 MUTATED OLFM1 WILD-TYPE
  FEMALE             4             168
  MALE              11             395
[1] 2 2
[1] FALSE
D1036V8, binary
                 cls
clus                0   1
  OLFM1 MUTATED     8   5
  OLFM1 WILD-TYPE 408  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      8    5
  OLFM1 WILD-TYPE  408   97
     clus
vv    OLFM1 MUTATED OLFM1 WILD-TYPE
  NO              8             408
  YES             5              97
[1] 2 2
[1] FALSE
D1036V9, continuous
[1] "Remove cluster labels:" "OLFM1 MUTATED"         
clus
  OLFM1 MUTATED OLFM1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EW 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"OLFM1 WILD-TYPE" "OLFM1 WILD-TYPE" 
D1036V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OLFM1 MUTATED       3                         0
  OLFM1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OLFM1 MUTATED                                           0     9
  OLFM1 WILD-TYPE                                         1   348
D1036V11, multiclass
                                           clus
vv                                          OLFM1 MUTATED OLFM1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V12, binary
                 cls
clus                0   1
  OLFM1 MUTATED     0  10
  OLFM1 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM1 MUTATED      0   10
  OLFM1 WILD-TYPE   10  388
                        clus
vv                       OLFM1 MUTATED OLFM1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(1037) Variable = KIF27 MUTATION ANALYSIS
D1037V1, survival
                 sevent
clus2               0   1
  KIF27 MUTATED    10   8
  KIF27 WILD-TYPE 328 208
  KIF27 MUTATED KIF27 WILD-TYPE 
             18             536 
  KIF27 MUTATED KIF27 WILD-TYPE 
              8             208 
$`KIF27 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A8NI TCGA-L5-A8NM TCGA-VR-A8EX TCGA-B7-5818 
       19.99        21.99        13.48         7.76        28.11        11.70 
TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8361 TCGA-BR-A4J6 TCGA-CD-A4MG TCGA-CG-5726 
       35.24        33.21        31.10         0.66         6.58        28.96 
TCGA-CG-5728 TCGA-D7-6528 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       65.10        15.22        26.47        22.68        38.14        26.04 

$`KIF27 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53        28.34        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        32.94        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIF27 MUTATED KIF27 WILD-TYPE 
           0.66            0.00 
  KIF27 MUTATED KIF27 WILD-TYPE 
           65.1           122.3 
  KIF27 MUTATED KIF27 WILD-TYPE 
          24.36           13.41 
[1] "0.7 - 65.1 (24.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.2"
D1037V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF27 MUTATED         0        1        4        1         3         2
  KIF27 WILD-TYPE      10       19       42       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF27 MUTATED           1          2          0          2        1         1
  KIF27 WILD-TYPE        28         82         62         37       42         3
D1037V3, multiclass
            clus
vv           KIF27 MUTATED KIF27 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KIF27 MUTATED       3   5   7   4
  KIF27 WILD-TYPE    51 130 254  98
D1037V4, multiclass
       clus
vv      KIF27 MUTATED KIF27 WILD-TYPE
  T0+T1             3              51
  T2                5             130
  T3                7             254
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KIF27 MUTATED     9   7   1   1
  KIF27 WILD-TYPE 186 166  88  84
D1037V5, multiclass
    clus
vv   KIF27 MUTATED KIF27 WILD-TYPE
  N0             9             186
  N1             7             166
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V6, binary
                 cls
clus                0   1
  KIF27 MUTATED    16   2
  KIF27 WILD-TYPE 466  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF27 MUTATED     16    2
  KIF27 WILD-TYPE  466   36
   clus
vv  KIF27 MUTATED KIF27 WILD-TYPE
  0            16             466
  1             2              36
[1] 2 2
[1] FALSE
D1037V7, binary
                 cls
clus                0   1
  KIF27 MUTATED    10  10
  KIF27 WILD-TYPE 162 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF27 MUTATED     10   10
  KIF27 WILD-TYPE  162  396
        clus
vv       KIF27 MUTATED KIF27 WILD-TYPE
  FEMALE            10             162
  MALE              10             396
[1] 2 2
[1] FALSE
D1037V8, binary
                 cls
clus                0   1
  KIF27 MUTATED    15   1
  KIF27 WILD-TYPE 401 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF27 MUTATED     15    1
  KIF27 WILD-TYPE  401  101
     clus
vv    KIF27 MUTATED KIF27 WILD-TYPE
  NO             15             401
  YES             1             101
[1] 2 2
[1] FALSE
D1037V9, continuous
[1] "Remove cluster labels:" "KIF27 MUTATED"         
clus
  KIF27 MUTATED KIF27 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
D1037V10, continuous
[1] "Remove cluster labels:" "KIF27 MUTATED"         
clus
  KIF27 MUTATED KIF27 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" "KIF27 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KIF27 MUTATED       2                         0
  KIF27 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF27 MUTATED                                           0    14
  KIF27 WILD-TYPE                                         1   343
D1037V11, multiclass
                                           clus
vv                                          KIF27 MUTATED KIF27 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V12, binary
                 cls
clus                0   1
  KIF27 MUTATED     0  11
  KIF27 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF27 MUTATED      0   11
  KIF27 WILD-TYPE   10  387
                        clus
vv                       KIF27 MUTATED KIF27 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1038) Variable = ARSJ MUTATION ANALYSIS
D1038V1, survival
                sevent
clus2              0   1
  ARSJ MUTATED     7   3
  ARSJ WILD-TYPE 331 213
  ARSJ MUTATED ARSJ WILD-TYPE 
            10            544 
  ARSJ MUTATED ARSJ WILD-TYPE 
             3            213 
$`ARSJ MUTATED`
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-LN-A49S TCGA-V5-AASV TCGA-CD-8536 TCGA-CG-5723 
        2.66        12.92        13.15        15.35        12.43       105.07 
TCGA-CG-5728 TCGA-D7-A4YV TCGA-F1-A72C TCGA-MX-A5UJ 
       65.10         5.92        11.38        19.73 

$`ARSJ WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ARSJ MUTATED ARSJ WILD-TYPE 
          2.66           0.00 
  ARSJ MUTATED ARSJ WILD-TYPE 
        105.07         122.30 
  ARSJ MUTATED ARSJ WILD-TYPE 
        13.035         13.630 
[1] "2.7 - 105.1 (13.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1038V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARSJ MUTATED         0        0        1        2         2         2
  ARSJ WILD-TYPE      10       20       45       29        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARSJ MUTATED           0          1          0          0        1         1
  ARSJ WILD-TYPE        29         83         62         39       42         3
D1038V3, multiclass
            clus
vv           ARSJ MUTATED ARSJ WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ARSJ MUTATED       2   2   6   0
  ARSJ WILD-TYPE    52 133 255 102
D1038V4, multiclass
       clus
vv      ARSJ MUTATED ARSJ WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               6            255
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ARSJ MUTATED     7   2   1   0
  ARSJ WILD-TYPE 188 171  88  85
D1038V5, multiclass
    clus
vv   ARSJ MUTATED ARSJ WILD-TYPE
  N0            7            188
  N1            2            171
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V6, binary
                cls
clus               0   1
  ARSJ MUTATED     7   2
  ARSJ WILD-TYPE 475  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      7    2
  ARSJ WILD-TYPE  475   36
   clus
vv  ARSJ MUTATED ARSJ WILD-TYPE
  0            7            475
  1            2             36
[1] 2 2
[1] FALSE
D1038V7, binary
                cls
clus               0   1
  ARSJ MUTATED     3   7
  ARSJ WILD-TYPE 169 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      3    7
  ARSJ WILD-TYPE  169  399
        clus
vv       ARSJ MUTATED ARSJ WILD-TYPE
  FEMALE            3            169
  MALE              7            399
[1] 2 2
[1] FALSE
D1038V8, binary
                cls
clus               0   1
  ARSJ MUTATED     6   2
  ARSJ WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      6    2
  ARSJ WILD-TYPE  410  100
     clus
vv    ARSJ MUTATED ARSJ WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D1038V9, continuous
[1] "Remove cluster labels:" "ARSJ MUTATED"          
clus
  ARSJ MUTATED ARSJ WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASW 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ARSJ WILD-TYPE" "ARSJ WILD-TYPE" 
D1038V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARSJ MUTATED       3                         1
  ARSJ WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARSJ MUTATED                                           0     4
  ARSJ WILD-TYPE                                         1   353
D1038V11, multiclass
                                           clus
vv                                          ARSJ MUTATED ARSJ WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V12, binary
                cls
clus               0   1
  ARSJ MUTATED     0   6
  ARSJ WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      0    6
  ARSJ WILD-TYPE   10  392
                        clus
vv                       ARSJ MUTATED ARSJ WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1039) Variable = PRICKLE4 MUTATION ANALYSIS
D1039V1, survival
                    sevent
clus2                  0   1
  PRICKLE4 MUTATED     3   2
  PRICKLE4 WILD-TYPE 335 214
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 5                549 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 2                214 
$`PRICKLE4 MUTATED`
TCGA-L5-A4OX TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GX 
        7.43        15.95       105.07        28.96        20.25 

$`PRICKLE4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
              7.43               0.00 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
            105.07             122.30 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
             20.25              13.51 
[1] "7.4 - 105.1 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1039V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRICKLE4 MUTATED         0        1        0        2         0         1
  PRICKLE4 WILD-TYPE      10       19       46       29        84        82
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRICKLE4 MUTATED           0          0          0          1        0
  PRICKLE4 WILD-TYPE        29         84         62         38       43
                    vv
clus                 STAGE IVA
  PRICKLE4 MUTATED           0
  PRICKLE4 WILD-TYPE         4
D1039V3, multiclass
            clus
vv           PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  2                 29
  STAGE IIA                 0                 84
  STAGE IIB                 1                 82
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PRICKLE4 MUTATED       1   3   1   1
  PRICKLE4 WILD-TYPE    53 132 260 101
D1039V4, multiclass
       clus
vv      PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  T0+T1                1                 53
  T2                   3                132
  T3                   1                260
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PRICKLE4 MUTATED     1   3   1   0
  PRICKLE4 WILD-TYPE 194 170  88  85
D1039V5, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  N0                1                194
  N1                3                170
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V6, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     6   0
  PRICKLE4 WILD-TYPE 476  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      6    0
  PRICKLE4 WILD-TYPE  476   38
   clus
vv  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  0                6                476
  1                0                 38
[1] 2 2
[1] FALSE
D1039V7, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     3   4
  PRICKLE4 WILD-TYPE 169 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      3    4
  PRICKLE4 WILD-TYPE  169  402
        clus
vv       PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  FEMALE                3                169
  MALE                  4                402
[1] 2 2
[1] FALSE
D1039V8, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     4   0
  PRICKLE4 WILD-TYPE 412 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      4    0
  PRICKLE4 WILD-TYPE  412  102
     clus
vv    PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  NO                 4                412
  YES                0                102
[1] 2 2
[1] FALSE
D1039V9, continuous
D1039V10, continuous
[1] "Remove cluster labels:" "PRICKLE4 MUTATED"      
clus
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A88S         TCGA-L5-A88V 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" "PRICKLE4 WILD-TYPE" 
        TCGA-Z6-AAPN 
"PRICKLE4 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PRICKLE4 MUTATED       1                         0
  PRICKLE4 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRICKLE4 MUTATED                                           0     3
  PRICKLE4 WILD-TYPE                                         1   354
D1039V11, multiclass
                                           clus
vv                                          PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V12, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     0   3
  PRICKLE4 WILD-TYPE  10 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      0    3
  PRICKLE4 WILD-TYPE   10  395
                        clus
vv                       PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                3                395
[1] 2 2
[1] FALSE

Clustering(1040) Variable = PIGO MUTATION ANALYSIS
D1040V1, survival
                sevent
clus2              0   1
  PIGO MUTATED    10   2
  PIGO WILD-TYPE 328 214
  PIGO MUTATED PIGO WILD-TYPE 
            12            542 
  PIGO MUTATED PIGO WILD-TYPE 
             2            214 
$`PIGO MUTATED`
TCGA-JY-A938 TCGA-2H-A9GJ TCGA-L5-A8NK TCGA-BR-6452 TCGA-BR-8366 TCGA-BR-8487 
       34.85        58.55        13.55        34.68         0.95         1.12 
TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A4MI TCGA-HF-7132 TCGA-HU-A4H3 
       31.96        12.30        12.43        11.77        77.29        29.00 

$`PIGO WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PIGO MUTATED PIGO WILD-TYPE 
          0.95           0.00 
  PIGO MUTATED PIGO WILD-TYPE 
         77.29         122.30 
  PIGO MUTATED PIGO WILD-TYPE 
        21.275         13.545 
[1] "0.9 - 77.3 (21.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.3"
D1040V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGO MUTATED         1        0        0        2         4         1
  PIGO WILD-TYPE       9       20       46       29        80        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGO MUTATED           0          1          0          1        2         0
  PIGO WILD-TYPE        29         83         62         38       41         4
D1040V3, multiclass
            clus
vv           PIGO MUTATED PIGO WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             4             80
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PIGO MUTATED       1   1   7   3
  PIGO WILD-TYPE    53 134 254  99
D1040V4, multiclass
       clus
vv      PIGO MUTATED PIGO WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               7            254
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PIGO MUTATED     8   2   1   1
  PIGO WILD-TYPE 187 171  88  84
D1040V5, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  N0            8            187
  N1            2            171
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V6, binary
                cls
clus               0   1
  PIGO MUTATED    10   2
  PIGO WILD-TYPE 472  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED     10    2
  PIGO WILD-TYPE  472   36
   clus
vv  PIGO MUTATED PIGO WILD-TYPE
  0           10            472
  1            2             36
[1] 2 2
[1] FALSE
D1040V7, binary
                cls
clus               0   1
  PIGO MUTATED     5   7
  PIGO WILD-TYPE 167 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      5    7
  PIGO WILD-TYPE  167  399
        clus
vv       PIGO MUTATED PIGO WILD-TYPE
  FEMALE            5            167
  MALE              7            399
[1] 2 2
[1] FALSE
D1040V8, binary
                cls
clus               0   1
  PIGO MUTATED     8   2
  PIGO WILD-TYPE 408 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      8    2
  PIGO WILD-TYPE  408  100
     clus
vv    PIGO MUTATED PIGO WILD-TYPE
  NO             8            408
  YES            2            100
[1] 2 2
[1] FALSE
D1040V9, continuous
D1040V10, continuous
[1] "Remove cluster labels:" "PIGO MUTATED"          
clus
  PIGO MUTATED PIGO WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" "PIGO WILD-TYPE" 
    TCGA-Z6-AAPN 
"PIGO WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGO MUTATED       5                         0
  PIGO WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGO MUTATED                                           0     5
  PIGO WILD-TYPE                                         1   352
D1040V11, multiclass
                                           clus
vv                                          PIGO MUTATED PIGO WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V12, binary
                cls
clus               0   1
  PIGO MUTATED     0   8
  PIGO WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      0    8
  PIGO WILD-TYPE   10  390
                        clus
vv                       PIGO MUTATED PIGO WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(1041) Variable = EFHC1 MUTATION ANALYSIS
D1041V1, survival
                 sevent
clus2               0   1
  EFHC1 MUTATED     7   3
  EFHC1 WILD-TYPE 331 213
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             544 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              3             213 
$`EFHC1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8081 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-8243 
       30.90        34.68        32.25         6.02        30.51         5.92 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H4 
       22.68        29.98         0.10        23.84 

$`EFHC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EFHC1 MUTATED EFHC1 WILD-TYPE 
            0.1             0.0 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          34.68          122.30 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          26.91           13.51 
[1] "0.1 - 34.7 (26.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1041V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHC1 MUTATED         0        0        0        0         2         3
  EFHC1 WILD-TYPE      10       20       46       31        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHC1 MUTATED           0          0          0          3        1         0
  EFHC1 WILD-TYPE        29         84         62         36       42         4
D1041V3, multiclass
            clus
vv           EFHC1 MUTATED EFHC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EFHC1 MUTATED       0   3   2   5
  EFHC1 WILD-TYPE    54 132 259  97
D1041V4, multiclass
       clus
vv      EFHC1 MUTATED EFHC1 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                2             259
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EFHC1 MUTATED     2   3   2   2
  EFHC1 WILD-TYPE 193 170  87  83
D1041V5, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  N0             2             193
  N1             3             170
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V6, binary
                 cls
clus                0   1
  EFHC1 MUTATED    10   0
  EFHC1 WILD-TYPE 472  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     10    0
  EFHC1 WILD-TYPE  472   38
   clus
vv  EFHC1 MUTATED EFHC1 WILD-TYPE
  0            10             472
  1             0              38
[1] 2 2
[1] FALSE
D1041V7, binary
                 cls
clus                0   1
  EFHC1 MUTATED     6   4
  EFHC1 WILD-TYPE 166 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      6    4
  EFHC1 WILD-TYPE  166  402
        clus
vv       EFHC1 MUTATED EFHC1 WILD-TYPE
  FEMALE             6             166
  MALE               4             402
[1] 2 2
[1] FALSE
D1041V8, binary
                 cls
clus                0   1
  EFHC1 MUTATED     9   1
  EFHC1 WILD-TYPE 407 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      9    1
  EFHC1 WILD-TYPE  407  101
     clus
vv    EFHC1 MUTATED EFHC1 WILD-TYPE
  NO              9             407
  YES             1             101
[1] 2 2
[1] FALSE
D1041V9, continuous
D1041V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHC1 MUTATED       5                         0
  EFHC1 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHC1 MUTATED                                           0     3
  EFHC1 WILD-TYPE                                         1   354
D1041V11, multiclass
                                           clus
vv                                          EFHC1 MUTATED EFHC1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V12, binary
                 cls
clus                0   1
  EFHC1 MUTATED     0   8
  EFHC1 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      0    8
  EFHC1 WILD-TYPE   10  390
                        clus
vv                       EFHC1 MUTATED EFHC1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1042) Variable = EPB41L5 MUTATION ANALYSIS
D1042V1, survival
                   sevent
clus2                 0   1
  EPB41L5 MUTATED     8   3
  EPB41L5 WILD-TYPE 330 213
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               11               543 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                3               213 
$`EPB41L5 MUTATED`
TCGA-CG-4460 TCGA-LN-A49U TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-8680 
       21.99        15.35         6.97        44.94        28.14        31.96 
TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        6.58        22.68        20.25        38.14        37.22 

$`EPB41L5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.41        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
             6.58              0.00 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
            44.94            122.30 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
            22.68             13.48 
[1] "6.6 - 44.9 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D1042V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB41L5 MUTATED         0        0        0        0         3         1
  EPB41L5 WILD-TYPE      10       20       46       31        81        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41L5 MUTATED           0          3          0          2        2
  EPB41L5 WILD-TYPE        29         81         62         37       41
                   vv
clus                STAGE IVA
  EPB41L5 MUTATED           0
  EPB41L5 WILD-TYPE         4
D1042V3, multiclass
            clus
vv           EPB41L5 MUTATED EPB41L5 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  EPB41L5 MUTATED       0   0   5   6
  EPB41L5 WILD-TYPE    54 135 256  96
D1042V4, multiclass
       clus
vv      EPB41L5 MUTATED EPB41L5 WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  5               256
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  EPB41L5 MUTATED     3   5   2   1
  EPB41L5 WILD-TYPE 192 168  87  84
D1042V5, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  N0               3               192
  N1               5               168
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V6, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     8   2
  EPB41L5 WILD-TYPE 474  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      8    2
  EPB41L5 WILD-TYPE  474   36
   clus
vv  EPB41L5 MUTATED EPB41L5 WILD-TYPE
  0               8               474
  1               2                36
[1] 2 2
[1] FALSE
D1042V7, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     4   7
  EPB41L5 WILD-TYPE 168 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      4    7
  EPB41L5 WILD-TYPE  168  399
        clus
vv       EPB41L5 MUTATED EPB41L5 WILD-TYPE
  FEMALE               4               168
  MALE                 7               399
[1] 2 2
[1] FALSE
D1042V8, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     8   3
  EPB41L5 WILD-TYPE 408  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      8    3
  EPB41L5 WILD-TYPE  408   99
     clus
vv    EPB41L5 MUTATED EPB41L5 WILD-TYPE
  NO                8               408
  YES               3                99
[1] 2 2
[1] FALSE
D1042V9, continuous
[1] "Remove cluster labels:" "EPB41L5 MUTATED"       
clus
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49V        TCGA-LN-A49W 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
D1042V10, continuous
[1] "Remove cluster labels:" "EPB41L5 MUTATED"       
clus
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" "EPB41L5 WILD-TYPE" 
       TCGA-Z6-AAPN 
"EPB41L5 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EPB41L5 MUTATED       5                         0
  EPB41L5 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB41L5 MUTATED                                           0     5
  EPB41L5 WILD-TYPE                                         1   352
D1042V11, multiclass
                                           clus
vv                                          EPB41L5 MUTATED EPB41L5 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V12, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     0   8
  EPB41L5 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      0    8
  EPB41L5 WILD-TYPE   10  390
                        clus
vv                       EPB41L5 MUTATED EPB41L5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(1043) Variable = OR52A5 MUTATION ANALYSIS
D1043V1, survival
                  sevent
clus2                0   1
  OR52A5 MUTATED     5   5
  OR52A5 WILD-TYPE 333 211
  OR52A5 MUTATED OR52A5 WILD-TYPE 
              10              544 
  OR52A5 MUTATED OR52A5 WILD-TYPE 
               5              211 
$`OR52A5 MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GR TCGA-L5-A8NE TCGA-BR-8680 TCGA-CG-4466 TCGA-D7-A4YU 
       31.27        32.45        55.50        31.96        18.97        16.44 
TCGA-HU-A4G6 TCGA-HU-A4GQ TCGA-IN-7808 TCGA-R5-A7ZR 
       24.26         0.10         3.45         6.08 

$`OR52A5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  OR52A5 MUTATED OR52A5 WILD-TYPE 
             0.1              0.0 
  OR52A5 MUTATED OR52A5 WILD-TYPE 
            55.5            122.3 
  OR52A5 MUTATED OR52A5 WILD-TYPE 
          21.615           13.510 
[1] "0.1 - 55.5 (21.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1043V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR52A5 MUTATED         1        1        1        0         1         2
  OR52A5 WILD-TYPE       9       19       45       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR52A5 MUTATED           1          0          1          1        1
  OR52A5 WILD-TYPE        28         84         61         38       42
                  vv
clus               STAGE IVA
  OR52A5 MUTATED           0
  OR52A5 WILD-TYPE         4
D1043V3, multiclass
            clus
vv           OR52A5 MUTATED OR52A5 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  OR52A5 MUTATED       3   2   4   2
  OR52A5 WILD-TYPE    51 133 257 100
D1043V4, multiclass
       clus
vv      OR52A5 MUTATED OR52A5 WILD-TYPE
  T0+T1              3               51
  T2                 2              133
  T3                 4              257
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  OR52A5 MUTATED     3   3   2   2
  OR52A5 WILD-TYPE 192 170  87  83
D1043V5, multiclass
    clus
vv   OR52A5 MUTATED OR52A5 WILD-TYPE
  N0              3              192
  N1              3              170
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V6, binary
                  cls
clus                 0   1
  OR52A5 MUTATED     8   2
  OR52A5 WILD-TYPE 474  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A5 MUTATED      8    2
  OR52A5 WILD-TYPE  474   36
   clus
vv  OR52A5 MUTATED OR52A5 WILD-TYPE
  0              8              474
  1              2               36
[1] 2 2
[1] FALSE
D1043V7, binary
                  cls
clus                 0   1
  OR52A5 MUTATED     2   9
  OR52A5 WILD-TYPE 170 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A5 MUTATED      2    9
  OR52A5 WILD-TYPE  170  397
        clus
vv       OR52A5 MUTATED OR52A5 WILD-TYPE
  FEMALE              2              170
  MALE                9              397
[1] 2 2
[1] FALSE
D1043V8, binary
                  cls
clus                 0   1
  OR52A5 MUTATED    11   0
  OR52A5 WILD-TYPE 405 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A5 MUTATED     11    0
  OR52A5 WILD-TYPE  405  102
     clus
vv    OR52A5 MUTATED OR52A5 WILD-TYPE
  NO              11              405
  YES              0              102
[1] 2 2
[1] FALSE
D1043V9, continuous
D1043V10, continuous
[1] "Remove cluster labels:" "OR52A5 MUTATED"        
clus
  OR52A5 MUTATED OR52A5 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" "OR52A5 WILD-TYPE" 
      TCGA-Z6-AAPN 
"OR52A5 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OR52A5 MUTATED       3                         2
  OR52A5 WILD-TYPE   130                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR52A5 MUTATED                                           0     3
  OR52A5 WILD-TYPE                                         1   354
D1043V11, multiclass
                                           clus
vv                                          OR52A5 MUTATED OR52A5 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V12, binary
                  cls
clus                 0   1
  OR52A5 MUTATED     0   7
  OR52A5 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A5 MUTATED      0    7
  OR52A5 WILD-TYPE   10  391
                        clus
vv                       OR52A5 MUTATED OR52A5 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(1044) Variable = ASB5 MUTATION ANALYSIS
D1044V1, survival
                sevent
clus2              0   1
  ASB5 MUTATED     5   6
  ASB5 WILD-TYPE 333 210
  ASB5 MUTATED ASB5 WILD-TYPE 
            11            543 
  ASB5 MUTATED ASB5 WILD-TYPE 
             6            210 
$`ASB5 MUTATED`
TCGA-R6-A6DN TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8680 
        8.02         6.97        30.90        14.79         1.12        31.96 
TCGA-CD-5802 TCGA-CG-4306 TCGA-D7-A6EY TCGA-R5-A7ZE TCGA-VQ-A8P2 
       13.35         1.02        11.44        18.21        38.14 

$`ASB5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.02        13.15        13.18        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        14.04        45.67         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ASB5 MUTATED ASB5 WILD-TYPE 
          1.02           0.00 
  ASB5 MUTATED ASB5 WILD-TYPE 
         38.14         122.30 
  ASB5 MUTATED ASB5 WILD-TYPE 
         13.35          13.58 
[1] "1.0 - 38.1 (13.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1044V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASB5 MUTATED         0        0        0        1         1         0
  ASB5 WILD-TYPE      10       20       46       30        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASB5 MUTATED           0          4          1          0        2         0
  ASB5 WILD-TYPE        29         80         61         39       41         4
D1044V3, multiclass
            clus
vv           ASB5 MUTATED ASB5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ASB5 MUTATED       0   1   6   3
  ASB5 WILD-TYPE    54 134 255  99
D1044V4, multiclass
       clus
vv      ASB5 MUTATED ASB5 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               6            255
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ASB5 MUTATED     2   3   3   1
  ASB5 WILD-TYPE 193 170  86  84
D1044V5, multiclass
    clus
vv   ASB5 MUTATED ASB5 WILD-TYPE
  N0            2            193
  N1            3            170
  N2            3             86
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V6, binary
                cls
clus               0   1
  ASB5 MUTATED     7   2
  ASB5 WILD-TYPE 475  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      7    2
  ASB5 WILD-TYPE  475   36
   clus
vv  ASB5 MUTATED ASB5 WILD-TYPE
  0            7            475
  1            2             36
[1] 2 2
[1] FALSE
D1044V7, binary
                cls
clus               0   1
  ASB5 MUTATED     5   6
  ASB5 WILD-TYPE 167 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      5    6
  ASB5 WILD-TYPE  167  400
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  FEMALE            5            167
  MALE              6            400
[1] 2 2
[1] FALSE
D1044V8, binary
                cls
clus               0   1
  ASB5 MUTATED     7   2
  ASB5 WILD-TYPE 409 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      7    2
  ASB5 WILD-TYPE  409  100
     clus
vv    ASB5 MUTATED ASB5 WILD-TYPE
  NO             7            409
  YES            2            100
[1] 2 2
[1] FALSE
D1044V9, continuous
D1044V10, continuous
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-Z6-AAPN 
"ASB5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ASB5 MUTATED       2                         0
  ASB5 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASB5 MUTATED                                           0     8
  ASB5 WILD-TYPE                                         1   349
D1044V11, multiclass
                                           clus
vv                                          ASB5 MUTATED ASB5 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V12, binary
                cls
clus               0   1
  ASB5 MUTATED     0   9
  ASB5 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      0    9
  ASB5 WILD-TYPE   10  389
                        clus
vv                       ASB5 MUTATED ASB5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(1045) Variable = MMP10 MUTATION ANALYSIS
D1045V1, survival
                 sevent
clus2               0   1
  MMP10 MUTATED     5   4
  MMP10 WILD-TYPE 333 212
  MMP10 MUTATED MMP10 WILD-TYPE 
              9             545 
  MMP10 MUTATED MMP10 WILD-TYPE 
              4             212 
$`MMP10 MUTATED`
TCGA-CG-4460 TCGA-L5-A4ON TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 
       21.99        18.35        28.14        31.96        16.14         6.02 
TCGA-CG-5733 TCGA-HU-A4G8 TCGA-HU-A4H3 
       21.07        22.68        29.00 

$`MMP10 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MMP10 MUTATED MMP10 WILD-TYPE 
           6.02            0.00 
  MMP10 MUTATED MMP10 WILD-TYPE 
          31.96          122.30 
  MMP10 MUTATED MMP10 WILD-TYPE 
          21.99           13.48 
[1] "6.0 - 32.0 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1045V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP10 MUTATED         0        0        0        0         0         3
  MMP10 WILD-TYPE      10       20       46       31        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP10 MUTATED           0          1          1          2        3         0
  MMP10 WILD-TYPE        29         83         61         37       40         4
D1045V3, multiclass
            clus
vv           MMP10 MUTATED MMP10 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MMP10 MUTATED       1   1   2   6
  MMP10 WILD-TYPE    53 134 259  96
D1045V4, multiclass
       clus
vv      MMP10 MUTATED MMP10 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                2             259
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MMP10 MUTATED     1   4   2   3
  MMP10 WILD-TYPE 194 169  87  82
D1045V5, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  N0             1             194
  N1             4             169
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V6, binary
                 cls
clus                0   1
  MMP10 MUTATED     7   2
  MMP10 WILD-TYPE 475  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      7    2
  MMP10 WILD-TYPE  475   36
   clus
vv  MMP10 MUTATED MMP10 WILD-TYPE
  0             7             475
  1             2              36
[1] 2 2
[1] FALSE
D1045V7, binary
                 cls
clus                0   1
  MMP10 MUTATED     5   5
  MMP10 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      5    5
  MMP10 WILD-TYPE  167  401
        clus
vv       MMP10 MUTATED MMP10 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D1045V8, binary
                 cls
clus                0   1
  MMP10 MUTATED     8   0
  MMP10 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      8    0
  MMP10 WILD-TYPE  408  102
     clus
vv    MMP10 MUTATED MMP10 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D1045V9, continuous
D1045V10, continuous
[1] "Remove cluster labels:" "MMP10 MUTATED"         
clus
  MMP10 MUTATED MMP10 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" "MMP10 WILD-TYPE" 
     TCGA-Z6-AAPN 
"MMP10 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MMP10 MUTATED       3                         0
  MMP10 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MMP10 MUTATED                                           0     4
  MMP10 WILD-TYPE                                         1   353
D1045V11, multiclass
                                           clus
vv                                          MMP10 MUTATED MMP10 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V12, binary
                 cls
clus                0   1
  MMP10 MUTATED     0   6
  MMP10 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      0    6
  MMP10 WILD-TYPE   10  392
                        clus
vv                       MMP10 MUTATED MMP10 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1046) Variable = FGF5 MUTATION ANALYSIS
D1046V1, survival
                sevent
clus2              0   1
  FGF5 MUTATED     3   4
  FGF5 WILD-TYPE 335 212
  FGF5 MUTATED FGF5 WILD-TYPE 
             7            547 
  FGF5 MUTATED FGF5 WILD-TYPE 
             4            212 
$`FGF5 MUTATED`
TCGA-JY-A93C TCGA-L5-A8NM TCGA-RE-A7BO TCGA-VR-A8EX TCGA-BR-A453 TCGA-HU-A4GX 
       23.18         7.76         7.00        28.11         6.08        20.25 
TCGA-HU-A4H8 
       14.07 

$`FGF5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  FGF5 MUTATED FGF5 WILD-TYPE 
          6.08           0.00 
  FGF5 MUTATED FGF5 WILD-TYPE 
         28.11         122.30 
  FGF5 MUTATED FGF5 WILD-TYPE 
         14.07          13.55 
[1] "6.1 - 28.1 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D1046V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF5 MUTATED         0        0        1        0         0         2
  FGF5 WILD-TYPE      10       20       45       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGF5 MUTATED           0          0          1          1        1         1
  FGF5 WILD-TYPE        29         84         61         38       42         3
D1046V3, multiclass
            clus
vv           FGF5 MUTATED FGF5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  FGF5 MUTATED       3   1   1   2
  FGF5 WILD-TYPE    51 134 260 100
D1046V4, multiclass
       clus
vv      FGF5 MUTATED FGF5 WILD-TYPE
  T0+T1            3             51
  T2               1            134
  T3               1            260
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  FGF5 MUTATED     0   5   2   1
  FGF5 WILD-TYPE 195 168  87  84
D1046V5, multiclass
    clus
vv   FGF5 MUTATED FGF5 WILD-TYPE
  N0            0            195
  N1            5            168
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V6, binary
                cls
clus               0   1
  FGF5 MUTATED     6   2
  FGF5 WILD-TYPE 476  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF5 MUTATED      6    2
  FGF5 WILD-TYPE  476   36
   clus
vv  FGF5 MUTATED FGF5 WILD-TYPE
  0            6            476
  1            2             36
[1] 2 2
[1] FALSE
D1046V7, binary
                cls
clus               0   1
  FGF5 MUTATED     4   4
  FGF5 WILD-TYPE 168 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF5 MUTATED      4    4
  FGF5 WILD-TYPE  168  402
        clus
vv       FGF5 MUTATED FGF5 WILD-TYPE
  FEMALE            4            168
  MALE              4            402
[1] 2 2
[1] FALSE
D1046V8, binary
                cls
clus               0   1
  FGF5 MUTATED     7   0
  FGF5 WILD-TYPE 409 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF5 MUTATED      7    0
  FGF5 WILD-TYPE  409  102
     clus
vv    FGF5 MUTATED FGF5 WILD-TYPE
  NO             7            409
  YES            0            102
[1] 2 2
[1] FALSE
D1046V9, continuous
[1] "Remove cluster labels:" "FGF5 MUTATED"          
clus
  FGF5 MUTATED FGF5 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
D1046V10, continuous
[1] "Remove cluster labels:" "FGF5 MUTATED"          
clus
  FGF5 MUTATED FGF5 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-V5-A7RB 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" "FGF5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FGF5 MUTATED       4                         0
  FGF5 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF5 MUTATED                                           0     3
  FGF5 WILD-TYPE                                         1   354
D1046V11, multiclass
                                           clus
vv                                          FGF5 MUTATED FGF5 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V12, binary
                cls
clus               0   1
  FGF5 MUTATED     0   5
  FGF5 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF5 MUTATED      0    5
  FGF5 WILD-TYPE   10  393
                        clus
vv                       FGF5 MUTATED FGF5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1047) Variable = CWH43 MUTATION ANALYSIS
D1047V1, survival
                 sevent
clus2               0   1
  CWH43 MUTATED     7   5
  CWH43 WILD-TYPE 331 211
  CWH43 MUTATED CWH43 WILD-TYPE 
             12             542 
  CWH43 MUTATED CWH43 WILD-TYPE 
              5             211 
$`CWH43 MUTATED`
TCGA-2H-A9GL TCGA-IG-A6QS TCGA-L5-A8NM TCGA-L5-A8NN TCGA-LN-A4A8 TCGA-XP-A8T8 
        5.92         9.96         7.76         5.49        15.52        14.37 
TCGA-B7-A5TI TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-A4QI TCGA-CG-5721 TCGA-D7-6817 
       19.56        31.10        25.18        21.44         6.02        12.79 

$`CWH43 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55        13.22        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       32.52        13.51        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CWH43 MUTATED CWH43 WILD-TYPE 
           5.49            0.00 
  CWH43 MUTATED CWH43 WILD-TYPE 
           31.1           122.3 
  CWH43 MUTATED CWH43 WILD-TYPE 
         13.580          13.565 
[1] "5.5 - 31.1 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1047V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CWH43 MUTATED         0        0        0        0         2         3
  CWH43 WILD-TYPE      10       20       46       31        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CWH43 MUTATED           2          2          0          2        1         0
  CWH43 WILD-TYPE        27         82         62         37       42         4
D1047V3, multiclass
            clus
vv           CWH43 MUTATED CWH43 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CWH43 MUTATED       1   4   3   4
  CWH43 WILD-TYPE    53 131 258  98
D1047V4, multiclass
       clus
vv      CWH43 MUTATED CWH43 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CWH43 MUTATED     2   7   1   2
  CWH43 WILD-TYPE 193 166  88  83
D1047V5, multiclass
    clus
vv   CWH43 MUTATED CWH43 WILD-TYPE
  N0             2             193
  N1             7             166
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V6, binary
                 cls
clus                0   1
  CWH43 MUTATED    12   0
  CWH43 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CWH43 MUTATED     12    0
  CWH43 WILD-TYPE  470   38
   clus
vv  CWH43 MUTATED CWH43 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D1047V7, binary
                 cls
clus                0   1
  CWH43 MUTATED     3   9
  CWH43 WILD-TYPE 169 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CWH43 MUTATED      3    9
  CWH43 WILD-TYPE  169  397
        clus
vv       CWH43 MUTATED CWH43 WILD-TYPE
  FEMALE             3             169
  MALE               9             397
[1] 2 2
[1] FALSE
D1047V8, binary
                 cls
clus                0   1
  CWH43 MUTATED    10   2
  CWH43 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CWH43 MUTATED     10    2
  CWH43 WILD-TYPE  406  100
     clus
vv    CWH43 MUTATED CWH43 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D1047V9, continuous
[1] "Remove cluster labels:" "CWH43 MUTATED"         
clus
  CWH43 MUTATED CWH43 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CWH43 WILD-TYPE" "CWH43 WILD-TYPE" 
D1047V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CWH43 MUTATED       1                         1
  CWH43 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CWH43 MUTATED                                           0     8
  CWH43 WILD-TYPE                                         1   349
D1047V11, multiclass
                                           clus
vv                                          CWH43 MUTATED CWH43 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V12, binary
                 cls
clus                0   1
  CWH43 MUTATED     1   7
  CWH43 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CWH43 MUTATED      1    7
  CWH43 WILD-TYPE    9  391
                        clus
vv                       CWH43 MUTATED CWH43 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1048) Variable = MTSS1 MUTATION ANALYSIS
D1048V1, survival
                 sevent
clus2               0   1
  MTSS1 MUTATED     7   7
  MTSS1 WILD-TYPE 331 209
  MTSS1 MUTATED MTSS1 WILD-TYPE 
             14             540 
  MTSS1 MUTATED MTSS1 WILD-TYPE 
              7             209 
$`MTSS1 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GR TCGA-IG-A8O2 TCGA-VR-AA4D TCGA-BR-4184 TCGA-BR-4201 
       19.99        32.45         4.67        46.19         6.97        30.90 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-A4MG 
       34.68        30.90        29.59        31.27        16.14         6.58 
TCGA-FP-7829 TCGA-HU-A4GN 
       19.53        29.98 

$`MTSS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MTSS1 MUTATED MTSS1 WILD-TYPE 
           4.67            0.00 
  MTSS1 MUTATED MTSS1 WILD-TYPE 
          46.19          122.30 
  MTSS1 MUTATED MTSS1 WILD-TYPE 
         29.785          13.445 
[1] "4.7 - 46.2 (29.8)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D1048V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTSS1 MUTATED         0        0        0        0         4         3
  MTSS1 WILD-TYPE      10       20       46       31        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTSS1 MUTATED           0          2          2          2        1         0
  MTSS1 WILD-TYPE        29         82         60         37       42         4
D1048V3, multiclass
            clus
vv           MTSS1 MUTATED MTSS1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MTSS1 MUTATED       1   2   9   3
  MTSS1 WILD-TYPE    53 133 252  99
D1048V4, multiclass
       clus
vv      MTSS1 MUTATED MTSS1 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                9             252
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MTSS1 MUTATED     4   4   3   3
  MTSS1 WILD-TYPE 191 169  86  82
D1048V5, multiclass
    clus
vv   MTSS1 MUTATED MTSS1 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V6, binary
                 cls
clus                0   1
  MTSS1 MUTATED    13   0
  MTSS1 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTSS1 MUTATED     13    0
  MTSS1 WILD-TYPE  469   38
   clus
vv  MTSS1 MUTATED MTSS1 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D1048V7, binary
                 cls
clus                0   1
  MTSS1 MUTATED     5  10
  MTSS1 WILD-TYPE 167 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTSS1 MUTATED      5   10
  MTSS1 WILD-TYPE  167  396
        clus
vv       MTSS1 MUTATED MTSS1 WILD-TYPE
  FEMALE             5             167
  MALE              10             396
[1] 2 2
[1] FALSE
D1048V8, binary
                 cls
clus                0   1
  MTSS1 MUTATED    11   2
  MTSS1 WILD-TYPE 405 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTSS1 MUTATED     11    2
  MTSS1 WILD-TYPE  405  100
     clus
vv    MTSS1 MUTATED MTSS1 WILD-TYPE
  NO             11             405
  YES             2             100
[1] 2 2
[1] FALSE
D1048V9, continuous
[1] "Remove cluster labels:" "MTSS1 MUTATED"         
clus
  MTSS1 MUTATED MTSS1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7B 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
D1048V10, continuous
[1] "Remove cluster labels:" "MTSS1 MUTATED"         
clus
  MTSS1 MUTATED MTSS1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" "MTSS1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTSS1 MUTATED       3                         0
  MTSS1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTSS1 MUTATED                                           0    11
  MTSS1 WILD-TYPE                                         1   346
D1048V11, multiclass
                                           clus
vv                                          MTSS1 MUTATED MTSS1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V12, binary
                 cls
clus                0   1
  MTSS1 MUTATED     0  12
  MTSS1 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTSS1 MUTATED      0   12
  MTSS1 WILD-TYPE   10  386
                        clus
vv                       MTSS1 MUTATED MTSS1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(1049) Variable = KIAA2018 MUTATION ANALYSIS
D1049V1, survival
                    sevent
clus2                  0   1
  KIAA2018 MUTATED    16  14
  KIAA2018 WILD-TYPE 322 202
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                30                524 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                14                202 
$`KIAA2018 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-2H-A9GI TCGA-2H-A9GR TCGA-IG-A4QS TCGA-KH-A6WC 
        4.31        19.99        14.30        32.45         3.88         6.28 
TCGA-L5-A4OJ TCGA-L5-A8NF TCGA-L5-A8NM TCGA-LN-A49M TCGA-LN-A7HW TCGA-R6-A6Y2 
       21.01         2.66         7.76        12.66        12.00         9.30 
TCGA-R6-A8W8 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-8361 
        2.89         6.97         9.67        34.68         9.17        31.10 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-4437 TCGA-CG-5726 
        1.12        12.79        27.12        31.96         8.05        28.96 
TCGA-CG-5728 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-IN-7808 TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       65.10        24.20        29.98         3.45        38.14        22.19 

$`KIAA2018 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.18         9.21        20.22         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40        36.36        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
              1.12               0.00 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
              65.1              122.3 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
            12.725             13.630 
[1] "1.1 - 65.1 (12.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1049V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA2018 MUTATED         2        3        1        1         6         4
  KIAA2018 WILD-TYPE       8       17       45       30        78        79
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA2018 MUTATED           1          2          3          2        1
  KIAA2018 WILD-TYPE        28         82         59         37       42
                    vv
clus                 STAGE IVA
  KIAA2018 MUTATED           1
  KIAA2018 WILD-TYPE         3
D1049V3, multiclass
            clus
vv           KIAA2018 MUTATED KIAA2018 WILD-TYPE
  STAGE I                   2                  8
  STAGE IA                  3                 17
  STAGE IB                  1                 45
  STAGE II                  1                 30
  STAGE IIA                 6                 78
  STAGE IIB                 4                 79
  STAGE III                 1                 28
  STAGE IIIA                2                 82
  STAGE IIIB                3                 59
  STAGE IIIC                2                 37
  STAGE IV                  1                 42
  STAGE IVA                 1                  3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  KIAA2018 MUTATED       7   6  10   6
  KIAA2018 WILD-TYPE    47 129 251  96
D1049V4, multiclass
       clus
vv      KIAA2018 MUTATED KIAA2018 WILD-TYPE
  T0+T1                7                 47
  T2                   6                129
  T3                  10                251
  T4                   6                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  KIAA2018 MUTATED    14   8   3   3
  KIAA2018 WILD-TYPE 181 165  86  82
D1049V5, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  N0               14                181
  N1                8                165
  N2                3                 86
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V6, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    23   3
  KIAA2018 WILD-TYPE 459  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     23    3
  KIAA2018 WILD-TYPE  459   35
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0               23                459
  1                3                 35
[1] 2 2
[1] FALSE
D1049V7, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    10  22
  KIAA2018 WILD-TYPE 162 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     10   22
  KIAA2018 WILD-TYPE  162  384
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  FEMALE               10                162
  MALE                 22                384
[1] 2 2
[1] FALSE
D1049V8, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    25   3
  KIAA2018 WILD-TYPE 391  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     25    3
  KIAA2018 WILD-TYPE  391   99
     clus
vv    KIAA2018 MUTATED KIAA2018 WILD-TYPE
  NO                25                391
  YES                3                 99
[1] 2 2
[1] FALSE
D1049V9, continuous
D1049V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA2018 MUTATED       5                         1
  KIAA2018 WILD-TYPE   128                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA2018 MUTATED                                           0    21
  KIAA2018 WILD-TYPE                                         1   336
D1049V11, multiclass
                                           clus
vv                                          KIAA2018 MUTATED KIAA2018 WILD-TYPE
  ASIAN                                                    5                128
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   21                336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V12, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED     1  19
  KIAA2018 WILD-TYPE   9 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      1   19
  KIAA2018 WILD-TYPE    9  379
                        clus
vv                       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               19                379
[1] 2 2
[1] FALSE

Clustering(1050) Variable = SMC5 MUTATION ANALYSIS
D1050V1, survival
                sevent
clus2              0   1
  SMC5 MUTATED     8   5
  SMC5 WILD-TYPE 330 211
  SMC5 MUTATED SMC5 WILD-TYPE 
            13            541 
  SMC5 MUTATED SMC5 WILD-TYPE 
             5            211 
$`SMC5 MUTATED`
TCGA-2H-A9GO TCGA-LN-A49W TCGA-Z6-A8JE TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8059 
       16.24        13.25         2.10         6.97         9.67        14.43 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8591 TCGA-BR-8680 TCGA-HF-7133 TCGA-HU-A4GT 
        0.26         4.31        28.14        31.96        63.06         6.51 
TCGA-VQ-A8P2 
       38.14 

$`SMC5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SMC5 MUTATED SMC5 WILD-TYPE 
          0.26           0.00 
  SMC5 MUTATED SMC5 WILD-TYPE 
         63.06         122.30 
  SMC5 MUTATED SMC5 WILD-TYPE 
         13.25          13.58 
[1] "0.3 - 63.1 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1050V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMC5 MUTATED         0        0        2        0         1         0
  SMC5 WILD-TYPE      10       20       44       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC5 MUTATED           2          3          0          1        2         1
  SMC5 WILD-TYPE        27         81         62         38       41         3
D1050V3, multiclass
            clus
vv           SMC5 MUTATED SMC5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             2             27
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SMC5 MUTATED       0   3   5   4
  SMC5 WILD-TYPE    54 132 256  98
D1050V4, multiclass
       clus
vv      SMC5 MUTATED SMC5 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SMC5 MUTATED     3   6   1   2
  SMC5 WILD-TYPE 192 167  88  83
D1050V5, multiclass
    clus
vv   SMC5 MUTATED SMC5 WILD-TYPE
  N0            3            192
  N1            6            167
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V6, binary
                cls
clus               0   1
  SMC5 MUTATED    10   2
  SMC5 WILD-TYPE 472  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED     10    2
  SMC5 WILD-TYPE  472   36
   clus
vv  SMC5 MUTATED SMC5 WILD-TYPE
  0           10            472
  1            2             36
[1] 2 2
[1] FALSE
D1050V7, binary
                cls
clus               0   1
  SMC5 MUTATED     5   8
  SMC5 WILD-TYPE 167 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      5    8
  SMC5 WILD-TYPE  167  398
        clus
vv       SMC5 MUTATED SMC5 WILD-TYPE
  FEMALE            5            167
  MALE              8            398
[1] 2 2
[1] FALSE
D1050V8, binary
                cls
clus               0   1
  SMC5 MUTATED    10   3
  SMC5 WILD-TYPE 406  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED     10    3
  SMC5 WILD-TYPE  406   99
     clus
vv    SMC5 MUTATED SMC5 WILD-TYPE
  NO            10            406
  YES            3             99
[1] 2 2
[1] FALSE
D1050V9, continuous
[1] "Remove cluster labels:" "SMC5 MUTATED"          
clus
  SMC5 MUTATED SMC5 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
D1050V10, continuous
[1] "Remove cluster labels:" "SMC5 MUTATED"          
clus
  SMC5 MUTATED SMC5 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" "SMC5 WILD-TYPE" 
    TCGA-Z6-AAPN 
"SMC5 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SMC5 MUTATED       3                         0
  SMC5 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMC5 MUTATED                                           0     8
  SMC5 WILD-TYPE                                         1   349
D1050V11, multiclass
                                           clus
vv                                          SMC5 MUTATED SMC5 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V12, binary
                cls
clus               0   1
  SMC5 MUTATED     0   9
  SMC5 WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      0    9
  SMC5 WILD-TYPE   10  389
                        clus
vv                       SMC5 MUTATED SMC5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(1051) Variable = BAG4 MUTATION ANALYSIS
D1051V1, survival
                sevent
clus2              0   1
  BAG4 MUTATED     2   1
  BAG4 WILD-TYPE 336 215
  BAG4 MUTATED BAG4 WILD-TYPE 
             3            551 
  BAG4 MUTATED BAG4 WILD-TYPE 
             1            215 
$`BAG4 MUTATED`
TCGA-D7-A4YV TCGA-HF-7132 TCGA-MX-A5UJ 
        5.92        77.29        19.73 

$`BAG4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  BAG4 MUTATED BAG4 WILD-TYPE 
          5.92           0.00 
  BAG4 MUTATED BAG4 WILD-TYPE 
         77.29         122.30 
  BAG4 MUTATED BAG4 WILD-TYPE 
         19.73          13.55 
[1] "5.9 - 77.3 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D1051V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAG4 MUTATED         0        0        1        1         0         1
  BAG4 WILD-TYPE      10       20       45       30        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAG4 MUTATED           0          1          0          0        0         0
  BAG4 WILD-TYPE        29         83         62         39       43         4
D1051V3, multiclass
            clus
vv           BAG4 MUTATED BAG4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BAG4 MUTATED       1   2   2   0
  BAG4 WILD-TYPE    53 133 259 102
D1051V4, multiclass
       clus
vv      BAG4 MUTATED BAG4 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               2            259
  T4               0            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BAG4 MUTATED     1   2   1   0
  BAG4 WILD-TYPE 194 171  88  85
D1051V5, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  N0            1            194
  N1            2            171
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V6, binary
                cls
clus               0   1
  BAG4 MUTATED     5   0
  BAG4 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    0
  BAG4 WILD-TYPE  477   38
   clus
vv  BAG4 MUTATED BAG4 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D1051V7, binary
                cls
clus               0   1
  BAG4 MUTATED     3   2
  BAG4 WILD-TYPE 169 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      3    2
  BAG4 WILD-TYPE  169  404
        clus
vv       BAG4 MUTATED BAG4 WILD-TYPE
  FEMALE            3            169
  MALE              2            404
[1] 2 2
[1] FALSE
D1051V8, binary
                cls
clus               0   1
  BAG4 MUTATED     2   1
  BAG4 WILD-TYPE 414 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      2    1
  BAG4 WILD-TYPE  414  101
     clus
vv    BAG4 MUTATED BAG4 WILD-TYPE
  NO             2            414
  YES            1            101
[1] 2 2
[1] FALSE
D1051V9, continuous
D1051V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAG4 MUTATED       0                         0
  BAG4 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAG4 MUTATED                                           0     3
  BAG4 WILD-TYPE                                         1   354
D1051V11, multiclass
                                           clus
vv                                          BAG4 MUTATED BAG4 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V12, binary
                cls
clus               0   1
  BAG4 MUTATED     0   3
  BAG4 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      0    3
  BAG4 WILD-TYPE   10  395
                        clus
vv                       BAG4 MUTATED BAG4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(1052) Variable = ZMYND8 MUTATION ANALYSIS
D1052V1, survival
                  sevent
clus2                0   1
  ZMYND8 MUTATED    15   4
  ZMYND8 WILD-TYPE 323 212
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              19              535 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               4              212 
$`ZMYND8 MUTATED`
TCGA-L5-A8NH TCGA-LN-A49V TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8372 
       12.92        12.59        26.70        34.68         4.31        31.27 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-A6EV TCGA-HF-7132 
        1.12        31.96        21.07        25.71        11.24        77.29 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-IN-A7NR 
       30.51        22.68        29.98         0.10        14.07         6.51 
TCGA-VQ-A8P2 
       38.14 

$`ZMYND8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 
       28.96        65.10         4.01        69.04         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
             0.1              0.0 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           77.29           122.30 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           22.68            13.51 
[1] "0.1 - 77.3 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D1052V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYND8 MUTATED         0        0        2        1         4         3
  ZMYND8 WILD-TYPE      10       20       44       30        80        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND8 MUTATED           0          3          0          3        3
  ZMYND8 WILD-TYPE        29         81         62         36       40
                  vv
clus               STAGE IVA
  ZMYND8 MUTATED           0
  ZMYND8 WILD-TYPE         4
D1052V3, multiclass
            clus
vv           ZMYND8 MUTATED ZMYND8 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               4               80
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZMYND8 MUTATED       2   6   5   6
  ZMYND8 WILD-TYPE    52 129 256  96
D1052V4, multiclass
       clus
vv      ZMYND8 MUTATED ZMYND8 WILD-TYPE
  T0+T1              2               52
  T2                 6              129
  T3                 5              256
  T4                 6               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZMYND8 MUTATED     6   6   4   4
  ZMYND8 WILD-TYPE 189 167  85  81
D1052V5, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  N0              6              189
  N1              6              167
  N2              4               85
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V6, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    18   3
  ZMYND8 WILD-TYPE 464  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     18    3
  ZMYND8 WILD-TYPE  464   35
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0             18              464
  1              3               35
[1] 2 2
[1] FALSE
D1052V7, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    12   9
  ZMYND8 WILD-TYPE 160 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     12    9
  ZMYND8 WILD-TYPE  160  397
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  FEMALE             12              160
  MALE                9              397
[1] 2 2
[1] FALSE
D1052V8, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    14   4
  ZMYND8 WILD-TYPE 402  98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     14    4
  ZMYND8 WILD-TYPE  402   98
     clus
vv    ZMYND8 MUTATED ZMYND8 WILD-TYPE
  NO              14              402
  YES              4               98
[1] 2 2
[1] FALSE
D1052V9, continuous
[1] "Remove cluster labels:" "ZMYND8 MUTATED"        
clus
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49W 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
D1052V10, continuous
[1] "Remove cluster labels:" "ZMYND8 MUTATED"        
clus
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" "ZMYND8 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZMYND8 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZMYND8 MUTATED       6                         0
  ZMYND8 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYND8 MUTATED                                           0    12
  ZMYND8 WILD-TYPE                                         1   345
D1052V11, multiclass
                                           clus
vv                                          ZMYND8 MUTATED ZMYND8 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V12, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED     0  16
  ZMYND8 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      0   16
  ZMYND8 WILD-TYPE   10  382
                        clus
vv                       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(1053) Variable = MPP5 MUTATION ANALYSIS
D1053V1, survival
                sevent
clus2              0   1
  MPP5 MUTATED     5   4
  MPP5 WILD-TYPE 333 212
  MPP5 MUTATED MPP5 WILD-TYPE 
             9            545 
  MPP5 MUTATED MPP5 WILD-TYPE 
             4            212 
$`MPP5 MUTATED`
TCGA-IG-A3YC TCGA-IG-A5B8 TCGA-L5-A8NM TCGA-LN-A9FP TCGA-VR-A8EZ TCGA-BR-6452 
       20.12         0.79         7.76        12.03        18.18        34.68 
TCGA-BR-8591 TCGA-D7-6527 TCGA-VQ-A8P2 
       28.14        10.26        38.14 

$`MPP5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
       33.27        35.21         0.85        20.78         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MPP5 MUTATED MPP5 WILD-TYPE 
          0.79           0.00 
  MPP5 MUTATED MPP5 WILD-TYPE 
         38.14         122.30 
  MPP5 MUTATED MPP5 WILD-TYPE 
         18.18          13.55 
[1] "0.8 - 38.1 (18.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1053V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MPP5 MUTATED         0        0        1        1         2         1
  MPP5 WILD-TYPE      10       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPP5 MUTATED           0          2          0          2        0         0
  MPP5 WILD-TYPE        29         82         62         37       43         4
D1053V3, multiclass
            clus
vv           MPP5 MUTATED MPP5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MPP5 MUTATED       0   3   4   2
  MPP5 WILD-TYPE    54 132 257 100
D1053V4, multiclass
       clus
vv      MPP5 MUTATED MPP5 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               4            257
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MPP5 MUTATED     3   4   0   2
  MPP5 WILD-TYPE 192 169  89  83
D1053V5, multiclass
    clus
vv   MPP5 MUTATED MPP5 WILD-TYPE
  N0            3            192
  N1            4            169
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V6, binary
                cls
clus               0   1
  MPP5 MUTATED     9   0
  MPP5 WILD-TYPE 473  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP5 MUTATED      9    0
  MPP5 WILD-TYPE  473   38
   clus
vv  MPP5 MUTATED MPP5 WILD-TYPE
  0            9            473
  1            0             38
[1] 2 2
[1] FALSE
D1053V7, binary
                cls
clus               0   1
  MPP5 MUTATED     3   6
  MPP5 WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP5 MUTATED      3    6
  MPP5 WILD-TYPE  169  400
        clus
vv       MPP5 MUTATED MPP5 WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D1053V8, binary
                cls
clus               0   1
  MPP5 MUTATED     6   3
  MPP5 WILD-TYPE 410  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP5 MUTATED      6    3
  MPP5 WILD-TYPE  410   99
     clus
vv    MPP5 MUTATED MPP5 WILD-TYPE
  NO             6            410
  YES            3             99
[1] 2 2
[1] FALSE
D1053V9, continuous
[1] "Remove cluster labels:" "MPP5 MUTATED"          
clus
  MPP5 MUTATED MPP5 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A51D     TCGA-IG-A5S3     TCGA-IG-A7DP 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8Q7 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"MPP5 WILD-TYPE" "MPP5 WILD-TYPE" 
D1053V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MPP5 MUTATED       1                         0
  MPP5 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MPP5 MUTATED                                           0     8
  MPP5 WILD-TYPE                                         1   349
D1053V11, multiclass
                                           clus
vv                                          MPP5 MUTATED MPP5 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V12, binary
                cls
clus               0   1
  MPP5 MUTATED     0   6
  MPP5 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP5 MUTATED      0    6
  MPP5 WILD-TYPE   10  392
                        clus
vv                       MPP5 MUTATED MPP5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1054) Variable = ECSIT MUTATION ANALYSIS
D1054V1, survival
                 sevent
clus2               0   1
  ECSIT MUTATED     4   4
  ECSIT WILD-TYPE 334 212
  ECSIT MUTATED ECSIT WILD-TYPE 
              8             546 
  ECSIT MUTATED ECSIT WILD-TYPE 
              4             212 
$`ECSIT MUTATED`
TCGA-L5-A4OI TCGA-MX-A663 TCGA-V5-A7RC TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-8487 
       19.99         9.86         3.42         6.61        14.43         1.12 
TCGA-HF-A5NB TCGA-HU-A4H8 
       30.51        14.07 

$`ECSIT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ECSIT MUTATED ECSIT WILD-TYPE 
           1.12            0.00 
  ECSIT MUTATED ECSIT WILD-TYPE 
          30.51          122.30 
  ECSIT MUTATED ECSIT WILD-TYPE 
         11.965          13.565 
[1] "1.1 - 30.5 (12.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1054V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ECSIT MUTATED         0        0        1        0         2         0
  ECSIT WILD-TYPE      10       20       45       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ECSIT MUTATED           2          0          0          2        0         0
  ECSIT WILD-TYPE        27         84         62         37       43         4
D1054V3, multiclass
            clus
vv           ECSIT MUTATED ECSIT WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              2              27
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ECSIT MUTATED       1   1   3   2
  ECSIT WILD-TYPE    53 134 258 100
D1054V4, multiclass
       clus
vv      ECSIT MUTATED ECSIT WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ECSIT MUTATED     2   3   0   2
  ECSIT WILD-TYPE 193 170  89  83
D1054V5, multiclass
    clus
vv   ECSIT MUTATED ECSIT WILD-TYPE
  N0             2             193
  N1             3             170
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V6, binary
                 cls
clus                0   1
  ECSIT MUTATED     6   0
  ECSIT WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      6    0
  ECSIT WILD-TYPE  476   38
   clus
vv  ECSIT MUTATED ECSIT WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1054V7, binary
                 cls
clus                0   1
  ECSIT MUTATED     3   5
  ECSIT WILD-TYPE 169 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      3    5
  ECSIT WILD-TYPE  169  401
        clus
vv       ECSIT MUTATED ECSIT WILD-TYPE
  FEMALE             3             169
  MALE               5             401
[1] 2 2
[1] FALSE
D1054V8, binary
                 cls
clus                0   1
  ECSIT MUTATED     6   2
  ECSIT WILD-TYPE 410 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      6    2
  ECSIT WILD-TYPE  410  100
     clus
vv    ECSIT MUTATED ECSIT WILD-TYPE
  NO              6             410
  YES             2             100
[1] 2 2
[1] FALSE
D1054V9, continuous
[1] "Remove cluster labels:" "ECSIT MUTATED"         
clus
  ECSIT MUTATED ECSIT WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RE      TCGA-V5-AASV 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
D1054V10, continuous
[1] "Remove cluster labels:" "ECSIT MUTATED"         
clus
  ECSIT MUTATED ECSIT WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" "ECSIT WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ECSIT MUTATED       1                         1
  ECSIT WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ECSIT MUTATED                                           0     5
  ECSIT WILD-TYPE                                         1   352
D1054V11, multiclass
                                           clus
vv                                          ECSIT MUTATED ECSIT WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V12, binary
                 cls
clus                0   1
  ECSIT MUTATED     0   6
  ECSIT WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      0    6
  ECSIT WILD-TYPE   10  392
                        clus
vv                       ECSIT MUTATED ECSIT WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1055) Variable = CSNK2A2 MUTATION ANALYSIS
D1055V1, survival
                   sevent
clus2                 0   1
  CSNK2A2 MUTATED     7   2
  CSNK2A2 WILD-TYPE 331 214
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                9               545 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                2               214 
$`CSNK2A2 MUTATED`
TCGA-R6-A6DQ TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8536 
        7.59        35.84        31.27        27.12        31.96        12.43 
TCGA-KB-A93J TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       36.95        38.14        22.19 

$`CSNK2A2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.41        37.22        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
             7.59              0.00 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            38.14            122.30 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            31.27             13.51 
[1] "7.6 - 38.1 (31.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.7"
D1055V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSNK2A2 MUTATED         0        0        1        2         0         0
  CSNK2A2 WILD-TYPE      10       20       45       29        84        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK2A2 MUTATED           0          1          2          1        1
  CSNK2A2 WILD-TYPE        29         83         60         38       42
                   vv
clus                STAGE IVA
  CSNK2A2 MUTATED           0
  CSNK2A2 WILD-TYPE         4
D1055V3, multiclass
            clus
vv           CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 2                29
  STAGE IIA                0                84
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               2                60
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CSNK2A2 MUTATED       0   2   2   4
  CSNK2A2 WILD-TYPE    54 133 259  98
D1055V4, multiclass
       clus
vv      CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  2               259
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CSNK2A2 MUTATED     2   3   1   2
  CSNK2A2 WILD-TYPE 193 170  88  83
D1055V5, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V6, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     7   1
  CSNK2A2 WILD-TYPE 475  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      7    1
  CSNK2A2 WILD-TYPE  475   37
   clus
vv  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  0               7               475
  1               1                37
[1] 2 2
[1] FALSE
D1055V7, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     2   7
  CSNK2A2 WILD-TYPE 170 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      2    7
  CSNK2A2 WILD-TYPE  170  399
        clus
vv       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  FEMALE               2               170
  MALE                 7               399
[1] 2 2
[1] FALSE
D1055V8, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     6   2
  CSNK2A2 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      6    2
  CSNK2A2 WILD-TYPE  410  100
     clus
vv    CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D1055V9, continuous
D1055V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK2A2 MUTATED       2                         0
  CSNK2A2 WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK2A2 MUTATED                                           0     7
  CSNK2A2 WILD-TYPE                                         1   350
D1055V11, multiclass
                                           clus
vv                                          CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V12, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     0   6
  CSNK2A2 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      0    6
  CSNK2A2 WILD-TYPE   10  392
                        clus
vv                       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1056) Variable = CCR9 MUTATION ANALYSIS
D1056V1, survival
                sevent
clus2              0   1
  CCR9 MUTATED     3   5
  CCR9 WILD-TYPE 335 211
  CCR9 MUTATED CCR9 WILD-TYPE 
             8            546 
  CCR9 MUTATED CCR9 WILD-TYPE 
             5            211 
$`CCR9 MUTATED`
TCGA-R6-A6DQ TCGA-VR-AA4D TCGA-BR-8382 TCGA-BR-8680 TCGA-D7-A6EZ TCGA-HU-A4H5 
        7.59        46.19        25.05        31.96        20.32        23.80 
TCGA-IN-A6RL TCGA-VQ-A8P2 
       13.35        38.14 

$`CCR9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CCR9 MUTATED CCR9 WILD-TYPE 
          7.59           0.00 
  CCR9 MUTATED CCR9 WILD-TYPE 
         46.19         122.30 
  CCR9 MUTATED CCR9 WILD-TYPE 
        24.425         13.510 
[1] "7.6 - 46.2 (24.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1056V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCR9 MUTATED         0        0        1        0         0         1
  CCR9 WILD-TYPE      10       20       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCR9 MUTATED           0          3          0          1        1         0
  CCR9 WILD-TYPE        29         81         62         38       42         4
D1056V3, multiclass
            clus
vv           CCR9 MUTATED CCR9 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CCR9 MUTATED       1   2   1   3
  CCR9 WILD-TYPE    53 133 260  99
D1056V4, multiclass
       clus
vv      CCR9 MUTATED CCR9 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               1            260
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CCR9 MUTATED     1   3   2   1
  CCR9 WILD-TYPE 194 170  87  84
D1056V5, multiclass
    clus
vv   CCR9 MUTATED CCR9 WILD-TYPE
  N0            1            194
  N1            3            170
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V6, binary
                cls
clus               0   1
  CCR9 MUTATED     6   1
  CCR9 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR9 MUTATED      6    1
  CCR9 WILD-TYPE  476   37
   clus
vv  CCR9 MUTATED CCR9 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D1056V7, binary
                cls
clus               0   1
  CCR9 MUTATED     2   6
  CCR9 WILD-TYPE 170 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR9 MUTATED      2    6
  CCR9 WILD-TYPE  170  400
        clus
vv       CCR9 MUTATED CCR9 WILD-TYPE
  FEMALE            2            170
  MALE              6            400
[1] 2 2
[1] FALSE
D1056V8, binary
                cls
clus               0   1
  CCR9 MUTATED     5   2
  CCR9 WILD-TYPE 411 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR9 MUTATED      5    2
  CCR9 WILD-TYPE  411  100
     clus
vv    CCR9 MUTATED CCR9 WILD-TYPE
  NO             5            411
  YES            2            100
[1] 2 2
[1] FALSE
D1056V9, continuous
[1] "Remove cluster labels:" "CCR9 MUTATED"          
clus
  CCR9 MUTATED CCR9 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7B 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CCR9 WILD-TYPE" "CCR9 WILD-TYPE" "CCR9 WILD-TYPE" 
D1056V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CCR9 MUTATED       2                         0
  CCR9 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCR9 MUTATED                                           0     6
  CCR9 WILD-TYPE                                         1   351
D1056V11, multiclass
                                           clus
vv                                          CCR9 MUTATED CCR9 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V12, binary
                cls
clus               0   1
  CCR9 MUTATED     0   6
  CCR9 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR9 MUTATED      0    6
  CCR9 WILD-TYPE   10  392
                        clus
vv                       CCR9 MUTATED CCR9 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1057) Variable = PODN MUTATION ANALYSIS
D1057V1, survival
                sevent
clus2              0   1
  PODN MUTATED     7   6
  PODN WILD-TYPE 331 210
  PODN MUTATED PODN WILD-TYPE 
            13            541 
  PODN MUTATED PODN WILD-TYPE 
             6            210 
$`PODN MUTATED`
TCGA-IG-A3Y9 TCGA-LN-A7HY TCGA-VR-A8EX TCGA-BR-4253 TCGA-BR-7715 TCGA-BR-8363 
        0.85        12.03        28.11         4.08        33.63         0.26 
TCGA-BR-8591 TCGA-CD-8529 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A74B TCGA-FP-A4BE 
       28.14        12.30        28.96        65.10         7.13        11.08 
TCGA-HU-A4GX 
       20.25 

$`PODN WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        35.21        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34        19.96         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PODN MUTATED PODN WILD-TYPE 
          0.26           0.00 
  PODN MUTATED PODN WILD-TYPE 
          65.1          122.3 
  PODN MUTATED PODN WILD-TYPE 
         12.30          13.58 
[1] "0.3 - 65.1 (12.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1057V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PODN MUTATED         0        1        2        0         2         0
  PODN WILD-TYPE      10       19       44       31        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PODN MUTATED           1          2          1          2        2         1
  PODN WILD-TYPE        28         82         61         37       41         3
D1057V3, multiclass
            clus
vv           PODN MUTATED PODN WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PODN MUTATED       2   2   5   5
  PODN WILD-TYPE    52 133 256  97
D1057V4, multiclass
       clus
vv      PODN MUTATED PODN WILD-TYPE
  T0+T1            2             52
  T2               2            133
  T3               5            256
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PODN MUTATED     7   4   2   2
  PODN WILD-TYPE 188 169  87  83
D1057V5, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  N0            7            188
  N1            4            169
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V6, binary
                cls
clus               0   1
  PODN MUTATED    13   2
  PODN WILD-TYPE 469  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED     13    2
  PODN WILD-TYPE  469   36
   clus
vv  PODN MUTATED PODN WILD-TYPE
  0           13            469
  1            2             36
[1] 2 2
[1] FALSE
D1057V7, binary
                cls
clus               0   1
  PODN MUTATED     7   8
  PODN WILD-TYPE 165 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      7    8
  PODN WILD-TYPE  165  398
        clus
vv       PODN MUTATED PODN WILD-TYPE
  FEMALE            7            165
  MALE              8            398
[1] 2 2
[1] FALSE
D1057V8, binary
                cls
clus               0   1
  PODN MUTATED     9   2
  PODN WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      9    2
  PODN WILD-TYPE  407  100
     clus
vv    PODN MUTATED PODN WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D1057V9, continuous
D1057V10, continuous
[1] "Remove cluster labels:" "PODN MUTATED"          
clus
  PODN MUTATED PODN WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" "PODN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PODN MUTATED       3                         1
  PODN WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PODN MUTATED                                           0     8
  PODN WILD-TYPE                                         1   349
D1057V11, multiclass
                                           clus
vv                                          PODN MUTATED PODN WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V12, binary
                cls
clus               0   1
  PODN MUTATED     0  12
  PODN WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      0   12
  PODN WILD-TYPE   10  386
                        clus
vv                       PODN MUTATED PODN WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1058) Variable = VWA1 MUTATION ANALYSIS
D1058V1, survival
                sevent
clus2              0   1
  VWA1 MUTATED     5   2
  VWA1 WILD-TYPE 333 214
  VWA1 MUTATED VWA1 WILD-TYPE 
             7            547 
  VWA1 MUTATED VWA1 WILD-TYPE 
             2            214 
$`VWA1 MUTATED`
TCGA-L5-A4OI TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 
       19.99        34.68        13.87        29.59         4.31         1.12 
TCGA-CD-A4MG 
        6.58 

$`VWA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        6.61        15.95        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  VWA1 MUTATED VWA1 WILD-TYPE 
          1.12           0.00 
  VWA1 MUTATED VWA1 WILD-TYPE 
         34.68         122.30 
  VWA1 MUTATED VWA1 WILD-TYPE 
         13.87          13.55 
[1] "1.1 - 34.7 (13.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1058V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VWA1 MUTATED         0        0        2        0         3         2
  VWA1 WILD-TYPE      10       20       44       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWA1 MUTATED           0          0          0          1        0         0
  VWA1 WILD-TYPE        29         84         62         38       43         4
D1058V3, multiclass
            clus
vv           VWA1 MUTATED VWA1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  VWA1 MUTATED       0   2   5   1
  VWA1 WILD-TYPE    54 133 256 101
D1058V4, multiclass
       clus
vv      VWA1 MUTATED VWA1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               5            256
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  VWA1 MUTATED     6   1   0   1
  VWA1 WILD-TYPE 189 172  89  84
D1058V5, multiclass
    clus
vv   VWA1 MUTATED VWA1 WILD-TYPE
  N0            6            189
  N1            1            172
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V6, binary
                cls
clus               0   1
  VWA1 MUTATED     7   0
  VWA1 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      7    0
  VWA1 WILD-TYPE  475   38
   clus
vv  VWA1 MUTATED VWA1 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D1058V7, binary
                cls
clus               0   1
  VWA1 MUTATED     4   4
  VWA1 WILD-TYPE 168 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      4    4
  VWA1 WILD-TYPE  168  402
        clus
vv       VWA1 MUTATED VWA1 WILD-TYPE
  FEMALE            4            168
  MALE              4            402
[1] 2 2
[1] FALSE
D1058V8, binary
                cls
clus               0   1
  VWA1 MUTATED     7   0
  VWA1 WILD-TYPE 409 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      7    0
  VWA1 WILD-TYPE  409  102
     clus
vv    VWA1 MUTATED VWA1 WILD-TYPE
  NO             7            409
  YES            0            102
[1] 2 2
[1] FALSE
D1058V9, continuous
D1058V10, continuous
[1] "Remove cluster labels:" "VWA1 MUTATED"          
clus
  VWA1 MUTATED VWA1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" "VWA1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"VWA1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  VWA1 MUTATED       1                         0
  VWA1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VWA1 MUTATED                                           0     6
  VWA1 WILD-TYPE                                         1   351
D1058V11, multiclass
                                           clus
vv                                          VWA1 MUTATED VWA1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V12, binary
                cls
clus               0   1
  VWA1 MUTATED     0   6
  VWA1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      0    6
  VWA1 WILD-TYPE   10  392
                        clus
vv                       VWA1 MUTATED VWA1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1059) Variable = PADI3 MUTATION ANALYSIS
D1059V1, survival
                 sevent
clus2               0   1
  PADI3 MUTATED     7   7
  PADI3 WILD-TYPE 331 209
  PADI3 MUTATED PADI3 WILD-TYPE 
             14             540 
  PADI3 MUTATED PADI3 WILD-TYPE 
              7             209 
$`PADI3 MUTATED`
TCGA-R6-A6Y0 TCGA-VR-A8ET TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8081 
       53.95         1.55         9.67        34.68        36.16        32.25 
TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-5577 
        6.18        31.10        11.77         1.02        28.96        25.71 
TCGA-D7-A6EY TCGA-HU-A4GU 
       11.44         6.58 

$`PADI3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PADI3 MUTATED PADI3 WILD-TYPE 
           1.02            0.00 
  PADI3 MUTATED PADI3 WILD-TYPE 
          53.95          122.30 
  PADI3 MUTATED PADI3 WILD-TYPE 
         18.740          13.565 
[1] "1.0 - 54.0 (18.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1059V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PADI3 MUTATED         0        2        1        0         3         2
  PADI3 WILD-TYPE      10       18       45       31        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PADI3 MUTATED           0          2          1          1        1         0
  PADI3 WILD-TYPE        29         82         61         38       42         4
D1059V3, multiclass
            clus
vv           PADI3 MUTATED PADI3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PADI3 MUTATED       2   3   6   2
  PADI3 WILD-TYPE    52 132 255 100
D1059V4, multiclass
       clus
vv      PADI3 MUTATED PADI3 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PADI3 MUTATED     7   2   2   2
  PADI3 WILD-TYPE 188 171  87  83
D1059V5, multiclass
    clus
vv   PADI3 MUTATED PADI3 WILD-TYPE
  N0             7             188
  N1             2             171
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V6, binary
                 cls
clus                0   1
  PADI3 MUTATED    13   1
  PADI3 WILD-TYPE 469  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED     13    1
  PADI3 WILD-TYPE  469   37
   clus
vv  PADI3 MUTATED PADI3 WILD-TYPE
  0            13             469
  1             1              37
[1] 2 2
[1] FALSE
D1059V7, binary
                 cls
clus                0   1
  PADI3 MUTATED     6   9
  PADI3 WILD-TYPE 166 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED      6    9
  PADI3 WILD-TYPE  166  397
        clus
vv       PADI3 MUTATED PADI3 WILD-TYPE
  FEMALE             6             166
  MALE               9             397
[1] 2 2
[1] FALSE
D1059V8, binary
                 cls
clus                0   1
  PADI3 MUTATED    12   0
  PADI3 WILD-TYPE 404 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED     12    0
  PADI3 WILD-TYPE  404  102
     clus
vv    PADI3 MUTATED PADI3 WILD-TYPE
  NO             12             404
  YES             0             102
[1] 2 2
[1] FALSE
D1059V9, continuous
[1] "Remove cluster labels:" "PADI3 MUTATED"         
clus
  PADI3 MUTATED PADI3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PADI3 WILD-TYPE" "PADI3 WILD-TYPE" "PADI3 WILD-TYPE" 
D1059V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PADI3 MUTATED       2                         0
  PADI3 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PADI3 MUTATED                                           0    10
  PADI3 WILD-TYPE                                         1   347
D1059V11, multiclass
                                           clus
vv                                          PADI3 MUTATED PADI3 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V12, binary
                 cls
clus                0   1
  PADI3 MUTATED     0  11
  PADI3 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED      0   11
  PADI3 WILD-TYPE   10  387
                        clus
vv                       PADI3 MUTATED PADI3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1060) Variable = BMPR2 MUTATION ANALYSIS
D1060V1, survival
                 sevent
clus2               0   1
  BMPR2 MUTATED    17   4
  BMPR2 WILD-TYPE 321 212
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             21             533 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              4             212 
$`BMPR2 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NW TCGA-LN-A4A1 TCGA-B7-A5TI TCGA-BR-4257 TCGA-BR-6852 
       19.99        46.09        12.59        19.56         9.67        44.94 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8588 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 
       29.59        32.25        12.79         6.58        12.62        15.95 
TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6524 TCGA-F1-6874 TCGA-HF-A5NB 
        9.01       105.07        65.10        17.85        14.47        30.51 
TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 
       22.68        20.25        38.14 

$`BMPR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        31.20        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44         0.69         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  BMPR2 MUTATED BMPR2 WILD-TYPE 
           6.58            0.00 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
         105.07          122.30 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          19.99           13.41 
[1] "6.6 - 105.1 (20.0)" "0.0 - 122.3 (13.4)"
[1] "hr=" "3"  
D1060V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BMPR2 MUTATED         0        0        4        3         3         5
  BMPR2 WILD-TYPE      10       20       42       28        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BMPR2 MUTATED           0          1          0          4        1         0
  BMPR2 WILD-TYPE        29         83         62         35       42         4
D1060V3, multiclass
            clus
vv           BMPR2 MUTATED BMPR2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               4              42
  STAGE II               3              28
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             4              35
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BMPR2 MUTATED       0   7   5   9
  BMPR2 WILD-TYPE    54 128 256  93
D1060V4, multiclass
       clus
vv      BMPR2 MUTATED BMPR2 WILD-TYPE
  T0+T1             0              54
  T2                7             128
  T3                5             256
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BMPR2 MUTATED    10   6   1   4
  BMPR2 WILD-TYPE 185 167  88  81
D1060V5, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  N0            10             185
  N1             6             167
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V6, binary
                 cls
clus                0   1
  BMPR2 MUTATED    20   1
  BMPR2 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     20    1
  BMPR2 WILD-TYPE  462   37
   clus
vv  BMPR2 MUTATED BMPR2 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D1060V7, binary
                 cls
clus                0   1
  BMPR2 MUTATED    10  12
  BMPR2 WILD-TYPE 162 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     10   12
  BMPR2 WILD-TYPE  162  394
        clus
vv       BMPR2 MUTATED BMPR2 WILD-TYPE
  FEMALE            10             162
  MALE              12             394
[1] 2 2
[1] FALSE
D1060V8, binary
                 cls
clus                0   1
  BMPR2 MUTATED    18   2
  BMPR2 WILD-TYPE 398 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     18    2
  BMPR2 WILD-TYPE  398  100
     clus
vv    BMPR2 MUTATED BMPR2 WILD-TYPE
  NO             18             398
  YES             2             100
[1] 2 2
[1] FALSE
D1060V9, continuous
[1] "Remove cluster labels:" "BMPR2 MUTATED"         
clus
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A2 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
D1060V10, continuous
[1] "Remove cluster labels:" "BMPR2 MUTATED"         
clus
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-LN-A49O      TCGA-LN-A49P 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" "BMPR2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BMPR2 MUTATED       5                         0
  BMPR2 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BMPR2 MUTATED                                           0    12
  BMPR2 WILD-TYPE                                         1   345
D1060V11, multiclass
                                           clus
vv                                          BMPR2 MUTATED BMPR2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V12, binary
                 cls
clus                0   1
  BMPR2 MUTATED     0  14
  BMPR2 WILD-TYPE  10 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED      0   14
  BMPR2 WILD-TYPE   10  384
                        clus
vv                       BMPR2 MUTATED BMPR2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(1061) Variable = SETD6 MUTATION ANALYSIS
D1061V1, survival
                 sevent
clus2               0   1
  SETD6 MUTATED     7   1
  SETD6 WILD-TYPE 331 215
  SETD6 MUTATED SETD6 WILD-TYPE 
              8             546 
  SETD6 MUTATED SETD6 WILD-TYPE 
              1             215 
$`SETD6 MUTATED`
TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8591 TCGA-FP-7998 
        7.76        26.70        34.68         6.18        28.14        22.29 
TCGA-HF-A5NB TCGA-R5-A7ZI 
       30.51        74.53 

$`SETD6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SETD6 MUTATED SETD6 WILD-TYPE 
           6.18            0.00 
  SETD6 MUTATED SETD6 WILD-TYPE 
          74.53          122.30 
  SETD6 MUTATED SETD6 WILD-TYPE 
          27.42           13.51 
[1] "6.2 - 74.5 (27.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.9"
D1061V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETD6 MUTATED         0        0        0        0         2         2
  SETD6 WILD-TYPE      10       20       46       31        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD6 MUTATED           0          0          0          3        1         0
  SETD6 WILD-TYPE        29         84         62         36       42         4
D1061V3, multiclass
            clus
vv           SETD6 MUTATED SETD6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SETD6 MUTATED       0   1   2   5
  SETD6 WILD-TYPE    54 134 259  97
D1061V4, multiclass
       clus
vv      SETD6 MUTATED SETD6 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SETD6 MUTATED     3   2   0   3
  SETD6 WILD-TYPE 192 171  89  82
D1061V5, multiclass
    clus
vv   SETD6 MUTATED SETD6 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V6, binary
                 cls
clus                0   1
  SETD6 MUTATED     6   1
  SETD6 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD6 MUTATED      6    1
  SETD6 WILD-TYPE  476   37
   clus
vv  SETD6 MUTATED SETD6 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D1061V7, binary
                 cls
clus                0   1
  SETD6 MUTATED     5   3
  SETD6 WILD-TYPE 167 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD6 MUTATED      5    3
  SETD6 WILD-TYPE  167  403
        clus
vv       SETD6 MUTATED SETD6 WILD-TYPE
  FEMALE             5             167
  MALE               3             403
[1] 2 2
[1] FALSE
D1061V8, binary
                 cls
clus                0   1
  SETD6 MUTATED     7   1
  SETD6 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD6 MUTATED      7    1
  SETD6 WILD-TYPE  409  101
     clus
vv    SETD6 MUTATED SETD6 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D1061V9, continuous
D1061V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SETD6 MUTATED       0                         0
  SETD6 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SETD6 MUTATED                                           0     7
  SETD6 WILD-TYPE                                         1   350
D1061V11, multiclass
                                           clus
vv                                          SETD6 MUTATED SETD6 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V12, binary
                 cls
clus                0   1
  SETD6 MUTATED     2   4
  SETD6 WILD-TYPE   8 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD6 MUTATED      2    4
  SETD6 WILD-TYPE    8  394
                        clus
vv                       SETD6 MUTATED SETD6 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1062) Variable = GPR84 MUTATION ANALYSIS
D1062V1, survival
                 sevent
clus2               0   1
  GPR84 MUTATED     4   1
  GPR84 WILD-TYPE 334 215
  GPR84 MUTATED GPR84 WILD-TYPE 
              5             549 
  GPR84 MUTATED GPR84 WILD-TYPE 
              1             215 
$`GPR84 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-IG-A3YB TCGA-BR-8487 TCGA-MX-A5UJ 
       19.99        21.99         2.63         1.12        19.73 

$`GPR84 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GPR84 MUTATED GPR84 WILD-TYPE 
           1.12            0.00 
  GPR84 MUTATED GPR84 WILD-TYPE 
          21.99          122.30 
  GPR84 MUTATED GPR84 WILD-TYPE 
          19.73           13.55 
[1] "1.1 - 22.0 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1062V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR84 MUTATED         0        0        0        0         1         0
  GPR84 WILD-TYPE      10       20       46       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR84 MUTATED           0          2          0          1        1         0
  GPR84 WILD-TYPE        29         82         62         38       42         4
D1062V3, multiclass
            clus
vv           GPR84 MUTATED GPR84 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GPR84 MUTATED       0   0   4   1
  GPR84 WILD-TYPE    54 135 257 101
D1062V4, multiclass
       clus
vv      GPR84 MUTATED GPR84 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                4             257
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GPR84 MUTATED     1   2   1   1
  GPR84 WILD-TYPE 194 171  88  84
D1062V5, multiclass
    clus
vv   GPR84 MUTATED GPR84 WILD-TYPE
  N0             1             194
  N1             2             171
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V6, binary
                 cls
clus                0   1
  GPR84 MUTATED     3   1
  GPR84 WILD-TYPE 479  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR84 MUTATED      3    1
  GPR84 WILD-TYPE  479   37
   clus
vv  GPR84 MUTATED GPR84 WILD-TYPE
  0             3             479
  1             1              37
[1] 2 2
[1] FALSE
D1062V7, binary
                 cls
clus                0   1
  GPR84 MUTATED     3   2
  GPR84 WILD-TYPE 169 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR84 MUTATED      3    2
  GPR84 WILD-TYPE  169  404
        clus
vv       GPR84 MUTATED GPR84 WILD-TYPE
  FEMALE             3             169
  MALE               2             404
[1] 2 2
[1] FALSE
D1062V8, binary
                 cls
clus                0   1
  GPR84 MUTATED     4   1
  GPR84 WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR84 MUTATED      4    1
  GPR84 WILD-TYPE  412  101
     clus
vv    GPR84 MUTATED GPR84 WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D1062V9, continuous
[1] "Remove cluster labels:" "GPR84 MUTATED"         
clus
  GPR84 MUTATED GPR84 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
D1062V10, continuous
[1] "Remove cluster labels:" "GPR84 MUTATED"         
clus
  GPR84 MUTATED GPR84 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" "GPR84 WILD-TYPE" 
     TCGA-Z6-AAPN 
"GPR84 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPR84 MUTATED       0                         0
  GPR84 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR84 MUTATED                                           0     4
  GPR84 WILD-TYPE                                         1   353
D1062V11, multiclass
                                           clus
vv                                          GPR84 MUTATED GPR84 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V12, binary
                 cls
clus                0   1
  GPR84 MUTATED     0   3
  GPR84 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR84 MUTATED      0    3
  GPR84 WILD-TYPE   10  395
                        clus
vv                       GPR84 MUTATED GPR84 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(1063) Variable = TTC3 MUTATION ANALYSIS
D1063V1, survival
                sevent
clus2              0   1
  TTC3 MUTATED    14  14
  TTC3 WILD-TYPE 324 202
  TTC3 MUTATED TTC3 WILD-TYPE 
            28            526 
  TTC3 MUTATED TTC3 WILD-TYPE 
            14            202 
$`TTC3 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GH TCGA-IG-A4P3 TCGA-L5-A4OT TCGA-L5-A893 
       19.99        21.99        31.27        18.64         4.90         3.02 
TCGA-LN-A5U7 TCGA-XP-A8T7 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8382 
       25.25        41.23         6.97        34.68         0.26        25.05 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A487 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5726 
       28.14        31.96        12.30        36.00         6.02        28.96 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-A4G9 
       69.04        12.66        11.44        21.27        26.47        24.20 
TCGA-HU-A4H8 TCGA-RD-A8N6 TCGA-VQ-A8P2 TCGA-VQ-AA64 
       14.07         8.94        38.14        18.41 

$`TTC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI 
        0.23        20.15         9.86        25.78        20.05        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
        7.07        30.97         6.97         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        12.03        15.02        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        25.71        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA 
      115.69       116.38        71.38        57.44        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TTC3 MUTATED TTC3 WILD-TYPE 
          0.26           0.00 
  TTC3 MUTATED TTC3 WILD-TYPE 
         69.04         122.30 
  TTC3 MUTATED TTC3 WILD-TYPE 
         21.63          13.41 
[1] "0.3 - 69.0 (21.6)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1"  
D1063V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTC3 MUTATED         1        2        4        1         3         3
  TTC3 WILD-TYPE       9       18       42       30        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTC3 MUTATED           0          6          3          3        5         0
  TTC3 WILD-TYPE        29         78         59         36       38         4
D1063V3, multiclass
            clus
vv           TTC3 MUTATED TTC3 WILD-TYPE
  STAGE I               1              9
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            6             78
  STAGE IIIB            3             59
  STAGE IIIC            3             36
  STAGE IV              5             38
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TTC3 MUTATED       6   9  10   7
  TTC3 WILD-TYPE    48 126 251  95
D1063V4, multiclass
       clus
vv      TTC3 MUTATED TTC3 WILD-TYPE
  T0+T1            6             48
  T2               9            126
  T3              10            251
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TTC3 MUTATED    10  11   4   6
  TTC3 WILD-TYPE 185 162  85  79
D1063V5, multiclass
    clus
vv   TTC3 MUTATED TTC3 WILD-TYPE
  N0           10            185
  N1           11            162
  N2            4             85
  N3            6             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V6, binary
                cls
clus               0   1
  TTC3 MUTATED    25   3
  TTC3 WILD-TYPE 457  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTC3 MUTATED     25    3
  TTC3 WILD-TYPE  457   35
   clus
vv  TTC3 MUTATED TTC3 WILD-TYPE
  0           25            457
  1            3             35
[1] 2 2
[1] FALSE
D1063V7, binary
                cls
clus               0   1
  TTC3 MUTATED    14  18
  TTC3 WILD-TYPE 158 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTC3 MUTATED     14   18
  TTC3 WILD-TYPE  158  388
        clus
vv       TTC3 MUTATED TTC3 WILD-TYPE
  FEMALE           14            158
  MALE             18            388
[1] 2 2
[1] FALSE
D1063V8, binary
                cls
clus               0   1
  TTC3 MUTATED    23   6
  TTC3 WILD-TYPE 393  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTC3 MUTATED     23    6
  TTC3 WILD-TYPE  393   96
     clus
vv    TTC3 MUTATED TTC3 WILD-TYPE
  NO            23            393
  YES            6             96
[1] 2 2
[1] FALSE
D1063V9, continuous
[1] "Remove cluster labels:" "TTC3 MUTATED"          
clus
  TTC3 MUTATED TTC3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A7HV 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T8 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"TTC3 WILD-TYPE" "TTC3 WILD-TYPE" 
D1063V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TTC3 MUTATED       5                         0
  TTC3 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TTC3 MUTATED                                           0    19
  TTC3 WILD-TYPE                                         1   338
D1063V11, multiclass
                                           clus
vv                                          TTC3 MUTATED TTC3 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V12, binary
                cls
clus               0   1
  TTC3 MUTATED     2  17
  TTC3 WILD-TYPE   8 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTC3 MUTATED      2   17
  TTC3 WILD-TYPE    8  381
                        clus
vv                       TTC3 MUTATED TTC3 WILD-TYPE
  HISPANIC OR LATINO                2              8
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(1064) Variable = PLK2 MUTATION ANALYSIS
D1064V1, survival
                sevent
clus2              0   1
  PLK2 MUTATED     5   2
  PLK2 WILD-TYPE 333 214
  PLK2 MUTATED PLK2 WILD-TYPE 
             7            547 
  PLK2 MUTATED PLK2 WILD-TYPE 
             2            214 
$`PLK2 MUTATED`
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HU-A4H3 TCGA-MX-A5UJ 
        1.12        31.96        16.14         6.58        29.00        19.73 
TCGA-VQ-A92D 
       66.81 

$`PLK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62        36.95         3.72        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PLK2 MUTATED PLK2 WILD-TYPE 
          1.12           0.00 
  PLK2 MUTATED PLK2 WILD-TYPE 
         66.81         122.30 
  PLK2 MUTATED PLK2 WILD-TYPE 
         19.73          13.51 
[1] "1.1 - 66.8 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.8"
D1064V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLK2 MUTATED         0        0        1        0         2         0
  PLK2 WILD-TYPE      10       20       45       31        82        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLK2 MUTATED           0          1          1          1        1         0
  PLK2 WILD-TYPE        29         83         61         38       42         4
D1064V3, multiclass
            clus
vv           PLK2 MUTATED PLK2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PLK2 MUTATED       0   1   4   2
  PLK2 WILD-TYPE    54 134 257 100
D1064V4, multiclass
       clus
vv      PLK2 MUTATED PLK2 WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               4            257
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PLK2 MUTATED     3   0   2   2
  PLK2 WILD-TYPE 192 173  87  83
D1064V5, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  N0            3            192
  N1            0            173
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V6, binary
                cls
clus               0   1
  PLK2 MUTATED     7   1
  PLK2 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      7    1
  PLK2 WILD-TYPE  475   37
   clus
vv  PLK2 MUTATED PLK2 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D1064V7, binary
                cls
clus               0   1
  PLK2 MUTATED     5   3
  PLK2 WILD-TYPE 167 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      5    3
  PLK2 WILD-TYPE  167  403
        clus
vv       PLK2 MUTATED PLK2 WILD-TYPE
  FEMALE            5            167
  MALE              3            403
[1] 2 2
[1] FALSE
D1064V8, binary
                cls
clus               0   1
  PLK2 MUTATED     6   0
  PLK2 WILD-TYPE 410 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      6    0
  PLK2 WILD-TYPE  410  102
     clus
vv    PLK2 MUTATED PLK2 WILD-TYPE
  NO             6            410
  YES            0            102
[1] 2 2
[1] FALSE
D1064V9, continuous
D1064V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PLK2 MUTATED       3                         0
  PLK2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLK2 MUTATED                                           0     5
  PLK2 WILD-TYPE                                         1   352
D1064V11, multiclass
                                           clus
vv                                          PLK2 MUTATED PLK2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V12, binary
                cls
clus               0   1
  PLK2 MUTATED     0   7
  PLK2 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      0    7
  PLK2 WILD-TYPE   10  391
                        clus
vv                       PLK2 MUTATED PLK2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(1065) Variable = ABCC2 MUTATION ANALYSIS
D1065V1, survival
                 sevent
clus2               0   1
  ABCC2 MUTATED    12   9
  ABCC2 WILD-TYPE 326 207
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             21             533 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              9             207 
$`ABCC2 MUTATED`
TCGA-Q9-A6FU TCGA-IG-A4QS TCGA-L5-A893 TCGA-L5-A8NQ TCGA-V5-AASV TCGA-VR-AA4D 
        5.16         3.88         3.02        21.37        15.35        46.19 
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-7717 TCGA-CD-5813 
       26.70         6.97         9.67        35.84        18.15        12.39 
TCGA-CG-5721 TCGA-D7-6528 TCGA-D7-8570 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G6 
        6.02        15.22        24.72        11.08        22.32        24.26 
TCGA-R5-A7O7 TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       45.67        38.14        26.04 

$`ABCC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        14.04        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        16.14        27.55        12.43        17.26 

  ABCC2 MUTATED ABCC2 WILD-TYPE 
           3.02            0.00 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
          46.19          122.30 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
          18.15           13.51 
[1] "3.0 - 46.2 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1065V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC2 MUTATED         1        1        2        1         3         4
  ABCC2 WILD-TYPE       9       19       44       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCC2 MUTATED           0          2          3          0        4         0
  ABCC2 WILD-TYPE        29         82         59         39       39         4
D1065V3, multiclass
            clus
vv           ABCC2 MUTATED ABCC2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             3              59
  STAGE IIIC             0              39
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCC2 MUTATED       3   3   9   6
  ABCC2 WILD-TYPE    51 132 252  96
D1065V4, multiclass
       clus
vv      ABCC2 MUTATED ABCC2 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCC2 MUTATED    11   6   3   1
  ABCC2 WILD-TYPE 184 167  86  84
D1065V5, multiclass
    clus
vv   ABCC2 MUTATED ABCC2 WILD-TYPE
  N0            11             184
  N1             6             167
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V6, binary
                 cls
clus                0   1
  ABCC2 MUTATED    19   1
  ABCC2 WILD-TYPE 463  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED     19    1
  ABCC2 WILD-TYPE  463   37
   clus
vv  ABCC2 MUTATED ABCC2 WILD-TYPE
  0            19             463
  1             1              37
[1] 2 2
[1] FALSE
D1065V7, binary
                 cls
clus                0   1
  ABCC2 MUTATED     8  14
  ABCC2 WILD-TYPE 164 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      8   14
  ABCC2 WILD-TYPE  164  392
        clus
vv       ABCC2 MUTATED ABCC2 WILD-TYPE
  FEMALE             8             164
  MALE              14             392
[1] 2 2
[1] FALSE
D1065V8, binary
                 cls
clus                0   1
  ABCC2 MUTATED    17   4
  ABCC2 WILD-TYPE 399  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED     17    4
  ABCC2 WILD-TYPE  399   98
     clus
vv    ABCC2 MUTATED ABCC2 WILD-TYPE
  NO             17             399
  YES             4              98
[1] 2 2
[1] FALSE
D1065V9, continuous
[1] "Remove cluster labels:" "ABCC2 MUTATED"         
clus
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCC2 WILD-TYPE" "ABCC2 WILD-TYPE" 
D1065V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC2 MUTATED       3                         2
  ABCC2 WILD-TYPE   130                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC2 MUTATED                                           0    16
  ABCC2 WILD-TYPE                                         1   341
D1065V11, multiclass
                                           clus
vv                                          ABCC2 MUTATED ABCC2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V12, binary
                 cls
clus                0   1
  ABCC2 MUTATED     1  15
  ABCC2 WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      1   15
  ABCC2 WILD-TYPE    9  383
                        clus
vv                       ABCC2 MUTATED ABCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(1066) Variable = CXXC1 MUTATION ANALYSIS
D1066V1, survival
                 sevent
clus2               0   1
  CXXC1 MUTATED    10   6
  CXXC1 WILD-TYPE 328 210
  CXXC1 MUTATED CXXC1 WILD-TYPE 
             16             538 
  CXXC1 MUTATED CXXC1 WILD-TYPE 
              6             210 
$`CXXC1 MUTATED`
TCGA-JY-A6FG TCGA-LN-A5U5 TCGA-BR-4257 TCGA-BR-6563 TCGA-BR-6852 TCGA-BR-8360 
       41.52         4.47         9.67        39.12        44.94         6.18 
TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-A4J7 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       31.10        25.05        32.52         6.02       105.07        28.96 
TCGA-HU-A4GC TCGA-HU-A4H8 TCGA-IN-8663 TCGA-R5-A7ZI 
        3.25        14.07         3.39        74.53 

$`CXXC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CXXC1 MUTATED CXXC1 WILD-TYPE 
           3.25            0.00 
  CXXC1 MUTATED CXXC1 WILD-TYPE 
         105.07          122.30 
  CXXC1 MUTATED CXXC1 WILD-TYPE 
         27.005          13.510 
[1] "3.2 - 105.1 (27.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D1066V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CXXC1 MUTATED         0        1        1        1         2         3
  CXXC1 WILD-TYPE      10       19       45       30        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CXXC1 MUTATED           1          0          1          2        3         0
  CXXC1 WILD-TYPE        28         84         61         37       40         4
D1066V3, multiclass
            clus
vv           CXXC1 MUTATED CXXC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CXXC1 MUTATED       2   2   5   6
  CXXC1 WILD-TYPE    52 133 256  96
D1066V4, multiclass
       clus
vv      CXXC1 MUTATED CXXC1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                5             256
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CXXC1 MUTATED     3   7   3   1
  CXXC1 WILD-TYPE 192 166  86  84
D1066V5, multiclass
    clus
vv   CXXC1 MUTATED CXXC1 WILD-TYPE
  N0             3             192
  N1             7             166
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V6, binary
                 cls
clus                0   1
  CXXC1 MUTATED    14   2
  CXXC1 WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC1 MUTATED     14    2
  CXXC1 WILD-TYPE  468   36
   clus
vv  CXXC1 MUTATED CXXC1 WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D1066V7, binary
                 cls
clus                0   1
  CXXC1 MUTATED     5  11
  CXXC1 WILD-TYPE 167 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC1 MUTATED      5   11
  CXXC1 WILD-TYPE  167  395
        clus
vv       CXXC1 MUTATED CXXC1 WILD-TYPE
  FEMALE             5             167
  MALE              11             395
[1] 2 2
[1] FALSE
D1066V8, binary
                 cls
clus                0   1
  CXXC1 MUTATED    15   0
  CXXC1 WILD-TYPE 401 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC1 MUTATED     15    0
  CXXC1 WILD-TYPE  401  102
     clus
vv    CXXC1 MUTATED CXXC1 WILD-TYPE
  NO             15             401
  YES             0             102
[1] 2 2
[1] FALSE
D1066V9, continuous
[1] "Remove cluster labels:" "CXXC1 MUTATED"         
clus
  CXXC1 MUTATED CXXC1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
D1066V10, continuous
[1] "Remove cluster labels:" "CXXC1 MUTATED"         
clus
  CXXC1 MUTATED CXXC1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" "CXXC1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"CXXC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CXXC1 MUTATED       4                         0
  CXXC1 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CXXC1 MUTATED                                           0     9
  CXXC1 WILD-TYPE                                         1   348
D1066V11, multiclass
                                           clus
vv                                          CXXC1 MUTATED CXXC1 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V12, binary
                 cls
clus                0   1
  CXXC1 MUTATED     1  11
  CXXC1 WILD-TYPE   9 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC1 MUTATED      1   11
  CXXC1 WILD-TYPE    9  387
                        clus
vv                       CXXC1 MUTATED CXXC1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1067) Variable = DGAT1 MUTATION ANALYSIS
D1067V1, survival
                 sevent
clus2               0   1
  DGAT1 MUTATED     8   1
  DGAT1 WILD-TYPE 330 215
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             545 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              1             215 
$`DGAT1 MUTATED`
TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8591 TCGA-CG-5718 TCGA-HU-A4G9 TCGA-HU-A4GT 
       29.59         4.31        28.14        36.00        24.20         6.51 
TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI 
       14.07        19.73        74.53 

$`DGAT1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DGAT1 MUTATED DGAT1 WILD-TYPE 
           4.31            0.00 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
          74.53          122.30 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
          24.20           13.51 
[1] "4.3 - 74.5 (24.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "5"  
D1067V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DGAT1 MUTATED         0        1        2        1         1         1
  DGAT1 WILD-TYPE      10       19       44       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DGAT1 MUTATED           0          1          0          1        1         0
  DGAT1 WILD-TYPE        29         83         62         38       42         4
D1067V3, multiclass
            clus
vv           DGAT1 MUTATED DGAT1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  DGAT1 MUTATED       2   2   2   3
  DGAT1 WILD-TYPE    52 133 259  99
D1067V4, multiclass
       clus
vv      DGAT1 MUTATED DGAT1 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  DGAT1 MUTATED     4   3   1   1
  DGAT1 WILD-TYPE 191 170  88  84
D1067V5, multiclass
    clus
vv   DGAT1 MUTATED DGAT1 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V6, binary
                 cls
clus                0   1
  DGAT1 MUTATED     8   1
  DGAT1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      8    1
  DGAT1 WILD-TYPE  474   37
   clus
vv  DGAT1 MUTATED DGAT1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D1067V7, binary
                 cls
clus                0   1
  DGAT1 MUTATED     7   2
  DGAT1 WILD-TYPE 165 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      7    2
  DGAT1 WILD-TYPE  165  404
        clus
vv       DGAT1 MUTATED DGAT1 WILD-TYPE
  FEMALE             7             165
  MALE               2             404
[1] 2 2
[1] FALSE
D1067V8, binary
                 cls
clus                0   1
  DGAT1 MUTATED     9   0
  DGAT1 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      9    0
  DGAT1 WILD-TYPE  407  102
     clus
vv    DGAT1 MUTATED DGAT1 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D1067V9, continuous
D1067V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DGAT1 MUTATED       3                         0
  DGAT1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DGAT1 MUTATED                                           0     5
  DGAT1 WILD-TYPE                                         1   352
D1067V11, multiclass
                                           clus
vv                                          DGAT1 MUTATED DGAT1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V12, binary
                 cls
clus                0   1
  DGAT1 MUTATED     1   7
  DGAT1 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      1    7
  DGAT1 WILD-TYPE    9  391
                        clus
vv                       DGAT1 MUTATED DGAT1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1068) Variable = ZNF506 MUTATION ANALYSIS
D1068V1, survival
                  sevent
clus2                0   1
  ZNF506 MUTATED     5   4
  ZNF506 WILD-TYPE 333 212
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               9              545 
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               4              212 
$`ZNF506 MUTATED`
TCGA-VR-A8EX TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-8680 TCGA-CG-5728 
       28.11        30.90         9.67         6.61        31.96        65.10 
TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-RD-A8N1 
        6.51        21.17       115.69 

$`ZNF506 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        5.13        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZNF506 MUTATED ZNF506 WILD-TYPE 
            6.51             0.00 
  ZNF506 MUTATED ZNF506 WILD-TYPE 
          115.69           122.30 
  ZNF506 MUTATED ZNF506 WILD-TYPE 
           28.11            13.51 
[1] "6.5 - 115.7 (28.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1068V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF506 MUTATED         0        0        1        0         1         0
  ZNF506 WILD-TYPE      10       20       45       31        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF506 MUTATED           1          1          1          0        1
  ZNF506 WILD-TYPE        28         83         61         39       42
                  vv
clus               STAGE IVA
  ZNF506 MUTATED           1
  ZNF506 WILD-TYPE         3
D1068V3, multiclass
            clus
vv           ZNF506 MUTATED ZNF506 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF506 MUTATED       1   3   3   1
  ZNF506 WILD-TYPE    53 132 258 101
D1068V4, multiclass
       clus
vv      ZNF506 MUTATED ZNF506 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF506 MUTATED     2   2   3   0
  ZNF506 WILD-TYPE 193 171  86  85
D1068V5, multiclass
    clus
vv   ZNF506 MUTATED ZNF506 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              3               86
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V6, binary
                  cls
clus                 0   1
  ZNF506 MUTATED     7   2
  ZNF506 WILD-TYPE 475  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF506 MUTATED      7    2
  ZNF506 WILD-TYPE  475   36
   clus
vv  ZNF506 MUTATED ZNF506 WILD-TYPE
  0              7              475
  1              2               36
[1] 2 2
[1] FALSE
D1068V7, binary
                  cls
clus                 0   1
  ZNF506 MUTATED     6   3
  ZNF506 WILD-TYPE 166 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF506 MUTATED      6    3
  ZNF506 WILD-TYPE  166  403
        clus
vv       ZNF506 MUTATED ZNF506 WILD-TYPE
  FEMALE              6              166
  MALE                3              403
[1] 2 2
[1] FALSE
D1068V8, binary
                  cls
clus                 0   1
  ZNF506 MUTATED     7   1
  ZNF506 WILD-TYPE 409 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF506 MUTATED      7    1
  ZNF506 WILD-TYPE  409  101
     clus
vv    ZNF506 MUTATED ZNF506 WILD-TYPE
  NO               7              409
  YES              1              101
[1] 2 2
[1] FALSE
D1068V9, continuous
[1] "Remove cluster labels:" "ZNF506 MUTATED"        
clus
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
D1068V10, continuous
[1] "Remove cluster labels:" "ZNF506 MUTATED"        
clus
  ZNF506 MUTATED ZNF506 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EZ 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" "ZNF506 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZNF506 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF506 MUTATED       3                         0
  ZNF506 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF506 MUTATED                                           0     4
  ZNF506 WILD-TYPE                                         1   353
D1068V11, multiclass
                                           clus
vv                                          ZNF506 MUTATED ZNF506 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V12, binary
                  cls
clus                 0   1
  ZNF506 MUTATED     0   7
  ZNF506 WILD-TYPE  10 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF506 MUTATED      0    7
  ZNF506 WILD-TYPE   10  391
                        clus
vv                       ZNF506 MUTATED ZNF506 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(1069) Variable = ATP2B1 MUTATION ANALYSIS
D1069V1, survival
                  sevent
clus2                0   1
  ATP2B1 MUTATED    14   4
  ATP2B1 WILD-TYPE 324 212
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
              18              536 
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
               4              212 
$`ATP2B1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4P3 TCGA-JY-A6FH TCGA-LN-A9FP TCGA-Z6-AAPN TCGA-B7-A5TI 
       19.99        18.64        47.38        12.03         2.66        19.56 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MI 
        6.97        34.68        32.78        29.59        31.96        11.77 
TCGA-CG-4306 TCGA-CG-4466 TCGA-HU-8238 TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-VQ-A8P2 
        1.02        18.97         1.51         6.58        19.73        38.14 

$`ATP2B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
            1.02             0.00 
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
           47.38           122.30 
  ATP2B1 MUTATED ATP2B1 WILD-TYPE 
          19.265           13.510 
[1] "1.0 - 47.4 (19.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2"  
D1069V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2B1 MUTATED         0        0        1        0         4         4
  ATP2B1 WILD-TYPE      10       20       45       31        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B1 MUTATED           0          4          0          2        2
  ATP2B1 WILD-TYPE        29         80         62         37       41
                  vv
clus               STAGE IVA
  ATP2B1 MUTATED           0
  ATP2B1 WILD-TYPE         4
D1069V3, multiclass
            clus
vv           ATP2B1 MUTATED ATP2B1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATP2B1 MUTATED       0   4  10   4
  ATP2B1 WILD-TYPE    54 131 251  98
D1069V4, multiclass
       clus
vv      ATP2B1 MUTATED ATP2B1 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                10              251
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP2B1 MUTATED     6   6   4   2
  ATP2B1 WILD-TYPE 189 167  85  83
D1069V5, multiclass
    clus
vv   ATP2B1 MUTATED ATP2B1 WILD-TYPE
  N0              6              189
  N1              6              167
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V6, binary
                  cls
clus                 0   1
  ATP2B1 MUTATED    15   2
  ATP2B1 WILD-TYPE 467  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B1 MUTATED     15    2
  ATP2B1 WILD-TYPE  467   36
   clus
vv  ATP2B1 MUTATED ATP2B1 WILD-TYPE
  0             15              467
  1              2               36
[1] 2 2
[1] FALSE
D1069V7, binary
                  cls
clus                 0   1
  ATP2B1 MUTATED     7  12
  ATP2B1 WILD-TYPE 165 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B1 MUTATED      7   12
  ATP2B1 WILD-TYPE  165  394
        clus
vv       ATP2B1 MUTATED ATP2B1 WILD-TYPE
  FEMALE              7              165
  MALE               12              394
[1] 2 2
[1] FALSE
D1069V8, binary
                  cls
clus                 0   1
  ATP2B1 MUTATED    14   3
  ATP2B1 WILD-TYPE 402  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B1 MUTATED     14    3
  ATP2B1 WILD-TYPE  402   99
     clus
vv    ATP2B1 MUTATED ATP2B1 WILD-TYPE
  NO              14              402
  YES              3               99
[1] 2 2
[1] FALSE
D1069V9, continuous
D1069V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP2B1 MUTATED       5                         0
  ATP2B1 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP2B1 MUTATED                                           0    12
  ATP2B1 WILD-TYPE                                         1   345
D1069V11, multiclass
                                           clus
vv                                          ATP2B1 MUTATED ATP2B1 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V12, binary
                  cls
clus                 0   1
  ATP2B1 MUTATED     0  14
  ATP2B1 WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B1 MUTATED      0   14
  ATP2B1 WILD-TYPE   10  384
                        clus
vv                       ATP2B1 MUTATED ATP2B1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE

Clustering(1070) Variable = PI16 MUTATION ANALYSIS
D1070V1, survival
                sevent
clus2              0   1
  PI16 MUTATED     1   4
  PI16 WILD-TYPE 337 212
  PI16 MUTATED PI16 WILD-TYPE 
             5            549 
  PI16 MUTATED PI16 WILD-TYPE 
             4            212 
$`PI16 MUTATED`
TCGA-L5-A8NM TCGA-BR-8591 TCGA-D7-A6EZ TCGA-HJ-7597 TCGA-R5-A7ZE 
        7.76        28.14        20.32        26.47        18.21 

$`PI16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PI16 MUTATED PI16 WILD-TYPE 
          7.76           0.00 
  PI16 MUTATED PI16 WILD-TYPE 
         28.14         122.30 
  PI16 MUTATED PI16 WILD-TYPE 
         20.32          13.51 
[1] "7.8 - 28.1 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1070V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PI16 MUTATED         0        0        1        0         0         1
  PI16 WILD-TYPE      10       20       45       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PI16 MUTATED           0          2          0          2        0         0
  PI16 WILD-TYPE        29         82         62         37       43         4
D1070V3, multiclass
            clus
vv           PI16 MUTATED PI16 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PI16 MUTATED       0   2   2   2
  PI16 WILD-TYPE    54 133 259 100
D1070V4, multiclass
       clus
vv      PI16 MUTATED PI16 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PI16 MUTATED     1   1   2   2
  PI16 WILD-TYPE 194 172  87  83
D1070V5, multiclass
    clus
vv   PI16 MUTATED PI16 WILD-TYPE
  N0            1            194
  N1            1            172
  N2            2             87
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V6, binary
                cls
clus               0   1
  PI16 MUTATED     5   0
  PI16 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      5    0
  PI16 WILD-TYPE  477   38
   clus
vv  PI16 MUTATED PI16 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D1070V7, binary
                cls
clus               0   1
  PI16 MUTATED     3   3
  PI16 WILD-TYPE 169 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      3    3
  PI16 WILD-TYPE  169  403
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  FEMALE            3            169
  MALE              3            403
[1] 2 2
[1] FALSE
D1070V8, binary
                cls
clus               0   1
  PI16 MUTATED     5   0
  PI16 WILD-TYPE 411 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      5    0
  PI16 WILD-TYPE  411  102
     clus
vv    PI16 MUTATED PI16 WILD-TYPE
  NO             5            411
  YES            0            102
[1] 2 2
[1] FALSE
D1070V9, continuous
D1070V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PI16 MUTATED       0                         0
  PI16 WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PI16 MUTATED                                           0     5
  PI16 WILD-TYPE                                         1   352
D1070V11, multiclass
                                           clus
vv                                          PI16 MUTATED PI16 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V12, binary
                cls
clus               0   1
  PI16 MUTATED     0   4
  PI16 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  PI16 MUTATED      0    4
  PI16 WILD-TYPE   10  394
                        clus
vv                       PI16 MUTATED PI16 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(1071) Variable = TOPBP1 MUTATION ANALYSIS
D1071V1, survival
                  sevent
clus2                0   1
  TOPBP1 MUTATED    12   7
  TOPBP1 WILD-TYPE 326 209
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              19              535 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
               7              209 
$`TOPBP1 MUTATED`
TCGA-2H-A9GL TCGA-IG-A7DP TCGA-L5-A88S TCGA-L5-A8NL TCGA-L5-A8NM TCGA-R6-A8W5 
        5.92        14.86        15.48        13.22         7.76        15.78 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8060 TCGA-BR-8368 TCGA-BR-8589 
        6.97        34.68        19.33        11.44         4.31        27.12 
TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5717 TCGA-D7-A6EV TCGA-HU-A4GT TCGA-HU-A4H2 
       12.43        15.95         6.97        11.24         6.51        12.95 
TCGA-SW-A7EA 
       19.04 

$`TOPBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        6.61        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
            4.31             0.00 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
           34.68           122.30 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
           12.95            13.68 
[1] "4.3 - 34.7 (12.9)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.2"
D1071V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TOPBP1 MUTATED         0        0        3        3         2         4
  TOPBP1 WILD-TYPE      10       20       43       28        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOPBP1 MUTATED           2          3          2          0        0
  TOPBP1 WILD-TYPE        27         81         60         39       43
                  vv
clus               STAGE IVA
  TOPBP1 MUTATED           1
  TOPBP1 WILD-TYPE         3
D1071V3, multiclass
            clus
vv           TOPBP1 MUTATED TOPBP1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TOPBP1 MUTATED       1   7  10   3
  TOPBP1 WILD-TYPE    53 128 251  99
D1071V4, multiclass
       clus
vv      TOPBP1 MUTATED TOPBP1 WILD-TYPE
  T0+T1              1               53
  T2                 7              128
  T3                10              251
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TOPBP1 MUTATED     7   9   2   1
  TOPBP1 WILD-TYPE 188 164  87  84
D1071V5, multiclass
    clus
vv   TOPBP1 MUTATED TOPBP1 WILD-TYPE
  N0              7              188
  N1              9              164
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V6, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    18   1
  TOPBP1 WILD-TYPE 464  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     18    1
  TOPBP1 WILD-TYPE  464   37
   clus
vv  TOPBP1 MUTATED TOPBP1 WILD-TYPE
  0             18              464
  1              1               37
[1] 2 2
[1] FALSE
D1071V7, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    13   9
  TOPBP1 WILD-TYPE 159 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     13    9
  TOPBP1 WILD-TYPE  159  397
        clus
vv       TOPBP1 MUTATED TOPBP1 WILD-TYPE
  FEMALE             13              159
  MALE                9              397
[1] 2 2
[1] FALSE
D1071V8, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    18   0
  TOPBP1 WILD-TYPE 398 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     18    0
  TOPBP1 WILD-TYPE  398  102
     clus
vv    TOPBP1 MUTATED TOPBP1 WILD-TYPE
  NO              18              398
  YES              0              102
[1] 2 2
[1] FALSE
D1071V9, continuous
[1] "Remove cluster labels:" "TOPBP1 MUTATED"        
clus
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
D1071V10, continuous
[1] "Remove cluster labels:" "TOPBP1 MUTATED"        
clus
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W8 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" "TOPBP1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TOPBP1 MUTATED       3                         0
  TOPBP1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TOPBP1 MUTATED                                           0    16
  TOPBP1 WILD-TYPE                                         1   341
D1071V11, multiclass
                                           clus
vv                                          TOPBP1 MUTATED TOPBP1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V12, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED     0  16
  TOPBP1 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED      0   16
  TOPBP1 WILD-TYPE   10  382
                        clus
vv                       TOPBP1 MUTATED TOPBP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(1072) Variable = CSF3R MUTATION ANALYSIS
D1072V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED    12   4
  CSF3R WILD-TYPE 326 212
  CSF3R MUTATED CSF3R WILD-TYPE 
             16             538 
  CSF3R MUTATED CSF3R WILD-TYPE 
              4             212 
$`CSF3R MUTATED`
TCGA-L5-A4OI TCGA-L5-A43E TCGA-LN-A49Y TCGA-R6-A6Y2 TCGA-V5-A7RB TCGA-BR-6452 
       19.99        30.25        12.46         9.30         5.29        34.68 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4437 
       33.21        29.59         4.31         6.58        15.95         8.05 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-HF-7134 TCGA-HF-A5NB 
        5.92        14.47        52.21        30.51 

$`CSF3R WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CSF3R MUTATED CSF3R WILD-TYPE 
           4.31            0.00 
  CSF3R MUTATED CSF3R WILD-TYPE 
          52.21          122.30 
  CSF3R MUTATED CSF3R WILD-TYPE 
          15.21           13.53 
[1] "4.3 - 52.2 (15.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1072V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSF3R MUTATED         1        1        3        2         3         2
  CSF3R WILD-TYPE       9       19       43       29        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSF3R MUTATED           0          1          0          2        0         0
  CSF3R WILD-TYPE        29         83         62         37       43         4
D1072V3, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CSF3R MUTATED       3   5   5   3
  CSF3R WILD-TYPE    51 130 256  99
D1072V4, multiclass
       clus
vv      CSF3R MUTATED CSF3R WILD-TYPE
  T0+T1             3              51
  T2                5             130
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CSF3R MUTATED     9   5   0   2
  CSF3R WILD-TYPE 186 168  89  83
D1072V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0             9             186
  N1             5             168
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V6, binary
                 cls
clus                0   1
  CSF3R MUTATED    14   0
  CSF3R WILD-TYPE 468  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     14    0
  CSF3R WILD-TYPE  468   38
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            14             468
  1             0              38
[1] 2 2
[1] FALSE
D1072V7, binary
                 cls
clus                0   1
  CSF3R MUTATED     5  12
  CSF3R WILD-TYPE 167 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      5   12
  CSF3R WILD-TYPE  167  394
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  FEMALE             5             167
  MALE              12             394
[1] 2 2
[1] FALSE
D1072V8, binary
                 cls
clus                0   1
  CSF3R MUTATED    15   1
  CSF3R WILD-TYPE 401 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     15    1
  CSF3R WILD-TYPE  401  101
     clus
vv    CSF3R MUTATED CSF3R WILD-TYPE
  NO             15             401
  YES             1             101
[1] 2 2
[1] FALSE
D1072V9, continuous
[1] "Remove cluster labels:" "CSF3R MUTATED"         
clus
  CSF3R MUTATED CSF3R WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A4A1      TCGA-LN-A4A2 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CSF3R WILD-TYPE" "CSF3R WILD-TYPE" 
D1072V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CSF3R MUTATED       2                         0
  CSF3R WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSF3R MUTATED                                           0     9
  CSF3R WILD-TYPE                                         1   348
D1072V11, multiclass
                                           clus
vv                                          CSF3R MUTATED CSF3R WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V12, binary
                 cls
clus                0   1
  CSF3R MUTATED     2   8
  CSF3R WILD-TYPE   8 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      2    8
  CSF3R WILD-TYPE    8  390
                        clus
vv                       CSF3R MUTATED CSF3R WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1073) Variable = LRP4 MUTATION ANALYSIS
D1073V1, survival
                sevent
clus2              0   1
  LRP4 MUTATED    14  11
  LRP4 WILD-TYPE 324 205
  LRP4 MUTATED LRP4 WILD-TYPE 
            25            529 
  LRP4 MUTATED LRP4 WILD-TYPE 
            11            205 
$`LRP4 MUTATED`
TCGA-2H-A9GJ TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A8NE TCGA-L5-A8NS TCGA-L7-A6VZ 
       58.55        32.61        18.35        55.50        13.41        10.36 
TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-BR-4184 TCGA-BR-6706 TCGA-BR-8081 TCGA-BR-8487 
       18.31        18.18         6.97        18.05        32.25         1.12 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-6526 TCGA-D7-8572 
       16.14        13.41         1.02         6.02        17.19        16.80 
TCGA-D7-A4YV TCGA-D7-A6EY TCGA-EQ-8122 TCGA-HF-7132 TCGA-HU-A4H2 TCGA-VQ-A8P2 
        5.92        11.44         7.99        77.29        12.95        38.14 
TCGA-VQ-A92D 
       66.81 

$`LRP4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        8.71        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        32.78        25.61        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.42         1.15        21.44         5.13        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  LRP4 MUTATED LRP4 WILD-TYPE 
          1.02           0.00 
  LRP4 MUTATED LRP4 WILD-TYPE 
         77.29         122.30 
  LRP4 MUTATED LRP4 WILD-TYPE 
         16.80          13.51 
[1] "1.0 - 77.3 (16.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1073V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP4 MUTATED         2        0        1        2         1         7
  LRP4 WILD-TYPE       8       20       45       29        83        76
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP4 MUTATED           0          4          3          2        3         0
  LRP4 WILD-TYPE        29         80         59         37       40         4
D1073V3, multiclass
            clus
vv           LRP4 MUTATED LRP4 WILD-TYPE
  STAGE I               2              8
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              2             29
  STAGE IIA             1             83
  STAGE IIB             7             76
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            3             59
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  LRP4 MUTATED       4   4  14   3
  LRP4 WILD-TYPE    50 131 247  99
D1073V4, multiclass
       clus
vv      LRP4 MUTATED LRP4 WILD-TYPE
  T0+T1            4             50
  T2               4            131
  T3              14            247
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  LRP4 MUTATED     7  10   3   5
  LRP4 WILD-TYPE 188 163  86  80
D1073V5, multiclass
    clus
vv   LRP4 MUTATED LRP4 WILD-TYPE
  N0            7            188
  N1           10            163
  N2            3             86
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V6, binary
                cls
clus               0   1
  LRP4 MUTATED    19   2
  LRP4 WILD-TYPE 463  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP4 MUTATED     19    2
  LRP4 WILD-TYPE  463   36
   clus
vv  LRP4 MUTATED LRP4 WILD-TYPE
  0           19            463
  1            2             36
[1] 2 2
[1] FALSE
D1073V7, binary
                cls
clus               0   1
  LRP4 MUTATED     8  17
  LRP4 WILD-TYPE 164 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP4 MUTATED      8   17
  LRP4 WILD-TYPE  164  389
        clus
vv       LRP4 MUTATED LRP4 WILD-TYPE
  FEMALE            8            164
  MALE             17            389
[1] 2 2
[1] FALSE
D1073V8, binary
                cls
clus               0   1
  LRP4 MUTATED    17   6
  LRP4 WILD-TYPE 399  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP4 MUTATED     17    6
  LRP4 WILD-TYPE  399   96
     clus
vv    LRP4 MUTATED LRP4 WILD-TYPE
  NO            17            399
  YES            6             96
[1] 2 2
[1] FALSE
D1073V9, continuous
[1] "Remove cluster labels:" "LRP4 MUTATED"          
clus
  LRP4 MUTATED LRP4 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8Q7 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"LRP4 WILD-TYPE" "LRP4 WILD-TYPE" 
D1073V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  LRP4 MUTATED       2                         0
  LRP4 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRP4 MUTATED                                           0    19
  LRP4 WILD-TYPE                                         1   338
D1073V11, multiclass
                                           clus
vv                                          LRP4 MUTATED LRP4 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V12, binary
                cls
clus               0   1
  LRP4 MUTATED     0  13
  LRP4 WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP4 MUTATED      0   13
  LRP4 WILD-TYPE   10  385
                        clus
vv                       LRP4 MUTATED LRP4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(1074) Variable = UGDH MUTATION ANALYSIS
D1074V1, survival
                sevent
clus2              0   1
  UGDH MUTATED     6   3
  UGDH WILD-TYPE 332 213
  UGDH MUTATED UGDH WILD-TYPE 
             9            545 
  UGDH MUTATED UGDH WILD-TYPE 
             3            213 
$`UGDH MUTATED`
TCGA-CG-5727 TCGA-L5-A8NM TCGA-LN-A4A2 TCGA-LN-A9FP TCGA-BR-4201 TCGA-BR-8591 
       79.07         7.76        12.49        12.03        30.90        28.14 
TCGA-BR-A4QL TCGA-CG-5728 TCGA-VQ-A8P2 
       16.14        65.10        38.14 

$`UGDH WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
        0.13        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  UGDH MUTATED UGDH WILD-TYPE 
          7.76           0.00 
  UGDH MUTATED UGDH WILD-TYPE 
         79.07         122.30 
  UGDH MUTATED UGDH WILD-TYPE 
         28.14          13.51 
[1] "7.8 - 79.1 (28.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D1074V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGDH MUTATED         0        0        1        1         2         1
  UGDH WILD-TYPE      10       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UGDH MUTATED           0          2          1          1        0         0
  UGDH WILD-TYPE        29         82         61         38       43         4
D1074V3, multiclass
            clus
vv           UGDH MUTATED UGDH WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  UGDH MUTATED       0   4   3   3
  UGDH WILD-TYPE    54 131 258  99
D1074V4, multiclass
       clus
vv      UGDH MUTATED UGDH WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  UGDH MUTATED     5   2   0   2
  UGDH WILD-TYPE 190 171  89  83
D1074V5, multiclass
    clus
vv   UGDH MUTATED UGDH WILD-TYPE
  N0            5            190
  N1            2            171
  N2            0             89
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V6, binary
                cls
clus               0   1
  UGDH MUTATED    11   0
  UGDH WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGDH MUTATED     11    0
  UGDH WILD-TYPE  471   38
   clus
vv  UGDH MUTATED UGDH WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D1074V7, binary
                cls
clus               0   1
  UGDH MUTATED     7   4
  UGDH WILD-TYPE 165 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGDH MUTATED      7    4
  UGDH WILD-TYPE  165  402
        clus
vv       UGDH MUTATED UGDH WILD-TYPE
  FEMALE            7            165
  MALE              4            402
[1] 2 2
[1] FALSE
D1074V8, binary
                cls
clus               0   1
  UGDH MUTATED     5   3
  UGDH WILD-TYPE 411  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGDH MUTATED      5    3
  UGDH WILD-TYPE  411   99
     clus
vv    UGDH MUTATED UGDH WILD-TYPE
  NO             5            411
  YES            3             99
[1] 2 2
[1] FALSE
D1074V9, continuous
[1] "Remove cluster labels:" "UGDH MUTATED"          
clus
  UGDH MUTATED UGDH WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"UGDH WILD-TYPE" "UGDH WILD-TYPE" "UGDH WILD-TYPE" 
D1074V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UGDH MUTATED       2                         0
  UGDH WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGDH MUTATED                                           0     7
  UGDH WILD-TYPE                                         1   350
D1074V11, multiclass
                                           clus
vv                                          UGDH MUTATED UGDH WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V12, binary
                cls
clus               0   1
  UGDH MUTATED     0   7
  UGDH WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGDH MUTATED      0    7
  UGDH WILD-TYPE   10  391
                        clus
vv                       UGDH MUTATED UGDH WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(1075) Variable = C1QA MUTATION ANALYSIS
D1075V1, survival
                sevent
clus2              0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 333 216
  C1QA MUTATED C1QA WILD-TYPE 
             5            549 
  C1QA MUTATED C1QA WILD-TYPE 
             0            216 
$`C1QA MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-5723 TCGA-CG-5728 TCGA-HU-A4GT 
       29.59         1.12       105.07        65.10         6.51 

$`C1QA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  C1QA MUTATED C1QA WILD-TYPE 
          1.12           0.00 
  C1QA MUTATED C1QA WILD-TYPE 
        105.07         122.30 
  C1QA MUTATED C1QA WILD-TYPE 
         29.59          13.55 
[1] "1.1 - 105.1 (29.6)" "0.0 - 122.3 (13.6)"
[1] "hr="     "9500000"
D1075V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1QA MUTATED         0        0        1        1         2         1
  C1QA WILD-TYPE      10       20       45       30        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1QA MUTATED           0          0          0          0        0         0
  C1QA WILD-TYPE        29         84         62         39       43         4
D1075V3, multiclass
            clus
vv           C1QA MUTATED C1QA WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  C1QA MUTATED       0   2   2   1
  C1QA WILD-TYPE    54 133 259 101
D1075V4, multiclass
       clus
vv      C1QA MUTATED C1QA WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  C1QA MUTATED     4   1   0   0
  C1QA WILD-TYPE 191 172  89  85
D1075V5, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  N0            4            191
  N1            1            172
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V6, binary
                cls
clus               0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      5    0
  C1QA WILD-TYPE  477   38
   clus
vv  C1QA MUTATED C1QA WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D1075V7, binary
                cls
clus               0   1
  C1QA MUTATED     4   1
  C1QA WILD-TYPE 168 405
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      4    1
  C1QA WILD-TYPE  168  405
        clus
vv       C1QA MUTATED C1QA WILD-TYPE
  FEMALE            4            168
  MALE              1            405
[1] 2 2
[1] FALSE
D1075V8, binary
                cls
clus               0   1
  C1QA MUTATED     4   0
  C1QA WILD-TYPE 412 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      4    0
  C1QA WILD-TYPE  412  102
     clus
vv    C1QA MUTATED C1QA WILD-TYPE
  NO             4            412
  YES            0            102
[1] 2 2
[1] FALSE
D1075V9, continuous
D1075V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  C1QA MUTATED       1                         0
  C1QA WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1QA MUTATED                                           0     2
  C1QA WILD-TYPE                                         1   355
D1075V11, multiclass
                                           clus
vv                                          C1QA MUTATED C1QA WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V12, binary
                cls
clus               0   1
  C1QA MUTATED     0   3
  C1QA WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      0    3
  C1QA WILD-TYPE   10  395
                        clus
vv                       C1QA MUTATED C1QA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(1076) Variable = ZC3H3 MUTATION ANALYSIS
D1076V1, survival
                 sevent
clus2               0   1
  ZC3H3 MUTATED    15   6
  ZC3H3 WILD-TYPE 323 210
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             21             533 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
              6             210 
$`ZC3H3 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-IG-A97I TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 
        4.31        24.00        12.16        26.70         9.67        34.68 
TCGA-BR-8368 TCGA-BR-8591 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4305 TCGA-D7-A4YT 
        4.31        28.14        12.43         6.58        15.95        14.27 
TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
        5.92        30.51        24.39        22.32        22.68        24.20 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-R5-A7ZE 
        6.51         6.58        18.21 

$`ZC3H3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        6.31        12.30        11.31        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        20.91        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        24.26         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
           4.31            0.00 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
          34.68          122.30 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
          15.95           13.51 
[1] "4.3 - 34.7 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1076V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H3 MUTATED         0        2        1        1         5         6
  ZC3H3 WILD-TYPE      10       18       45       30        79        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZC3H3 MUTATED           0          2          1          2        1         0
  ZC3H3 WILD-TYPE        29         82         61         37       42         4
D1076V3, multiclass
            clus
vv           ZC3H3 MUTATED ZC3H3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              6              77
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZC3H3 MUTATED       2   4  10   5
  ZC3H3 WILD-TYPE    52 131 251  97
D1076V4, multiclass
       clus
vv      ZC3H3 MUTATED ZC3H3 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3               10             251
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZC3H3 MUTATED    11   4   3   3
  ZC3H3 WILD-TYPE 184 169  86  82
D1076V5, multiclass
    clus
vv   ZC3H3 MUTATED ZC3H3 WILD-TYPE
  N0            11             184
  N1             4             169
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V6, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    20   0
  ZC3H3 WILD-TYPE 462  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     20    0
  ZC3H3 WILD-TYPE  462   38
   clus
vv  ZC3H3 MUTATED ZC3H3 WILD-TYPE
  0            20             462
  1             0              38
[1] 2 2
[1] FALSE
D1076V7, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    13   9
  ZC3H3 WILD-TYPE 159 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     13    9
  ZC3H3 WILD-TYPE  159  397
        clus
vv       ZC3H3 MUTATED ZC3H3 WILD-TYPE
  FEMALE            13             159
  MALE               9             397
[1] 2 2
[1] FALSE
D1076V8, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    17   3
  ZC3H3 WILD-TYPE 399  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     17    3
  ZC3H3 WILD-TYPE  399   99
     clus
vv    ZC3H3 MUTATED ZC3H3 WILD-TYPE
  NO             17             399
  YES             3              99
[1] 2 2
[1] FALSE
D1076V9, continuous
D1076V10, continuous
[1] "Remove cluster labels:" "ZC3H3 MUTATED"         
clus
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A4OG      TCGA-L5-A4OI 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL      TCGA-IG-A3Y9 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" "ZC3H3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H3 MUTATED       8                         0
  ZC3H3 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H3 MUTATED                                           0    12
  ZC3H3 WILD-TYPE                                         1   345
D1076V11, multiclass
                                           clus
vv                                          ZC3H3 MUTATED ZC3H3 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V12, binary
                 cls
clus                0   1
  ZC3H3 MUTATED     0  18
  ZC3H3 WILD-TYPE  10 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED      0   18
  ZC3H3 WILD-TYPE   10  380
                        clus
vv                       ZC3H3 MUTATED ZC3H3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(1077) Variable = CHMP7 MUTATION ANALYSIS
D1077V1, survival
                 sevent
clus2               0   1
  CHMP7 MUTATED     2   3
  CHMP7 WILD-TYPE 336 213
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              5             549 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              3             213 
$`CHMP7 MUTATED`
TCGA-CG-4460 TCGA-VR-A8EQ TCGA-BR-A4QL TCGA-CG-5728 TCGA-HU-A4GX 
       21.99        22.82        16.14        65.10        20.25 

$`CHMP7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CHMP7 MUTATED CHMP7 WILD-TYPE 
          16.14            0.00 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
           65.1           122.3 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
          21.99           13.51 
[1] "16.1 - 65.1 (22.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1077V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHMP7 MUTATED         0        0        1        0         0         0
  CHMP7 WILD-TYPE      10       20       45       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHMP7 MUTATED           1          0          1          1        2         0
  CHMP7 WILD-TYPE        28         84         61         38       41         4
D1077V3, multiclass
            clus
vv           CHMP7 MUTATED CHMP7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CHMP7 MUTATED       0   1   2   3
  CHMP7 WILD-TYPE    54 134 259  99
D1077V4, multiclass
       clus
vv      CHMP7 MUTATED CHMP7 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                2             259
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CHMP7 MUTATED     1   2   2   1
  CHMP7 WILD-TYPE 194 171  87  84
D1077V5, multiclass
    clus
vv   CHMP7 MUTATED CHMP7 WILD-TYPE
  N0             1             194
  N1             2             171
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V6, binary
                 cls
clus                0   1
  CHMP7 MUTATED     5   1
  CHMP7 WILD-TYPE 477  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      5    1
  CHMP7 WILD-TYPE  477   37
   clus
vv  CHMP7 MUTATED CHMP7 WILD-TYPE
  0             5             477
  1             1              37
[1] 2 2
[1] FALSE
D1077V7, binary
                 cls
clus                0   1
  CHMP7 MUTATED     5   1
  CHMP7 WILD-TYPE 167 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      5    1
  CHMP7 WILD-TYPE  167  405
        clus
vv       CHMP7 MUTATED CHMP7 WILD-TYPE
  FEMALE             5             167
  MALE               1             405
[1] 2 2
[1] FALSE
D1077V8, binary
                 cls
clus                0   1
  CHMP7 MUTATED     3   1
  CHMP7 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      3    1
  CHMP7 WILD-TYPE  413  101
     clus
vv    CHMP7 MUTATED CHMP7 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D1077V9, continuous
[1] "Remove cluster labels:" "CHMP7 MUTATED"         
clus
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" "CHMP7 WILD-TYPE" 
D1077V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHMP7 MUTATED       1                         0
  CHMP7 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHMP7 MUTATED                                           0     3
  CHMP7 WILD-TYPE                                         1   354
D1077V11, multiclass
                                           clus
vv                                          CHMP7 MUTATED CHMP7 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V12, binary
                 cls
clus                0   1
  CHMP7 MUTATED     0   3
  CHMP7 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      0    3
  CHMP7 WILD-TYPE   10  395
                        clus
vv                       CHMP7 MUTATED CHMP7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(1078) Variable = PTPRT MUTATION ANALYSIS
D1078V1, survival
                 sevent
clus2               0   1
  PTPRT MUTATED    42  11
  PTPRT WILD-TYPE 296 205
  PTPRT MUTATED PTPRT WILD-TYPE 
             53             501 
  PTPRT MUTATED PTPRT WILD-TYPE 
             11             205 
$`PTPRT MUTATED`
TCGA-L5-A4OI TCGA-S8-A6BV TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-JY-A93E TCGA-L5-A4OH 
       19.99        20.02        32.45         0.85        25.22        32.61 
TCGA-L5-A4OS TCGA-L5-A8NK TCGA-L7-A6VZ TCGA-LN-A4A4 TCGA-LN-A4MR TCGA-LN-A8HZ 
       58.59        13.55        10.36        12.59        13.22        12.33 
TCGA-VR-A8EW TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-6802 
        8.12         6.97         9.34        34.68        18.05        30.90 
TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
       44.94        14.43        31.10        14.04        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MJ 
        9.21         1.12        31.96        12.30         6.58        12.62 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-5721 TCGA-CG-5723 
       15.95         1.02         7.99        14.01         6.02       105.07 
TCGA-CG-5728 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-F1-A448 TCGA-HU-8238 TCGA-HU-A4G6 
       65.10        14.27        22.29        21.27         1.51        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-IN-AB1X 
       24.20        11.77         8.98        29.00        23.80        13.51 
TCGA-RD-A7BT TCGA-RD-A8N1 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-AA6A 
        8.61       115.69        38.14        37.22        38.93 

$`PTPRT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       16.24         4.21         7.69        33.27        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53         7.17        12.33        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 
       11.31        12.43        11.61        12.20        11.77        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        3.02        27.02         8.05        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        22.68         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PTPRT MUTATED PTPRT WILD-TYPE 
           0.85            0.00 
  PTPRT MUTATED PTPRT WILD-TYPE 
         115.69          122.30 
  PTPRT MUTATED PTPRT WILD-TYPE 
          14.43           13.41 
[1] "0.8 - 115.7 (14.4)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2.3"
D1078V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPRT MUTATED         1        4        6        2        10         1
  PTPRT WILD-TYPE       9       16       40       29        74        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRT MUTATED           2         12          4          6        6         0
  PTPRT WILD-TYPE        27         72         58         33       37         4
D1078V3, multiclass
            clus
vv           PTPRT MUTATED PTPRT WILD-TYPE
  STAGE I                1               9
  STAGE IA               4              16
  STAGE IB               6              40
  STAGE II               2              29
  STAGE IIA             10              74
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA            12              72
  STAGE IIIB             4              58
  STAGE IIIC             6              33
  STAGE IV               6              37
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PTPRT MUTATED       5  14  24  13
  PTPRT WILD-TYPE    49 121 237  89
D1078V4, multiclass
       clus
vv      PTPRT MUTATED PTPRT WILD-TYPE
  T0+T1             5              49
  T2               14             121
  T3               24             237
  T4               13              89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PTPRT MUTATED    22  15  10   9
  PTPRT WILD-TYPE 173 158  79  76
D1078V5, multiclass
    clus
vv   PTPRT MUTATED PTPRT WILD-TYPE
  N0            22             173
  N1            15             158
  N2            10              79
  N3             9              76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V6, binary
                 cls
clus                0   1
  PTPRT MUTATED    49   3
  PTPRT WILD-TYPE 433  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     49    3
  PTPRT WILD-TYPE  433   35
   clus
vv  PTPRT MUTATED PTPRT WILD-TYPE
  0            49             433
  1             3              35
[1] 2 2
[1] FALSE
D1078V7, binary
                 cls
clus                0   1
  PTPRT MUTATED    16  41
  PTPRT WILD-TYPE 156 365
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     16   41
  PTPRT WILD-TYPE  156  365
        clus
vv       PTPRT MUTATED PTPRT WILD-TYPE
  FEMALE            16             156
  MALE              41             365
[1] 2 2
[1] FALSE
D1078V8, binary
                 cls
clus                0   1
  PTPRT MUTATED    39  10
  PTPRT WILD-TYPE 377  92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED     39   10
  PTPRT WILD-TYPE  377   92
     clus
vv    PTPRT MUTATED PTPRT WILD-TYPE
  NO             39             377
  YES            10              92
[1] 2 2
[1] FALSE
D1078V9, continuous
D1078V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPRT MUTATED      16                         0
  PTPRT WILD-TYPE   117                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPRT MUTATED                                           1    31
  PTPRT WILD-TYPE                                         0   326
D1078V11, multiclass
                                           clus
vv                                          PTPRT MUTATED PTPRT WILD-TYPE
  ASIAN                                                16             117
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                31             326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V12, binary
                 cls
clus                0   1
  PTPRT MUTATED     1  38
  PTPRT WILD-TYPE   9 360
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRT MUTATED      1   38
  PTPRT WILD-TYPE    9  360
                        clus
vv                       PTPRT MUTATED PTPRT WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            38             360
[1] 2 2
[1] FALSE

Clustering(1079) Variable = ZNF687 MUTATION ANALYSIS
D1079V1, survival
                  sevent
clus2                0   1
  ZNF687 MUTATED     8   4
  ZNF687 WILD-TYPE 330 212
  ZNF687 MUTATED ZNF687 WILD-TYPE 
              12              542 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
               4              212 
$`ZNF687 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-R6-A6Y2 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       19.99         7.76         9.30         1.12        28.14        31.96 
TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-5721 TCGA-F1-6874 TCGA-F1-A448 TCGA-VQ-A8P2 
       16.14         1.02         6.02        14.47        21.27        38.14 

$`ZNF687 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35        53.95        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZNF687 MUTATED ZNF687 WILD-TYPE 
            1.02             0.00 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
           38.14           122.30 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
          15.305           13.530 
[1] "1.0 - 38.1 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1079V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF687 MUTATED         0        0        1        0         1         1
  ZNF687 WILD-TYPE      10       20       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF687 MUTATED           0          1          2          2        4
  ZNF687 WILD-TYPE        29         83         60         37       39
                  vv
clus               STAGE IVA
  ZNF687 MUTATED           0
  ZNF687 WILD-TYPE         4
D1079V3, multiclass
            clus
vv           ZNF687 MUTATED ZNF687 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF687 MUTATED       1   2   5   5
  ZNF687 WILD-TYPE    53 133 256  97
D1079V4, multiclass
       clus
vv      ZNF687 MUTATED ZNF687 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 5              256
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF687 MUTATED     2   3   3   4
  ZNF687 WILD-TYPE 193 170  86  81
D1079V5, multiclass
    clus
vv   ZNF687 MUTATED ZNF687 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V6, binary
                  cls
clus                 0   1
  ZNF687 MUTATED    10   2
  ZNF687 WILD-TYPE 472  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED     10    2
  ZNF687 WILD-TYPE  472   36
   clus
vv  ZNF687 MUTATED ZNF687 WILD-TYPE
  0             10              472
  1              2               36
[1] 2 2
[1] FALSE
D1079V7, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     5   9
  ZNF687 WILD-TYPE 167 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      5    9
  ZNF687 WILD-TYPE  167  397
        clus
vv       ZNF687 MUTATED ZNF687 WILD-TYPE
  FEMALE              5              167
  MALE                9              397
[1] 2 2
[1] FALSE
D1079V8, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     9   2
  ZNF687 WILD-TYPE 407 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      9    2
  ZNF687 WILD-TYPE  407  100
     clus
vv    ZNF687 MUTATED ZNF687 WILD-TYPE
  NO               9              407
  YES              2              100
[1] 2 2
[1] FALSE
D1079V9, continuous
D1079V10, continuous
[1] "Remove cluster labels:" "ZNF687 MUTATED"        
clus
  ZNF687 MUTATED ZNF687 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" "ZNF687 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF687 MUTATED       1                         0
  ZNF687 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF687 MUTATED                                           0    11
  ZNF687 WILD-TYPE                                         1   346
D1079V11, multiclass
                                           clus
vv                                          ZNF687 MUTATED ZNF687 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V12, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     2   7
  ZNF687 WILD-TYPE   8 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      2    7
  ZNF687 WILD-TYPE    8  391
                        clus
vv                       ZNF687 MUTATED ZNF687 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(1080) Variable = FAM111A MUTATION ANALYSIS
D1080V1, survival
                   sevent
clus2                 0   1
  FAM111A MUTATED     7   5
  FAM111A WILD-TYPE 331 211
  FAM111A MUTATED FAM111A WILD-TYPE 
               12               542 
  FAM111A MUTATED FAM111A WILD-TYPE 
                5               211 
$`FAM111A MUTATED`
TCGA-CG-4460 TCGA-JY-A6FA TCGA-L5-A8NR TCGA-L5-A8NW TCGA-LN-A49L TCGA-BR-4256 
       21.99        44.75         8.71        46.09        10.45         9.34 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PD TCGA-CD-A48A TCGA-CG-4305 TCGA-HU-A4GU 
        1.12        31.96        20.65        12.43        15.95         6.58 

$`FAM111A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
        5.49        21.37        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FAM111A MUTATED FAM111A WILD-TYPE 
             1.12              0.00 
  FAM111A MUTATED FAM111A WILD-TYPE 
            46.09            122.30 
  FAM111A MUTATED FAM111A WILD-TYPE 
           14.190            13.565 
[1] "1.1 - 46.1 (14.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1080V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM111A MUTATED         0        0        1        1         3         3
  FAM111A WILD-TYPE      10       20       45       30        81        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM111A MUTATED           1          0          0          0        2
  FAM111A WILD-TYPE        28         84         62         39       41
                   vv
clus                STAGE IVA
  FAM111A MUTATED           0
  FAM111A WILD-TYPE         4
D1080V3, multiclass
            clus
vv           FAM111A MUTATED FAM111A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                3                80
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM111A MUTATED       1   4   4   3
  FAM111A WILD-TYPE    53 131 257  99
D1080V4, multiclass
       clus
vv      FAM111A MUTATED FAM111A WILD-TYPE
  T0+T1               1                53
  T2                  4               131
  T3                  4               257
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM111A MUTATED     4   7   1   0
  FAM111A WILD-TYPE 191 166  88  85
D1080V5, multiclass
    clus
vv   FAM111A MUTATED FAM111A WILD-TYPE
  N0               4               191
  N1               7               166
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V6, binary
                   cls
clus                  0   1
  FAM111A MUTATED    11   2
  FAM111A WILD-TYPE 471  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED     11    2
  FAM111A WILD-TYPE  471   36
   clus
vv  FAM111A MUTATED FAM111A WILD-TYPE
  0              11               471
  1               2                36
[1] 2 2
[1] FALSE
D1080V7, binary
                   cls
clus                  0   1
  FAM111A MUTATED     5   8
  FAM111A WILD-TYPE 167 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED      5    8
  FAM111A WILD-TYPE  167  398
        clus
vv       FAM111A MUTATED FAM111A WILD-TYPE
  FEMALE               5               167
  MALE                 8               398
[1] 2 2
[1] FALSE
D1080V8, binary
                   cls
clus                  0   1
  FAM111A MUTATED    10   2
  FAM111A WILD-TYPE 406 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED     10    2
  FAM111A WILD-TYPE  406  100
     clus
vv    FAM111A MUTATED FAM111A WILD-TYPE
  NO               10               406
  YES               2               100
[1] 2 2
[1] FALSE
D1080V9, continuous
[1] "Remove cluster labels:" "FAM111A MUTATED"       
clus
  FAM111A MUTATED FAM111A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49M 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
D1080V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM111A MUTATED       5                         0
  FAM111A WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM111A MUTATED                                           0     5
  FAM111A WILD-TYPE                                         1   352
D1080V11, multiclass
                                           clus
vv                                          FAM111A MUTATED FAM111A WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V12, binary
                   cls
clus                  0   1
  FAM111A MUTATED     0   8
  FAM111A WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED      0    8
  FAM111A WILD-TYPE   10  390
                        clus
vv                       FAM111A MUTATED FAM111A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(1081) Variable = INTS8 MUTATION ANALYSIS
D1081V1, survival
                 sevent
clus2               0   1
  INTS8 MUTATED    11   5
  INTS8 WILD-TYPE 327 211
  INTS8 MUTATED INTS8 WILD-TYPE 
             16             538 
  INTS8 MUTATED INTS8 WILD-TYPE 
              5             211 
$`INTS8 MUTATED`
TCGA-L5-A4OG TCGA-IG-A3YB TCGA-JY-A6F8 TCGA-L5-A8NF TCGA-R6-A8WG TCGA-V5-AASX 
        4.70         2.63       122.10         2.66        12.69         8.98 
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CG-4305 
        6.97        30.90        32.25        31.27        16.14        15.95 
TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-8604 TCGA-MX-A666 
       14.47        22.32        22.82        14.04 

$`INTS8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85        20.78        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         6.61         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8608 
       26.47         1.51         5.92        24.39        28.96        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       19.73        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  INTS8 MUTATED INTS8 WILD-TYPE 
           2.63            0.00 
  INTS8 MUTATED INTS8 WILD-TYPE 
          122.1           122.3 
  INTS8 MUTATED INTS8 WILD-TYPE 
          15.21           13.51 
[1] "2.6 - 122.1 (15.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1081V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INTS8 MUTATED         2        0        1        1         2         2
  INTS8 WILD-TYPE       8       20       45       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INTS8 MUTATED           0          3          1          2        1         1
  INTS8 WILD-TYPE        29         81         61         37       42         3
D1081V3, multiclass
            clus
vv           INTS8 MUTATED INTS8 WILD-TYPE
  STAGE I                2               8
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  INTS8 MUTATED       3   4   4   6
  INTS8 WILD-TYPE    51 131 257  96
D1081V4, multiclass
       clus
vv      INTS8 MUTATED INTS8 WILD-TYPE
  T0+T1             3              51
  T2                4             131
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  INTS8 MUTATED     8   3   1   3
  INTS8 WILD-TYPE 187 170  88  82
D1081V5, multiclass
    clus
vv   INTS8 MUTATED INTS8 WILD-TYPE
  N0             8             187
  N1             3             170
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V6, binary
                 cls
clus                0   1
  INTS8 MUTATED    15   1
  INTS8 WILD-TYPE 467  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS8 MUTATED     15    1
  INTS8 WILD-TYPE  467   37
   clus
vv  INTS8 MUTATED INTS8 WILD-TYPE
  0            15             467
  1             1              37
[1] 2 2
[1] FALSE
D1081V7, binary
                 cls
clus                0   1
  INTS8 MUTATED     9  11
  INTS8 WILD-TYPE 163 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS8 MUTATED      9   11
  INTS8 WILD-TYPE  163  395
        clus
vv       INTS8 MUTATED INTS8 WILD-TYPE
  FEMALE             9             163
  MALE              11             395
[1] 2 2
[1] FALSE
D1081V8, binary
                 cls
clus                0   1
  INTS8 MUTATED    14   1
  INTS8 WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS8 MUTATED     14    1
  INTS8 WILD-TYPE  402  101
     clus
vv    INTS8 MUTATED INTS8 WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D1081V9, continuous
[1] "Remove cluster labels:" "INTS8 MUTATED"         
clus
  INTS8 MUTATED INTS8 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
D1081V10, continuous
[1] "Remove cluster labels:" "INTS8 MUTATED"         
clus
  INTS8 MUTATED INTS8 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" "INTS8 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  INTS8 MUTATED       2                         0
  INTS8 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INTS8 MUTATED                                           0    16
  INTS8 WILD-TYPE                                         1   341
D1081V11, multiclass
                                           clus
vv                                          INTS8 MUTATED INTS8 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V12, binary
                 cls
clus                0   1
  INTS8 MUTATED     1  14
  INTS8 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS8 MUTATED      1   14
  INTS8 WILD-TYPE    9  384
                        clus
vv                       INTS8 MUTATED INTS8 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(1082) Variable = IL1R2 MUTATION ANALYSIS
D1082V1, survival
                 sevent
clus2               0   1
  IL1R2 MUTATED     7   4
  IL1R2 WILD-TYPE 331 212
  IL1R2 MUTATED IL1R2 WILD-TYPE 
             11             543 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              4             212 
$`IL1R2 MUTATED`
TCGA-L7-A6VZ TCGA-VR-A8ER TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-7715 TCGA-BR-8487 
       10.36        12.43        32.78        18.05        33.63         1.12 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HU-A4GT TCGA-VQ-A8P2 
       31.96        16.14         6.58         6.51        38.14 

$`IL1R2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        46.09        10.85         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 
       39.12        26.10         9.17        25.61        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IL1R2 MUTATED IL1R2 WILD-TYPE 
           1.12            0.00 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
          38.14          122.30 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
          16.14           13.55 
[1] "1.1 - 38.1 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1082V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL1R2 MUTATED         0        0        0        0         5         0
  IL1R2 WILD-TYPE      10       20       46       31        79        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL1R2 MUTATED           1          2          1          2        1         0
  IL1R2 WILD-TYPE        28         82         61         37       42         4
D1082V3, multiclass
            clus
vv           IL1R2 MUTATED IL1R2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IL1R2 MUTATED       0   0   8   4
  IL1R2 WILD-TYPE    54 135 253  98
D1082V4, multiclass
       clus
vv      IL1R2 MUTATED IL1R2 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IL1R2 MUTATED     5   3   1   3
  IL1R2 WILD-TYPE 190 170  88  82
D1082V5, multiclass
    clus
vv   IL1R2 MUTATED IL1R2 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V6, binary
                 cls
clus                0   1
  IL1R2 MUTATED    10   1
  IL1R2 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED     10    1
  IL1R2 WILD-TYPE  472   37
   clus
vv  IL1R2 MUTATED IL1R2 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D1082V7, binary
                 cls
clus                0   1
  IL1R2 MUTATED     4   8
  IL1R2 WILD-TYPE 168 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      4    8
  IL1R2 WILD-TYPE  168  398
        clus
vv       IL1R2 MUTATED IL1R2 WILD-TYPE
  FEMALE             4             168
  MALE               8             398
[1] 2 2
[1] FALSE
D1082V8, binary
                 cls
clus                0   1
  IL1R2 MUTATED     9   3
  IL1R2 WILD-TYPE 407  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      9    3
  IL1R2 WILD-TYPE  407   99
     clus
vv    IL1R2 MUTATED IL1R2 WILD-TYPE
  NO              9             407
  YES             3              99
[1] 2 2
[1] FALSE
D1082V9, continuous
[1] "Remove cluster labels:" "IL1R2 MUTATED"         
clus
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
D1082V10, continuous
[1] "Remove cluster labels:" "IL1R2 MUTATED"         
clus
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"IL1R2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IL1R2 MUTATED       3                         0
  IL1R2 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL1R2 MUTATED                                           0     8
  IL1R2 WILD-TYPE                                         1   349
D1082V11, multiclass
                                           clus
vv                                          IL1R2 MUTATED IL1R2 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V12, binary
                 cls
clus                0   1
  IL1R2 MUTATED     0  10
  IL1R2 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      0   10
  IL1R2 WILD-TYPE   10  388
                        clus
vv                       IL1R2 MUTATED IL1R2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(1083) Variable = ALCAM MUTATION ANALYSIS
D1083V1, survival
                 sevent
clus2               0   1
  ALCAM MUTATED     5   7
  ALCAM WILD-TYPE 333 209
  ALCAM MUTATED ALCAM WILD-TYPE 
             12             542 
  ALCAM MUTATED ALCAM WILD-TYPE 
              7             209 
$`ALCAM MUTATED`
TCGA-L5-A8NM TCGA-XP-A8T7 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8360 
        7.76        41.23        26.70         6.97        30.90         6.18 
TCGA-BR-8487 TCGA-CD-5801 TCGA-CG-5718 TCGA-CG-5721 TCGA-D7-A6EZ TCGA-EQ-8122 
        1.12        13.18        36.00         6.02        20.32         7.99 

$`ALCAM WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ALCAM MUTATED ALCAM WILD-TYPE 
           1.12            0.00 
  ALCAM MUTATED ALCAM WILD-TYPE 
          41.23          122.30 
  ALCAM MUTATED ALCAM WILD-TYPE 
         10.585          13.630 
[1] "1.1 - 41.2 (10.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1083V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALCAM MUTATED         1        0        1        1         3         3
  ALCAM WILD-TYPE       9       20       45       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALCAM MUTATED           0          3          0          0        1         0
  ALCAM WILD-TYPE        29         81         62         39       42         4
D1083V3, multiclass
            clus
vv           ALCAM MUTATED ALCAM WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ALCAM MUTATED       1   5   6   2
  ALCAM WILD-TYPE    53 130 255 100
D1083V4, multiclass
       clus
vv      ALCAM MUTATED ALCAM WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ALCAM MUTATED     5   7   1   0
  ALCAM WILD-TYPE 190 166  88  85
D1083V5, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  N0             5             190
  N1             7             166
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V6, binary
                 cls
clus                0   1
  ALCAM MUTATED    11   0
  ALCAM WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED     11    0
  ALCAM WILD-TYPE  471   38
   clus
vv  ALCAM MUTATED ALCAM WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D1083V7, binary
                 cls
clus                0   1
  ALCAM MUTATED     7   7
  ALCAM WILD-TYPE 165 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      7    7
  ALCAM WILD-TYPE  165  399
        clus
vv       ALCAM MUTATED ALCAM WILD-TYPE
  FEMALE             7             165
  MALE               7             399
[1] 2 2
[1] FALSE
D1083V8, binary
                 cls
clus                0   1
  ALCAM MUTATED    12   1
  ALCAM WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED     12    1
  ALCAM WILD-TYPE  404  101
     clus
vv    ALCAM MUTATED ALCAM WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D1083V9, continuous
[1] "Remove cluster labels:" "ALCAM MUTATED"         
clus
  ALCAM MUTATED ALCAM WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
D1083V10, continuous
[1] "Remove cluster labels:" "ALCAM MUTATED"         
clus
  ALCAM MUTATED ALCAM WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T8 
"ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" "ALCAM WILD-TYPE" 
     TCGA-Z6-AAPN 
"ALCAM WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALCAM MUTATED       1                         1
  ALCAM WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALCAM MUTATED                                           0     9
  ALCAM WILD-TYPE                                         1   348
D1083V11, multiclass
                                           clus
vv                                          ALCAM MUTATED ALCAM WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V12, binary
                 cls
clus                0   1
  ALCAM MUTATED     1   9
  ALCAM WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      1    9
  ALCAM WILD-TYPE    9  389
                        clus
vv                       ALCAM MUTATED ALCAM WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1084) Variable = TIA1 MUTATION ANALYSIS
D1084V1, survival
                sevent
clus2              0   1
  TIA1 MUTATED     3   3
  TIA1 WILD-TYPE 335 213
  TIA1 MUTATED TIA1 WILD-TYPE 
             6            548 
  TIA1 MUTATED TIA1 WILD-TYPE 
             3            213 
$`TIA1 MUTATED`
TCGA-L5-A43J TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL TCGA-HF-A5NB TCGA-HU-A4GQ 
        4.31        31.27        31.96        16.14        30.51         0.10 

$`TIA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TIA1 MUTATED TIA1 WILD-TYPE 
           0.1            0.0 
  TIA1 MUTATED TIA1 WILD-TYPE 
         31.96         122.30 
  TIA1 MUTATED TIA1 WILD-TYPE 
        23.325         13.530 
[1] "0.1 - 32.0 (23.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1084V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIA1 MUTATED         0        0        0        0         0         1
  TIA1 WILD-TYPE      10       20       46       31        84        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIA1 MUTATED           0          0          1          3        1         0
  TIA1 WILD-TYPE        29         84         61         36       42         4
D1084V3, multiclass
            clus
vv           TIA1 MUTATED TIA1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TIA1 MUTATED       0   0   2   4
  TIA1 WILD-TYPE    54 135 259  98
D1084V4, multiclass
       clus
vv      TIA1 MUTATED TIA1 WILD-TYPE
  T0+T1            0             54
  T2               0            135
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TIA1 MUTATED     1   0   2   3
  TIA1 WILD-TYPE 194 173  87  82
D1084V5, multiclass
    clus
vv   TIA1 MUTATED TIA1 WILD-TYPE
  N0            1            194
  N1            0            173
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V6, binary
                cls
clus               0   1
  TIA1 MUTATED     4   1
  TIA1 WILD-TYPE 478  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIA1 MUTATED      4    1
  TIA1 WILD-TYPE  478   37
   clus
vv  TIA1 MUTATED TIA1 WILD-TYPE
  0            4            478
  1            1             37
[1] 2 2
[1] FALSE
D1084V7, binary
                cls
clus               0   1
  TIA1 MUTATED     2   4
  TIA1 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIA1 MUTATED      2    4
  TIA1 WILD-TYPE  170  402
        clus
vv       TIA1 MUTATED TIA1 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D1084V8, binary
                cls
clus               0   1
  TIA1 MUTATED     4   1
  TIA1 WILD-TYPE 412 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIA1 MUTATED      4    1
  TIA1 WILD-TYPE  412  101
     clus
vv    TIA1 MUTATED TIA1 WILD-TYPE
  NO             4            412
  YES            1            101
[1] 2 2
[1] FALSE
D1084V9, continuous
D1084V10, continuous
[1] "Remove cluster labels:" "TIA1 MUTATED"          
clus
  TIA1 MUTATED TIA1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A4OE     TCGA-L5-A4OG 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" "TIA1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"TIA1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TIA1 MUTATED       2                         0
  TIA1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIA1 MUTATED                                           0     3
  TIA1 WILD-TYPE                                         1   354
D1084V11, multiclass
                                           clus
vv                                          TIA1 MUTATED TIA1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V12, binary
                cls
clus               0   1
  TIA1 MUTATED     0   4
  TIA1 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIA1 MUTATED      0    4
  TIA1 WILD-TYPE   10  394
                        clus
vv                       TIA1 MUTATED TIA1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(1085) Variable = C6ORF72 MUTATION ANALYSIS
D1085V1, survival
                   sevent
clus2                 0   1
  C6ORF72 MUTATED     6   1
  C6ORF72 WILD-TYPE 332 215
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                7               547 
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                1               215 
$`C6ORF72 MUTATED`
TCGA-LN-A49R TCGA-Q9-A6FW TCGA-BR-6452 TCGA-CG-5721 TCGA-HU-A4GH TCGA-HU-A4GX 
       13.38         7.82        34.68         6.02        11.77        20.25 
TCGA-RD-A8N6 
        8.94 

$`C6ORF72 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S 
       10.45        12.66        12.43        13.41        12.33        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
             6.02              0.00 
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
            34.68            122.30 
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
            11.77             13.68 
[1] "6.0 - 34.7 (11.8)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "2.3"
D1085V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C6ORF72 MUTATED         0        1        1        0         1         0
  C6ORF72 WILD-TYPE      10       19       45       31        83        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF72 MUTATED           1          1          1          1        1
  C6ORF72 WILD-TYPE        28         83         61         38       42
                   vv
clus                STAGE IVA
  C6ORF72 MUTATED           0
  C6ORF72 WILD-TYPE         4
D1085V3, multiclass
            clus
vv           C6ORF72 MUTATED C6ORF72 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C6ORF72 MUTATED       1   2   3   2
  C6ORF72 WILD-TYPE    53 133 258 100
D1085V4, multiclass
       clus
vv      C6ORF72 MUTATED C6ORF72 WILD-TYPE
  T0+T1               1                53
  T2                  2               133
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C6ORF72 MUTATED     3   2   3   0
  C6ORF72 WILD-TYPE 192 171  86  85
D1085V5, multiclass
    clus
vv   C6ORF72 MUTATED C6ORF72 WILD-TYPE
  N0               3               192
  N1               2               171
  N2               3                86
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V6, binary
                   cls
clus                  0   1
  C6ORF72 MUTATED     7   0
  C6ORF72 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF72 MUTATED      7    0
  C6ORF72 WILD-TYPE  475   38
   clus
vv  C6ORF72 MUTATED C6ORF72 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D1085V7, binary
                   cls
clus                  0   1
  C6ORF72 MUTATED     4   4
  C6ORF72 WILD-TYPE 168 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF72 MUTATED      4    4
  C6ORF72 WILD-TYPE  168  402
        clus
vv       C6ORF72 MUTATED C6ORF72 WILD-TYPE
  FEMALE               4               168
  MALE                 4               402
[1] 2 2
[1] FALSE
D1085V8, binary
                   cls
clus                  0   1
  C6ORF72 MUTATED     6   2
  C6ORF72 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF72 MUTATED      6    2
  C6ORF72 WILD-TYPE  410  100
     clus
vv    C6ORF72 MUTATED C6ORF72 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D1085V9, continuous
[1] "Remove cluster labels:" "C6ORF72 MUTATED"       
clus
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
D1085V10, continuous
[1] "Remove cluster labels:" "C6ORF72 MUTATED"       
clus
  C6ORF72 MUTATED C6ORF72 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49S        TCGA-LN-A49U 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-R6-A6DN        TCGA-R6-A6L4 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" "C6ORF72 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C6ORF72 MUTATED       3                         0
  C6ORF72 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6ORF72 MUTATED                                           0     3
  C6ORF72 WILD-TYPE                                         1   354
D1085V11, multiclass
                                           clus
vv                                          C6ORF72 MUTATED C6ORF72 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V12, binary
                   cls
clus                  0   1
  C6ORF72 MUTATED     0   6
  C6ORF72 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF72 MUTATED      0    6
  C6ORF72 WILD-TYPE   10  392
                        clus
vv                       C6ORF72 MUTATED C6ORF72 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1086) Variable = DEK MUTATION ANALYSIS
D1086V1, survival
               sevent
clus2             0   1
  DEK MUTATED     8   1
  DEK WILD-TYPE 330 215
  DEK MUTATED DEK WILD-TYPE 
            9           545 
  DEK MUTATED DEK WILD-TYPE 
            1           215 
$`DEK MUTATED`
TCGA-Z6-A8JD TCGA-BR-8680 TCGA-CG-5723 TCGA-CG-5730 TCGA-HF-A5NB TCGA-HJ-7597 
        3.42        31.96       105.07         4.01        30.51        26.47 
TCGA-HU-A4GX TCGA-IP-7968 TCGA-VQ-A8P2 
       20.25         2.53        38.14 

$`DEK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DEK MUTATED DEK WILD-TYPE 
         2.53          0.00 
  DEK MUTATED DEK WILD-TYPE 
       105.07        122.30 
  DEK MUTATED DEK WILD-TYPE 
        26.47         13.51 
[1] "2.5 - 105.1 (26.5)" "0.0 - 122.3 (13.5)"
[1] "hr=" "5"  
D1086V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DEK MUTATED         0        0        1        1         0         1
  DEK WILD-TYPE      10       20       45       30        84        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEK MUTATED           0          1          1          2        2         0
  DEK WILD-TYPE        29         83         61         37       41         4
D1086V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             1            45
  STAGE II             1            30
  STAGE IIA            0            84
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           1            61
  STAGE IIIC           2            37
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  DEK MUTATED       0   3   2   4
  DEK WILD-TYPE    54 132 259  98
D1086V4, multiclass
       clus
vv      DEK MUTATED DEK WILD-TYPE
  T0+T1           0            54
  T2              3           132
  T3              2           259
  T4              4            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DEK MUTATED     2   3   3   1
  DEK WILD-TYPE 193 170  86  84
D1086V5, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  N0           2           193
  N1           3           170
  N2           3            86
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V6, binary
               cls
clus              0   1
  DEK MUTATED     5   2
  DEK WILD-TYPE 477  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    2
  DEK WILD-TYPE  477   36
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           5           477
  1           2            36
[1] 2 2
[1] FALSE
D1086V7, binary
               cls
clus              0   1
  DEK MUTATED     4   5
  DEK WILD-TYPE 168 401
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    5
  DEK WILD-TYPE  168  401
        clus
vv       DEK MUTATED DEK WILD-TYPE
  FEMALE           4           168
  MALE             5           401
[1] 2 2
[1] FALSE
D1086V8, binary
               cls
clus              0   1
  DEK MUTATED     5   2
  DEK WILD-TYPE 411 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    2
  DEK WILD-TYPE  411  100
     clus
vv    DEK MUTATED DEK WILD-TYPE
  NO            5           411
  YES           2           100
[1] 2 2
[1] FALSE
D1086V9, continuous
[1] "Remove cluster labels:" "DEK MUTATED"           
clus
  DEK MUTATED DEK WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-V5-AASW    TCGA-V5-AASX    TCGA-VR-A8EO    TCGA-VR-A8EP    TCGA-VR-A8EQ 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-VR-A8ER    TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-VR-A8EY    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-VR-AA7B    TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7 
"DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" "DEK WILD-TYPE" 
   TCGA-XP-A8T8    TCGA-Z6-A8JE 
"DEK WILD-TYPE" "DEK WILD-TYPE" 
D1086V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DEK MUTATED       2                         0
  DEK WILD-TYPE   131                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEK MUTATED                                           0     4
  DEK WILD-TYPE                                         1   353
D1086V11, multiclass
                                           clus
vv                                          DEK MUTATED DEK WILD-TYPE
  ASIAN                                               2           131
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V12, binary
               cls
clus              0   1
  DEK MUTATED     0   5
  DEK WILD-TYPE  10 393
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      0    5
  DEK WILD-TYPE   10  393
                        clus
vv                       DEK MUTATED DEK WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           5           393
[1] 2 2
[1] FALSE

Clustering(1087) Variable = UBXN6 MUTATION ANALYSIS
D1087V1, survival
                 sevent
clus2               0   1
  UBXN6 MUTATED     9   5
  UBXN6 WILD-TYPE 329 211
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             14             540 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              5             211 
$`UBXN6 MUTATED`
TCGA-L5-A4OI TCGA-IG-A4QT TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-A4MG 
       19.99         9.30        26.70        30.90         1.12         6.58 
TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4H3 
       12.62         8.05        21.07        21.27        29.98        29.00 
TCGA-HU-A4H8 TCGA-VQ-AA64 
       14.07        18.41 

$`UBXN6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  UBXN6 MUTATED UBXN6 WILD-TYPE 
           1.12            0.00 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
           30.9           122.3 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
          19.20           13.51 
[1] "1.1 - 30.9 (19.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1087V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBXN6 MUTATED         0        0        2        1         4         1
  UBXN6 WILD-TYPE      10       20       44       30        80        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBXN6 MUTATED           0          1          2          2        0         0
  UBXN6 WILD-TYPE        29         83         60         37       43         4
D1087V3, multiclass
            clus
vv           UBXN6 MUTATED UBXN6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  UBXN6 MUTATED       1   5   6   2
  UBXN6 WILD-TYPE    53 130 255 100
D1087V4, multiclass
       clus
vv      UBXN6 MUTATED UBXN6 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  UBXN6 MUTATED     5   3   2   3
  UBXN6 WILD-TYPE 190 170  87  82
D1087V5, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V6, binary
                 cls
clus                0   1
  UBXN6 MUTATED    13   0
  UBXN6 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED     13    0
  UBXN6 WILD-TYPE  469   38
   clus
vv  UBXN6 MUTATED UBXN6 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D1087V7, binary
                 cls
clus                0   1
  UBXN6 MUTATED     5   9
  UBXN6 WILD-TYPE 167 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      5    9
  UBXN6 WILD-TYPE  167  397
        clus
vv       UBXN6 MUTATED UBXN6 WILD-TYPE
  FEMALE             5             167
  MALE               9             397
[1] 2 2
[1] FALSE
D1087V8, binary
                 cls
clus                0   1
  UBXN6 MUTATED    10   3
  UBXN6 WILD-TYPE 406  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED     10    3
  UBXN6 WILD-TYPE  406   99
     clus
vv    UBXN6 MUTATED UBXN6 WILD-TYPE
  NO             10             406
  YES             3              99
[1] 2 2
[1] FALSE
D1087V9, continuous
D1087V10, continuous
[1] "Remove cluster labels:" "UBXN6 MUTATED"         
clus
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  UBXN6 MUTATED       5                         0
  UBXN6 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBXN6 MUTATED                                           0     7
  UBXN6 WILD-TYPE                                         1   350
D1087V11, multiclass
                                           clus
vv                                          UBXN6 MUTATED UBXN6 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V12, binary
                 cls
clus                0   1
  UBXN6 MUTATED     1   9
  UBXN6 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      1    9
  UBXN6 WILD-TYPE    9  389
                        clus
vv                       UBXN6 MUTATED UBXN6 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1088) Variable = FGF13 MUTATION ANALYSIS
D1088V1, survival
                 sevent
clus2               0   1
  FGF13 MUTATED    12   5
  FGF13 WILD-TYPE 326 211
  FGF13 MUTATED FGF13 WILD-TYPE 
             17             537 
  FGF13 MUTATED FGF13 WILD-TYPE 
              5             211 
$`FGF13 MUTATED`
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-L5-A4OJ TCGA-L5-A4OT TCGA-B7-5816 TCGA-BR-4201 
       35.97         5.16        21.01         4.90        26.70        30.90 
TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-8531 TCGA-CG-5723 TCGA-D7-A4Z0 TCGA-HF-A5NB 
       44.94        29.59        12.59       105.07        14.76        30.51 
TCGA-HU-A4H8 TCGA-R5-A7ZE TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       14.07        18.21        37.41        38.14        17.85 

$`FGF13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        3.32         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        13.78        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       43.36        37.22        22.19         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FGF13 MUTATED FGF13 WILD-TYPE 
            4.9             0.0 
  FGF13 MUTATED FGF13 WILD-TYPE 
         105.07          122.30 
  FGF13 MUTATED FGF13 WILD-TYPE 
          26.70           13.41 
[1] "4.9 - 105.1 (26.7)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D1088V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF13 MUTATED         1        0        2        1         1         3
  FGF13 WILD-TYPE       9       20       44       30        83        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGF13 MUTATED           1          3          2          1        2         0
  FGF13 WILD-TYPE        28         81         60         38       41         4
D1088V3, multiclass
            clus
vv           FGF13 MUTATED FGF13 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  FGF13 MUTATED       3   4   8   4
  FGF13 WILD-TYPE    51 131 253  98
D1088V4, multiclass
       clus
vv      FGF13 MUTATED FGF13 WILD-TYPE
  T0+T1             3              51
  T2                4             131
  T3                8             253
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  FGF13 MUTATED     5   7   3   2
  FGF13 WILD-TYPE 190 166  86  83
D1088V5, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  N0             5             190
  N1             7             166
  N2             3              86
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V6, binary
                 cls
clus                0   1
  FGF13 MUTATED    17   2
  FGF13 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     17    2
  FGF13 WILD-TYPE  465   36
   clus
vv  FGF13 MUTATED FGF13 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D1088V7, binary
                 cls
clus                0   1
  FGF13 MUTATED    12   7
  FGF13 WILD-TYPE 160 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     12    7
  FGF13 WILD-TYPE  160  399
        clus
vv       FGF13 MUTATED FGF13 WILD-TYPE
  FEMALE            12             160
  MALE               7             399
[1] 2 2
[1] FALSE
D1088V8, binary
                 cls
clus                0   1
  FGF13 MUTATED    14   4
  FGF13 WILD-TYPE 402  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     14    4
  FGF13 WILD-TYPE  402   98
     clus
vv    FGF13 MUTATED FGF13 WILD-TYPE
  NO             14             402
  YES             4              98
[1] 2 2
[1] FALSE
D1088V9, continuous
D1088V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FGF13 MUTATED       2                         0
  FGF13 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF13 MUTATED                                           0    15
  FGF13 WILD-TYPE                                         1   342
D1088V11, multiclass
                                           clus
vv                                          FGF13 MUTATED FGF13 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V12, binary
                 cls
clus                0   1
  FGF13 MUTATED     0  11
  FGF13 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED      0   11
  FGF13 WILD-TYPE   10  387
                        clus
vv                       FGF13 MUTATED FGF13 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1089) Variable = CHD1 MUTATION ANALYSIS
D1089V1, survival
                sevent
clus2              0   1
  CHD1 MUTATED    14   6
  CHD1 WILD-TYPE 324 210
  CHD1 MUTATED CHD1 WILD-TYPE 
            20            534 
  CHD1 MUTATED CHD1 WILD-TYPE 
             6            210 
$`CHD1 MUTATED`
TCGA-JY-A6FA TCGA-JY-A93D TCGA-L5-A43H TCGA-L5-A4OU TCGA-L5-A8NM TCGA-LN-A7HV 
       44.75        31.56         0.30        29.00         7.76        10.52 
TCGA-LN-A8HZ TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 
       12.33        19.56         6.97         9.67        34.68        32.78 
TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-5579 TCGA-MX-A5UJ TCGA-R5-A7ZI 
       31.96        15.95         6.02        20.91        19.73        74.53 
TCGA-VQ-A8P2 TCGA-VQ-A91V 
       38.14        42.64 

$`CHD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D 
       17.85         1.87        15.65        20.81         1.71        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CHD1 MUTATED CHD1 WILD-TYPE 
           0.3            0.0 
  CHD1 MUTATED CHD1 WILD-TYPE 
         74.53         122.30 
  CHD1 MUTATED CHD1 WILD-TYPE 
        20.320         13.495 
[1] "0.3 - 74.5 (20.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1089V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHD1 MUTATED         0        0        0        1         5         2
  CHD1 WILD-TYPE      10       20       46       30        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD1 MUTATED           1          5          0          2        3         0
  CHD1 WILD-TYPE        28         79         62         37       40         4
D1089V3, multiclass
            clus
vv           CHD1 MUTATED CHD1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            5             79
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CHD1 MUTATED       0   6   8   5
  CHD1 WILD-TYPE    54 129 253  97
D1089V4, multiclass
       clus
vv      CHD1 MUTATED CHD1 WILD-TYPE
  T0+T1            0             54
  T2               6            129
  T3               8            253
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CHD1 MUTATED     5   8   4   2
  CHD1 WILD-TYPE 190 165  85  83
D1089V5, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  N0            5            190
  N1            8            165
  N2            4             85
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V6, binary
                cls
clus               0   1
  CHD1 MUTATED    17   2
  CHD1 WILD-TYPE 465  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     17    2
  CHD1 WILD-TYPE  465   36
   clus
vv  CHD1 MUTATED CHD1 WILD-TYPE
  0           17            465
  1            2             36
[1] 2 2
[1] FALSE
D1089V7, binary
                cls
clus               0   1
  CHD1 MUTATED     6  14
  CHD1 WILD-TYPE 166 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      6   14
  CHD1 WILD-TYPE  166  392
        clus
vv       CHD1 MUTATED CHD1 WILD-TYPE
  FEMALE            6            166
  MALE             14            392
[1] 2 2
[1] FALSE
D1089V8, binary
                cls
clus               0   1
  CHD1 MUTATED    15   5
  CHD1 WILD-TYPE 401  97
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     15    5
  CHD1 WILD-TYPE  401   97
     clus
vv    CHD1 MUTATED CHD1 WILD-TYPE
  NO            15            401
  YES            5             97
[1] 2 2
[1] FALSE
D1089V9, continuous
[1] "Remove cluster labels:" "CHD1 MUTATED"          
clus
  CHD1 MUTATED CHD1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CHD1 WILD-TYPE" "CHD1 WILD-TYPE" "CHD1 WILD-TYPE" 
D1089V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CHD1 MUTATED       4                         0
  CHD1 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHD1 MUTATED                                           0    13
  CHD1 WILD-TYPE                                         1   344
D1089V11, multiclass
                                           clus
vv                                          CHD1 MUTATED CHD1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V12, binary
                cls
clus               0   1
  CHD1 MUTATED     1  10
  CHD1 WILD-TYPE   9 388
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      1   10
  CHD1 WILD-TYPE    9  388
                        clus
vv                       CHD1 MUTATED CHD1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           10            388
[1] 2 2
[1] FALSE

Clustering(1090) Variable = SLC30A5 MUTATION ANALYSIS
D1090V1, survival
                   sevent
clus2                 0   1
  SLC30A5 MUTATED     2   6
  SLC30A5 WILD-TYPE 336 210
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                8               546 
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                6               210 
$`SLC30A5 MUTATED`
TCGA-JY-A93D TCGA-L5-A4OJ TCGA-L5-A8NM TCGA-R6-A6Y2 TCGA-VR-A8ER TCGA-BR-8589 
       31.56        21.01         7.76         9.30        12.43        27.12 
TCGA-CG-4306 TCGA-CG-5726 
        1.02        28.96 

$`SLC30A5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
             1.02              0.00 
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
            31.56            122.30 
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
           16.720            13.565 
[1] "1.0 - 31.6 (16.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D1090V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC30A5 MUTATED         1        1        0        0         0         1
  SLC30A5 WILD-TYPE       9       19       46       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC30A5 MUTATED           1          0          1          1        1
  SLC30A5 WILD-TYPE        28         84         61         38       42
                   vv
clus                STAGE IVA
  SLC30A5 MUTATED           0
  SLC30A5 WILD-TYPE         4
D1090V3, multiclass
            clus
vv           SLC30A5 MUTATED SLC30A5 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 1                19
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SLC30A5 MUTATED       2   2   1   2
  SLC30A5 WILD-TYPE    52 133 260 100
D1090V4, multiclass
       clus
vv      SLC30A5 MUTATED SLC30A5 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  1               260
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SLC30A5 MUTATED     2   3   1   1
  SLC30A5 WILD-TYPE 193 170  88  84
D1090V5, multiclass
    clus
vv   SLC30A5 MUTATED SLC30A5 WILD-TYPE
  N0               2               193
  N1               3               170
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V6, binary
                   cls
clus                  0   1
  SLC30A5 MUTATED     6   1
  SLC30A5 WILD-TYPE 476  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A5 MUTATED      6    1
  SLC30A5 WILD-TYPE  476   37
   clus
vv  SLC30A5 MUTATED SLC30A5 WILD-TYPE
  0               6               476
  1               1                37
[1] 2 2
[1] FALSE
D1090V7, binary
                   cls
clus                  0   1
  SLC30A5 MUTATED     2   6
  SLC30A5 WILD-TYPE 170 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A5 MUTATED      2    6
  SLC30A5 WILD-TYPE  170  400
        clus
vv       SLC30A5 MUTATED SLC30A5 WILD-TYPE
  FEMALE               2               170
  MALE                 6               400
[1] 2 2
[1] FALSE
D1090V8, binary
                   cls
clus                  0   1
  SLC30A5 MUTATED     4   2
  SLC30A5 WILD-TYPE 412 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A5 MUTATED      4    2
  SLC30A5 WILD-TYPE  412  100
     clus
vv    SLC30A5 MUTATED SLC30A5 WILD-TYPE
  NO                4               412
  YES               2               100
[1] 2 2
[1] FALSE
D1090V9, continuous
[1] "Remove cluster labels:" "SLC30A5 MUTATED"       
clus
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
D1090V10, continuous
[1] "Remove cluster labels:" "SLC30A5 MUTATED"       
clus
  SLC30A5 MUTATED SLC30A5 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A8W5 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8EU 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" "SLC30A5 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC30A5 MUTATED       0                         0
  SLC30A5 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC30A5 MUTATED                                           0     5
  SLC30A5 WILD-TYPE                                         1   352
D1090V11, multiclass
                                           clus
vv                                          SLC30A5 MUTATED SLC30A5 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V12, binary
                   cls
clus                  0   1
  SLC30A5 MUTATED     1   1
  SLC30A5 WILD-TYPE   9 397
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A5 MUTATED      1    1
  SLC30A5 WILD-TYPE    9  397
                        clus
vv                       SLC30A5 MUTATED SLC30A5 WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               1               397
[1] 2 2
[1] FALSE

Clustering(1091) Variable = PHACTR2 MUTATION ANALYSIS
D1091V1, survival
                   sevent
clus2                 0   1
  PHACTR2 MUTATED    12   6
  PHACTR2 WILD-TYPE 326 210
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               18               536 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                6               210 
$`PHACTR2 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GI TCGA-JY-A6FG TCGA-L5-A4OU TCGA-BR-6452 TCGA-BR-8373 
       21.99        14.30        41.52        29.00        34.68        14.79 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A4PE TCGA-BR-A4PF 
        1.12        28.14        31.96        32.58        20.42         1.15 
TCGA-CD-A4MJ TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       12.62        11.44        22.32         0.10        38.14        22.19 

$`PHACTR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53        26.73        24.79         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
              0.1               0.0 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            41.52            122.30 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
           22.090            13.445 
[1] "0.1 - 41.5 (22.1)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D1091V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR2 MUTATED         0        0        2        0         3         2
  PHACTR2 WILD-TYPE      10       20       44       31        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR2 MUTATED           2          2          3          2        2
  PHACTR2 WILD-TYPE        27         82         59         37       41
                   vv
clus                STAGE IVA
  PHACTR2 MUTATED           0
  PHACTR2 WILD-TYPE         4
D1091V3, multiclass
            clus
vv           PHACTR2 MUTATED PHACTR2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                2                27
  STAGE IIIA               2                82
  STAGE IIIB               3                59
  STAGE IIIC               2                37
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PHACTR2 MUTATED       0   2   7   9
  PHACTR2 WILD-TYPE    54 133 254  93
D1091V4, multiclass
       clus
vv      PHACTR2 MUTATED PHACTR2 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  7               254
  T4                  9                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PHACTR2 MUTATED     7   5   3   3
  PHACTR2 WILD-TYPE 188 168  86  82
D1091V5, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  N0               7               188
  N1               5               168
  N2               3                86
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V6, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED    16   2
  PHACTR2 WILD-TYPE 466  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED     16    2
  PHACTR2 WILD-TYPE  466   36
   clus
vv  PHACTR2 MUTATED PHACTR2 WILD-TYPE
  0              16               466
  1               2                36
[1] 2 2
[1] FALSE
D1091V7, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     7  11
  PHACTR2 WILD-TYPE 165 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      7   11
  PHACTR2 WILD-TYPE  165  395
        clus
vv       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  FEMALE               7               165
  MALE                11               395
[1] 2 2
[1] FALSE
D1091V8, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED    17   1
  PHACTR2 WILD-TYPE 399 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED     17    1
  PHACTR2 WILD-TYPE  399  101
     clus
vv    PHACTR2 MUTATED PHACTR2 WILD-TYPE
  NO               17               399
  YES               1               101
[1] 2 2
[1] FALSE
D1091V9, continuous
D1091V10, continuous
[1] "Remove cluster labels:" "PHACTR2 MUTATED"       
clus
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR2 MUTATED       5                         0
  PHACTR2 WILD-TYPE   128                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR2 MUTATED                                           0    11
  PHACTR2 WILD-TYPE                                         1   346
D1091V11, multiclass
                                           clus
vv                                          PHACTR2 MUTATED PHACTR2 WILD-TYPE
  ASIAN                                                   5               128
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V12, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     0  12
  PHACTR2 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      0   12
  PHACTR2 WILD-TYPE   10  386
                        clus
vv                       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(1092) Variable = YIF1A MUTATION ANALYSIS
D1092V1, survival
                 sevent
clus2               0   1
  YIF1A MUTATED     3   1
  YIF1A WILD-TYPE 335 215
  YIF1A MUTATED YIF1A WILD-TYPE 
              4             550 
  YIF1A MUTATED YIF1A WILD-TYPE 
              1             215 
$`YIF1A MUTATED`
TCGA-BR-7717 TCGA-BR-8591 TCGA-D7-A6F0 TCGA-VQ-A8P2 
       18.15        28.14        22.29        38.14 

$`YIF1A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  YIF1A MUTATED YIF1A WILD-TYPE 
          18.15            0.00 
  YIF1A MUTATED YIF1A WILD-TYPE 
          38.14          122.30 
  YIF1A MUTATED YIF1A WILD-TYPE 
         25.215          13.510 
[1] "18.1 - 38.1 (25.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D1092V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YIF1A MUTATED         0        0        1        0         0         0
  YIF1A WILD-TYPE      10       20       45       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YIF1A MUTATED           0          2          0          1        1         0
  YIF1A WILD-TYPE        29         82         62         38       42         4
D1092V3, multiclass
            clus
vv           YIF1A MUTATED YIF1A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  YIF1A MUTATED       0   1   0   4
  YIF1A WILD-TYPE    54 134 261  98
D1092V4, multiclass
       clus
vv      YIF1A MUTATED YIF1A WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                0             261
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  YIF1A MUTATED     2   2   0   1
  YIF1A WILD-TYPE 193 171  89  84
D1092V5, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  N0             2             193
  N1             2             171
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V6, binary
                 cls
clus                0   1
  YIF1A MUTATED     5   0
  YIF1A WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      5    0
  YIF1A WILD-TYPE  477   38
   clus
vv  YIF1A MUTATED YIF1A WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D1092V7, binary
                 cls
clus                0   1
  YIF1A MUTATED     2   3
  YIF1A WILD-TYPE 170 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      2    3
  YIF1A WILD-TYPE  170  403
        clus
vv       YIF1A MUTATED YIF1A WILD-TYPE
  FEMALE             2             170
  MALE               3             403
[1] 2 2
[1] FALSE
D1092V8, binary
                 cls
clus                0   1
  YIF1A MUTATED     3   1
  YIF1A WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      3    1
  YIF1A WILD-TYPE  413  101
     clus
vv    YIF1A MUTATED YIF1A WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D1092V9, continuous
D1092V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YIF1A MUTATED       0                         0
  YIF1A WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YIF1A MUTATED                                           0     5
  YIF1A WILD-TYPE                                         1   352
D1092V11, multiclass
                                           clus
vv                                          YIF1A MUTATED YIF1A WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V12, binary
                 cls
clus                0   1
  YIF1A MUTATED     0   4
  YIF1A WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      0    4
  YIF1A WILD-TYPE   10  394
                        clus
vv                       YIF1A MUTATED YIF1A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1093) Variable = ARID3A MUTATION ANALYSIS
D1093V1, survival
                  sevent
clus2                0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 332 216
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              548 
  ARID3A MUTATED ARID3A WILD-TYPE 
               0              216 
$`ARID3A MUTATED`
TCGA-BR-6452 TCGA-CG-5721 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-IN-8462 
       34.68         6.02        24.20        29.98         6.51        18.81 

$`ARID3A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36         3.45         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ARID3A MUTATED ARID3A WILD-TYPE 
            6.02             0.00 
  ARID3A MUTATED ARID3A WILD-TYPE 
           34.68           122.30 
  ARID3A MUTATED ARID3A WILD-TYPE 
          21.505           13.530 
[1] "6.0 - 34.7 (21.5)"  "0.0 - 122.3 (13.5)"
[1] "hr="     "9100000"
D1093V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID3A MUTATED         0        1        0        0         3         1
  ARID3A WILD-TYPE      10       19       46       31        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID3A MUTATED           0          0          0          0        1
  ARID3A WILD-TYPE        29         84         62         39       42
                  vv
clus               STAGE IVA
  ARID3A MUTATED           0
  ARID3A WILD-TYPE         4
D1093V3, multiclass
            clus
vv           ARID3A MUTATED ARID3A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ARID3A MUTATED       1   2   2   1
  ARID3A WILD-TYPE    53 133 259 101
D1093V4, multiclass
       clus
vv      ARID3A MUTATED ARID3A WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 2              259
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID3A MUTATED     3   3   0   0
  ARID3A WILD-TYPE 192 170  89  85
D1093V5, multiclass
    clus
vv   ARID3A MUTATED ARID3A WILD-TYPE
  N0              3              192
  N1              3              170
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V6, binary
                  cls
clus                 0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      6    0
  ARID3A WILD-TYPE  476   38
   clus
vv  ARID3A MUTATED ARID3A WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D1093V7, binary
                  cls
clus                 0   1
  ARID3A MUTATED     3   3
  ARID3A WILD-TYPE 169 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      3    3
  ARID3A WILD-TYPE  169  403
        clus
vv       ARID3A MUTATED ARID3A WILD-TYPE
  FEMALE              3              169
  MALE                3              403
[1] 2 2
[1] FALSE
D1093V8, binary
                  cls
clus                 0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      6    0
  ARID3A WILD-TYPE  410  102
     clus
vv    ARID3A MUTATED ARID3A WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D1093V9, continuous
D1093V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID3A MUTATED       3                         0
  ARID3A WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID3A MUTATED                                           0     2
  ARID3A WILD-TYPE                                         1   355
D1093V11, multiclass
                                           clus
vv                                          ARID3A MUTATED ARID3A WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V12, binary
                  cls
clus                 0   1
  ARID3A MUTATED     0   5
  ARID3A WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      0    5
  ARID3A WILD-TYPE   10  393
                        clus
vv                       ARID3A MUTATED ARID3A WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1094) Variable = IRF2BP2 MUTATION ANALYSIS
D1094V1, survival
                   sevent
clus2                 0   1
  IRF2BP2 MUTATED     4   3
  IRF2BP2 WILD-TYPE 334 213
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                7               547 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                3               213 
$`IRF2BP2 MUTATED`
TCGA-L5-A4OI TCGA-V5-AASW TCGA-VR-AA4D TCGA-B7-A5TK TCGA-D7-A6EY TCGA-D7-A748 
       19.99         9.27        46.19         9.47        11.44         4.34 
TCGA-IN-8462 
       18.81 

$`IRF2BP2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
             4.34              0.00 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
            46.19            122.30 
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
            11.44             13.58 
[1] "4.3 - 46.2 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1094V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRF2BP2 MUTATED         0        0        0        0         0         2
  IRF2BP2 WILD-TYPE      10       20       46       31        84        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRF2BP2 MUTATED           0          1          1          1        1
  IRF2BP2 WILD-TYPE        29         83         61         38       42
                   vv
clus                STAGE IVA
  IRF2BP2 MUTATED           0
  IRF2BP2 WILD-TYPE         4
D1094V3, multiclass
            clus
vv           IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  IRF2BP2 MUTATED       1   1   2   2
  IRF2BP2 WILD-TYPE    53 134 259 100
D1094V4, multiclass
       clus
vv      IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  2               259
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  IRF2BP2 MUTATED     0   2   0   3
  IRF2BP2 WILD-TYPE 195 171  89  82
D1094V5, multiclass
    clus
vv   IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  N0               0               195
  N1               2               171
  N2               0                89
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V6, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     4   1
  IRF2BP2 WILD-TYPE 478  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      4    1
  IRF2BP2 WILD-TYPE  478   37
   clus
vv  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  0               4               478
  1               1                37
[1] 2 2
[1] FALSE
D1094V7, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     2   5
  IRF2BP2 WILD-TYPE 170 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      2    5
  IRF2BP2 WILD-TYPE  170  401
        clus
vv       IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  FEMALE               2               170
  MALE                 5               401
[1] 2 2
[1] FALSE
D1094V8, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     4   3
  IRF2BP2 WILD-TYPE 412  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      4    3
  IRF2BP2 WILD-TYPE  412   99
     clus
vv    IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  NO                4               412
  YES               3                99
[1] 2 2
[1] FALSE
D1094V9, continuous
[1] "Remove cluster labels:" "IRF2BP2 MUTATED"       
clus
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
D1094V10, continuous
[1] "Remove cluster labels:" "IRF2BP2 MUTATED"       
clus
  IRF2BP2 MUTATED IRF2BP2 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" "IRF2BP2 WILD-TYPE" 
       TCGA-Z6-AAPN 
"IRF2BP2 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  IRF2BP2 MUTATED       0                         0
  IRF2BP2 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRF2BP2 MUTATED                                           0     7
  IRF2BP2 WILD-TYPE                                         1   350
D1094V11, multiclass
                                           clus
vv                                          IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V12, binary
                   cls
clus                  0   1
  IRF2BP2 MUTATED     0   5
  IRF2BP2 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IRF2BP2 MUTATED      0    5
  IRF2BP2 WILD-TYPE   10  393
                        clus
vv                       IRF2BP2 MUTATED IRF2BP2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(1095) Variable = ABCF3 MUTATION ANALYSIS
D1095V1, survival
                 sevent
clus2               0   1
  ABCF3 MUTATED    11   2
  ABCF3 WILD-TYPE 327 214
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             13             541 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              2             214 
$`ABCF3 MUTATED`
TCGA-IC-A6RF TCGA-VR-A8EO TCGA-BR-4184 TCGA-BR-8078 TCGA-CG-4305 TCGA-CG-5721 
       15.68        25.81         6.97        29.59        15.95         6.02 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-RD-A7C1 
       11.08        30.51        29.98        20.25        29.00        16.67 
TCGA-VQ-A8P2 
       38.14 

$`ABCF3 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ABCF3 MUTATED ABCF3 WILD-TYPE 
           6.02            0.00 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
          38.14          122.30 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
          20.25           13.48 
[1] "6.0 - 38.1 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.2"
D1095V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCF3 MUTATED         0        1        1        1         3         1
  ABCF3 WILD-TYPE      10       19       45       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCF3 MUTATED           0          2          0          3        1         0
  ABCF3 WILD-TYPE        29         82         62         36       42         4
D1095V3, multiclass
            clus
vv           ABCF3 MUTATED ABCF3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCF3 MUTATED       1   3   3   6
  ABCF3 WILD-TYPE    53 132 258  96
D1095V4, multiclass
       clus
vv      ABCF3 MUTATED ABCF3 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCF3 MUTATED     5   5   1   2
  ABCF3 WILD-TYPE 190 168  88  83
D1095V5, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  N0             5             190
  N1             5             168
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V6, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   0
  ABCF3 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    0
  ABCF3 WILD-TYPE  470   38
   clus
vv  ABCF3 MUTATED ABCF3 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D1095V7, binary
                 cls
clus                0   1
  ABCF3 MUTATED     5   8
  ABCF3 WILD-TYPE 167 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      5    8
  ABCF3 WILD-TYPE  167  398
        clus
vv       ABCF3 MUTATED ABCF3 WILD-TYPE
  FEMALE             5             167
  MALE               8             398
[1] 2 2
[1] FALSE
D1095V8, binary
                 cls
clus                0   1
  ABCF3 MUTATED     8   4
  ABCF3 WILD-TYPE 408  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      8    4
  ABCF3 WILD-TYPE  408   98
     clus
vv    ABCF3 MUTATED ABCF3 WILD-TYPE
  NO              8             408
  YES             4              98
[1] 2 2
[1] FALSE
D1095V9, continuous
[1] "Remove cluster labels:" "ABCF3 MUTATED"         
clus
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EP 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
D1095V10, continuous
[1] "Remove cluster labels:" "ABCF3 MUTATED"         
clus
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              1              97 
     TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" "ABCF3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ABCF3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCF3 MUTATED       3                         1
  ABCF3 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCF3 MUTATED                                           0     6
  ABCF3 WILD-TYPE                                         1   351
D1095V11, multiclass
                                           clus
vv                                          ABCF3 MUTATED ABCF3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V12, binary
                 cls
clus                0   1
  ABCF3 MUTATED     0   8
  ABCF3 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      0    8
  ABCF3 WILD-TYPE   10  390
                        clus
vv                       ABCF3 MUTATED ABCF3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1096) Variable = DTNBP1 MUTATION ANALYSIS
D1096V1, survival
                  sevent
clus2                0   1
  DTNBP1 MUTATED     3   3
  DTNBP1 WILD-TYPE 335 213
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               6              548 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               3              213 
$`DTNBP1 MUTATED`
TCGA-L5-A4OI TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-8363 TCGA-BR-A4IY TCGA-D7-A4YV 
       19.99         9.67        30.90         0.26        12.89         5.92 

$`DTNBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        27.55        28.57         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
            0.26             0.00 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
            30.9            122.3 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
           11.28            13.63 
[1] "0.3 - 30.9 (11.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D1096V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DTNBP1 MUTATED         0        0        1        0         0         2
  DTNBP1 WILD-TYPE      10       20       45       31        84        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DTNBP1 MUTATED           0          2          0          1        0
  DTNBP1 WILD-TYPE        29         82         62         38       43
                  vv
clus               STAGE IVA
  DTNBP1 MUTATED           0
  DTNBP1 WILD-TYPE         4
D1096V3, multiclass
            clus
vv           DTNBP1 MUTATED DTNBP1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DTNBP1 MUTATED       0   1   3   2
  DTNBP1 WILD-TYPE    54 134 258 100
D1096V4, multiclass
       clus
vv      DTNBP1 MUTATED DTNBP1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DTNBP1 MUTATED     3   1   1   1
  DTNBP1 WILD-TYPE 192 172  88  84
D1096V5, multiclass
    clus
vv   DTNBP1 MUTATED DTNBP1 WILD-TYPE
  N0              3              192
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V6, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     6   0
  DTNBP1 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      6    0
  DTNBP1 WILD-TYPE  476   38
   clus
vv  DTNBP1 MUTATED DTNBP1 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D1096V7, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     4   3
  DTNBP1 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      4    3
  DTNBP1 WILD-TYPE  168  403
        clus
vv       DTNBP1 MUTATED DTNBP1 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D1096V8, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     6   0
  DTNBP1 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      6    0
  DTNBP1 WILD-TYPE  410  102
     clus
vv    DTNBP1 MUTATED DTNBP1 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D1096V9, continuous
D1096V10, continuous
[1] "Remove cluster labels:" "DTNBP1 MUTATED"        
clus
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" "DTNBP1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"DTNBP1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DTNBP1 MUTATED       1                         0
  DTNBP1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DTNBP1 MUTATED                                           0     6
  DTNBP1 WILD-TYPE                                         1   351
D1096V11, multiclass
                                           clus
vv                                          DTNBP1 MUTATED DTNBP1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V12, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     0   6
  DTNBP1 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      0    6
  DTNBP1 WILD-TYPE   10  392
                        clus
vv                       DTNBP1 MUTATED DTNBP1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(1097) Variable = CHST15 MUTATION ANALYSIS
D1097V1, survival
                  sevent
clus2                0   1
  CHST15 MUTATED     8   8
  CHST15 WILD-TYPE 330 208
  CHST15 MUTATED CHST15 WILD-TYPE 
              16              538 
  CHST15 MUTATED CHST15 WILD-TYPE 
               8              208 
$`CHST15 MUTATED`
TCGA-2H-A9GL TCGA-L5-A891 TCGA-L5-A8NN TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 
        5.92         3.75         5.49        26.70         6.97        30.90 
TCGA-BR-8360 TCGA-BR-8365 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4PE TCGA-CD-8536 
        6.18        17.52        25.05         1.12        20.42        12.43 
TCGA-CG-4306 TCGA-CG-5726 TCGA-HF-7132 TCGA-HU-A4GQ 
        1.02        28.96        77.29         0.10 

$`CHST15 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        7.40        31.10         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CHST15 MUTATED CHST15 WILD-TYPE 
             0.1              0.0 
  CHST15 MUTATED CHST15 WILD-TYPE 
           77.29           122.30 
  CHST15 MUTATED CHST15 WILD-TYPE 
            9.70            13.63 
[1] "0.1 - 77.3 (9.7)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1097V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHST15 MUTATED         0        1        1        2         3         1
  CHST15 WILD-TYPE      10       19       45       29        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHST15 MUTATED           2          2          0          2        1
  CHST15 WILD-TYPE        27         82         62         37       42
                  vv
clus               STAGE IVA
  CHST15 MUTATED           0
  CHST15 WILD-TYPE         4
D1097V3, multiclass
            clus
vv           CHST15 MUTATED CHST15 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                2               29
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CHST15 MUTATED       1   3   9   4
  CHST15 WILD-TYPE    53 132 252  98
D1097V4, multiclass
       clus
vv      CHST15 MUTATED CHST15 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 9              252
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CHST15 MUTATED     8   5   2   1
  CHST15 WILD-TYPE 187 168  87  84
D1097V5, multiclass
    clus
vv   CHST15 MUTATED CHST15 WILD-TYPE
  N0              8              187
  N1              5              168
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V6, binary
                  cls
clus                 0   1
  CHST15 MUTATED    15   1
  CHST15 WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     15    1
  CHST15 WILD-TYPE  467   37
   clus
vv  CHST15 MUTATED CHST15 WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D1097V7, binary
                  cls
clus                 0   1
  CHST15 MUTATED     7  10
  CHST15 WILD-TYPE 165 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED      7   10
  CHST15 WILD-TYPE  165  396
        clus
vv       CHST15 MUTATED CHST15 WILD-TYPE
  FEMALE              7              165
  MALE               10              396
[1] 2 2
[1] FALSE
D1097V8, binary
                  cls
clus                 0   1
  CHST15 MUTATED    12   1
  CHST15 WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED     12    1
  CHST15 WILD-TYPE  404  101
     clus
vv    CHST15 MUTATED CHST15 WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D1097V9, continuous
D1097V10, continuous
[1] "Remove cluster labels:" "CHST15 MUTATED"        
clus
  CHST15 MUTATED CHST15 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NQ 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" "CHST15 WILD-TYPE" 
      TCGA-Z6-AAPN 
"CHST15 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CHST15 MUTATED       2                         0
  CHST15 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHST15 MUTATED                                           0    11
  CHST15 WILD-TYPE                                         1   346
D1097V11, multiclass
                                           clus
vv                                          CHST15 MUTATED CHST15 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V12, binary
                  cls
clus                 0   1
  CHST15 MUTATED     0  11
  CHST15 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHST15 MUTATED      0   11
  CHST15 WILD-TYPE   10  387
                        clus
vv                       CHST15 MUTATED CHST15 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(1098) Variable = SI MUTATION ANALYSIS
D1098V1, survival
              sevent
clus2            0   1
  SI MUTATED    29  18
  SI WILD-TYPE 309 198
  SI MUTATED SI WILD-TYPE 
          47          507 
  SI MUTATED SI WILD-TYPE 
          18          198 
$`SI MUTATED`
TCGA-FP-A8CX TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO TCGA-JY-A6FG TCGA-L5-A4ON 
        0.23        31.27         5.92        16.24        41.52        18.35 
TCGA-L5-A4OT TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A4A4 
        4.90        16.47         5.49        10.45        13.41        12.59 
TCGA-R6-A6KZ TCGA-R6-A8WG TCGA-VR-A8EY TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7197 
        5.06        12.69        33.70         6.61        34.68         9.21 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
        6.18        31.10         0.26        25.05         1.12        28.14 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4306 
       31.96         9.86        10.68         6.58        12.20         1.02 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5728 TCGA-D7-6526 TCGA-D7-6822 
        6.97         6.02        15.02        65.10        17.19        12.33 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-8631 TCGA-HU-8604 
       36.43        14.76        22.29        21.27         0.56        22.82 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-A6RJ TCGA-RD-A7BS TCGA-VQ-A8P2 
        6.58        23.84        12.46        11.05        38.14 

$`SI WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07        16.24        20.15         9.86        25.78        20.05 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         7.63        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        47.93         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P 
       10.85        10.36         5.92        12.66        12.43        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        7.40        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58        20.88         8.22        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 
        0.00         9.01        18.97         7.07        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SI MUTATED SI WILD-TYPE 
        0.23         0.00 
  SI MUTATED SI WILD-TYPE 
        65.1        122.3 
  SI MUTATED SI WILD-TYPE 
       12.59        13.78 
[1] "0.2 - 65.1 (12.6)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D1098V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  SI MUTATED         0        1        5        2         9         6         6
  SI WILD-TYPE      10       19       41       29        75        77        23
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SI MUTATED            5          3          4        4         1
  SI WILD-TYPE         79         59         35       39         3
D1098V3, multiclass
            clus
vv           SI MUTATED SI WILD-TYPE
  STAGE I             0           10
  STAGE IA            1           19
  STAGE IB            5           41
  STAGE II            2           29
  STAGE IIA           9           75
  STAGE IIB           6           77
  STAGE III           6           23
  STAGE IIIA          5           79
  STAGE IIIB          3           59
  STAGE IIIC          4           35
  STAGE IV            4           39
  STAGE IVA           1            3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T0+T1  T2  T3  T4
  SI MUTATED       3  10  24   9
  SI WILD-TYPE    51 125 237  93
D1098V4, multiclass
       clus
vv      SI MUTATED SI WILD-TYPE
  T0+T1          3           51
  T2            10          125
  T3            24          237
  T4             9           93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2  N3
  SI MUTATED    17  16   8   5
  SI WILD-TYPE 178 157  81  80
D1098V5, multiclass
    clus
vv   SI MUTATED SI WILD-TYPE
  N0         17          178
  N1         16          157
  N2          8           81
  N3          5           80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V6, binary
              cls
clus             0   1
  SI MUTATED    39   4
  SI WILD-TYPE 443  34
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     39    4
  SI WILD-TYPE  443   34
   clus
vv  SI MUTATED SI WILD-TYPE
  0         39          443
  1          4           34
[1] 2 2
[1] FALSE
D1098V7, binary
              cls
clus             0   1
  SI MUTATED    16  32
  SI WILD-TYPE 156 374
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     16   32
  SI WILD-TYPE  156  374
        clus
vv       SI MUTATED SI WILD-TYPE
  FEMALE         16          156
  MALE           32          374
[1] 2 2
[1] FALSE
D1098V8, binary
              cls
clus             0   1
  SI MUTATED    34   8
  SI WILD-TYPE 382  94
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED     34    8
  SI WILD-TYPE  382   94
     clus
vv    SI MUTATED SI WILD-TYPE
  NO          34          382
  YES          8           94
[1] 2 2
[1] FALSE
D1098V9, continuous
D1098V10, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN
  SI MUTATED      10                         0
  SI WILD-TYPE   123                        14
              vv
clus           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SI MUTATED                                           0    30
  SI WILD-TYPE                                         1   327
D1098V11, multiclass
                                           clus
vv                                          SI MUTATED SI WILD-TYPE
  ASIAN                                             10          123
  BLACK OR AFRICAN AMERICAN                          0           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0            1
  WHITE                                             30          327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V12, binary
              cls
clus             0   1
  SI MUTATED     2  31
  SI WILD-TYPE   8 367
[1] "tbl2"
              cls
clus           [,1] [,2]
  SI MUTATED      2   31
  SI WILD-TYPE    8  367
                        clus
vv                       SI MUTATED SI WILD-TYPE
  HISPANIC OR LATINO              2            8
  NOT HISPANIC OR LATINO         31          367
[1] 2 2
[1] FALSE

Clustering(1099) Variable = RP1L1 MUTATION ANALYSIS
D1099V1, survival
                 sevent
clus2               0   1
  RP1L1 MUTATED    25  14
  RP1L1 WILD-TYPE 313 202
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             39             515 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             14             202 
$`RP1L1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A8NL TCGA-L5-A8NM 
       19.99        21.01         7.13         7.40        13.22         7.76 
TCGA-LN-A4A8 TCGA-LN-A8I1 TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 
       15.52        13.18         2.10        26.70         6.97        30.90 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8384 TCGA-BR-8680 TCGA-BR-A44U 
        9.67        34.68        35.84         3.72        31.96        13.87 
TCGA-BR-A452 TCGA-BR-A4PE TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
        7.53        20.42        12.30        12.43         6.58        11.77 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-6818 TCGA-F1-A448 TCGA-FP-7829 
        6.02        65.10         7.99        12.36        21.27        19.53 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-MX-A5UJ TCGA-VQ-A8DT 
       22.32        24.20        13.35        19.53        19.73        48.79 
TCGA-VQ-A8P2 TCGA-VQ-AA64 TCGA-VQ-AA6I 
       38.14        18.41        16.14 

$`RP1L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        34.13         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       28.34         0.66        32.52        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.33        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       15.02        28.96         4.01        69.04        21.07        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.99        14.47        72.23        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39        18.38        12.46         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        11.24        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  RP1L1 MUTATED RP1L1 WILD-TYPE 
            2.1             0.0 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
           65.1           122.3 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          15.52           13.51 
[1] "2.1 - 65.1 (15.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1099V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RP1L1 MUTATED         1        1        3        1         6         5
  RP1L1 WILD-TYPE       9       19       43       30        78        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RP1L1 MUTATED           1          9          5          2        3         0
  RP1L1 WILD-TYPE        28         75         57         37       40         4
D1099V3, multiclass
            clus
vv           RP1L1 MUTATED RP1L1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              6              78
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             9              75
  STAGE IIIB             5              57
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RP1L1 MUTATED       4  10  16   8
  RP1L1 WILD-TYPE    50 125 245  94
D1099V4, multiclass
       clus
vv      RP1L1 MUTATED RP1L1 WILD-TYPE
  T0+T1             4              50
  T2               10             125
  T3               16             245
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RP1L1 MUTATED    13  13   5   6
  RP1L1 WILD-TYPE 182 160  84  79
D1099V5, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  N0            13             182
  N1            13             160
  N2             5              84
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V6, binary
                 cls
clus                0   1
  RP1L1 MUTATED    36   2
  RP1L1 WILD-TYPE 446  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     36    2
  RP1L1 WILD-TYPE  446   36
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0            36             446
  1             2              36
[1] 2 2
[1] FALSE
D1099V7, binary
                 cls
clus                0   1
  RP1L1 MUTATED    17  23
  RP1L1 WILD-TYPE 155 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     17   23
  RP1L1 WILD-TYPE  155  383
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  FEMALE            17             155
  MALE              23             383
[1] 2 2
[1] FALSE
D1099V8, binary
                 cls
clus                0   1
  RP1L1 MUTATED    28   8
  RP1L1 WILD-TYPE 388  94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     28    8
  RP1L1 WILD-TYPE  388   94
     clus
vv    RP1L1 MUTATED RP1L1 WILD-TYPE
  NO             28             388
  YES             8              94
[1] 2 2
[1] FALSE
D1099V9, continuous
[1] "Remove cluster labels:" "RP1L1 MUTATED"         
clus
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
D1099V10, continuous
[1] "Remove cluster labels:" "RP1L1 MUTATED"         
clus
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX      TCGA-L5-A88S 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" "RP1L1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RP1L1 MUTATED      10                         0
  RP1L1 WILD-TYPE   123                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RP1L1 MUTATED                                           0    25
  RP1L1 WILD-TYPE                                         1   332
D1099V11, multiclass
                                           clus
vv                                          RP1L1 MUTATED RP1L1 WILD-TYPE
  ASIAN                                                10             123
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                25             332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V12, binary
                 cls
clus                0   1
  RP1L1 MUTATED     1  26
  RP1L1 WILD-TYPE   9 372
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      1   26
  RP1L1 WILD-TYPE    9  372
                        clus
vv                       RP1L1 MUTATED RP1L1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            26             372
[1] 2 2
[1] FALSE

Clustering(1100) Variable = ITGAL MUTATION ANALYSIS
D1100V1, survival
                 sevent
clus2               0   1
  ITGAL MUTATED    13  10
  ITGAL WILD-TYPE 325 206
  ITGAL MUTATED ITGAL WILD-TYPE 
             23             531 
  ITGAL MUTATED ITGAL WILD-TYPE 
             10             206 
$`ITGAL MUTATED`
TCGA-2H-A9GG TCGA-IG-A625 TCGA-JY-A6FA TCGA-L5-A8NH TCGA-V5-A7RB TCGA-V5-AASW 
       20.05        12.82        44.75        12.92         5.29         9.27 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 
        9.67        34.68        35.84        25.05        27.12        31.96 
TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8533 TCGA-CD-A4MG TCGA-CG-5721 TCGA-FP-7829 
       20.42        13.18        15.39         6.58         6.02        19.53 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-IN-A7NR TCGA-VQ-AA6I 
       22.68         6.51         6.58         6.51        16.14 

$`ITGAL WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        7.00        20.38         3.42        16.44        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         0.10        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ITGAL MUTATED ITGAL WILD-TYPE 
           5.29            0.00 
  ITGAL MUTATED ITGAL WILD-TYPE 
          44.75          122.30 
  ITGAL MUTATED ITGAL WILD-TYPE 
          15.39           13.55 
[1] "5.3 - 44.8 (15.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1100V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAL MUTATED         1        0        2        1         3         4
  ITGAL WILD-TYPE       9       20       44       30        81        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAL MUTATED           1          1          3          1        4         0
  ITGAL WILD-TYPE        28         83         59         38       39         4
D1100V3, multiclass
            clus
vv           ITGAL MUTATED ITGAL WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             3              59
  STAGE IIIC             1              38
  STAGE IV               4              39
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGAL MUTATED       4   3  12   4
  ITGAL WILD-TYPE    50 132 249  98
D1100V4, multiclass
       clus
vv      ITGAL MUTATED ITGAL WILD-TYPE
  T0+T1             4              50
  T2                3             132
  T3               12             249
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGAL MUTATED     7  10   2   3
  ITGAL WILD-TYPE 188 163  87  82
D1100V5, multiclass
    clus
vv   ITGAL MUTATED ITGAL WILD-TYPE
  N0             7             188
  N1            10             163
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V6, binary
                 cls
clus                0   1
  ITGAL MUTATED    20   3
  ITGAL WILD-TYPE 462  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED     20    3
  ITGAL WILD-TYPE  462   35
   clus
vv  ITGAL MUTATED ITGAL WILD-TYPE
  0            20             462
  1             3              35
[1] 2 2
[1] FALSE
D1100V7, binary
                 cls
clus                0   1
  ITGAL MUTATED    10  16
  ITGAL WILD-TYPE 162 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED     10   16
  ITGAL WILD-TYPE  162  390
        clus
vv       ITGAL MUTATED ITGAL WILD-TYPE
  FEMALE            10             162
  MALE              16             390
[1] 2 2
[1] FALSE
D1100V8, binary
                 cls
clus                0   1
  ITGAL MUTATED    20   2
  ITGAL WILD-TYPE 396 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED     20    2
  ITGAL WILD-TYPE  396  100
     clus
vv    ITGAL MUTATED ITGAL WILD-TYPE
  NO             20             396
  YES             2             100
[1] 2 2
[1] FALSE
D1100V9, continuous
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
D1100V10, continuous
[1] "Remove cluster labels:" "ITGAL MUTATED"         
clus
  ITGAL MUTATED ITGAL WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RC 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" "ITGAL WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGAL MUTATED       9                         1
  ITGAL WILD-TYPE   124                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGAL MUTATED                                           0    13
  ITGAL WILD-TYPE                                         1   344
D1100V11, multiclass
                                           clus
vv                                          ITGAL MUTATED ITGAL WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V12, binary
                 cls
clus                0   1
  ITGAL MUTATED     1  20
  ITGAL WILD-TYPE   9 378
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAL MUTATED      1   20
  ITGAL WILD-TYPE    9  378
                        clus
vv                       ITGAL MUTATED ITGAL WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            20             378
[1] 2 2
[1] FALSE

Clustering(1101) Variable = PCLO MUTATION ANALYSIS
D1101V1, survival
                sevent
clus2              0   1
  PCLO MUTATED    65  36
  PCLO WILD-TYPE 273 180
  PCLO MUTATED PCLO WILD-TYPE 
           101            453 
  PCLO MUTATED PCLO WILD-TYPE 
            36            180 
$`PCLO MUTATED`
TCGA-FP-A8CX TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        0.23        25.78         5.92        32.45         7.69         3.88 
TCGA-IG-A51D TCGA-IG-A6QS TCGA-IG-A97H TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OP 
       17.03         9.96        14.50        30.25        21.01         7.17 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L7-A56G 
        4.90        29.00        55.50        13.48         7.76        10.85 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ 
       12.59        22.39        12.23         0.13        12.85         5.06 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-AASX TCGA-VR-A8EY TCGA-VR-AA4G TCGA-Z6-A8JE 
        2.30        12.69         8.98        33.70        18.05         2.10 
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 
       11.70         6.97        30.90         9.34         6.61        34.68 
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-8059 TCGA-BR-8078 
       19.33         9.21        35.24        28.73        14.43        29.59 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.40        31.10         4.31         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A452 
        1.12        27.12        28.14        31.96        10.68         7.53 
TCGA-BR-A4PF TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4304 
        1.15        12.07        12.82         6.58        11.77        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 
       15.95         1.02         7.99         4.01        12.03        18.97 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5734 TCGA-D7-6527 TCGA-D7-6822 
        7.07        36.00         6.02         7.99        10.26        12.33 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-7132 
       20.91        16.44        14.76        21.27        11.08        77.29 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       22.82        22.68        24.20        22.75        11.77         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.10         6.58        20.25        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A7NT TCGA-R5-A7ZE TCGA-R5-A7ZI 
       14.07         3.45         3.39        10.62        18.21        74.53 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-VQ-A8P2 TCGA-VQ-AA68 TCGA-VQ-AA6I 
        9.24         8.61        38.14        43.66        16.14 

$`PCLO WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       79.07        16.24        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         9.30         0.53         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       26.33        32.61        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.67         6.18         9.57        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        44.94        21.90        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
       25.05         3.72         9.21        12.79         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        34.13        13.87         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
       12.39        12.59        11.64        15.39        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
       20.02         3.02         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       19.07         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        69.04        21.07        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        14.66        21.14        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        72.23        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY 
        3.25        25.81        21.37        29.98         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        21.17        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       14.04        45.67         8.52         6.08         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PCLO MUTATED PCLO WILD-TYPE 
           0.1            0.0 
  PCLO MUTATED PCLO WILD-TYPE 
         77.29         122.30 
  PCLO MUTATED PCLO WILD-TYPE 
         12.69          13.87 
[1] "0.1 - 77.3 (12.7)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1"  
D1101V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCLO MUTATED         3        5        9        8        15        15
  PCLO WILD-TYPE       7       15       37       23        69        68
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCLO MUTATED           5         12          9          8        9         0
  PCLO WILD-TYPE        24         72         53         31       34         4
D1101V3, multiclass
            clus
vv           PCLO MUTATED PCLO WILD-TYPE
  STAGE I               3              7
  STAGE IA              5             15
  STAGE IB              9             37
  STAGE II              8             23
  STAGE IIA            15             69
  STAGE IIB            15             68
  STAGE III             5             24
  STAGE IIIA           12             72
  STAGE IIIB            9             53
  STAGE IIIC            8             31
  STAGE IV              9             34
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PCLO MUTATED      12  27  42  20
  PCLO WILD-TYPE    42 108 219  82
D1101V4, multiclass
       clus
vv      PCLO MUTATED PCLO WILD-TYPE
  T0+T1           12             42
  T2              27            108
  T3              42            219
  T4              20             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PCLO MUTATED    33  37  16  14
  PCLO WILD-TYPE 162 136  73  71
D1101V5, multiclass
    clus
vv   PCLO MUTATED PCLO WILD-TYPE
  N0           33            162
  N1           37            136
  N2           16             73
  N3           14             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V6, binary
                cls
clus               0   1
  PCLO MUTATED    94   6
  PCLO WILD-TYPE 388  32
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     94    6
  PCLO WILD-TYPE  388   32
   clus
vv  PCLO MUTATED PCLO WILD-TYPE
  0           94            388
  1            6             32
[1] 2 2
[1] FALSE
D1101V7, binary
                cls
clus               0   1
  PCLO MUTATED    37  72
  PCLO WILD-TYPE 135 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     37   72
  PCLO WILD-TYPE  135  334
        clus
vv       PCLO MUTATED PCLO WILD-TYPE
  FEMALE           37            135
  MALE             72            334
[1] 2 2
[1] FALSE
D1101V8, binary
                cls
clus               0   1
  PCLO MUTATED    80  11
  PCLO WILD-TYPE 336  91
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     80   11
  PCLO WILD-TYPE  336   91
     clus
vv    PCLO MUTATED PCLO WILD-TYPE
  NO            80            336
  YES           11             91
[1] 2 2
[1] FALSE
D1101V9, continuous
D1101V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PCLO MUTATED      26                         3
  PCLO WILD-TYPE   107                        11
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCLO MUTATED                                           1    63
  PCLO WILD-TYPE                                         0   294
D1101V11, multiclass
                                           clus
vv                                          PCLO MUTATED PCLO WILD-TYPE
  ASIAN                                               26            107
  BLACK OR AFRICAN AMERICAN                            3             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               63            294
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V12, binary
                cls
clus               0   1
  PCLO MUTATED     3  77
  PCLO WILD-TYPE   7 321
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      3   77
  PCLO WILD-TYPE    7  321
                        clus
vv                       PCLO MUTATED PCLO WILD-TYPE
  HISPANIC OR LATINO                3              7
  NOT HISPANIC OR LATINO           77            321
[1] 2 2
[1] FALSE

Clustering(1102) Variable = NPR3 MUTATION ANALYSIS
D1102V1, survival
                sevent
clus2              0   1
  NPR3 MUTATED     8   1
  NPR3 WILD-TYPE 330 215
  NPR3 MUTATED NPR3 WILD-TYPE 
             9            545 
  NPR3 MUTATED NPR3 WILD-TYPE 
             1            215 
$`NPR3 MUTATED`
TCGA-L5-A4OI TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-CG-4305 
       19.99         6.97        32.25        31.96        13.51        15.95 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4G8 
        6.02       105.07        22.68 

$`NPR3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NPR3 MUTATED NPR3 WILD-TYPE 
          6.02           0.00 
  NPR3 MUTATED NPR3 WILD-TYPE 
        105.07         122.30 
  NPR3 MUTATED NPR3 WILD-TYPE 
         19.99          13.51 
[1] "6.0 - 105.1 (20.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "4.9"
D1102V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NPR3 MUTATED         0        0        0        2         0         2
  NPR3 WILD-TYPE      10       20       46       29        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NPR3 MUTATED           0          2          1          2        2         0
  NPR3 WILD-TYPE        29         82         61         37       41         4
D1102V3, multiclass
            clus
vv           NPR3 MUTATED NPR3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              2             29
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NPR3 MUTATED       0   2   4   5
  NPR3 WILD-TYPE    54 133 257  97
D1102V4, multiclass
       clus
vv      NPR3 MUTATED NPR3 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NPR3 MUTATED     2   5   1   3
  NPR3 WILD-TYPE 193 168  88  82
D1102V5, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  N0            2            193
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V6, binary
                cls
clus               0   1
  NPR3 MUTATED     8   1
  NPR3 WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      8    1
  NPR3 WILD-TYPE  474   37
   clus
vv  NPR3 MUTATED NPR3 WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D1102V7, binary
                cls
clus               0   1
  NPR3 MUTATED     5   6
  NPR3 WILD-TYPE 167 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      5    6
  NPR3 WILD-TYPE  167  400
        clus
vv       NPR3 MUTATED NPR3 WILD-TYPE
  FEMALE            5            167
  MALE              6            400
[1] 2 2
[1] FALSE
D1102V8, binary
                cls
clus               0   1
  NPR3 MUTATED    10   0
  NPR3 WILD-TYPE 406 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED     10    0
  NPR3 WILD-TYPE  406  102
     clus
vv    NPR3 MUTATED NPR3 WILD-TYPE
  NO            10            406
  YES            0            102
[1] 2 2
[1] FALSE
D1102V9, continuous
D1102V10, continuous
[1] "Remove cluster labels:" "NPR3 MUTATED"          
clus
  NPR3 MUTATED NPR3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" "NPR3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"NPR3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NPR3 MUTATED       2                         0
  NPR3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPR3 MUTATED                                           0     6
  NPR3 WILD-TYPE                                         1   351
D1102V11, multiclass
                                           clus
vv                                          NPR3 MUTATED NPR3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V12, binary
                cls
clus               0   1
  NPR3 MUTATED     0   7
  NPR3 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      0    7
  NPR3 WILD-TYPE   10  391
                        clus
vv                       NPR3 MUTATED NPR3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(1103) Variable = PTPN12 MUTATION ANALYSIS
D1103V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED     9   2
  PTPN12 WILD-TYPE 329 214
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              11              543 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               2              214 
$`PTPN12 MUTATED`
TCGA-L5-A8NJ TCGA-BR-8368 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5723 TCGA-D7-A4YY 
       16.47         4.31        28.14        31.96       105.07        13.78 
TCGA-D7-A6EY TCGA-EQ-5647 TCGA-HU-A4G3 TCGA-HU-A4GX TCGA-MX-A666 
       11.44         0.62         5.59        20.25        14.04 

$`PTPN12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            0.62             0.00 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
          105.07           122.30 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           14.04            13.51 
[1] "0.6 - 105.1 (14.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.4"
D1103V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN12 MUTATED         0        0        1        1         1         1
  PTPN12 WILD-TYPE      10       20       45       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN12 MUTATED           1          1          2          2        2
  PTPN12 WILD-TYPE        28         83         60         37       41
                  vv
clus               STAGE IVA
  PTPN12 MUTATED           0
  PTPN12 WILD-TYPE         4
D1103V3, multiclass
            clus
vv           PTPN12 MUTATED PTPN12 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              2               37
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PTPN12 MUTATED       0   4   3   5
  PTPN12 WILD-TYPE    54 131 258  97
D1103V4, multiclass
       clus
vv      PTPN12 MUTATED PTPN12 WILD-TYPE
  T0+T1              0               54
  T2                 4              131
  T3                 3              258
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PTPN12 MUTATED     2   2   3   4
  PTPN12 WILD-TYPE 193 171  86  81
D1103V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              3               86
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V6, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    10   2
  PTPN12 WILD-TYPE 472  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     10    2
  PTPN12 WILD-TYPE  472   36
   clus
vv  PTPN12 MUTATED PTPN12 WILD-TYPE
  0             10              472
  1              2               36
[1] 2 2
[1] FALSE
D1103V7, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     5   8
  PTPN12 WILD-TYPE 167 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      5    8
  PTPN12 WILD-TYPE  167  398
        clus
vv       PTPN12 MUTATED PTPN12 WILD-TYPE
  FEMALE              5              167
  MALE                8              398
[1] 2 2
[1] FALSE
D1103V8, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    10   1
  PTPN12 WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     10    1
  PTPN12 WILD-TYPE  406  101
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D1103V9, continuous
D1103V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN12 MUTATED       3                         0
  PTPN12 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN12 MUTATED                                           0     9
  PTPN12 WILD-TYPE                                         1   348
D1103V11, multiclass
                                           clus
vv                                          PTPN12 MUTATED PTPN12 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V12, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     0  11
  PTPN12 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      0   11
  PTPN12 WILD-TYPE   10  387
                        clus
vv                       PTPN12 MUTATED PTPN12 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(1104) Variable = MTSS1L MUTATION ANALYSIS
D1104V1, survival
                  sevent
clus2                0   1
  MTSS1L MUTATED     6   5
  MTSS1L WILD-TYPE 332 211
  MTSS1L MUTATED MTSS1L WILD-TYPE 
              11              543 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
               5              211 
$`MTSS1L MUTATED`
TCGA-2H-A9GG TCGA-L5-A8NS TCGA-BR-6706 TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 
       20.05        13.41        18.05        30.90        31.27         1.12 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-HF-A5NB TCGA-HU-A4H3 
       16.14         6.58         1.02        30.51        29.00 

$`MTSS1L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        25.61        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  MTSS1L MUTATED MTSS1L WILD-TYPE 
            1.02             0.00 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
           31.27           122.30 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
           18.05            13.51 
[1] "1.0 - 31.3 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1104V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTSS1L MUTATED         0        0        0        0         2         1
  MTSS1L WILD-TYPE      10       20       46       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTSS1L MUTATED           1          2          1          3        1
  MTSS1L WILD-TYPE        28         82         61         36       42
                  vv
clus               STAGE IVA
  MTSS1L MUTATED           0
  MTSS1L WILD-TYPE         4
D1104V3, multiclass
            clus
vv           MTSS1L MUTATED MTSS1L WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MTSS1L MUTATED       0   0   9   3
  MTSS1L WILD-TYPE    54 135 252  99
D1104V4, multiclass
       clus
vv      MTSS1L MUTATED MTSS1L WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 9              252
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MTSS1L MUTATED     3   2   2   4
  MTSS1L WILD-TYPE 192 171  87  81
D1104V5, multiclass
    clus
vv   MTSS1L MUTATED MTSS1L WILD-TYPE
  N0              3              192
  N1              2              171
  N2              2               87
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V6, binary
                  cls
clus                 0   1
  MTSS1L MUTATED    10   1
  MTSS1L WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED     10    1
  MTSS1L WILD-TYPE  472   37
   clus
vv  MTSS1L MUTATED MTSS1L WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D1104V7, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     5   7
  MTSS1L WILD-TYPE 167 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      5    7
  MTSS1L WILD-TYPE  167  399
        clus
vv       MTSS1L MUTATED MTSS1L WILD-TYPE
  FEMALE              5              167
  MALE                7              399
[1] 2 2
[1] FALSE
D1104V8, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     7   2
  MTSS1L WILD-TYPE 409 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      7    2
  MTSS1L WILD-TYPE  409  100
     clus
vv    MTSS1L MUTATED MTSS1L WILD-TYPE
  NO               7              409
  YES              2              100
[1] 2 2
[1] FALSE
D1104V9, continuous
D1104V10, continuous
[1] "Remove cluster labels:" "MTSS1L MUTATED"        
clus
  MTSS1L MUTATED MTSS1L WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NW       TCGA-LN-A49O 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" "MTSS1L WILD-TYPE" 
      TCGA-Z6-AAPN 
"MTSS1L WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MTSS1L MUTATED       2                         0
  MTSS1L WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTSS1L MUTATED                                           0     7
  MTSS1L WILD-TYPE                                         1   350
D1104V11, multiclass
                                           clus
vv                                          MTSS1L MUTATED MTSS1L WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V12, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     0   8
  MTSS1L WILD-TYPE  10 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      0    8
  MTSS1L WILD-TYPE   10  390
                        clus
vv                       MTSS1L MUTATED MTSS1L WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(1105) Variable = ABCA7 MUTATION ANALYSIS
D1105V1, survival
                 sevent
clus2               0   1
  ABCA7 MUTATED    16   7
  ABCA7 WILD-TYPE 322 209
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             23             531 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              7             209 
$`ABCA7 MUTATED`
TCGA-EQ-A4SO TCGA-IG-A6QS TCGA-JY-A6FH TCGA-LN-A4A9 TCGA-LN-A7HX TCGA-R6-A8W5 
       16.24         9.96        47.38        11.54        12.23        15.78 
TCGA-B7-A5TI TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8680 TCGA-CD-A4MG 
       19.56        29.59         6.18        14.04        31.96         6.58 
TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-8602 
        1.02         6.02        11.44        14.47        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       22.68        24.20         0.10        74.53        38.14 

$`ABCA7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.26         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ABCA7 MUTATED ABCA7 WILD-TYPE 
            0.1             0.0 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
          74.53          122.30 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
          15.78           13.51 
[1] "0.1 - 74.5 (15.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1105V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA7 MUTATED         0        1        1        0         4         5
  ABCA7 WILD-TYPE      10       19       45       31        80        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCA7 MUTATED           0          3          3          3        4         1
  ABCA7 WILD-TYPE        29         81         59         36       39         3
D1105V3, multiclass
            clus
vv           ABCA7 MUTATED ABCA7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             3              36
  STAGE IV               4              39
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCA7 MUTATED       1   5   8  11
  ABCA7 WILD-TYPE    53 130 253  91
D1105V4, multiclass
       clus
vv      ABCA7 MUTATED ABCA7 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                8             253
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCA7 MUTATED     9   9   3   4
  ABCA7 WILD-TYPE 186 164  86  81
D1105V5, multiclass
    clus
vv   ABCA7 MUTATED ABCA7 WILD-TYPE
  N0             9             186
  N1             9             164
  N2             3              86
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V6, binary
                 cls
clus                0   1
  ABCA7 MUTATED    20   4
  ABCA7 WILD-TYPE 462  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED     20    4
  ABCA7 WILD-TYPE  462   34
   clus
vv  ABCA7 MUTATED ABCA7 WILD-TYPE
  0            20             462
  1             4              34
[1] 2 2
[1] FALSE
D1105V7, binary
                 cls
clus                0   1
  ABCA7 MUTATED     9  16
  ABCA7 WILD-TYPE 163 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      9   16
  ABCA7 WILD-TYPE  163  390
        clus
vv       ABCA7 MUTATED ABCA7 WILD-TYPE
  FEMALE             9             163
  MALE              16             390
[1] 2 2
[1] FALSE
D1105V8, binary
                 cls
clus                0   1
  ABCA7 MUTATED    18   5
  ABCA7 WILD-TYPE 398  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED     18    5
  ABCA7 WILD-TYPE  398   97
     clus
vv    ABCA7 MUTATED ABCA7 WILD-TYPE
  NO             18             398
  YES             5              97
[1] 2 2
[1] FALSE
D1105V9, continuous
[1] "Remove cluster labels:" "ABCA7 MUTATED"         
clus
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ABCA7 WILD-TYPE" "ABCA7 WILD-TYPE" 
D1105V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA7 MUTATED       8                         0
  ABCA7 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA7 MUTATED                                           0    13
  ABCA7 WILD-TYPE                                         1   344
D1105V11, multiclass
                                           clus
vv                                          ABCA7 MUTATED ABCA7 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V12, binary
                 cls
clus                0   1
  ABCA7 MUTATED     1  18
  ABCA7 WILD-TYPE   9 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      1   18
  ABCA7 WILD-TYPE    9  380
                        clus
vv                       ABCA7 MUTATED ABCA7 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(1106) Variable = OR1L3 MUTATION ANALYSIS
D1106V1, survival
                 sevent
clus2               0   1
  OR1L3 MUTATED     6   2
  OR1L3 WILD-TYPE 332 214
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              8             546 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              2             214 
$`OR1L3 MUTATED`
TCGA-2H-A9GO TCGA-BR-7722 TCGA-BR-8680 TCGA-CG-4436 TCGA-FP-7829 TCGA-FP-8211 
       16.24        15.32        31.96         7.99        19.53        13.58 
TCGA-HF-7132 TCGA-VQ-A8P2 
       77.29        38.14 

$`OR1L3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  OR1L3 MUTATED OR1L3 WILD-TYPE 
           7.99            0.00 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
          77.29          122.30 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
         17.885          13.495 
[1] "8.0 - 77.3 (17.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D1106V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR1L3 MUTATED         0        0        1        1         0         3
  OR1L3 WILD-TYPE      10       20       45       30        84        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR1L3 MUTATED           0          1          0          0        1         1
  OR1L3 WILD-TYPE        29         83         62         39       42         3
D1106V3, multiclass
            clus
vv           OR1L3 MUTATED OR1L3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OR1L3 MUTATED       0   2   4   2
  OR1L3 WILD-TYPE    54 133 257 100
D1106V4, multiclass
       clus
vv      OR1L3 MUTATED OR1L3 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OR1L3 MUTATED     1   6   1   0
  OR1L3 WILD-TYPE 194 167  88  85
D1106V5, multiclass
    clus
vv   OR1L3 MUTATED OR1L3 WILD-TYPE
  N0             1             194
  N1             6             167
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V6, binary
                 cls
clus                0   1
  OR1L3 MUTATED     5   2
  OR1L3 WILD-TYPE 477  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      5    2
  OR1L3 WILD-TYPE  477   36
   clus
vv  OR1L3 MUTATED OR1L3 WILD-TYPE
  0             5             477
  1             2              36
[1] 2 2
[1] FALSE
D1106V7, binary
                 cls
clus                0   1
  OR1L3 MUTATED     0   8
  OR1L3 WILD-TYPE 172 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      0    8
  OR1L3 WILD-TYPE  172  398
        clus
vv       OR1L3 MUTATED OR1L3 WILD-TYPE
  FEMALE             0             172
  MALE               8             398
[1] 2 2
[1] FALSE
D1106V8, binary
                 cls
clus                0   1
  OR1L3 MUTATED     4   4
  OR1L3 WILD-TYPE 412  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      4    4
  OR1L3 WILD-TYPE  412   98
     clus
vv    OR1L3 MUTATED OR1L3 WILD-TYPE
  NO              4             412
  YES             4              98
[1] 2 2
[1] FALSE
D1106V9, continuous
D1106V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR1L3 MUTATED       1                         0
  OR1L3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR1L3 MUTATED                                           0     4
  OR1L3 WILD-TYPE                                         1   353
D1106V11, multiclass
                                           clus
vv                                          OR1L3 MUTATED OR1L3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V12, binary
                 cls
clus                0   1
  OR1L3 MUTATED     0   4
  OR1L3 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      0    4
  OR1L3 WILD-TYPE   10  394
                        clus
vv                       OR1L3 MUTATED OR1L3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1107) Variable = HOOK1 MUTATION ANALYSIS
D1107V1, survival
                 sevent
clus2               0   1
  HOOK1 MUTATED     5   5
  HOOK1 WILD-TYPE 333 211
  HOOK1 MUTATED HOOK1 WILD-TYPE 
             10             544 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              5             211 
$`HOOK1 MUTATED`
TCGA-L5-A43I TCGA-2H-A9GF TCGA-L5-A43E TCGA-V5-A7RB TCGA-BR-6452 TCGA-BR-8081 
       18.28        25.78        30.25         5.29        34.68        32.25 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5717 TCGA-VQ-A8P2 
        1.12        16.14         6.97        38.14 

$`HOOK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        30.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  HOOK1 MUTATED HOOK1 WILD-TYPE 
           1.12            0.00 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          38.14          122.30 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          22.03           13.51 
[1] "1.1 - 38.1 (22.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1107V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOOK1 MUTATED         1        0        0        1         2         1
  HOOK1 WILD-TYPE       9       20       46       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOOK1 MUTATED           1          3          1          0        0         0
  HOOK1 WILD-TYPE        28         81         61         39       43         4
D1107V3, multiclass
            clus
vv           HOOK1 MUTATED HOOK1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HOOK1 MUTATED       2   1   5   3
  HOOK1 WILD-TYPE    52 134 256  99
D1107V4, multiclass
       clus
vv      HOOK1 MUTATED HOOK1 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HOOK1 MUTATED     5   5   0   1
  HOOK1 WILD-TYPE 190 168  89  84
D1107V5, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  N0             5             190
  N1             5             168
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V6, binary
                 cls
clus                0   1
  HOOK1 MUTATED     9   0
  HOOK1 WILD-TYPE 473  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      9    0
  HOOK1 WILD-TYPE  473   38
   clus
vv  HOOK1 MUTATED HOOK1 WILD-TYPE
  0             9             473
  1             0              38
[1] 2 2
[1] FALSE
D1107V7, binary
                 cls
clus                0   1
  HOOK1 MUTATED     5   6
  HOOK1 WILD-TYPE 167 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      5    6
  HOOK1 WILD-TYPE  167  400
        clus
vv       HOOK1 MUTATED HOOK1 WILD-TYPE
  FEMALE             5             167
  MALE               6             400
[1] 2 2
[1] FALSE
D1107V8, binary
                 cls
clus                0   1
  HOOK1 MUTATED     8   2
  HOOK1 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      8    2
  HOOK1 WILD-TYPE  408  100
     clus
vv    HOOK1 MUTATED HOOK1 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D1107V9, continuous
[1] "Remove cluster labels:" "HOOK1 MUTATED"         
clus
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" "HOOK1 WILD-TYPE" 
D1107V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOOK1 MUTATED       0                         0
  HOOK1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOOK1 MUTATED                                           0     8
  HOOK1 WILD-TYPE                                         1   349
D1107V11, multiclass
                                           clus
vv                                          HOOK1 MUTATED HOOK1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V12, binary
                 cls
clus                0   1
  HOOK1 MUTATED     1   5
  HOOK1 WILD-TYPE   9 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      1    5
  HOOK1 WILD-TYPE    9  393
                        clus
vv                       HOOK1 MUTATED HOOK1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1108) Variable = MAP7D1 MUTATION ANALYSIS
D1108V1, survival
                  sevent
clus2                0   1
  MAP7D1 MUTATED    10   6
  MAP7D1 WILD-TYPE 328 210
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              16              538 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               6              210 
$`MAP7D1 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NH TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8363 
        4.31        12.92        30.90         9.34        34.68         0.26 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-8535 TCGA-CD-8536 
        4.31        14.04         0.72        13.15        12.82        12.43 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-HU-8244 TCGA-VQ-A8P2 
       12.62         6.02        24.39        38.14 

$`MAP7D1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        0.95        26.33         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       15.39        12.07         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
            0.26             0.00 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           38.14           122.30 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
          12.720           13.825 
[1] "0.3 - 38.1 (12.7)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.2"
D1108V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP7D1 MUTATED         0        1        3        2         1         1
  MAP7D1 WILD-TYPE      10       19       43       29        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D1 MUTATED           0          3          1          0        2
  MAP7D1 WILD-TYPE        29         81         61         39       41
                  vv
clus               STAGE IVA
  MAP7D1 MUTATED           0
  MAP7D1 WILD-TYPE         4
D1108V3, multiclass
            clus
vv           MAP7D1 MUTATED MAP7D1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  MAP7D1 MUTATED       2   4   6   3
  MAP7D1 WILD-TYPE    52 131 255  99
D1108V4, multiclass
       clus
vv      MAP7D1 MUTATED MAP7D1 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 6              255
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  MAP7D1 MUTATED     9   5   0   1
  MAP7D1 WILD-TYPE 186 168  89  84
D1108V5, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  N0              9              186
  N1              5              168
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V6, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    15   1
  MAP7D1 WILD-TYPE 467  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     15    1
  MAP7D1 WILD-TYPE  467   37
   clus
vv  MAP7D1 MUTATED MAP7D1 WILD-TYPE
  0             15              467
  1              1               37
[1] 2 2
[1] FALSE
D1108V7, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     7  10
  MAP7D1 WILD-TYPE 165 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      7   10
  MAP7D1 WILD-TYPE  165  396
        clus
vv       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  FEMALE              7              165
  MALE               10              396
[1] 2 2
[1] FALSE
D1108V8, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    12   1
  MAP7D1 WILD-TYPE 404 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     12    1
  MAP7D1 WILD-TYPE  404  101
     clus
vv    MAP7D1 MUTATED MAP7D1 WILD-TYPE
  NO              12              404
  YES              1              101
[1] 2 2
[1] FALSE
D1108V9, continuous
D1108V10, continuous
[1] "Remove cluster labels:" "MAP7D1 MUTATED"        
clus
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A4OE       TCGA-L5-A4OG 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" "MAP7D1 WILD-TYPE" 
      TCGA-Z6-AAPN 
"MAP7D1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP7D1 MUTATED       6                         0
  MAP7D1 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP7D1 MUTATED                                           0    10
  MAP7D1 WILD-TYPE                                         1   347
D1108V11, multiclass
                                           clus
vv                                          MAP7D1 MUTATED MAP7D1 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V12, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     0  13
  MAP7D1 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      0   13
  MAP7D1 WILD-TYPE   10  385
                        clus
vv                       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(1109) Variable = VPRBP MUTATION ANALYSIS
D1109V1, survival
                 sevent
clus2               0   1
  VPRBP MUTATED     6   3
  VPRBP WILD-TYPE 332 213
  VPRBP MUTATED VPRBP WILD-TYPE 
              9             545 
  VPRBP MUTATED VPRBP WILD-TYPE 
              3             213 
$`VPRBP MUTATED`
TCGA-JY-A93D TCGA-L5-A8NL TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-6457 TCGA-BR-8680 
       31.56        13.22         7.76        26.70        13.68        31.96 
TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 
       12.43        15.95         1.02 

$`VPRBP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
        2.66        12.92        13.48        16.47        13.55         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  VPRBP MUTATED VPRBP WILD-TYPE 
           1.02            0.00 
  VPRBP MUTATED VPRBP WILD-TYPE 
          31.96          122.30 
  VPRBP MUTATED VPRBP WILD-TYPE 
          13.68           13.55 
[1] "1.0 - 32.0 (13.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1109V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPRBP MUTATED         0        0        1        2         1         2
  VPRBP WILD-TYPE      10       20       45       29        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VPRBP MUTATED           1          0          0          1        2         0
  VPRBP WILD-TYPE        28         84         62         38       41         4
D1109V3, multiclass
            clus
vv           VPRBP MUTATED VPRBP WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               2              29
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  VPRBP MUTATED       0   4   4   2
  VPRBP WILD-TYPE    54 131 257 100
D1109V4, multiclass
       clus
vv      VPRBP MUTATED VPRBP WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  VPRBP MUTATED     4   4   2   1
  VPRBP WILD-TYPE 191 169  87  84
D1109V5, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V6, binary
                 cls
clus                0   1
  VPRBP MUTATED     9   2
  VPRBP WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      9    2
  VPRBP WILD-TYPE  473   36
   clus
vv  VPRBP MUTATED VPRBP WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D1109V7, binary
                 cls
clus                0   1
  VPRBP MUTATED     3   8
  VPRBP WILD-TYPE 169 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      3    8
  VPRBP WILD-TYPE  169  398
        clus
vv       VPRBP MUTATED VPRBP WILD-TYPE
  FEMALE             3             169
  MALE               8             398
[1] 2 2
[1] FALSE
D1109V8, binary
                 cls
clus                0   1
  VPRBP MUTATED     6   1
  VPRBP WILD-TYPE 410 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      6    1
  VPRBP WILD-TYPE  410  101
     clus
vv    VPRBP MUTATED VPRBP WILD-TYPE
  NO              6             410
  YES             1             101
[1] 2 2
[1] FALSE
D1109V9, continuous
D1109V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  VPRBP MUTATED       2                         0
  VPRBP WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPRBP MUTATED                                           0     6
  VPRBP WILD-TYPE                                         1   351
D1109V11, multiclass
                                           clus
vv                                          VPRBP MUTATED VPRBP WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V12, binary
                 cls
clus                0   1
  VPRBP MUTATED     0   5
  VPRBP WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      0    5
  VPRBP WILD-TYPE   10  393
                        clus
vv                       VPRBP MUTATED VPRBP WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1110) Variable = OR2M5 MUTATION ANALYSIS
D1110V1, survival
                 sevent
clus2               0   1
  OR2M5 MUTATED     7   7
  OR2M5 WILD-TYPE 331 209
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             14             540 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              7             209 
$`OR2M5 MUTATED`
TCGA-L5-A4OX TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-7723 TCGA-BR-8384 TCGA-BR-8686 
        7.43        11.01         9.67        28.73         3.72        20.88 
TCGA-BR-8687 TCGA-CD-A48C TCGA-D7-6527 TCGA-D7-A4YU TCGA-HU-A4G3 TCGA-HU-A4G9 
        8.22        11.61        10.26        16.44         5.59        24.20 
TCGA-IN-A7NU TCGA-VQ-A8P2 
       11.70        38.14 

$`OR2M5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        31.96        32.58         9.86        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.43         6.31        12.30        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  OR2M5 MUTATED OR2M5 WILD-TYPE 
           3.72            0.00 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          38.14          122.30 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          11.31           13.73 
[1] "3.7 - 38.1 (11.3)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.6"
D1110V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR2M5 MUTATED         0        1        1        1         0         5
  OR2M5 WILD-TYPE      10       19       45       30        84        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2M5 MUTATED           0          1          4          2        0         0
  OR2M5 WILD-TYPE        29         83         58         37       43         4
D1110V3, multiclass
            clus
vv           OR2M5 MUTATED OR2M5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              5              78
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             4              58
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OR2M5 MUTATED       1   4   4   6
  OR2M5 WILD-TYPE    53 131 257  96
D1110V4, multiclass
       clus
vv      OR2M5 MUTATED OR2M5 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OR2M5 MUTATED     3   5   3   3
  OR2M5 WILD-TYPE 192 168  86  82
D1110V5, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  N0             3             192
  N1             5             168
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V6, binary
                 cls
clus                0   1
  OR2M5 MUTATED    16   0
  OR2M5 WILD-TYPE 466  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED     16    0
  OR2M5 WILD-TYPE  466   38
   clus
vv  OR2M5 MUTATED OR2M5 WILD-TYPE
  0            16             466
  1             0              38
[1] 2 2
[1] FALSE
D1110V7, binary
                 cls
clus                0   1
  OR2M5 MUTATED     4  12
  OR2M5 WILD-TYPE 168 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      4   12
  OR2M5 WILD-TYPE  168  394
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  FEMALE             4             168
  MALE              12             394
[1] 2 2
[1] FALSE
D1110V8, binary
                 cls
clus                0   1
  OR2M5 MUTATED    13   2
  OR2M5 WILD-TYPE 403 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED     13    2
  OR2M5 WILD-TYPE  403  100
     clus
vv    OR2M5 MUTATED OR2M5 WILD-TYPE
  NO             13             403
  YES             2             100
[1] 2 2
[1] FALSE
D1110V9, continuous
D1110V10, continuous
[1] "Remove cluster labels:" "OR2M5 MUTATED"         
clus
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" "OR2M5 WILD-TYPE" 
     TCGA-Z6-AAPN 
"OR2M5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR2M5 MUTATED       4                         0
  OR2M5 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR2M5 MUTATED                                           0    11
  OR2M5 WILD-TYPE                                         1   346
D1110V11, multiclass
                                           clus
vv                                          OR2M5 MUTATED OR2M5 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V12, binary
                 cls
clus                0   1
  OR2M5 MUTATED     0  13
  OR2M5 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      0   13
  OR2M5 WILD-TYPE   10  385
                        clus
vv                       OR2M5 MUTATED OR2M5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(1111) Variable = RANBP3 MUTATION ANALYSIS
D1111V1, survival
                  sevent
clus2                0   1
  RANBP3 MUTATED    10   2
  RANBP3 WILD-TYPE 328 214
  RANBP3 MUTATED RANBP3 WILD-TYPE 
              12              542 
  RANBP3 MUTATED RANBP3 WILD-TYPE 
               2              214 
$`RANBP3 MUTATED`
TCGA-L5-A4OJ TCGA-LN-A9FP TCGA-X8-AAAR TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-8536 
       21.01        12.03        18.21         4.31        31.96        12.43 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-7132 
       12.30         6.58         1.02         6.02        11.08        77.29 

$`RANBP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07        12.82         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  RANBP3 MUTATED RANBP3 WILD-TYPE 
            1.02             0.00 
  RANBP3 MUTATED RANBP3 WILD-TYPE 
           77.29           122.30 
  RANBP3 MUTATED RANBP3 WILD-TYPE 
          12.165           13.730 
[1] "1.0 - 77.3 (12.2)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "2.2"
D1111V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RANBP3 MUTATED         1        0        2        2         3         2
  RANBP3 WILD-TYPE       9       20       44       29        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP3 MUTATED           0          0          0          0        3
  RANBP3 WILD-TYPE        29         84         62         39       40
                  vv
clus               STAGE IVA
  RANBP3 MUTATED           0
  RANBP3 WILD-TYPE         4
D1111V3, multiclass
            clus
vv           RANBP3 MUTATED RANBP3 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                2               29
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  RANBP3 MUTATED       2   4   5   3
  RANBP3 WILD-TYPE    52 131 256  99
D1111V4, multiclass
       clus
vv      RANBP3 MUTATED RANBP3 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 5              256
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  RANBP3 MUTATED     8   4   2   0
  RANBP3 WILD-TYPE 187 169  87  85
D1111V5, multiclass
    clus
vv   RANBP3 MUTATED RANBP3 WILD-TYPE
  N0              8              187
  N1              4              169
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V6, binary
                  cls
clus                 0   1
  RANBP3 MUTATED    11   2
  RANBP3 WILD-TYPE 471  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP3 MUTATED     11    2
  RANBP3 WILD-TYPE  471   36
   clus
vv  RANBP3 MUTATED RANBP3 WILD-TYPE
  0             11              471
  1              2               36
[1] 2 2
[1] FALSE
D1111V7, binary
                  cls
clus                 0   1
  RANBP3 MUTATED     3  11
  RANBP3 WILD-TYPE 169 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP3 MUTATED      3   11
  RANBP3 WILD-TYPE  169  395
        clus
vv       RANBP3 MUTATED RANBP3 WILD-TYPE
  FEMALE              3              169
  MALE               11              395
[1] 2 2
[1] FALSE
D1111V8, binary
                  cls
clus                 0   1
  RANBP3 MUTATED     9   3
  RANBP3 WILD-TYPE 407  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP3 MUTATED      9    3
  RANBP3 WILD-TYPE  407   99
     clus
vv    RANBP3 MUTATED RANBP3 WILD-TYPE
  NO               9              407
  YES              3               99
[1] 2 2
[1] FALSE
D1111V9, continuous
D1111V10, continuous
[1] "Remove cluster labels:" "RANBP3 MUTATED"        
clus
  RANBP3 MUTATED RANBP3 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" "RANBP3 WILD-TYPE" 
      TCGA-Z6-AAPN 
"RANBP3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RANBP3 MUTATED       5                         1
  RANBP3 WILD-TYPE   128                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RANBP3 MUTATED                                           0     4
  RANBP3 WILD-TYPE                                         1   353
D1111V11, multiclass
                                           clus
vv                                          RANBP3 MUTATED RANBP3 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V12, binary
                  cls
clus                 0   1
  RANBP3 MUTATED     0   9
  RANBP3 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP3 MUTATED      0    9
  RANBP3 WILD-TYPE   10  389
                        clus
vv                       RANBP3 MUTATED RANBP3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1112) Variable = PLK1 MUTATION ANALYSIS
D1112V1, survival
                sevent
clus2              0   1
  PLK1 MUTATED     9   8
  PLK1 WILD-TYPE 329 208
  PLK1 MUTATED PLK1 WILD-TYPE 
            17            537 
  PLK1 MUTATED PLK1 WILD-TYPE 
             8            208 
$`PLK1 MUTATED`
TCGA-L5-A8NF TCGA-L5-A8NM TCGA-BR-4280 TCGA-BR-8285 TCGA-BR-8682 TCGA-CD-A4MI 
        2.66         7.76         6.61         0.56        32.58        11.77 
TCGA-CG-5721 TCGA-FP-7998 TCGA-HU-8238 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4H3 
        6.02        22.29         1.51        21.07         0.10        29.00 
TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA64 
       19.73         8.61        19.04        38.14        18.41 

$`PLK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         8.05        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        14.07        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 
        5.92        24.39        28.96        22.32        22.82         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 
       20.81         1.71        42.64        66.81        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PLK1 MUTATED PLK1 WILD-TYPE 
           0.1            0.0 
  PLK1 MUTATED PLK1 WILD-TYPE 
         38.14         122.30 
  PLK1 MUTATED PLK1 WILD-TYPE 
         11.77          13.58 
[1] "0.1 - 38.1 (11.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1112V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLK1 MUTATED         0        0        2        0         0         2
  PLK1 WILD-TYPE      10       20       44       31        84        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLK1 MUTATED           1          3          2          4        2         1
  PLK1 WILD-TYPE        28         81         60         35       41         3
D1112V3, multiclass
            clus
vv           PLK1 MUTATED PLK1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             0             84
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            4             35
  STAGE IV              2             41
  STAGE IVA             1              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PLK1 MUTATED       1   4   5   8
  PLK1 WILD-TYPE    53 131 256  94
D1112V4, multiclass
       clus
vv      PLK1 MUTATED PLK1 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               5            256
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PLK1 MUTATED     4   5   5   4
  PLK1 WILD-TYPE 191 168  84  81
D1112V5, multiclass
    clus
vv   PLK1 MUTATED PLK1 WILD-TYPE
  N0            4            191
  N1            5            168
  N2            5             84
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V6, binary
                cls
clus               0   1
  PLK1 MUTATED    16   1
  PLK1 WILD-TYPE 466  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED     16    1
  PLK1 WILD-TYPE  466   37
   clus
vv  PLK1 MUTATED PLK1 WILD-TYPE
  0           16            466
  1            1             37
[1] 2 2
[1] FALSE
D1112V7, binary
                cls
clus               0   1
  PLK1 MUTATED     6  12
  PLK1 WILD-TYPE 166 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED      6   12
  PLK1 WILD-TYPE  166  394
        clus
vv       PLK1 MUTATED PLK1 WILD-TYPE
  FEMALE            6            166
  MALE             12            394
[1] 2 2
[1] FALSE
D1112V8, binary
                cls
clus               0   1
  PLK1 MUTATED    13   3
  PLK1 WILD-TYPE 403  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED     13    3
  PLK1 WILD-TYPE  403   99
     clus
vv    PLK1 MUTATED PLK1 WILD-TYPE
  NO            13            403
  YES            3             99
[1] 2 2
[1] FALSE
D1112V9, continuous
D1112V10, continuous
[1] "Remove cluster labels:" "PLK1 MUTATED"          
clus
  PLK1 MUTATED PLK1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" "PLK1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PLK1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PLK1 MUTATED       6                         0
  PLK1 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLK1 MUTATED                                           1     9
  PLK1 WILD-TYPE                                         0   348
D1112V11, multiclass
                                           clus
vv                                          PLK1 MUTATED PLK1 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V12, binary
                cls
clus               0   1
  PLK1 MUTATED     1  11
  PLK1 WILD-TYPE   9 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED      1   11
  PLK1 WILD-TYPE    9  387
                        clus
vv                       PLK1 MUTATED PLK1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(1113) Variable = BRPF3 MUTATION ANALYSIS
D1113V1, survival
                 sevent
clus2               0   1
  BRPF3 MUTATED     7   5
  BRPF3 WILD-TYPE 331 211
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             12             542 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
              5             211 
$`BRPF3 MUTATED`
TCGA-L5-A8NQ TCGA-VR-A8EO TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8078 TCGA-CD-A4MG 
       21.37        25.81         6.97         9.34        29.59         6.58 
TCGA-CD-A4MI TCGA-CG-4437 TCGA-CG-5728 TCGA-D7-A4YT TCGA-F1-6874 TCGA-HU-8602 
       11.77         8.05        65.10        14.27        14.47        22.32 

$`BRPF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BRPF3 MUTATED BRPF3 WILD-TYPE 
           6.58            0.00 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
           65.1           122.3 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
          14.37           13.53 
[1] "6.6 - 65.1 (14.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1113V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRPF3 MUTATED         0        0        2        1         3         2
  BRPF3 WILD-TYPE      10       20       44       30        81        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRPF3 MUTATED           0          3          0          0        0         0
  BRPF3 WILD-TYPE        29         81         62         39       43         4
D1113V3, multiclass
            clus
vv           BRPF3 MUTATED BRPF3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BRPF3 MUTATED       0   5   4   2
  BRPF3 WILD-TYPE    54 130 257 100
D1113V4, multiclass
       clus
vv      BRPF3 MUTATED BRPF3 WILD-TYPE
  T0+T1             0              54
  T2                5             130
  T3                4             257
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BRPF3 MUTATED     7   4   0   1
  BRPF3 WILD-TYPE 188 169  89  84
D1113V5, multiclass
    clus
vv   BRPF3 MUTATED BRPF3 WILD-TYPE
  N0             7             188
  N1             4             169
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V6, binary
                 cls
clus                0   1
  BRPF3 MUTATED    12   0
  BRPF3 WILD-TYPE 470  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED     12    0
  BRPF3 WILD-TYPE  470   38
   clus
vv  BRPF3 MUTATED BRPF3 WILD-TYPE
  0            12             470
  1             0              38
[1] 2 2
[1] FALSE
D1113V7, binary
                 cls
clus                0   1
  BRPF3 MUTATED     4   9
  BRPF3 WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED      4    9
  BRPF3 WILD-TYPE  168  397
        clus
vv       BRPF3 MUTATED BRPF3 WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D1113V8, binary
                 cls
clus                0   1
  BRPF3 MUTATED    10   1
  BRPF3 WILD-TYPE 406 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED     10    1
  BRPF3 WILD-TYPE  406  101
     clus
vv    BRPF3 MUTATED BRPF3 WILD-TYPE
  NO             10             406
  YES             1             101
[1] 2 2
[1] FALSE
D1113V9, continuous
[1] "Remove cluster labels:" "BRPF3 MUTATED"         
clus
  BRPF3 MUTATED BRPF3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EP 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
D1113V10, continuous
[1] "Remove cluster labels:" "BRPF3 MUTATED"         
clus
  BRPF3 MUTATED BRPF3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" "BRPF3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"BRPF3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRPF3 MUTATED       3                         0
  BRPF3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRPF3 MUTATED                                           0     8
  BRPF3 WILD-TYPE                                         1   349
D1113V11, multiclass
                                           clus
vv                                          BRPF3 MUTATED BRPF3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V12, binary
                 cls
clus                0   1
  BRPF3 MUTATED     0   9
  BRPF3 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED      0    9
  BRPF3 WILD-TYPE   10  389
                        clus
vv                       BRPF3 MUTATED BRPF3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1114) Variable = CSNK1G3 MUTATION ANALYSIS
D1114V1, survival
                   sevent
clus2                 0   1
  CSNK1G3 MUTATED     6   2
  CSNK1G3 WILD-TYPE 332 214
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                8               546 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                2               214 
$`CSNK1G3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8487 TCGA-CG-5721 TCGA-HF-7132 
        6.97        34.68        32.25         1.12         6.02        77.29 
TCGA-HU-8602 TCGA-HU-A4GQ 
       22.32         0.10 

$`CSNK1G3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
              0.1               0.0 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
            77.29            122.30 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
           14.645            13.565 
[1] "0.1 - 77.3 (14.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1114V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSNK1G3 MUTATED         1        0        0        1         2         2
  CSNK1G3 WILD-TYPE       9       20       46       30        82        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1G3 MUTATED           0          1          0          1        1
  CSNK1G3 WILD-TYPE        29         83         62         38       42
                   vv
clus                STAGE IVA
  CSNK1G3 MUTATED           0
  CSNK1G3 WILD-TYPE         4
D1114V3, multiclass
            clus
vv           CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CSNK1G3 MUTATED       1   1   3   4
  CSNK1G3 WILD-TYPE    53 134 258  98
D1114V4, multiclass
       clus
vv      CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  3               258
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CSNK1G3 MUTATED     4   4   1   0
  CSNK1G3 WILD-TYPE 191 169  88  85
D1114V5, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  N0               4               191
  N1               4               169
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V6, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     7   0
  CSNK1G3 WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      7    0
  CSNK1G3 WILD-TYPE  475   38
   clus
vv  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D1114V7, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     4   5
  CSNK1G3 WILD-TYPE 168 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      4    5
  CSNK1G3 WILD-TYPE  168  401
        clus
vv       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  FEMALE               4               168
  MALE                 5               401
[1] 2 2
[1] FALSE
D1114V8, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     8   1
  CSNK1G3 WILD-TYPE 408 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      8    1
  CSNK1G3 WILD-TYPE  408  101
     clus
vv    CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  NO                8               408
  YES               1               101
[1] 2 2
[1] FALSE
D1114V9, continuous
D1114V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK1G3 MUTATED       2                         1
  CSNK1G3 WILD-TYPE   131                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK1G3 MUTATED                                           0     4
  CSNK1G3 WILD-TYPE                                         1   353
D1114V11, multiclass
                                           clus
vv                                          CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V12, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     0   7
  CSNK1G3 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      0    7
  CSNK1G3 WILD-TYPE   10  391
                        clus
vv                       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(1115) Variable = STX12 MUTATION ANALYSIS
D1115V1, survival
                 sevent
clus2               0   1
  STX12 MUTATED     2   1
  STX12 WILD-TYPE 336 215
  STX12 MUTATED STX12 WILD-TYPE 
              3             551 
  STX12 MUTATED STX12 WILD-TYPE 
              1             215 
$`STX12 MUTATED`
TCGA-2H-A9GG TCGA-HU-A4GX TCGA-IN-A6RN 
       20.05        20.25        19.53 

$`STX12 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  STX12 MUTATED STX12 WILD-TYPE 
          19.53            0.00 
  STX12 MUTATED STX12 WILD-TYPE 
          20.25          122.30 
  STX12 MUTATED STX12 WILD-TYPE 
          20.05           13.51 
[1] "19.5 - 20.2 (20.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1115V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STX12 MUTATED         0        0        0        0         1         1
  STX12 WILD-TYPE      10       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STX12 MUTATED           1          0          0          1        0         0
  STX12 WILD-TYPE        28         84         62         38       43         4
D1115V3, multiclass
            clus
vv           STX12 MUTATED STX12 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  STX12 MUTATED       1   0   1   2
  STX12 WILD-TYPE    53 135 260 100
D1115V4, multiclass
       clus
vv      STX12 MUTATED STX12 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  STX12 MUTATED     1   1   2   0
  STX12 WILD-TYPE 194 172  87  85
D1115V5, multiclass
    clus
vv   STX12 MUTATED STX12 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V6, binary
                 cls
clus                0   1
  STX12 MUTATED     4   0
  STX12 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX12 MUTATED      4    0
  STX12 WILD-TYPE  478   38
   clus
vv  STX12 MUTATED STX12 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D1115V7, binary
                 cls
clus                0   1
  STX12 MUTATED     2   2
  STX12 WILD-TYPE 170 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX12 MUTATED      2    2
  STX12 WILD-TYPE  170  404
        clus
vv       STX12 MUTATED STX12 WILD-TYPE
  FEMALE             2             170
  MALE               2             404
[1] 2 2
[1] FALSE
D1115V8, binary
                 cls
clus                0   1
  STX12 MUTATED     4   0
  STX12 WILD-TYPE 412 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX12 MUTATED      4    0
  STX12 WILD-TYPE  412  102
     clus
vv    STX12 MUTATED STX12 WILD-TYPE
  NO              4             412
  YES             0             102
[1] 2 2
[1] FALSE
D1115V9, continuous
D1115V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STX12 MUTATED       1                         0
  STX12 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STX12 MUTATED                                           0     2
  STX12 WILD-TYPE                                         1   355
D1115V11, multiclass
                                           clus
vv                                          STX12 MUTATED STX12 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V12, binary
                 cls
clus                0   1
  STX12 MUTATED     0   3
  STX12 WILD-TYPE  10 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX12 MUTATED      0    3
  STX12 WILD-TYPE   10  395
                        clus
vv                       STX12 MUTATED STX12 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             3             395
[1] 2 2
[1] FALSE

Clustering(1116) Variable = KRTAP10-9 MUTATION ANALYSIS
D1116V1, survival
                     sevent
clus2                   0   1
  KRTAP10-9 MUTATED     6   2
  KRTAP10-9 WILD-TYPE 332 214
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  8                 546 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  2                 214 
$`KRTAP10-9 MUTATED`
TCGA-L5-A8NG TCGA-BR-4184 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 
       35.97         6.97        28.14        31.96        11.77        15.95 
TCGA-CG-5723 TCGA-CG-5730 
      105.07         4.01 

$`KRTAP10-9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82         0.36        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
               4.01                0.00 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
             105.07              122.30 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
             22.045              13.530 
[1] "4.0 - 105.1 (22.0)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D1116V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP10-9 MUTATED         1        0        0        2         0         0
  KRTAP10-9 WILD-TYPE       9       20       46       29        84        83
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP10-9 MUTATED           1          2          0          1        2
  KRTAP10-9 WILD-TYPE        28         82         62         38       41
                     vv
clus                  STAGE IVA
  KRTAP10-9 MUTATED           0
  KRTAP10-9 WILD-TYPE         4
D1116V3, multiclass
            clus
vv           KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  STAGE I                    1                   9
  STAGE IA                   0                  20
  STAGE IB                   0                  46
  STAGE II                   2                  29
  STAGE IIA                  0                  84
  STAGE IIB                  0                  83
  STAGE III                  1                  28
  STAGE IIIA                 2                  82
  STAGE IIIB                 0                  62
  STAGE IIIC                 1                  38
  STAGE IV                   2                  41
  STAGE IVA                  0                   4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T0+T1  T2  T3  T4
  KRTAP10-9 MUTATED       1   3   3   2
  KRTAP10-9 WILD-TYPE    53 132 258 100
D1116V4, multiclass
       clus
vv      KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  T0+T1                 1                  53
  T2                    3                 132
  T3                    3                 258
  T4                    2                 100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2  N3
  KRTAP10-9 MUTATED     0   7   1   1
  KRTAP10-9 WILD-TYPE 195 166  88  84
D1116V5, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  N0                 0                 195
  N1                 7                 166
  N2                 1                  88
  N3                 1                  84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V6, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     5   2
  KRTAP10-9 WILD-TYPE 477  36
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      5    2
  KRTAP10-9 WILD-TYPE  477   36
   clus
vv  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  0                 5                 477
  1                 2                  36
[1] 2 2
[1] FALSE
D1116V7, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     1   8
  KRTAP10-9 WILD-TYPE 171 398
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      1    8
  KRTAP10-9 WILD-TYPE  171  398
        clus
vv       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  FEMALE                 1                 171
  MALE                   8                 398
[1] 2 2
[1] FALSE
D1116V8, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     8   0
  KRTAP10-9 WILD-TYPE 408 102
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      8    0
  KRTAP10-9 WILD-TYPE  408  102
     clus
vv    KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  NO                  8                 408
  YES                 0                 102
[1] 2 2
[1] FALSE
D1116V9, continuous
D1116V10, continuous
[1] "Remove cluster labels:" "KRTAP10-9 MUTATED"     
clus
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  1                  97 
         TCGA-IC-A6RF          TCGA-L5-A43I          TCGA-L5-A43J 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A4OE          TCGA-L5-A4OG          TCGA-L5-A4OI 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A88T          TCGA-L5-A88Y          TCGA-L5-A8NT 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-Q9-A6FU          TCGA-IC-A6RE          TCGA-IG-A3QL 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-IG-A3Y9          TCGA-IG-A3YA          TCGA-IG-A3YC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-IG-A4P3          TCGA-IG-A4QT          TCGA-IG-A50L 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-IG-A5B8          TCGA-IG-A6QS          TCGA-IG-A8O2 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-IG-A97H          TCGA-JY-A6FA          TCGA-JY-A6FE 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-JY-A6FG          TCGA-JY-A6FH          TCGA-KH-A6WC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A43C          TCGA-L5-A43E          TCGA-L5-A43H 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A4OH          TCGA-L5-A4OM          TCGA-L5-A4ON 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A4OO          TCGA-L5-A4OP          TCGA-L5-A4OQ 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A4OT          TCGA-L5-A4OU          TCGA-L5-A4OW 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A4OX          TCGA-L5-A88S          TCGA-L5-A88V 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A893          TCGA-L5-A8NE          TCGA-L5-A8NF 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A8NK          TCGA-L5-A8NN          TCGA-L5-A8NQ 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-L5-A8NR          TCGA-L5-A8NS          TCGA-L5-A8NW 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A49O          TCGA-LN-A49P          TCGA-LN-A49R 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A49S          TCGA-LN-A49U          TCGA-LN-A49V 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A49W          TCGA-LN-A4A3          TCGA-LN-A4A6 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A4A9          TCGA-LN-A5U6          TCGA-LN-A5U7 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A7HV          TCGA-LN-A7HW          TCGA-LN-A7HX 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-LN-A7HZ          TCGA-LN-A8HZ          TCGA-LN-A8I0 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-M9-A5M8          TCGA-Q9-A6FW          TCGA-R6-A6DN 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-R6-A6L4          TCGA-R6-A6XQ          TCGA-R6-A6Y2 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-R6-A8W5          TCGA-R6-A8W8          TCGA-R6-A8WC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-RE-A7BO          TCGA-V5-A7RB          TCGA-V5-A7RC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-V5-AASV          TCGA-VR-A8EP          TCGA-VR-A8ER 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-VR-A8EU          TCGA-VR-A8EW          TCGA-VR-A8EX 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-VR-A8EZ          TCGA-VR-A8Q7          TCGA-VR-AA4G 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-VR-AA7D          TCGA-VR-AA7I          TCGA-X8-AAAR 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-XP-A8T6          TCGA-XP-A8T7          TCGA-XP-A8T8 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-Z6-AAPN 
"KRTAP10-9 WILD-TYPE" 
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  KRTAP10-9 MUTATED       2                         1
  KRTAP10-9 WILD-TYPE   131                        13
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRTAP10-9 MUTATED                                           0     3
  KRTAP10-9 WILD-TYPE                                         1   354
D1116V11, multiclass
                                           clus
vv                                          KRTAP10-9 MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     3
                                           clus
vv                                          KRTAP10-9 WILD-TYPE
  ASIAN                                                     131
  BLACK OR AFRICAN AMERICAN                                  13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V12, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     0   5
  KRTAP10-9 WILD-TYPE  10 393
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      0    5
  KRTAP10-9 WILD-TYPE   10  393
                        clus
vv                       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  HISPANIC OR LATINO                     0                  10
  NOT HISPANIC OR LATINO                 5                 393
[1] 2 2
[1] FALSE

Clustering(1117) Variable = LOXL2 MUTATION ANALYSIS
D1117V1, survival
                 sevent
clus2               0   1
  LOXL2 MUTATED    11   6
  LOXL2 WILD-TYPE 327 210
  LOXL2 MUTATED LOXL2 WILD-TYPE 
             17             537 
  LOXL2 MUTATED LOXL2 WILD-TYPE 
              6             210 
$`LOXL2 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-2H-A9GI TCGA-L5-A4ON TCGA-L5-A4OW TCGA-L5-A8NE 
       19.99        21.99        14.30        18.35         7.13        55.50 
TCGA-L5-A8NL TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8487 
       13.22         9.34         9.67        34.68        32.25         1.12 
TCGA-BR-8588 TCGA-BR-8591 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4H3 
       12.79        28.14        11.08        22.68        29.00 

$`LOXL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        0.30        26.33        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         4.08         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  LOXL2 MUTATED LOXL2 WILD-TYPE 
           1.12            0.00 
  LOXL2 MUTATED LOXL2 WILD-TYPE 
           55.5           122.3 
  LOXL2 MUTATED LOXL2 WILD-TYPE 
          18.35           13.51 
[1] "1.1 - 55.5 (18.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1117V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LOXL2 MUTATED         1        0        0        0         3         6
  LOXL2 WILD-TYPE       9       20       46       31        81        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LOXL2 MUTATED           2          0          0          3        1         0
  LOXL2 WILD-TYPE        27         84         62         36       42         4
D1117V3, multiclass
            clus
vv           LOXL2 MUTATED LOXL2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              6              77
  STAGE III              2              27
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LOXL2 MUTATED       2   2   7   5
  LOXL2 WILD-TYPE    52 133 254  97
D1117V4, multiclass
       clus
vv      LOXL2 MUTATED LOXL2 WILD-TYPE
  T0+T1             2              52
  T2                2             133
  T3                7             254
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LOXL2 MUTATED     5   9   0   3
  LOXL2 WILD-TYPE 190 164  89  82
D1117V5, multiclass
    clus
vv   LOXL2 MUTATED LOXL2 WILD-TYPE
  N0             5             190
  N1             9             164
  N2             0              89
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V6, binary
                 cls
clus                0   1
  LOXL2 MUTATED    14   1
  LOXL2 WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LOXL2 MUTATED     14    1
  LOXL2 WILD-TYPE  468   37
   clus
vv  LOXL2 MUTATED LOXL2 WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D1117V7, binary
                 cls
clus                0   1
  LOXL2 MUTATED     9   9
  LOXL2 WILD-TYPE 163 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LOXL2 MUTATED      9    9
  LOXL2 WILD-TYPE  163  397
        clus
vv       LOXL2 MUTATED LOXL2 WILD-TYPE
  FEMALE             9             163
  MALE               9             397
[1] 2 2
[1] FALSE
D1117V8, binary
                 cls
clus                0   1
  LOXL2 MUTATED    14   1
  LOXL2 WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LOXL2 MUTATED     14    1
  LOXL2 WILD-TYPE  402  101
     clus
vv    LOXL2 MUTATED LOXL2 WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D1117V9, continuous
D1117V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LOXL2 MUTATED       2                         2
  LOXL2 WILD-TYPE   131                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LOXL2 MUTATED                                           0    11
  LOXL2 WILD-TYPE                                         1   346
D1117V11, multiclass
                                           clus
vv                                          LOXL2 MUTATED LOXL2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V12, binary
                 cls
clus                0   1
  LOXL2 MUTATED     0  11
  LOXL2 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LOXL2 MUTATED      0   11
  LOXL2 WILD-TYPE   10  387
                        clus
vv                       LOXL2 MUTATED LOXL2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1118) Variable = SLC25A41 MUTATION ANALYSIS
D1118V1, survival
                    sevent
clus2                  0   1
  SLC25A41 MUTATED     3   2
  SLC25A41 WILD-TYPE 335 214
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
                 5                549 
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
                 2                214 
$`SLC25A41 MUTATED`
TCGA-L5-A43J TCGA-BR-8361 TCGA-HU-A4G8 TCGA-R5-A7ZI TCGA-R5-A7ZR 
        4.31        31.10        22.68        74.53         6.08 

$`SLC25A41 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 
       19.73        14.04        45.67        18.21         8.52         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
              4.31               0.00 
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
             74.53             122.30 
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
             22.68              13.55 
[1] "4.3 - 74.5 (22.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1118V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC25A41 MUTATED         1        0        0        0         0         2
  SLC25A41 WILD-TYPE       9       20       46       31        84        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A41 MUTATED           1          0          0          1        1
  SLC25A41 WILD-TYPE        28         84         62         38       42
                    vv
clus                 STAGE IVA
  SLC25A41 MUTATED           0
  SLC25A41 WILD-TYPE         4
D1118V3, multiclass
            clus
vv           SLC25A41 MUTATED SLC25A41 WILD-TYPE
  STAGE I                   1                  9
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 0                 84
  STAGE IIB                 2                 81
  STAGE III                 1                 28
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SLC25A41 MUTATED       1   0   3   2
  SLC25A41 WILD-TYPE    53 135 258 100
D1118V4, multiclass
       clus
vv      SLC25A41 MUTATED SLC25A41 WILD-TYPE
  T0+T1                1                 53
  T2                   0                135
  T3                   3                258
  T4                   2                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SLC25A41 MUTATED     1   3   1   0
  SLC25A41 WILD-TYPE 194 170  88  85
D1118V5, multiclass
    clus
vv   SLC25A41 MUTATED SLC25A41 WILD-TYPE
  N0                1                194
  N1                3                170
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V6, binary
                    cls
clus                   0   1
  SLC25A41 MUTATED     3   1
  SLC25A41 WILD-TYPE 479  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A41 MUTATED      3    1
  SLC25A41 WILD-TYPE  479   37
   clus
vv  SLC25A41 MUTATED SLC25A41 WILD-TYPE
  0                3                479
  1                1                 37
[1] 2 2
[1] FALSE
D1118V7, binary
                    cls
clus                   0   1
  SLC25A41 MUTATED     4   2
  SLC25A41 WILD-TYPE 168 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A41 MUTATED      4    2
  SLC25A41 WILD-TYPE  168  404
        clus
vv       SLC25A41 MUTATED SLC25A41 WILD-TYPE
  FEMALE                4                168
  MALE                  2                404
[1] 2 2
[1] FALSE
D1118V8, binary
                    cls
clus                   0   1
  SLC25A41 MUTATED     5   0
  SLC25A41 WILD-TYPE 411 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A41 MUTATED      5    0
  SLC25A41 WILD-TYPE  411  102
     clus
vv    SLC25A41 MUTATED SLC25A41 WILD-TYPE
  NO                 5                411
  YES                0                102
[1] 2 2
[1] FALSE
D1118V9, continuous
D1118V10, continuous
[1] "Remove cluster labels:" "SLC25A41 MUTATED"      
clus
  SLC25A41 MUTATED SLC25A41 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A4OE 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A4OX         TCGA-L5-A88S         TCGA-L5-A88V 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A893         TCGA-L5-A8NE         TCGA-L5-A8NF 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A8NK         TCGA-L5-A8NN         TCGA-L5-A8NQ 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-L5-A8NR         TCGA-L5-A8NS         TCGA-L5-A8NW 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A49O         TCGA-LN-A49P         TCGA-LN-A49R 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A49S         TCGA-LN-A49U         TCGA-LN-A49V 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A49W         TCGA-LN-A4A3         TCGA-LN-A4A6 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A5U6         TCGA-LN-A5U7 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-LN-A7HZ         TCGA-LN-A8HZ         TCGA-LN-A8I0 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-M9-A5M8         TCGA-Q9-A6FW         TCGA-R6-A6DN 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-R6-A6L4         TCGA-R6-A6XQ         TCGA-R6-A6Y2 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-R6-A8W5         TCGA-R6-A8W8         TCGA-R6-A8WC 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-RE-A7BO         TCGA-V5-A7RB         TCGA-V5-A7RC 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-V5-AASV         TCGA-VR-A8EP         TCGA-VR-A8ER 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-VR-A8EU         TCGA-VR-A8EW         TCGA-VR-A8EX 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-VR-A8EZ         TCGA-VR-A8Q7         TCGA-VR-AA4G 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-VR-AA7D         TCGA-VR-AA7I         TCGA-X8-AAAR 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-XP-A8T6         TCGA-XP-A8T7         TCGA-XP-A8T8 
"SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" "SLC25A41 WILD-TYPE" 
        TCGA-Z6-AAPN 
"SLC25A41 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC25A41 MUTATED       1                         2
  SLC25A41 WILD-TYPE   132                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC25A41 MUTATED                                           0     3
  SLC25A41 WILD-TYPE                                         1   354
D1118V11, multiclass
                                           clus
vv                                          SLC25A41 MUTATED SLC25A41 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                2                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V12, binary
                    cls
clus                   0   1
  SLC25A41 MUTATED     1   4
  SLC25A41 WILD-TYPE   9 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A41 MUTATED      1    4
  SLC25A41 WILD-TYPE    9  394
                        clus
vv                       SLC25A41 MUTATED SLC25A41 WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO                4                394
[1] 2 2
[1] FALSE

Clustering(1119) Variable = MAP9 MUTATION ANALYSIS
D1119V1, survival
                sevent
clus2              0   1
  MAP9 MUTATED     6   6
  MAP9 WILD-TYPE 332 210
  MAP9 MUTATED MAP9 WILD-TYPE 
            12            542 
  MAP9 MUTATED MAP9 WILD-TYPE 
             6            210 
$`MAP9 MUTATED`
TCGA-L5-A8NV TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 
       52.57         6.97        30.90        25.05        28.14         7.53 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-FP-A4BE TCGA-HJ-7597 TCGA-VQ-AA68 
       31.96         6.58        12.62        11.08        26.47        43.66 

$`MAP9 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       12.79        27.12         9.34         6.28        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  MAP9 MUTATED MAP9 WILD-TYPE 
          6.58           0.00 
  MAP9 MUTATED MAP9 WILD-TYPE 
         52.57         122.30 
  MAP9 MUTATED MAP9 WILD-TYPE 
         25.76          13.53 
[1] "6.6 - 52.6 (25.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1119V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP9 MUTATED         1        0        3        0         3         0
  MAP9 WILD-TYPE       9       20       43       31        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP9 MUTATED           0          1          1          3        1         0
  MAP9 WILD-TYPE        29         83         61         36       42         4
D1119V3, multiclass
            clus
vv           MAP9 MUTATED MAP9 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            3             36
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MAP9 MUTATED       1   4   5   4
  MAP9 WILD-TYPE    53 131 256  98
D1119V4, multiclass
       clus
vv      MAP9 MUTATED MAP9 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MAP9 MUTATED     6   2   1   4
  MAP9 WILD-TYPE 189 171  88  81
D1119V5, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  N0            6            189
  N1            2            171
  N2            1             88
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V6, binary
                cls
clus               0   1
  MAP9 MUTATED    10   1
  MAP9 WILD-TYPE 472  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     10    1
  MAP9 WILD-TYPE  472   37
   clus
vv  MAP9 MUTATED MAP9 WILD-TYPE
  0           10            472
  1            1             37
[1] 2 2
[1] FALSE
D1119V7, binary
                cls
clus               0   1
  MAP9 MUTATED     5   9
  MAP9 WILD-TYPE 167 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      5    9
  MAP9 WILD-TYPE  167  397
        clus
vv       MAP9 MUTATED MAP9 WILD-TYPE
  FEMALE            5            167
  MALE              9            397
[1] 2 2
[1] FALSE
D1119V8, binary
                cls
clus               0   1
  MAP9 MUTATED    12   2
  MAP9 WILD-TYPE 404 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     12    2
  MAP9 WILD-TYPE  404  100
     clus
vv    MAP9 MUTATED MAP9 WILD-TYPE
  NO            12            404
  YES            2            100
[1] 2 2
[1] FALSE
D1119V9, continuous
D1119V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MAP9 MUTATED       3                         2
  MAP9 WILD-TYPE   130                        12
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP9 MUTATED                                           0     9
  MAP9 WILD-TYPE                                         1   348
D1119V11, multiclass
                                           clus
vv                                          MAP9 MUTATED MAP9 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            2             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V12, binary
                cls
clus               0   1
  MAP9 MUTATED     0  12
  MAP9 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      0   12
  MAP9 WILD-TYPE   10  386
                        clus
vv                       MAP9 MUTATED MAP9 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1120) Variable = SLC9A2 MUTATION ANALYSIS
D1120V1, survival
                  sevent
clus2                0   1
  SLC9A2 MUTATED     8   7
  SLC9A2 WILD-TYPE 330 209
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              15              539 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               7              209 
$`SLC9A2 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GI TCGA-L5-A4OT TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8078 
       19.99        14.30         4.90        39.78        14.43        29.59 
TCGA-BR-8366 TCGA-CD-5801 TCGA-CD-A4MI TCGA-CG-4437 TCGA-D7-A4YV TCGA-HU-A4G8 
        0.95        13.18        11.77         8.05         5.92        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX 
       29.98         0.10        20.25 

$`SLC9A2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.77        21.37         8.98         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
             0.1              0.0 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
           39.78           122.30 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
           14.30            13.55 
[1] "0.1 - 39.8 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1120V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A2 MUTATED         0        0        0        1         2         4
  SLC9A2 WILD-TYPE      10       20       46       30        82        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A2 MUTATED           2          2          0          3        1
  SLC9A2 WILD-TYPE        27         82         62         36       42
                  vv
clus               STAGE IVA
  SLC9A2 MUTATED           0
  SLC9A2 WILD-TYPE         4
D1120V3, multiclass
            clus
vv           SLC9A2 MUTATED SLC9A2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               4               79
  STAGE III               2               27
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SLC9A2 MUTATED       0   2   9   4
  SLC9A2 WILD-TYPE    54 133 252  98
D1120V4, multiclass
       clus
vv      SLC9A2 MUTATED SLC9A2 WILD-TYPE
  T0+T1              0               54
  T2                 2              133
  T3                 9              252
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SLC9A2 MUTATED     2  10   2   1
  SLC9A2 WILD-TYPE 193 163  87  84
D1120V5, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  N0              2              193
  N1             10              163
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V6, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED    13   1
  SLC9A2 WILD-TYPE 469  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED     13    1
  SLC9A2 WILD-TYPE  469   37
   clus
vv  SLC9A2 MUTATED SLC9A2 WILD-TYPE
  0             13              469
  1              1               37
[1] 2 2
[1] FALSE
D1120V7, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     6   9
  SLC9A2 WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      6    9
  SLC9A2 WILD-TYPE  166  397
        clus
vv       SLC9A2 MUTATED SLC9A2 WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D1120V8, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED    15   0
  SLC9A2 WILD-TYPE 401 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED     15    0
  SLC9A2 WILD-TYPE  401  102
     clus
vv    SLC9A2 MUTATED SLC9A2 WILD-TYPE
  NO              15              401
  YES              0              102
[1] 2 2
[1] FALSE
D1120V9, continuous
D1120V10, continuous
[1] "Remove cluster labels:" "SLC9A2 MUTATED"        
clus
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" "SLC9A2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A2 MUTATED       6                         0
  SLC9A2 WILD-TYPE   127                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A2 MUTATED                                           0     7
  SLC9A2 WILD-TYPE                                         1   350
D1120V11, multiclass
                                           clus
vv                                          SLC9A2 MUTATED SLC9A2 WILD-TYPE
  ASIAN                                                  6              127
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V12, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     0  11
  SLC9A2 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      0   11
  SLC9A2 WILD-TYPE   10  387
                        clus
vv                       SLC9A2 MUTATED SLC9A2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(1121) Variable = SEC31B MUTATION ANALYSIS
D1121V1, survival
                  sevent
clus2                0   1
  SEC31B MUTATED    16   5
  SEC31B WILD-TYPE 322 211
  SEC31B MUTATED SEC31B WILD-TYPE 
              21              533 
  SEC31B MUTATED SEC31B WILD-TYPE 
               5              211 
$`SEC31B MUTATED`
TCGA-2H-A9GO TCGA-L5-A4OT TCGA-L5-A8NM TCGA-L5-A8NV TCGA-BR-8078 TCGA-BR-8589 
       16.24         4.90         7.76        52.57        29.59        27.12 
TCGA-BR-A4PE TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8579 TCGA-HF-A5NB TCGA-HU-8602 
       20.42         6.02        65.10        20.91        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 
       22.68        29.98         0.10         6.58        29.00        14.07 
TCGA-IN-7806 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       36.36        37.41        38.14 

$`SEC31B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37         8.98         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.02        43.36        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SEC31B MUTATED SEC31B WILD-TYPE 
             0.1              0.0 
  SEC31B MUTATED SEC31B WILD-TYPE 
            65.1            122.3 
  SEC31B MUTATED SEC31B WILD-TYPE 
           22.68            13.41 
[1] "0.1 - 65.1 (22.7)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.3"
D1121V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SEC31B MUTATED         0        0        3        0         2         7
  SEC31B WILD-TYPE      10       20       43       31        82        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC31B MUTATED           0          1          1          3        3
  SEC31B WILD-TYPE        29         83         61         36       40
                  vv
clus               STAGE IVA
  SEC31B MUTATED           1
  SEC31B WILD-TYPE         3
D1121V3, multiclass
            clus
vv           SEC31B MUTATED SEC31B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                3               43
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               7               76
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                3               40
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SEC31B MUTATED       1   5   8   8
  SEC31B WILD-TYPE    53 130 253  94
D1121V4, multiclass
       clus
vv      SEC31B MUTATED SEC31B WILD-TYPE
  T0+T1              1               53
  T2                 5              130
  T3                 8              253
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SEC31B MUTATED     5  12   2   2
  SEC31B WILD-TYPE 190 161  87  83
D1121V5, multiclass
    clus
vv   SEC31B MUTATED SEC31B WILD-TYPE
  N0              5              190
  N1             12              161
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V6, binary
                  cls
clus                 0   1
  SEC31B MUTATED    18   3
  SEC31B WILD-TYPE 464  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31B MUTATED     18    3
  SEC31B WILD-TYPE  464   35
   clus
vv  SEC31B MUTATED SEC31B WILD-TYPE
  0             18              464
  1              3               35
[1] 2 2
[1] FALSE
D1121V7, binary
                  cls
clus                 0   1
  SEC31B MUTATED    10  12
  SEC31B WILD-TYPE 162 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31B MUTATED     10   12
  SEC31B WILD-TYPE  162  394
        clus
vv       SEC31B MUTATED SEC31B WILD-TYPE
  FEMALE             10              162
  MALE               12              394
[1] 2 2
[1] FALSE
D1121V8, binary
                  cls
clus                 0   1
  SEC31B MUTATED    16   3
  SEC31B WILD-TYPE 400  99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31B MUTATED     16    3
  SEC31B WILD-TYPE  400   99
     clus
vv    SEC31B MUTATED SEC31B WILD-TYPE
  NO              16              400
  YES              3               99
[1] 2 2
[1] FALSE
D1121V9, continuous
D1121V10, continuous
[1] "Remove cluster labels:" "SEC31B MUTATED"        
clus
  SEC31B MUTATED SEC31B WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" "SEC31B WILD-TYPE" 
      TCGA-Z6-AAPN 
"SEC31B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SEC31B MUTATED       7                         0
  SEC31B WILD-TYPE   126                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SEC31B MUTATED                                           0    11
  SEC31B WILD-TYPE                                         1   346
D1121V11, multiclass
                                           clus
vv                                          SEC31B MUTATED SEC31B WILD-TYPE
  ASIAN                                                  7              126
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V12, binary
                  cls
clus                 0   1
  SEC31B MUTATED     0  13
  SEC31B WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31B MUTATED      0   13
  SEC31B WILD-TYPE   10  385
                        clus
vv                       SEC31B MUTATED SEC31B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(1122) Variable = MINA MUTATION ANALYSIS
D1122V1, survival
                sevent
clus2              0   1
  MINA MUTATED     4   4
  MINA WILD-TYPE 334 212
  MINA MUTATED MINA WILD-TYPE 
             8            546 
  MINA MUTATED MINA WILD-TYPE 
             4            212 
$`MINA MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-CG-4465 TCGA-CG-5733 
        6.97        34.68        29.59         0.26         9.01        21.07 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`MINA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  MINA MUTATED MINA WILD-TYPE 
          0.26           0.00 
  MINA MUTATED MINA WILD-TYPE 
         38.14         122.30 
  MINA MUTATED MINA WILD-TYPE 
         20.40          13.53 
[1] "0.3 - 38.1 (20.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1122V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MINA MUTATED         0        0        1        0         1         1
  MINA WILD-TYPE      10       20       45       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MINA MUTATED           0          4          0          0        1         0
  MINA WILD-TYPE        29         80         62         39       42         4
D1122V3, multiclass
            clus
vv           MINA MUTATED MINA WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MINA MUTATED       0   2   3   3
  MINA WILD-TYPE    54 133 258  99
D1122V4, multiclass
       clus
vv      MINA MUTATED MINA WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MINA MUTATED     3   2   2   1
  MINA WILD-TYPE 192 171  87  84
D1122V5, multiclass
    clus
vv   MINA MUTATED MINA WILD-TYPE
  N0            3            192
  N1            2            171
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V6, binary
                cls
clus               0   1
  MINA MUTATED     6   1
  MINA WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    1
  MINA WILD-TYPE  476   37
   clus
vv  MINA MUTATED MINA WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D1122V7, binary
                cls
clus               0   1
  MINA MUTATED     6   2
  MINA WILD-TYPE 166 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    2
  MINA WILD-TYPE  166  404
        clus
vv       MINA MUTATED MINA WILD-TYPE
  FEMALE            6            166
  MALE              2            404
[1] 2 2
[1] FALSE
D1122V8, binary
                cls
clus               0   1
  MINA MUTATED     6   1
  MINA WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    1
  MINA WILD-TYPE  410  101
     clus
vv    MINA MUTATED MINA WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D1122V9, continuous
D1122V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MINA MUTATED       0                         0
  MINA WILD-TYPE   133                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MINA MUTATED                                           0     6
  MINA WILD-TYPE                                         1   351
D1122V11, multiclass
                                           clus
vv                                          MINA MUTATED MINA WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V12, binary
                cls
clus               0   1
  MINA MUTATED     0   5
  MINA WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      0    5
  MINA WILD-TYPE   10  393
                        clus
vv                       MINA MUTATED MINA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1123) Variable = CAB39L MUTATION ANALYSIS
D1123V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     4   3
  CAB39L WILD-TYPE 334 213
  CAB39L MUTATED CAB39L WILD-TYPE 
               7              547 
  CAB39L MUTATED CAB39L WILD-TYPE 
               3              213 
$`CAB39L MUTATED`
TCGA-L5-A8NM TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8680 TCGA-BR-A4QL 
        7.76         9.67        34.68         6.18        31.96        16.14 
TCGA-HU-8602 
       22.32 

$`CAB39L WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CAB39L MUTATED CAB39L WILD-TYPE 
            6.18             0.00 
  CAB39L MUTATED CAB39L WILD-TYPE 
           34.68           122.30 
  CAB39L MUTATED CAB39L WILD-TYPE 
           16.14            13.55 
[1] "6.2 - 34.7 (16.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1123V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CAB39L MUTATED         0        0        0        0         2         2
  CAB39L WILD-TYPE      10       20       46       31        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAB39L MUTATED           0          0          1          1        1
  CAB39L WILD-TYPE        29         84         61         38       42
                  vv
clus               STAGE IVA
  CAB39L MUTATED           0
  CAB39L WILD-TYPE         4
D1123V3, multiclass
            clus
vv           CAB39L MUTATED CAB39L WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CAB39L MUTATED       0   1   3   3
  CAB39L WILD-TYPE    54 134 258  99
D1123V4, multiclass
       clus
vv      CAB39L MUTATED CAB39L WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CAB39L MUTATED     3   1   1   2
  CAB39L WILD-TYPE 192 172  88  83
D1123V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  N0              3              192
  N1              1              172
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V6, binary
                  cls
clus                 0   1
  CAB39L MUTATED     7   1
  CAB39L WILD-TYPE 475  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      7    1
  CAB39L WILD-TYPE  475   37
   clus
vv  CAB39L MUTATED CAB39L WILD-TYPE
  0              7              475
  1              1               37
[1] 2 2
[1] FALSE
D1123V7, binary
                  cls
clus                 0   1
  CAB39L MUTATED     5   3
  CAB39L WILD-TYPE 167 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      5    3
  CAB39L WILD-TYPE  167  403
        clus
vv       CAB39L MUTATED CAB39L WILD-TYPE
  FEMALE              5              167
  MALE                3              403
[1] 2 2
[1] FALSE
D1123V8, binary
                  cls
clus                 0   1
  CAB39L MUTATED     7   0
  CAB39L WILD-TYPE 409 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      7    0
  CAB39L WILD-TYPE  409  102
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               7              409
  YES              0              102
[1] 2 2
[1] FALSE
D1123V9, continuous
D1123V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CAB39L MUTATED       2                         0
  CAB39L WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CAB39L MUTATED                                           0     5
  CAB39L WILD-TYPE                                         1   352
D1123V11, multiclass
                                           clus
vv                                          CAB39L MUTATED CAB39L WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V12, binary
                  cls
clus                 0   1
  CAB39L MUTATED     0   6
  CAB39L WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      0    6
  CAB39L WILD-TYPE   10  392
                        clus
vv                       CAB39L MUTATED CAB39L WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(1124) Variable = GPR137B MUTATION ANALYSIS
D1124V1, survival
                   sevent
clus2                 0   1
  GPR137B MUTATED     6   1
  GPR137B WILD-TYPE 332 215
  GPR137B MUTATED GPR137B WILD-TYPE 
                7               547 
  GPR137B MUTATED GPR137B WILD-TYPE 
                1               215 
$`GPR137B MUTATED`
TCGA-L5-A8NN TCGA-Z6-A8JE TCGA-BR-8487 TCGA-BR-8683 TCGA-HU-8602 TCGA-MX-A5UJ 
        5.49         2.10         1.12         9.86        22.32        19.73 
TCGA-R5-A7O7 
       45.67 

$`GPR137B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE 
        5.56        63.62        36.95         3.72        14.04        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GPR137B MUTATED GPR137B WILD-TYPE 
             1.12              0.00 
  GPR137B MUTATED GPR137B WILD-TYPE 
            45.67            122.30 
  GPR137B MUTATED GPR137B WILD-TYPE 
             9.86             13.58 
[1] "1.1 - 45.7 (9.9)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "2.2"
D1124V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR137B MUTATED         0        0        0        0         1         2
  GPR137B WILD-TYPE      10       20       46       31        83        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR137B MUTATED           1          2          1          0        1
  GPR137B WILD-TYPE        28         82         61         39       42
                   vv
clus                STAGE IVA
  GPR137B MUTATED           0
  GPR137B WILD-TYPE         4
D1124V3, multiclass
            clus
vv           GPR137B MUTATED GPR137B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                1                83
  STAGE IIB                2                81
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  GPR137B MUTATED       0   0   5   3
  GPR137B WILD-TYPE    54 135 256  99
D1124V4, multiclass
       clus
vv      GPR137B MUTATED GPR137B WILD-TYPE
  T0+T1               0                54
  T2                  0               135
  T3                  5               256
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  GPR137B MUTATED     3   3   2   0
  GPR137B WILD-TYPE 192 170  87  85
D1124V5, multiclass
    clus
vv   GPR137B MUTATED GPR137B WILD-TYPE
  N0               3               192
  N1               3               170
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V6, binary
                   cls
clus                  0   1
  GPR137B MUTATED     7   1
  GPR137B WILD-TYPE 475  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      7    1
  GPR137B WILD-TYPE  475   37
   clus
vv  GPR137B MUTATED GPR137B WILD-TYPE
  0               7               475
  1               1                37
[1] 2 2
[1] FALSE
D1124V7, binary
                   cls
clus                  0   1
  GPR137B MUTATED     3   5
  GPR137B WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      3    5
  GPR137B WILD-TYPE  169  401
        clus
vv       GPR137B MUTATED GPR137B WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D1124V8, binary
                   cls
clus                  0   1
  GPR137B MUTATED     8   0
  GPR137B WILD-TYPE 408 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      8    0
  GPR137B WILD-TYPE  408  102
     clus
vv    GPR137B MUTATED GPR137B WILD-TYPE
  NO                8               408
  YES               0               102
[1] 2 2
[1] FALSE
D1124V9, continuous
[1] "Remove cluster labels:" "GPR137B MUTATED"       
clus
  GPR137B MUTATED GPR137B WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-A8JD 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
D1124V10, continuous
[1] "Remove cluster labels:" "GPR137B MUTATED"       
clus
  GPR137B MUTATED GPR137B WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NQ 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" "GPR137B WILD-TYPE" 
       TCGA-Z6-AAPN 
"GPR137B WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPR137B MUTATED       2                         0
  GPR137B WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR137B MUTATED                                           0     6
  GPR137B WILD-TYPE                                         1   351
D1124V11, multiclass
                                           clus
vv                                          GPR137B MUTATED GPR137B WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V12, binary
                   cls
clus                  0   1
  GPR137B MUTATED     1   6
  GPR137B WILD-TYPE   9 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      1    6
  GPR137B WILD-TYPE    9  392
                        clus
vv                       GPR137B MUTATED GPR137B WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1125) Variable = IL1F7 MUTATION ANALYSIS
D1125V1, survival
                 sevent
clus2               0   1
  IL1F7 MUTATED     3   1
  IL1F7 WILD-TYPE 335 215
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              4             550 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              1             215 
$`IL1F7 MUTATED`
TCGA-LN-A7HV TCGA-BR-4280 TCGA-BR-8368 TCGA-MX-A5UJ 
       10.52         6.61         4.31        19.73 

$`IL1F7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  IL1F7 MUTATED IL1F7 WILD-TYPE 
           4.31            0.00 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
          19.73          122.30 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
          8.565          13.630 
[1] "4.3 - 19.7 (8.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1125V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL1F7 MUTATED         0        0        1        0         1         0
  IL1F7 WILD-TYPE      10       20       45       31        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL1F7 MUTATED           1          1          0          0        0         0
  IL1F7 WILD-TYPE        28         83         62         39       43         4
D1125V3, multiclass
            clus
vv           IL1F7 MUTATED IL1F7 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IL1F7 MUTATED       0   3   1   0
  IL1F7 WILD-TYPE    54 132 260 102
D1125V4, multiclass
       clus
vv      IL1F7 MUTATED IL1F7 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                1             260
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IL1F7 MUTATED     2   1   1   0
  IL1F7 WILD-TYPE 193 172  88  85
D1125V5, multiclass
    clus
vv   IL1F7 MUTATED IL1F7 WILD-TYPE
  N0             2             193
  N1             1             172
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V6, binary
                 cls
clus                0   1
  IL1F7 MUTATED     4   0
  IL1F7 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      4    0
  IL1F7 WILD-TYPE  478   38
   clus
vv  IL1F7 MUTATED IL1F7 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D1125V7, binary
                 cls
clus                0   1
  IL1F7 MUTATED     3   1
  IL1F7 WILD-TYPE 169 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      3    1
  IL1F7 WILD-TYPE  169  405
        clus
vv       IL1F7 MUTATED IL1F7 WILD-TYPE
  FEMALE             3             169
  MALE               1             405
[1] 2 2
[1] FALSE
D1125V8, binary
                 cls
clus                0   1
  IL1F7 MUTATED     3   1
  IL1F7 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      3    1
  IL1F7 WILD-TYPE  413  101
     clus
vv    IL1F7 MUTATED IL1F7 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D1125V9, continuous
[1] "Remove cluster labels:" "IL1F7 MUTATED"         
clus
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
D1125V10, continuous
[1] "Remove cluster labels:" "IL1F7 MUTATED"         
clus
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" "IL1F7 WILD-TYPE" 
     TCGA-Z6-AAPN 
"IL1F7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IL1F7 MUTATED       1                         0
  IL1F7 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL1F7 MUTATED                                           0     3
  IL1F7 WILD-TYPE                                         1   354
D1125V11, multiclass
                                           clus
vv                                          IL1F7 MUTATED IL1F7 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V12, binary
                 cls
clus                0   1
  IL1F7 MUTATED     0   4
  IL1F7 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      0    4
  IL1F7 WILD-TYPE   10  394
                        clus
vv                       IL1F7 MUTATED IL1F7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1126) Variable = TM7SF3 MUTATION ANALYSIS
D1126V1, survival
                  sevent
clus2                0   1
  TM7SF3 MUTATED     6   1
  TM7SF3 WILD-TYPE 332 215
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               7              547 
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               1              215 
$`TM7SF3 MUTATED`
TCGA-L5-A4OI TCGA-XP-A8T8 TCGA-BR-6452 TCGA-BR-8361 TCGA-CG-4436 TCGA-D7-A4YV 
       19.99        14.37        34.68        31.10         7.99         5.92 
TCGA-HF-A5NB 
       30.51 

$`TM7SF3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
            5.92             0.00 
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
           34.68           122.30 
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
           19.99            13.51 
[1] "5.9 - 34.7 (20.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.2"
D1126V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM7SF3 MUTATED         0        0        1        0         1         2
  TM7SF3 WILD-TYPE      10       20       45       31        83        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF3 MUTATED           0          0          0          3        0
  TM7SF3 WILD-TYPE        29         84         62         36       43
                  vv
clus               STAGE IVA
  TM7SF3 MUTATED           0
  TM7SF3 WILD-TYPE         4
D1126V3, multiclass
            clus
vv           TM7SF3 MUTATED TM7SF3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TM7SF3 MUTATED       1   1   3   2
  TM7SF3 WILD-TYPE    53 134 258 100
D1126V4, multiclass
       clus
vv      TM7SF3 MUTATED TM7SF3 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TM7SF3 MUTATED     2   2   1   2
  TM7SF3 WILD-TYPE 193 171  88  83
D1126V5, multiclass
    clus
vv   TM7SF3 MUTATED TM7SF3 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V6, binary
                  cls
clus                 0   1
  TM7SF3 MUTATED     6   0
  TM7SF3 WILD-TYPE 476  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF3 MUTATED      6    0
  TM7SF3 WILD-TYPE  476   38
   clus
vv  TM7SF3 MUTATED TM7SF3 WILD-TYPE
  0              6              476
  1              0               38
[1] 2 2
[1] FALSE
D1126V7, binary
                  cls
clus                 0   1
  TM7SF3 MUTATED     4   3
  TM7SF3 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF3 MUTATED      4    3
  TM7SF3 WILD-TYPE  168  403
        clus
vv       TM7SF3 MUTATED TM7SF3 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D1126V8, binary
                  cls
clus                 0   1
  TM7SF3 MUTATED     5   2
  TM7SF3 WILD-TYPE 411 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF3 MUTATED      5    2
  TM7SF3 WILD-TYPE  411  100
     clus
vv    TM7SF3 MUTATED TM7SF3 WILD-TYPE
  NO               5              411
  YES              2              100
[1] 2 2
[1] FALSE
D1126V9, continuous
[1] "Remove cluster labels:" "TM7SF3 MUTATED"        
clus
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
D1126V10, continuous
[1] "Remove cluster labels:" "TM7SF3 MUTATED"        
clus
  TM7SF3 MUTATED TM7SF3 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-Z6-AAPN 
"TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" "TM7SF3 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM7SF3 MUTATED       0                         1
  TM7SF3 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM7SF3 MUTATED                                           0     4
  TM7SF3 WILD-TYPE                                         1   353
D1126V11, multiclass
                                           clus
vv                                          TM7SF3 MUTATED TM7SF3 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V12, binary
                  cls
clus                 0   1
  TM7SF3 MUTATED     1   3
  TM7SF3 WILD-TYPE   9 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF3 MUTATED      1    3
  TM7SF3 WILD-TYPE    9  395
                        clus
vv                       TM7SF3 MUTATED TM7SF3 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(1127) Variable = TTK MUTATION ANALYSIS
D1127V1, survival
               sevent
clus2             0   1
  TTK MUTATED    14   7
  TTK WILD-TYPE 324 209
  TTK MUTATED TTK WILD-TYPE 
           21           533 
  TTK MUTATED TTK WILD-TYPE 
            7           209 
$`TTK MUTATED`
TCGA-L5-A4OI TCGA-CG-5727 TCGA-L5-A8NS TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO 
       19.99        79.07        13.41        16.44         8.98        25.81 
TCGA-VR-A8EQ TCGA-ZR-A9CJ TCGA-BR-4256 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8680 
       22.82        19.73         9.34        29.56        29.59        31.96 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6822 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-F1-6874 
        6.58         6.02        12.33         5.92        11.44        14.47 
TCGA-F1-A448 TCGA-HU-8602 TCGA-R5-A805 
       21.27        22.32         9.24 

$`TTK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO 
        5.16        20.02        47.05        21.99        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         6.08         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  TTK MUTATED TTK WILD-TYPE 
         5.92          0.00 
  TTK MUTATED TTK WILD-TYPE 
        79.07        122.30 
  TTK MUTATED TTK WILD-TYPE 
        16.44         13.51 
[1] "5.9 - 79.1 (16.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1127V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTK MUTATED         1        0        3        1         2         4
  TTK WILD-TYPE       9       20       43       30        82        79
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTK MUTATED           1          0          4          2        2         0
  TTK WILD-TYPE        28         84         58         37       41         4
D1127V3, multiclass
            clus
vv           TTK MUTATED TTK WILD-TYPE
  STAGE I              1             9
  STAGE IA             0            20
  STAGE IB             3            43
  STAGE II             1            30
  STAGE IIA            2            82
  STAGE IIB            4            79
  STAGE III            1            28
  STAGE IIIA           0            84
  STAGE IIIB           4            58
  STAGE IIIC           2            37
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  TTK MUTATED       2   2  11   5
  TTK WILD-TYPE    52 133 250  97
D1127V4, multiclass
       clus
vv      TTK MUTATED TTK WILD-TYPE
  T0+T1           2            52
  T2              2           133
  T3             11           250
  T4              5            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  TTK MUTATED    10   5   2   4
  TTK WILD-TYPE 185 168  87  81
D1127V5, multiclass
    clus
vv   TTK MUTATED TTK WILD-TYPE
  N0          10           185
  N1           5           168
  N2           2            87
  N3           4            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V6, binary
               cls
clus              0   1
  TTK MUTATED    17   1
  TTK WILD-TYPE 465  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED     17    1
  TTK WILD-TYPE  465   37
   clus
vv  TTK MUTATED TTK WILD-TYPE
  0          17           465
  1           1            37
[1] 2 2
[1] FALSE
D1127V7, binary
               cls
clus              0   1
  TTK MUTATED     4  18
  TTK WILD-TYPE 168 388
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      4   18
  TTK WILD-TYPE  168  388
        clus
vv       TTK MUTATED TTK WILD-TYPE
  FEMALE           4           168
  MALE            18           388
[1] 2 2
[1] FALSE
D1127V8, binary
               cls
clus              0   1
  TTK MUTATED    15   5
  TTK WILD-TYPE 401  97
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED     15    5
  TTK WILD-TYPE  401   97
     clus
vv    TTK MUTATED TTK WILD-TYPE
  NO           15           401
  YES           5            97
[1] 2 2
[1] FALSE
D1127V9, continuous
D1127V10, continuous
[1] "Remove cluster labels:" "TTK MUTATED"           
clus
  TTK MUTATED TTK WILD-TYPE 
            2            96 
   TCGA-IC-A6RF    TCGA-L5-A43I    TCGA-L5-A43J    TCGA-L5-A4OE    TCGA-L5-A4OG 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-L5-A88T    TCGA-L5-A88Y    TCGA-L5-A8NG    TCGA-L5-A8NT    TCGA-Q9-A6FU 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-IC-A6RE    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YC 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-IG-A4P3    TCGA-IG-A4QT    TCGA-IG-A50L    TCGA-IG-A5B8    TCGA-IG-A6QS 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-IG-A8O2    TCGA-IG-A97H    TCGA-JY-A6FA    TCGA-JY-A6FE    TCGA-JY-A6FG 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-JY-A6FH    TCGA-KH-A6WC    TCGA-L5-A43C    TCGA-L5-A43E    TCGA-L5-A43H 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-L5-A4OH    TCGA-L5-A4OM    TCGA-L5-A4ON    TCGA-L5-A4OO    TCGA-L5-A4OP 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-L5-A4OQ    TCGA-L5-A4OT    TCGA-L5-A4OU    TCGA-L5-A4OW    TCGA-L5-A4OX 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-L5-A88S    TCGA-L5-A88V    TCGA-L5-A893    TCGA-L5-A8NE    TCGA-L5-A8NF 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-L5-A8NK    TCGA-L5-A8NN    TCGA-L5-A8NQ    TCGA-L5-A8NR    TCGA-L5-A8NW 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-LN-A49O    TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-LN-A49V    TCGA-LN-A49W    TCGA-LN-A4A3    TCGA-LN-A4A6    TCGA-LN-A4A9 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-LN-A5U6    TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-LN-A8HZ    TCGA-LN-A8I0    TCGA-M9-A5M8    TCGA-Q9-A6FW 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-R6-A6DN    TCGA-R6-A6L4    TCGA-R6-A6XQ    TCGA-R6-A6Y2    TCGA-R6-A8W5 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-R6-A8W8    TCGA-R6-A8WC    TCGA-RE-A7BO    TCGA-V5-A7RB    TCGA-V5-A7RC 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-V5-AASV    TCGA-VR-A8EP    TCGA-VR-A8ER    TCGA-VR-A8EU    TCGA-VR-A8EW 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-VR-A8EX    TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4G    TCGA-VR-AA7D 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-VR-AA7I    TCGA-X8-AAAR    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" "TTK WILD-TYPE" 
   TCGA-Z6-AAPN 
"TTK WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  TTK MUTATED       3                         1
  TTK WILD-TYPE   130                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TTK MUTATED                                           0    16
  TTK WILD-TYPE                                         1   341
D1127V11, multiclass
                                           clus
vv                                          TTK MUTATED TTK WILD-TYPE
  ASIAN                                               3           130
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              16           341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V12, binary
               cls
clus              0   1
  TTK MUTATED     1  15
  TTK WILD-TYPE   9 383
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      1   15
  TTK WILD-TYPE    9  383
                        clus
vv                       TTK MUTATED TTK WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          15           383
[1] 2 2
[1] FALSE

Clustering(1128) Variable = SLFN13 MUTATION ANALYSIS
D1128V1, survival
                  sevent
clus2                0   1
  SLFN13 MUTATED     6   1
  SLFN13 WILD-TYPE 332 215
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               7              547 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               1              215 
$`SLFN13 MUTATED`
TCGA-L5-A4OI TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8589 TCGA-CG-5721 
       19.99        34.68        29.59         6.18        27.12         6.02 
TCGA-VQ-A8PM 
        1.87 

$`SLFN13 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19        17.85        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SLFN13 MUTATED SLFN13 WILD-TYPE 
            1.87             0.00 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
           34.68           122.30 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
           19.99            13.55 
[1] "1.9 - 34.7 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.8"
D1128V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLFN13 MUTATED         1        0        1        0         2         1
  SLFN13 WILD-TYPE       9       20       45       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN13 MUTATED           0          0          1          1        2
  SLFN13 WILD-TYPE        29         84         61         38       41
                  vv
clus               STAGE IVA
  SLFN13 MUTATED           0
  SLFN13 WILD-TYPE         4
D1128V3, multiclass
            clus
vv           SLFN13 MUTATED SLFN13 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SLFN13 MUTATED       1   1   3   4
  SLFN13 WILD-TYPE    53 134 258  98
D1128V4, multiclass
       clus
vv      SLFN13 MUTATED SLFN13 WILD-TYPE
  T0+T1              1               53
  T2                 1              134
  T3                 3              258
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SLFN13 MUTATED     4   4   0   2
  SLFN13 WILD-TYPE 191 169  89  83
D1128V5, multiclass
    clus
vv   SLFN13 MUTATED SLFN13 WILD-TYPE
  N0              4              191
  N1              4              169
  N2              0               89
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V6, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     8   0
  SLFN13 WILD-TYPE 474  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      8    0
  SLFN13 WILD-TYPE  474   38
   clus
vv  SLFN13 MUTATED SLFN13 WILD-TYPE
  0              8              474
  1              0               38
[1] 2 2
[1] FALSE
D1128V7, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     3   7
  SLFN13 WILD-TYPE 169 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      3    7
  SLFN13 WILD-TYPE  169  399
        clus
vv       SLFN13 MUTATED SLFN13 WILD-TYPE
  FEMALE              3              169
  MALE                7              399
[1] 2 2
[1] FALSE
D1128V8, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     8   0
  SLFN13 WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      8    0
  SLFN13 WILD-TYPE  408  102
     clus
vv    SLFN13 MUTATED SLFN13 WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D1128V9, continuous
D1128V10, continuous
[1] "Remove cluster labels:" "SLFN13 MUTATED"        
clus
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" "SLFN13 WILD-TYPE" 
      TCGA-Z6-AAPN 
"SLFN13 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SLFN13 MUTATED       0                         1
  SLFN13 WILD-TYPE   133                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLFN13 MUTATED                                           0     7
  SLFN13 WILD-TYPE                                         1   350
D1128V11, multiclass
                                           clus
vv                                          SLFN13 MUTATED SLFN13 WILD-TYPE
  ASIAN                                                  0              133
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V12, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     0   6
  SLFN13 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      0    6
  SLFN13 WILD-TYPE   10  392
                        clus
vv                       SLFN13 MUTATED SLFN13 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(1129) Variable = RBBP8 MUTATION ANALYSIS
D1129V1, survival
                 sevent
clus2               0   1
  RBBP8 MUTATED     6   2
  RBBP8 WILD-TYPE 332 214
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              8             546 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              2             214 
$`RBBP8 MUTATED`
TCGA-L5-A4OI TCGA-IG-A3YA TCGA-L5-A4OJ TCGA-BR-4256 TCGA-BR-8059 TCGA-BR-8078 
       19.99        20.78        21.01         9.34        14.43        29.59 
TCGA-BR-8589 TCGA-CG-4305 
       27.12        15.95 

$`RBBP8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       35.21         0.85         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RBBP8 MUTATED RBBP8 WILD-TYPE 
           9.34            0.00 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
          29.59          122.30 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
         20.385          13.495 
[1] "9.3 - 29.6 (20.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D1129V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBBP8 MUTATED         1        0        0        1         0         1
  RBBP8 WILD-TYPE       9       20       46       30        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBBP8 MUTATED           1          1          1          1        0         0
  RBBP8 WILD-TYPE        28         83         61         38       43         4
D1129V3, multiclass
            clus
vv           RBBP8 MUTATED RBBP8 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RBBP8 MUTATED       1   1   1   4
  RBBP8 WILD-TYPE    53 134 260  98
D1129V4, multiclass
       clus
vv      RBBP8 MUTATED RBBP8 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                1             260
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RBBP8 MUTATED     3   4   0   1
  RBBP8 WILD-TYPE 192 169  89  84
D1129V5, multiclass
    clus
vv   RBBP8 MUTATED RBBP8 WILD-TYPE
  N0             3             192
  N1             4             169
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V6, binary
                 cls
clus                0   1
  RBBP8 MUTATED     7   0
  RBBP8 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      7    0
  RBBP8 WILD-TYPE  475   38
   clus
vv  RBBP8 MUTATED RBBP8 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D1129V7, binary
                 cls
clus                0   1
  RBBP8 MUTATED     2   6
  RBBP8 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      2    6
  RBBP8 WILD-TYPE  170  400
        clus
vv       RBBP8 MUTATED RBBP8 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D1129V8, binary
                 cls
clus                0   1
  RBBP8 MUTATED     8   0
  RBBP8 WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      8    0
  RBBP8 WILD-TYPE  408  102
     clus
vv    RBBP8 MUTATED RBBP8 WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D1129V9, continuous
[1] "Remove cluster labels:" "RBBP8 MUTATED"         
clus
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YB 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
D1129V10, continuous
[1] "Remove cluster labels:" "RBBP8 MUTATED"         
clus
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QT 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS      TCGA-IG-A8O2 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE      TCGA-JY-A6FG 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C      TCGA-L5-A43E 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM      TCGA-L5-A4ON 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OT 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX      TCGA-L5-A88S 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RBBP8 MUTATED       0                         0
  RBBP8 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBBP8 MUTATED                                           0     7
  RBBP8 WILD-TYPE                                         1   350
D1129V11, multiclass
                                           clus
vv                                          RBBP8 MUTATED RBBP8 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V12, binary
                 cls
clus                0   1
  RBBP8 MUTATED     0   5
  RBBP8 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      0    5
  RBBP8 WILD-TYPE   10  393
                        clus
vv                       RBBP8 MUTATED RBBP8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1130) Variable = SPANXC MUTATION ANALYSIS
D1130V1, survival
                  sevent
clus2                0   1
  SPANXC MUTATED     6   3
  SPANXC WILD-TYPE 332 213
  SPANXC MUTATED SPANXC WILD-TYPE 
               9              545 
  SPANXC MUTATED SPANXC WILD-TYPE 
               3              213 
$`SPANXC MUTATED`
TCGA-V5-A7RB TCGA-VR-A8EX TCGA-VR-AA7B TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-4436 
        5.29        28.11        11.24        29.59         6.58         7.99 
TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4H3 
       30.51        29.98        29.00 

$`SPANXC WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SPANXC MUTATED SPANXC WILD-TYPE 
            5.29             0.00 
  SPANXC MUTATED SPANXC WILD-TYPE 
           30.51           122.30 
  SPANXC MUTATED SPANXC WILD-TYPE 
           28.11            13.55 
[1] "5.3 - 30.5 (28.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1130V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPANXC MUTATED         0        0        2        0         2         1
  SPANXC WILD-TYPE      10       20       44       31        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXC MUTATED           0          0          0          2        1
  SPANXC WILD-TYPE        29         84         62         37       42
                  vv
clus               STAGE IVA
  SPANXC MUTATED           1
  SPANXC WILD-TYPE         3
D1130V3, multiclass
            clus
vv           SPANXC MUTATED SPANXC WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SPANXC MUTATED       3   3   2   3
  SPANXC WILD-TYPE    51 132 259  99
D1130V4, multiclass
       clus
vv      SPANXC MUTATED SPANXC WILD-TYPE
  T0+T1              3               51
  T2                 3              132
  T3                 2              259
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SPANXC MUTATED     4   3   0   3
  SPANXC WILD-TYPE 191 170  89  82
D1130V5, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  N0              4              191
  N1              3              170
  N2              0               89
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V6, binary
                  cls
clus                 0   1
  SPANXC MUTATED     8   2
  SPANXC WILD-TYPE 474  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      8    2
  SPANXC WILD-TYPE  474   36
   clus
vv  SPANXC MUTATED SPANXC WILD-TYPE
  0              8              474
  1              2               36
[1] 2 2
[1] FALSE
D1130V7, binary
                  cls
clus                 0   1
  SPANXC MUTATED     5   6
  SPANXC WILD-TYPE 167 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      5    6
  SPANXC WILD-TYPE  167  400
        clus
vv       SPANXC MUTATED SPANXC WILD-TYPE
  FEMALE              5              167
  MALE                6              400
[1] 2 2
[1] FALSE
D1130V8, binary
                  cls
clus                 0   1
  SPANXC MUTATED     7   1
  SPANXC WILD-TYPE 409 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      7    1
  SPANXC WILD-TYPE  409  101
     clus
vv    SPANXC MUTATED SPANXC WILD-TYPE
  NO               7              409
  YES              1              101
[1] 2 2
[1] FALSE
D1130V9, continuous
D1130V10, continuous
[1] "Remove cluster labels:" "SPANXC MUTATED"        
clus
  SPANXC MUTATED SPANXC WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" "SPANXC WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPANXC MUTATED       3                         0
  SPANXC WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPANXC MUTATED                                           0     3
  SPANXC WILD-TYPE                                         1   354
D1130V11, multiclass
                                           clus
vv                                          SPANXC MUTATED SPANXC WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V12, binary
                  cls
clus                 0   1
  SPANXC MUTATED     1   5
  SPANXC WILD-TYPE   9 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      1    5
  SPANXC WILD-TYPE    9  393
                        clus
vv                       SPANXC MUTATED SPANXC WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1131) Variable = MSL3 MUTATION ANALYSIS
D1131V1, survival
                sevent
clus2              0   1
  MSL3 MUTATED     6   3
  MSL3 WILD-TYPE 332 213
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            545 
  MSL3 MUTATED MSL3 WILD-TYPE 
             3            213 
$`MSL3 MUTATED`
TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5721 
       18.15        32.25         1.12        31.96        13.18         6.02 
TCGA-D7-6522 TCGA-F1-6874 TCGA-HJ-7597 
       18.61        14.47        26.47 

$`MSL3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59         9.60         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MSL3 MUTATED MSL3 WILD-TYPE 
          1.12           0.00 
  MSL3 MUTATED MSL3 WILD-TYPE 
         32.25         122.30 
  MSL3 MUTATED MSL3 WILD-TYPE 
         18.15          13.51 
[1] "1.1 - 32.2 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1131V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MSL3 MUTATED         0        0        3        0         1         1
  MSL3 WILD-TYPE      10       20       43       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSL3 MUTATED           0          1          0          0        3         0
  MSL3 WILD-TYPE        29         83         62         39       40         4
D1131V3, multiclass
            clus
vv           MSL3 MUTATED MSL3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              3             43
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              3             40
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  MSL3 MUTATED       0   3   2   4
  MSL3 WILD-TYPE    54 132 259  98
D1131V4, multiclass
       clus
vv      MSL3 MUTATED MSL3 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               2            259
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  MSL3 MUTATED     5   3   1   0
  MSL3 WILD-TYPE 190 170  88  85
D1131V5, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  N0            5            190
  N1            3            170
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V6, binary
                cls
clus               0   1
  MSL3 MUTATED     7   1
  MSL3 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      7    1
  MSL3 WILD-TYPE  475   37
   clus
vv  MSL3 MUTATED MSL3 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D1131V7, binary
                cls
clus               0   1
  MSL3 MUTATED     3   6
  MSL3 WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      3    6
  MSL3 WILD-TYPE  169  400
        clus
vv       MSL3 MUTATED MSL3 WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D1131V8, binary
                cls
clus               0   1
  MSL3 MUTATED     9   0
  MSL3 WILD-TYPE 407 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      9    0
  MSL3 WILD-TYPE  407  102
     clus
vv    MSL3 MUTATED MSL3 WILD-TYPE
  NO             9            407
  YES            0            102
[1] 2 2
[1] FALSE
D1131V9, continuous
D1131V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MSL3 MUTATED       2                         0
  MSL3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSL3 MUTATED                                           0     6
  MSL3 WILD-TYPE                                         1   351
D1131V11, multiclass
                                           clus
vv                                          MSL3 MUTATED MSL3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V12, binary
                cls
clus               0   1
  MSL3 MUTATED     0   8
  MSL3 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      0    8
  MSL3 WILD-TYPE   10  390
                        clus
vv                       MSL3 MUTATED MSL3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(1132) Variable = EGLN1 MUTATION ANALYSIS
D1132V1, survival
                 sevent
clus2               0   1
  EGLN1 MUTATED     4   1
  EGLN1 WILD-TYPE 334 215
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              5             549 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              1             215 
$`EGLN1 MUTATED`
TCGA-XP-A8T7 TCGA-BR-6452 TCGA-BR-8297 TCGA-BR-8487 TCGA-D7-A4YV 
       41.23        34.68         7.40         1.12         5.92 

$`EGLN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  EGLN1 MUTATED EGLN1 WILD-TYPE 
           1.12            0.00 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
          41.23          122.30 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
           7.40           13.58 
[1] "1.1 - 41.2 (7.4)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1132V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EGLN1 MUTATED         0        0        0        0         3         1
  EGLN1 WILD-TYPE      10       20       46       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGLN1 MUTATED           0          0          0          1        1         0
  EGLN1 WILD-TYPE        29         84         62         38       42         4
D1132V3, multiclass
            clus
vv           EGLN1 MUTATED EGLN1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EGLN1 MUTATED       0   1   3   2
  EGLN1 WILD-TYPE    54 134 258 100
D1132V4, multiclass
       clus
vv      EGLN1 MUTATED EGLN1 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EGLN1 MUTATED     3   1   1   1
  EGLN1 WILD-TYPE 192 172  88  84
D1132V5, multiclass
    clus
vv   EGLN1 MUTATED EGLN1 WILD-TYPE
  N0             3             192
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V6, binary
                 cls
clus                0   1
  EGLN1 MUTATED     6   0
  EGLN1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      6    0
  EGLN1 WILD-TYPE  476   38
   clus
vv  EGLN1 MUTATED EGLN1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1132V7, binary
                 cls
clus                0   1
  EGLN1 MUTATED     5   1
  EGLN1 WILD-TYPE 167 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      5    1
  EGLN1 WILD-TYPE  167  405
        clus
vv       EGLN1 MUTATED EGLN1 WILD-TYPE
  FEMALE             5             167
  MALE               1             405
[1] 2 2
[1] FALSE
D1132V8, binary
                 cls
clus                0   1
  EGLN1 MUTATED     5   0
  EGLN1 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      5    0
  EGLN1 WILD-TYPE  411  102
     clus
vv    EGLN1 MUTATED EGLN1 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D1132V9, continuous
[1] "Remove cluster labels:" "EGLN1 MUTATED"         
clus
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-AA7B      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
D1132V10, continuous
[1] "Remove cluster labels:" "EGLN1 MUTATED"         
clus
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T8 
"EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" "EGLN1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"EGLN1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EGLN1 MUTATED       0                         0
  EGLN1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EGLN1 MUTATED                                           0     6
  EGLN1 WILD-TYPE                                         1   351
D1132V11, multiclass
                                           clus
vv                                          EGLN1 MUTATED EGLN1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V12, binary
                 cls
clus                0   1
  EGLN1 MUTATED     1   5
  EGLN1 WILD-TYPE   9 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      1    5
  EGLN1 WILD-TYPE    9  393
                        clus
vv                       EGLN1 MUTATED EGLN1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1133) Variable = ARNT MUTATION ANALYSIS
D1133V1, survival
                sevent
clus2              0   1
  ARNT MUTATED     5   2
  ARNT WILD-TYPE 333 214
  ARNT MUTATED ARNT WILD-TYPE 
             7            547 
  ARNT MUTATED ARNT WILD-TYPE 
             2            214 
$`ARNT MUTATED`
TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-A487 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-R5-A7ZI 
       31.27        31.96        12.30         6.58         5.92        74.53 
TCGA-VQ-A8P2 
       38.14 

$`ARNT WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        6.31        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ARNT MUTATED ARNT WILD-TYPE 
          5.92           0.00 
  ARNT MUTATED ARNT WILD-TYPE 
         74.53         122.30 
  ARNT MUTATED ARNT WILD-TYPE 
         31.27          13.55 
[1] "5.9 - 74.5 (31.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D1133V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARNT MUTATED         0        0        1        0         1         2
  ARNT WILD-TYPE      10       20       45       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARNT MUTATED           0          1          0          1        2         0
  ARNT WILD-TYPE        29         83         62         38       41         4
D1133V3, multiclass
            clus
vv           ARNT MUTATED ARNT WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ARNT MUTATED       0   1   3   4
  ARNT WILD-TYPE    54 134 258  98
D1133V4, multiclass
       clus
vv      ARNT MUTATED ARNT WILD-TYPE
  T0+T1            0             54
  T2               1            134
  T3               3            258
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ARNT MUTATED     2   4   1   1
  ARNT WILD-TYPE 193 169  88  84
D1133V5, multiclass
    clus
vv   ARNT MUTATED ARNT WILD-TYPE
  N0            2            193
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V6, binary
                cls
clus               0   1
  ARNT MUTATED     6   2
  ARNT WILD-TYPE 476  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      6    2
  ARNT WILD-TYPE  476   36
   clus
vv  ARNT MUTATED ARNT WILD-TYPE
  0            6            476
  1            2             36
[1] 2 2
[1] FALSE
D1133V7, binary
                cls
clus               0   1
  ARNT MUTATED     2   6
  ARNT WILD-TYPE 170 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      2    6
  ARNT WILD-TYPE  170  400
        clus
vv       ARNT MUTATED ARNT WILD-TYPE
  FEMALE            2            170
  MALE              6            400
[1] 2 2
[1] FALSE
D1133V8, binary
                cls
clus               0   1
  ARNT MUTATED     6   1
  ARNT WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      6    1
  ARNT WILD-TYPE  410  101
     clus
vv    ARNT MUTATED ARNT WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D1133V9, continuous
D1133V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARNT MUTATED       3                         0
  ARNT WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARNT MUTATED                                           0     4
  ARNT WILD-TYPE                                         1   353
D1133V11, multiclass
                                           clus
vv                                          ARNT MUTATED ARNT WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V12, binary
                cls
clus               0   1
  ARNT MUTATED     1   5
  ARNT WILD-TYPE   9 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      1    5
  ARNT WILD-TYPE    9  393
                        clus
vv                       ARNT MUTATED ARNT WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1134) Variable = SCN9A MUTATION ANALYSIS
D1134V1, survival
                 sevent
clus2               0   1
  SCN9A MUTATED    25  15
  SCN9A WILD-TYPE 313 201
  SCN9A MUTATED SCN9A WILD-TYPE 
             40             514 
  SCN9A MUTATED SCN9A WILD-TYPE 
             15             201 
$`SCN9A MUTATED`
TCGA-S8-A6BV TCGA-CG-4460 TCGA-2H-A9GR TCGA-IG-A4QS TCGA-L5-A4OT TCGA-L5-A891 
       20.02        21.99        32.45         3.88         4.90         3.75 
TCGA-L5-A893 TCGA-L5-A8NM TCGA-L5-A8NN TCGA-R6-A6XQ TCGA-RE-A7BO TCGA-BR-4184 
        3.02         7.76         5.49         6.35         7.00         6.97 
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8373 
       34.68         6.18        31.10         4.31        31.27        14.79 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-CD-8527 
        9.21         1.12        31.96        28.34        32.52         7.17 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-6525 
       15.95         6.02        28.96        65.10        69.04        13.35 
TCGA-D7-6527 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4H3 
       10.26        11.08         6.21        24.26        11.77        29.00 
TCGA-HU-A4H4 TCGA-IP-7968 TCGA-R5-A7ZE TCGA-RD-A7BT 
       23.84         2.53        18.21         8.61 

$`SCN9A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       27.12         5.16        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
        7.43        15.48         2.60        25.12         7.40        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98         0.72        14.17         0.53         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       12.10        12.39        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SCN9A MUTATED SCN9A WILD-TYPE 
           1.12            0.00 
  SCN9A MUTATED SCN9A WILD-TYPE 
          69.04          122.30 
  SCN9A MUTATED SCN9A WILD-TYPE 
         11.425          13.730 
[1] "1.1 - 69.0 (11.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D1134V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCN9A MUTATED         1        3        2        3         5         5
  SCN9A WILD-TYPE       9       17       44       28        79        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN9A MUTATED           1          7          2          5        6         0
  SCN9A WILD-TYPE        28         77         60         34       37         4
D1134V3, multiclass
            clus
vv           SCN9A MUTATED SCN9A WILD-TYPE
  STAGE I                1               9
  STAGE IA               3              17
  STAGE IB               2              44
  STAGE II               3              28
  STAGE IIA              5              79
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             7              77
  STAGE IIIB             2              60
  STAGE IIIC             5              34
  STAGE IV               6              37
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SCN9A MUTATED       6   9  14  13
  SCN9A WILD-TYPE    48 126 247  89
D1134V4, multiclass
       clus
vv      SCN9A MUTATED SCN9A WILD-TYPE
  T0+T1             6              48
  T2                9             126
  T3               14             247
  T4               13              89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SCN9A MUTATED    13  15   7   6
  SCN9A WILD-TYPE 182 158  82  79
D1134V5, multiclass
    clus
vv   SCN9A MUTATED SCN9A WILD-TYPE
  N0            13             182
  N1            15             158
  N2             7              82
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V6, binary
                 cls
clus                0   1
  SCN9A MUTATED    36   3
  SCN9A WILD-TYPE 446  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED     36    3
  SCN9A WILD-TYPE  446   35
   clus
vv  SCN9A MUTATED SCN9A WILD-TYPE
  0            36             446
  1             3              35
[1] 2 2
[1] FALSE
D1134V7, binary
                 cls
clus                0   1
  SCN9A MUTATED    16  27
  SCN9A WILD-TYPE 156 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED     16   27
  SCN9A WILD-TYPE  156  379
        clus
vv       SCN9A MUTATED SCN9A WILD-TYPE
  FEMALE            16             156
  MALE              27             379
[1] 2 2
[1] FALSE
D1134V8, binary
                 cls
clus                0   1
  SCN9A MUTATED    33   3
  SCN9A WILD-TYPE 383  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED     33    3
  SCN9A WILD-TYPE  383   99
     clus
vv    SCN9A MUTATED SCN9A WILD-TYPE
  NO             33             383
  YES             3              99
[1] 2 2
[1] FALSE
D1134V9, continuous
D1134V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SCN9A MUTATED       8                         1
  SCN9A WILD-TYPE   125                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCN9A MUTATED                                           1    25
  SCN9A WILD-TYPE                                         0   332
D1134V11, multiclass
                                           clus
vv                                          SCN9A MUTATED SCN9A WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                25             332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V12, binary
                 cls
clus                0   1
  SCN9A MUTATED     0  30
  SCN9A WILD-TYPE  10 368
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN9A MUTATED      0   30
  SCN9A WILD-TYPE   10  368
                        clus
vv                       SCN9A MUTATED SCN9A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            30             368
[1] 2 2
[1] FALSE

Clustering(1135) Variable = AMHR2 MUTATION ANALYSIS
D1135V1, survival
                 sevent
clus2               0   1
  AMHR2 MUTATED     7   1
  AMHR2 WILD-TYPE 331 215
  AMHR2 MUTATED AMHR2 WILD-TYPE 
              8             546 
  AMHR2 MUTATED AMHR2 WILD-TYPE 
              1             215 
$`AMHR2 MUTATED`
TCGA-L5-A4OI TCGA-VR-A8ET TCGA-BR-6852 TCGA-BR-7707 TCGA-CG-4305 TCGA-HU-A4H3 
       19.99         1.55        44.94        35.84        15.95        29.00 
TCGA-R5-A7O7 TCGA-VQ-A8P2 
       45.67        38.14 

$`AMHR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        14.04        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  AMHR2 MUTATED AMHR2 WILD-TYPE 
           1.55            0.00 
  AMHR2 MUTATED AMHR2 WILD-TYPE 
          45.67          122.30 
  AMHR2 MUTATED AMHR2 WILD-TYPE 
         32.420          13.495 
[1] "1.6 - 45.7 (32.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.8"
D1135V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMHR2 MUTATED         1        0        1        1         2         0
  AMHR2 WILD-TYPE       9       20       45       30        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMHR2 MUTATED           0          1          0          2        1         0
  AMHR2 WILD-TYPE        29         83         62         37       42         4
D1135V3, multiclass
            clus
vv           AMHR2 MUTATED AMHR2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  AMHR2 MUTATED       1   3   3   2
  AMHR2 WILD-TYPE    53 132 258 100
D1135V4, multiclass
       clus
vv      AMHR2 MUTATED AMHR2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  AMHR2 MUTATED     3   5   0   2
  AMHR2 WILD-TYPE 192 168  89  83
D1135V5, multiclass
    clus
vv   AMHR2 MUTATED AMHR2 WILD-TYPE
  N0             3             192
  N1             5             168
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V6, binary
                 cls
clus                0   1
  AMHR2 MUTATED     7   1
  AMHR2 WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMHR2 MUTATED      7    1
  AMHR2 WILD-TYPE  475   37
   clus
vv  AMHR2 MUTATED AMHR2 WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D1135V7, binary
                 cls
clus                0   1
  AMHR2 MUTATED     4   6
  AMHR2 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMHR2 MUTATED      4    6
  AMHR2 WILD-TYPE  168  400
        clus
vv       AMHR2 MUTATED AMHR2 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D1135V8, binary
                 cls
clus                0   1
  AMHR2 MUTATED     7   1
  AMHR2 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMHR2 MUTATED      7    1
  AMHR2 WILD-TYPE  409  101
     clus
vv    AMHR2 MUTATED AMHR2 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D1135V9, continuous
[1] "Remove cluster labels:" "AMHR2 MUTATED"         
clus
  AMHR2 MUTATED AMHR2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8EU 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
D1135V10, continuous
[1] "Remove cluster labels:" "AMHR2 MUTATED"         
clus
  AMHR2 MUTATED AMHR2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" "AMHR2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"AMHR2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AMHR2 MUTATED       1                         1
  AMHR2 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMHR2 MUTATED                                           0     7
  AMHR2 WILD-TYPE                                         1   350
D1135V11, multiclass
                                           clus
vv                                          AMHR2 MUTATED AMHR2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V12, binary
                 cls
clus                0   1
  AMHR2 MUTATED     1   5
  AMHR2 WILD-TYPE   9 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMHR2 MUTATED      1    5
  AMHR2 WILD-TYPE    9  393
                        clus
vv                       AMHR2 MUTATED AMHR2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1136) Variable = BRCA1 MUTATION ANALYSIS
D1136V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED    14   4
  BRCA1 WILD-TYPE 324 212
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             18             536 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              4             212 
$`BRCA1 MUTATED`
TCGA-KH-A6WC TCGA-L5-A8NS TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6Y2 TCGA-X8-AAAR 
        6.28        13.41        12.03        12.26         9.30        18.21 
TCGA-BR-8360 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4306 
        6.18        27.12        28.14        31.96         6.58         1.02 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5728 TCGA-HU-8243 TCGA-HU-A4GN TCGA-HU-A4H3 
       29.98        19.07        65.10         5.92        29.98        29.00 

$`BRCA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
        9.21        20.22         1.12        12.79         9.34         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           1.02            0.00 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
           65.1           122.3 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         15.810          13.565 
[1] "1.0 - 65.1 (15.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D1136V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRCA1 MUTATED         0        2        2        1         4         3
  BRCA1 WILD-TYPE      10       18       44       30        80        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA1 MUTATED           0          0          1          3        2         0
  BRCA1 WILD-TYPE        29         84         61         36       41         4
D1136V3, multiclass
            clus
vv           BRCA1 MUTATED BRCA1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               2              18
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             3              36
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BRCA1 MUTATED       3   6   4   6
  BRCA1 WILD-TYPE    51 129 257  96
D1136V4, multiclass
       clus
vv      BRCA1 MUTATED BRCA1 WILD-TYPE
  T0+T1             3              51
  T2                6             129
  T3                4             257
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BRCA1 MUTATED     9   6   2   3
  BRCA1 WILD-TYPE 186 167  87  82
D1136V5, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  N0             9             186
  N1             6             167
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V6, binary
                 cls
clus                0   1
  BRCA1 MUTATED    17   2
  BRCA1 WILD-TYPE 465  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     17    2
  BRCA1 WILD-TYPE  465   36
   clus
vv  BRCA1 MUTATED BRCA1 WILD-TYPE
  0            17             465
  1             2              36
[1] 2 2
[1] FALSE
D1136V7, binary
                 cls
clus                0   1
  BRCA1 MUTATED     4  17
  BRCA1 WILD-TYPE 168 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      4   17
  BRCA1 WILD-TYPE  168  389
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  FEMALE             4             168
  MALE              17             389
[1] 2 2
[1] FALSE
D1136V8, binary
                 cls
clus                0   1
  BRCA1 MUTATED    11   4
  BRCA1 WILD-TYPE 405  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     11    4
  BRCA1 WILD-TYPE  405   98
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO             11             405
  YES             4              98
[1] 2 2
[1] FALSE
D1136V9, continuous
[1] "Remove cluster labels:" "BRCA1 MUTATED"         
clus
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" "BRCA1 WILD-TYPE" 
D1136V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRCA1 MUTATED       7                         0
  BRCA1 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRCA1 MUTATED                                           0     9
  BRCA1 WILD-TYPE                                         1   348
D1136V11, multiclass
                                           clus
vv                                          BRCA1 MUTATED BRCA1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V12, binary
                 cls
clus                0   1
  BRCA1 MUTATED     1  14
  BRCA1 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      1   14
  BRCA1 WILD-TYPE    9  384
                        clus
vv                       BRCA1 MUTATED BRCA1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(1137) Variable = AMICA1 MUTATION ANALYSIS
D1137V1, survival
                  sevent
clus2                0   1
  AMICA1 MUTATED     2   3
  AMICA1 WILD-TYPE 336 213
  AMICA1 MUTATED AMICA1 WILD-TYPE 
               5              549 
  AMICA1 MUTATED AMICA1 WILD-TYPE 
               3              213 
$`AMICA1 MUTATED`
TCGA-L5-A8NH TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-6528 
       12.92        31.96         9.01        28.96        15.22 

$`AMICA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMICA1 MUTATED AMICA1 WILD-TYPE 
            9.01             0.00 
  AMICA1 MUTATED AMICA1 WILD-TYPE 
           31.96           122.30 
  AMICA1 MUTATED AMICA1 WILD-TYPE 
           15.22            13.55 
[1] "9.0 - 32.0 (15.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1137V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMICA1 MUTATED         0        1        1        0         0         0
  AMICA1 WILD-TYPE      10       19       45       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMICA1 MUTATED           0          1          0          0        3
  AMICA1 WILD-TYPE        29         83         62         39       40
                  vv
clus               STAGE IVA
  AMICA1 MUTATED           0
  AMICA1 WILD-TYPE         4
D1137V3, multiclass
            clus
vv           AMICA1 MUTATED AMICA1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  AMICA1 MUTATED       2   1   1   3
  AMICA1 WILD-TYPE    52 134 260  99
D1137V4, multiclass
       clus
vv      AMICA1 MUTATED AMICA1 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 1              260
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  AMICA1 MUTATED     4   1   1   1
  AMICA1 WILD-TYPE 191 172  88  84
D1137V5, multiclass
    clus
vv   AMICA1 MUTATED AMICA1 WILD-TYPE
  N0              4              191
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V6, binary
                  cls
clus                 0   1
  AMICA1 MUTATED     4   3
  AMICA1 WILD-TYPE 478  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMICA1 MUTATED      4    3
  AMICA1 WILD-TYPE  478   35
   clus
vv  AMICA1 MUTATED AMICA1 WILD-TYPE
  0              4              478
  1              3               35
[1] 2 2
[1] FALSE
D1137V7, binary
                  cls
clus                 0   1
  AMICA1 MUTATED     4   4
  AMICA1 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMICA1 MUTATED      4    4
  AMICA1 WILD-TYPE  168  402
        clus
vv       AMICA1 MUTATED AMICA1 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D1137V8, binary
                  cls
clus                 0   1
  AMICA1 MUTATED     2   0
  AMICA1 WILD-TYPE 414 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMICA1 MUTATED      2    0
  AMICA1 WILD-TYPE  414  102
     clus
vv    AMICA1 MUTATED AMICA1 WILD-TYPE
  NO               2              414
  YES              0              102
[1] 2 2
[1] FALSE
D1137V9, continuous
D1137V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AMICA1 MUTATED       1                         0
  AMICA1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMICA1 MUTATED                                           0     5
  AMICA1 WILD-TYPE                                         1   352
D1137V11, multiclass
                                           clus
vv                                          AMICA1 MUTATED AMICA1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V12, binary
                  cls
clus                 0   1
  AMICA1 MUTATED     0   5
  AMICA1 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMICA1 MUTATED      0    5
  AMICA1 WILD-TYPE   10  393
                        clus
vv                       AMICA1 MUTATED AMICA1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1138) Variable = OXCT2 MUTATION ANALYSIS
D1138V1, survival
                 sevent
clus2               0   1
  OXCT2 MUTATED     5   1
  OXCT2 WILD-TYPE 333 215
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              6             548 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              1             215 
$`OXCT2 MUTATED`
TCGA-Z6-AAPN TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-A4J6 TCGA-HU-A4GN TCGA-IN-A6RS 
        2.66        35.84         0.26         0.66        29.98        12.59 

$`OXCT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53        28.34        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
       12.46        13.35        19.53         6.44         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  OXCT2 MUTATED OXCT2 WILD-TYPE 
           0.26            0.00 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
          35.84          122.30 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
          7.625          13.630 
[1] "0.3 - 35.8 (7.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1138V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OXCT2 MUTATED         0        1        2        0         3         0
  OXCT2 WILD-TYPE      10       19       44       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OXCT2 MUTATED           0          0          0          0        0         0
  OXCT2 WILD-TYPE        29         84         62         39       43         4
D1138V3, multiclass
            clus
vv           OXCT2 MUTATED OXCT2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  OXCT2 MUTATED       1   3   2   0
  OXCT2 WILD-TYPE    53 132 259 102
D1138V4, multiclass
       clus
vv      OXCT2 MUTATED OXCT2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                2             259
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  OXCT2 MUTATED     5   1   0   0
  OXCT2 WILD-TYPE 190 172  89  85
D1138V5, multiclass
    clus
vv   OXCT2 MUTATED OXCT2 WILD-TYPE
  N0             5             190
  N1             1             172
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V6, binary
                 cls
clus                0   1
  OXCT2 MUTATED     6   0
  OXCT2 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      6    0
  OXCT2 WILD-TYPE  476   38
   clus
vv  OXCT2 MUTATED OXCT2 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1138V7, binary
                 cls
clus                0   1
  OXCT2 MUTATED     3   3
  OXCT2 WILD-TYPE 169 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      3    3
  OXCT2 WILD-TYPE  169  403
        clus
vv       OXCT2 MUTATED OXCT2 WILD-TYPE
  FEMALE             3             169
  MALE               3             403
[1] 2 2
[1] FALSE
D1138V8, binary
                 cls
clus                0   1
  OXCT2 MUTATED     6   0
  OXCT2 WILD-TYPE 410 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      6    0
  OXCT2 WILD-TYPE  410  102
     clus
vv    OXCT2 MUTATED OXCT2 WILD-TYPE
  NO              6             410
  YES             0             102
[1] 2 2
[1] FALSE
D1138V9, continuous
D1138V10, continuous
[1] "Remove cluster labels:" "OXCT2 MUTATED"         
clus
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" "OXCT2 WILD-TYPE" 
     TCGA-XP-A8T8 
"OXCT2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OXCT2 MUTATED       1                         0
  OXCT2 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OXCT2 MUTATED                                           0     5
  OXCT2 WILD-TYPE                                         1   352
D1138V11, multiclass
                                           clus
vv                                          OXCT2 MUTATED OXCT2 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V12, binary
                 cls
clus                0   1
  OXCT2 MUTATED     0   6
  OXCT2 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      0    6
  OXCT2 WILD-TYPE   10  392
                        clus
vv                       OXCT2 MUTATED OXCT2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1139) Variable = WWC1 MUTATION ANALYSIS
D1139V1, survival
                sevent
clus2              0   1
  WWC1 MUTATED    11   7
  WWC1 WILD-TYPE 327 209
  WWC1 MUTATED WWC1 WILD-TYPE 
            18            536 
  WWC1 MUTATED WWC1 WILD-TYPE 
             7            209 
$`WWC1 MUTATED`
TCGA-EQ-A4SO TCGA-2H-A9GJ TCGA-KH-A6WC TCGA-L5-A88W TCGA-L5-A8NH TCGA-LN-A49Y 
       16.24        58.55         6.28        25.12        12.92        12.46 
TCGA-VR-A8EY TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7707 
       33.70         6.97         9.34        34.68        18.05        35.84 
TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-6820 TCGA-D7-A4YV 
        6.18         1.12        31.96         6.02        11.31         5.92 

$`WWC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       79.07         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  WWC1 MUTATED WWC1 WILD-TYPE 
          1.12           0.00 
  WWC1 MUTATED WWC1 WILD-TYPE 
         58.55         122.30 
  WWC1 MUTATED WWC1 WILD-TYPE 
         12.69          13.63 
[1] "1.1 - 58.5 (12.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1139V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WWC1 MUTATED         1        1        1        0         6         2
  WWC1 WILD-TYPE       9       19       45       31        78        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WWC1 MUTATED           0          3          1          0        4         0
  WWC1 WILD-TYPE        29         81         61         39       39         4
D1139V3, multiclass
            clus
vv           WWC1 MUTATED WWC1 WILD-TYPE
  STAGE I               1              9
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             6             78
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WWC1 MUTATED       3   2   9   5
  WWC1 WILD-TYPE    51 133 252  97
D1139V4, multiclass
       clus
vv      WWC1 MUTATED WWC1 WILD-TYPE
  T0+T1            3             51
  T2               2            133
  T3               9            252
  T4               5             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WWC1 MUTATED    11   7   2   0
  WWC1 WILD-TYPE 184 166  87  85
D1139V5, multiclass
    clus
vv   WWC1 MUTATED WWC1 WILD-TYPE
  N0           11            184
  N1            7            166
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V6, binary
                cls
clus               0   1
  WWC1 MUTATED    15   2
  WWC1 WILD-TYPE 467  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC1 MUTATED     15    2
  WWC1 WILD-TYPE  467   36
   clus
vv  WWC1 MUTATED WWC1 WILD-TYPE
  0           15            467
  1            2             36
[1] 2 2
[1] FALSE
D1139V7, binary
                cls
clus               0   1
  WWC1 MUTATED     7  13
  WWC1 WILD-TYPE 165 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC1 MUTATED      7   13
  WWC1 WILD-TYPE  165  393
        clus
vv       WWC1 MUTATED WWC1 WILD-TYPE
  FEMALE            7            165
  MALE             13            393
[1] 2 2
[1] FALSE
D1139V8, binary
                cls
clus               0   1
  WWC1 MUTATED    14   3
  WWC1 WILD-TYPE 402  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC1 MUTATED     14    3
  WWC1 WILD-TYPE  402   99
     clus
vv    WWC1 MUTATED WWC1 WILD-TYPE
  NO            14            402
  YES            3             99
[1] 2 2
[1] FALSE
D1139V9, continuous
D1139V10, continuous
[1] "Remove cluster labels:" "WWC1 MUTATED"          
clus
  WWC1 MUTATED WWC1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-L5-A43C 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" "WWC1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"WWC1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WWC1 MUTATED       2                         0
  WWC1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WWC1 MUTATED                                           0    16
  WWC1 WILD-TYPE                                         1   341
D1139V11, multiclass
                                           clus
vv                                          WWC1 MUTATED WWC1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V12, binary
                cls
clus               0   1
  WWC1 MUTATED     0  15
  WWC1 WILD-TYPE  10 383
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC1 MUTATED      0   15
  WWC1 WILD-TYPE   10  383
                        clus
vv                       WWC1 MUTATED WWC1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           15            383
[1] 2 2
[1] FALSE

Clustering(1140) Variable = ATF5 MUTATION ANALYSIS
D1140V1, survival
                sevent
clus2              0   1
  ATF5 MUTATED     2   1
  ATF5 WILD-TYPE 336 215
  ATF5 MUTATED ATF5 WILD-TYPE 
             3            551 
  ATF5 MUTATED ATF5 WILD-TYPE 
             1            215 
$`ATF5 MUTATED`
TCGA-CG-4460 TCGA-BR-8361 TCGA-CG-5723 
       21.99        31.10       105.07 

$`ATF5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ATF5 MUTATED ATF5 WILD-TYPE 
         21.99           0.00 
  ATF5 MUTATED ATF5 WILD-TYPE 
        105.07         122.30 
  ATF5 MUTATED ATF5 WILD-TYPE 
         31.10          13.51 
[1] "22.0 - 105.1 (31.1)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "2.7"
D1140V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATF5 MUTATED         1        0        0        1         0         0
  ATF5 WILD-TYPE       9       20       46       30        84        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATF5 MUTATED           0          1          0          1        1         0
  ATF5 WILD-TYPE        29         83         62         38       42         4
D1140V3, multiclass
            clus
vv           ATF5 MUTATED ATF5 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ATF5 MUTATED       1   1   0   3
  ATF5 WILD-TYPE    53 134 261  99
D1140V4, multiclass
       clus
vv      ATF5 MUTATED ATF5 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               0            261
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ATF5 MUTATED     1   3   1   0
  ATF5 WILD-TYPE 194 170  88  85
D1140V5, multiclass
    clus
vv   ATF5 MUTATED ATF5 WILD-TYPE
  N0            1            194
  N1            3            170
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V6, binary
                cls
clus               0   1
  ATF5 MUTATED     3   1
  ATF5 WILD-TYPE 479  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF5 MUTATED      3    1
  ATF5 WILD-TYPE  479   37
   clus
vv  ATF5 MUTATED ATF5 WILD-TYPE
  0            3            479
  1            1             37
[1] 2 2
[1] FALSE
D1140V7, binary
                cls
clus               0   1
  ATF5 MUTATED     3   2
  ATF5 WILD-TYPE 169 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF5 MUTATED      3    2
  ATF5 WILD-TYPE  169  404
        clus
vv       ATF5 MUTATED ATF5 WILD-TYPE
  FEMALE            3            169
  MALE              2            404
[1] 2 2
[1] FALSE
D1140V8, binary
                cls
clus               0   1
  ATF5 MUTATED     4   0
  ATF5 WILD-TYPE 412 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF5 MUTATED      4    0
  ATF5 WILD-TYPE  412  102
     clus
vv    ATF5 MUTATED ATF5 WILD-TYPE
  NO             4            412
  YES            0            102
[1] 2 2
[1] FALSE
D1140V9, continuous
D1140V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ATF5 MUTATED       0                         1
  ATF5 WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATF5 MUTATED                                           0     2
  ATF5 WILD-TYPE                                         1   355
D1140V11, multiclass
                                           clus
vv                                          ATF5 MUTATED ATF5 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V12, binary
                cls
clus               0   1
  ATF5 MUTATED     0   3
  ATF5 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF5 MUTATED      0    3
  ATF5 WILD-TYPE   10  395
                        clus
vv                       ATF5 MUTATED ATF5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(1141) Variable = EP300 MUTATION ANALYSIS
D1141V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    19  14
  EP300 WILD-TYPE 319 202
  EP300 MUTATED EP300 WILD-TYPE 
             33             521 
  EP300 MUTATED EP300 WILD-TYPE 
             14             202 
$`EP300 MUTATED`
TCGA-L5-A4OI TCGA-CG-4460 TCGA-EQ-A4SO TCGA-2H-A9GF TCGA-IG-A5B8 TCGA-IG-A6QS 
       19.99        21.99        16.24        25.78         0.79         9.96 
TCGA-JY-A6FD TCGA-L5-A4OH TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A9FO TCGA-R6-A6L4 
       68.02        32.61        12.33        12.59         0.13        16.31 
TCGA-R6-A6Y0 TCGA-ZR-A9CJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 
       53.95        19.73         6.97        30.90         9.34        32.78 
TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 
       44.94        31.27         7.36        25.05        28.14        31.96 
TCGA-BR-8686 TCGA-BR-A4QL TCGA-CD-A4MH TCGA-CG-4441 TCGA-CG-5721 TCGA-D7-A6EY 
       20.88        16.14        12.20        14.01         6.02        11.44 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-SW-A7EA 
       29.98         6.51        19.04 

$`EP300 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX 
        5.16        20.02        47.05        22.98        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15         9.86        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03        23.41        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        13.38        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38        13.18        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        4.64         7.43        18.35         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        32.58         9.86         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        1.02         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  EP300 MUTATED EP300 WILD-TYPE 
           0.13            0.00 
  EP300 MUTATED EP300 WILD-TYPE 
          68.02          122.30 
  EP300 MUTATED EP300 WILD-TYPE 
          19.04           13.41 
[1] "0.1 - 68.0 (19.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D1141V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EP300 MUTATED         1        0        3        0         9         2
  EP300 WILD-TYPE       9       20       43       31        75        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP300 MUTATED           1          3          4          5        3         0
  EP300 WILD-TYPE        28         81         58         34       40         4
D1141V3, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              9              75
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             4              58
  STAGE IIIC             5              34
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EP300 MUTATED       2   7  15   9
  EP300 WILD-TYPE    52 128 246  93
D1141V4, multiclass
       clus
vv      EP300 MUTATED EP300 WILD-TYPE
  T0+T1             2              52
  T2                7             128
  T3               15             246
  T4                9              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EP300 MUTATED    13  10   2   7
  EP300 WILD-TYPE 182 163  87  78
D1141V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            13             182
  N1            10             163
  N2             2              87
  N3             7              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V6, binary
                 cls
clus                0   1
  EP300 MUTATED    28   2
  EP300 WILD-TYPE 454  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     28    2
  EP300 WILD-TYPE  454   36
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            28             454
  1             2              36
[1] 2 2
[1] FALSE
D1141V7, binary
                 cls
clus                0   1
  EP300 MUTATED    13  23
  EP300 WILD-TYPE 159 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     13   23
  EP300 WILD-TYPE  159  383
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            13             159
  MALE              23             383
[1] 2 2
[1] FALSE
D1141V8, binary
                 cls
clus                0   1
  EP300 MUTATED    28   4
  EP300 WILD-TYPE 388  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     28    4
  EP300 WILD-TYPE  388   98
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             28             388
  YES             4              98
[1] 2 2
[1] FALSE
D1141V9, continuous
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49R 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49W      TCGA-LN-A49X 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2      TCGA-LN-A4A3 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6      TCGA-LN-A4A8 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR      TCGA-LN-A5U5 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ      TCGA-V5-A7RB 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 
D1141V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EP300 MUTATED       9                         0
  EP300 WILD-TYPE   124                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EP300 MUTATED                                           0    22
  EP300 WILD-TYPE                                         1   335
D1141V11, multiclass
                                           clus
vv                                          EP300 MUTATED EP300 WILD-TYPE
  ASIAN                                                 9             124
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                22             335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V12, binary
                 cls
clus                0   1
  EP300 MUTATED     0  28
  EP300 WILD-TYPE  10 370
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED      0   28
  EP300 WILD-TYPE   10  370
                        clus
vv                       EP300 MUTATED EP300 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            28             370
[1] 2 2
[1] FALSE

Clustering(1142) Variable = DLD MUTATION ANALYSIS
D1142V1, survival
               sevent
clus2             0   1
  DLD MUTATED    10   4
  DLD WILD-TYPE 328 212
  DLD MUTATED DLD WILD-TYPE 
           14           540 
  DLD MUTATED DLD WILD-TYPE 
            4           212 
$`DLD MUTATED`
TCGA-L5-A43J TCGA-KB-A93G TCGA-IC-A6RE TCGA-IG-A8O2 TCGA-LN-A8I0 TCGA-CD-A4MH 
        4.31        20.15         7.69         4.67        13.38        12.20 
TCGA-CG-5733 TCGA-D7-6526 TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-IN-A6RS TCGA-R5-A7ZI 
       21.07        17.19        30.51        23.84        12.59        74.53 
TCGA-VQ-A8E7 TCGA-VQ-A8PE 
       37.41        22.19 

$`DLD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PK 
       13.25        13.02        43.36        38.14        37.22        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  DLD MUTATED DLD WILD-TYPE 
         4.31          0.00 
  DLD MUTATED DLD WILD-TYPE 
        74.53        122.30 
  DLD MUTATED DLD WILD-TYPE 
        18.67         13.53 
[1] "4.3 - 74.5 (18.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1142V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLD MUTATED         0        1        1        0         2         3
  DLD WILD-TYPE      10       19       45       31        82        80
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DLD MUTATED           0          2          2          1        2         0
  DLD WILD-TYPE        29         82         60         38       41         4
D1142V3, multiclass
            clus
vv           DLD MUTATED DLD WILD-TYPE
  STAGE I              0            10
  STAGE IA             1            19
  STAGE IB             1            45
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            3            80
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           2            60
  STAGE IIIC           1            38
  STAGE IV             2            41
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  DLD MUTATED       2   4   6   2
  DLD WILD-TYPE    52 131 255 100
D1142V4, multiclass
       clus
vv      DLD MUTATED DLD WILD-TYPE
  T0+T1           2            52
  T2              4           131
  T3              6           255
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  DLD MUTATED     5   3   4   2
  DLD WILD-TYPE 190 170  85  83
D1142V5, multiclass
    clus
vv   DLD MUTATED DLD WILD-TYPE
  N0           5           190
  N1           3           170
  N2           4            85
  N3           2            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V6, binary
               cls
clus              0   1
  DLD MUTATED    11   2
  DLD WILD-TYPE 471  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  DLD MUTATED     11    2
  DLD WILD-TYPE  471   36
   clus
vv  DLD MUTATED DLD WILD-TYPE
  0          11           471
  1           2            36
[1] 2 2
[1] FALSE
D1142V7, binary
               cls
clus              0   1
  DLD MUTATED     6   8
  DLD WILD-TYPE 166 398
[1] "tbl2"
               cls
clus            [,1] [,2]
  DLD MUTATED      6    8
  DLD WILD-TYPE  166  398
        clus
vv       DLD MUTATED DLD WILD-TYPE
  FEMALE           6           166
  MALE             8           398
[1] 2 2
[1] FALSE
D1142V8, binary
               cls
clus              0   1
  DLD MUTATED    10   2
  DLD WILD-TYPE 406 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  DLD MUTATED     10    2
  DLD WILD-TYPE  406  100
     clus
vv    DLD MUTATED DLD WILD-TYPE
  NO           10           406
  YES           2           100
[1] 2 2
[1] FALSE
D1142V9, continuous
D1142V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DLD MUTATED       4                         0
  DLD WILD-TYPE   129                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLD MUTATED                                           0     8
  DLD WILD-TYPE                                         1   349
D1142V11, multiclass
                                           clus
vv                                          DLD MUTATED DLD WILD-TYPE
  ASIAN                                               4           129
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               8           349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V12, binary
               cls
clus              0   1
  DLD MUTATED     1   7
  DLD WILD-TYPE   9 391
[1] "tbl2"
               cls
clus            [,1] [,2]
  DLD MUTATED      1    7
  DLD WILD-TYPE    9  391
                        clus
vv                       DLD MUTATED DLD WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO           7           391
[1] 2 2
[1] FALSE

Clustering(1143) Variable = BIRC3 MUTATION ANALYSIS
D1143V1, survival
                 sevent
clus2               0   1
  BIRC3 MUTATED     4   7
  BIRC3 WILD-TYPE 334 209
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             11             543 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
              7             209 
$`BIRC3 MUTATED`
TCGA-CG-4460 TCGA-JY-A6FG TCGA-L5-A8NQ TCGA-BR-6455 TCGA-BR-8363 TCGA-BR-8487 
       21.99        41.52        21.37        13.87         0.26         1.12 
TCGA-CD-A489 TCGA-CG-5722 TCGA-HF-7132 TCGA-VQ-A8DU TCGA-VQ-A8P2 
       11.31         0.99        77.29         5.46        38.14 

$`BIRC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BIRC3 MUTATED BIRC3 WILD-TYPE 
           0.26            0.00 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          77.29          122.30 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          13.87           13.55 
[1] "0.3 - 77.3 (13.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1143V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BIRC3 MUTATED         0        0        1        1         3         1
  BIRC3 WILD-TYPE      10       20       45       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIRC3 MUTATED           1          2          0          0        2         0
  BIRC3 WILD-TYPE        28         82         62         39       41         4
D1143V3, multiclass
            clus
vv           BIRC3 MUTATED BIRC3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BIRC3 MUTATED       0   3   6   2
  BIRC3 WILD-TYPE    54 132 255 100
D1143V4, multiclass
       clus
vv      BIRC3 MUTATED BIRC3 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BIRC3 MUTATED     4   6   2   0
  BIRC3 WILD-TYPE 191 167  87  85
D1143V5, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  N0             4             191
  N1             6             167
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V6, binary
                 cls
clus                0   1
  BIRC3 MUTATED    10   2
  BIRC3 WILD-TYPE 472  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED     10    2
  BIRC3 WILD-TYPE  472   36
   clus
vv  BIRC3 MUTATED BIRC3 WILD-TYPE
  0            10             472
  1             2              36
[1] 2 2
[1] FALSE
D1143V7, binary
                 cls
clus                0   1
  BIRC3 MUTATED     5   7
  BIRC3 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      5    7
  BIRC3 WILD-TYPE  167  399
        clus
vv       BIRC3 MUTATED BIRC3 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D1143V8, binary
                 cls
clus                0   1
  BIRC3 MUTATED     8   2
  BIRC3 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      8    2
  BIRC3 WILD-TYPE  408  100
     clus
vv    BIRC3 MUTATED BIRC3 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D1143V9, continuous
D1143V10, continuous
[1] "Remove cluster labels:" "BIRC3 MUTATED"         
clus
  BIRC3 MUTATED BIRC3 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NR 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" "BIRC3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BIRC3 MUTATED       1                         0
  BIRC3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BIRC3 MUTATED                                           0     8
  BIRC3 WILD-TYPE                                         1   349
D1143V11, multiclass
                                           clus
vv                                          BIRC3 MUTATED BIRC3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V12, binary
                 cls
clus                0   1
  BIRC3 MUTATED     0   5
  BIRC3 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      0    5
  BIRC3 WILD-TYPE   10  393
                        clus
vv                       BIRC3 MUTATED BIRC3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1144) Variable = NOS1 MUTATION ANALYSIS
D1144V1, survival
                sevent
clus2              0   1
  NOS1 MUTATED    22  11
  NOS1 WILD-TYPE 316 205
  NOS1 MUTATED NOS1 WILD-TYPE 
            33            521 
  NOS1 MUTATED NOS1 WILD-TYPE 
            11            205 
$`NOS1 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NM TCGA-R6-A6DN TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EW 
       21.99         7.76         8.02        16.44        25.81         8.12 
TCGA-VR-AA7B TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8361 
       11.24        11.01         6.97        30.90        29.59        31.10 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8683 
       31.27         1.12        27.12        28.14        31.96         9.86 
TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-5577 TCGA-D7-8576 
        0.53        16.14         6.02       105.07        25.71        14.66 
TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H8 
       11.44        22.32        24.20        11.77         6.58        14.07 
TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
       74.53        19.04        38.14 

$`NOS1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       33.21        37.25        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        9.21        20.22        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  NOS1 MUTATED NOS1 WILD-TYPE 
          0.53           0.00 
  NOS1 MUTATED NOS1 WILD-TYPE 
        105.07         122.30 
  NOS1 MUTATED NOS1 WILD-TYPE 
         16.44          13.48 
[1] "0.5 - 105.1 (16.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1144V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOS1 MUTATED         0        2        4        1         2         5
  NOS1 WILD-TYPE      10       18       42       30        82        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOS1 MUTATED           0          4          7          3        6         0
  NOS1 WILD-TYPE        29         80         55         36       37         4
D1144V3, multiclass
            clus
vv           NOS1 MUTATED NOS1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             5             78
  STAGE III             0             29
  STAGE IIIA            4             80
  STAGE IIIB            7             55
  STAGE IIIC            3             36
  STAGE IV              6             37
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  NOS1 MUTATED       5   6   9  16
  NOS1 WILD-TYPE    49 129 252  86
D1144V4, multiclass
       clus
vv      NOS1 MUTATED NOS1 WILD-TYPE
  T0+T1            5             49
  T2               6            129
  T3               9            252
  T4              16             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  NOS1 MUTATED    10  10   6   7
  NOS1 WILD-TYPE 185 163  83  78
D1144V5, multiclass
    clus
vv   NOS1 MUTATED NOS1 WILD-TYPE
  N0           10            185
  N1           10            163
  N2            6             83
  N3            7             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V6, binary
                cls
clus               0   1
  NOS1 MUTATED    31   4
  NOS1 WILD-TYPE 451  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     31    4
  NOS1 WILD-TYPE  451   34
   clus
vv  NOS1 MUTATED NOS1 WILD-TYPE
  0           31            451
  1            4             34
[1] 2 2
[1] FALSE
D1144V7, binary
                cls
clus               0   1
  NOS1 MUTATED    18  19
  NOS1 WILD-TYPE 154 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     18   19
  NOS1 WILD-TYPE  154  387
        clus
vv       NOS1 MUTATED NOS1 WILD-TYPE
  FEMALE           18            154
  MALE             19            387
[1] 2 2
[1] FALSE
D1144V8, binary
                cls
clus               0   1
  NOS1 MUTATED    28   3
  NOS1 WILD-TYPE 388  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     28    3
  NOS1 WILD-TYPE  388   99
     clus
vv    NOS1 MUTATED NOS1 WILD-TYPE
  NO            28            388
  YES            3             99
[1] 2 2
[1] FALSE
D1144V9, continuous
D1144V10, continuous
[1] "Remove cluster labels:" "NOS1 MUTATED"          
clus
  NOS1 MUTATED NOS1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" "NOS1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOS1 MUTATED       9                         0
  NOS1 WILD-TYPE   124                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOS1 MUTATED                                           0    24
  NOS1 WILD-TYPE                                         1   333
D1144V11, multiclass
                                           clus
vv                                          NOS1 MUTATED NOS1 WILD-TYPE
  ASIAN                                                9            124
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               24            333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V12, binary
                cls
clus               0   1
  NOS1 MUTATED     1  27
  NOS1 WILD-TYPE   9 371
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED      1   27
  NOS1 WILD-TYPE    9  371
                        clus
vv                       NOS1 MUTATED NOS1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           27            371
[1] 2 2
[1] FALSE

Clustering(1145) Variable = NOTCH1 MUTATION ANALYSIS
D1145V1, survival
                  sevent
clus2                0   1
  NOTCH1 MUTATED    29  13
  NOTCH1 WILD-TYPE 309 203
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              42              512 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              13              203 
$`NOTCH1 MUTATED`
TCGA-L5-A43J TCGA-L5-A88T TCGA-CG-4460 TCGA-2H-A9GN TCGA-IG-A3Y9 TCGA-IG-A50L 
        4.31        22.82        21.99         8.94         0.85         0.53 
TCGA-IG-A5S3 TCGA-KH-A6WC TCGA-L5-A4OU TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49V 
       23.41         6.28        29.00        10.85        12.43        12.59 
TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A9FR TCGA-R6-A6Y2 TCGA-V5-AASV TCGA-VR-A8EY 
       12.59        12.33        12.26         9.30        15.35        33.70 
TCGA-VR-A8EZ TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 
       18.18        26.70        19.56         6.97         6.61        35.84 
TCGA-BR-8078 TCGA-BR-A4J7 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MJ TCGA-CG-4305 
       29.59        32.52        12.43         6.31        12.62        15.95 
TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6526 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HJ-7597 
       28.96        65.10        17.19         5.92        21.27        26.47 
TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       22.32        24.26        22.68        24.20        14.07        38.14 

$`NOTCH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       21.70        23.18        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.66        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33        13.22         4.47        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        28.11        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34         0.66        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 
       12.59        11.64        15.39        12.07        12.82        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        15.02         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4GC 
       22.82        21.07         0.76        24.30         5.59         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            0.53             0.00 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
            65.1            122.3 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
          16.570           13.495 
[1] "0.5 - 65.1 (16.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1145V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOTCH1 MUTATED         0        4        6        2         5        13
  NOTCH1 WILD-TYPE      10       16       40       29        79        70
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOTCH1 MUTATED           2          6          1          2        1
  NOTCH1 WILD-TYPE        27         78         61         37       42
                  vv
clus               STAGE IVA
  NOTCH1 MUTATED           0
  NOTCH1 WILD-TYPE         4
D1145V3, multiclass
            clus
vv           NOTCH1 MUTATED NOTCH1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                4               16
  STAGE IB                6               40
  STAGE II                2               29
  STAGE IIA               5               79
  STAGE IIB              13               70
  STAGE III               2               27
  STAGE IIIA              6               78
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  NOTCH1 MUTATED       5  11  17   9
  NOTCH1 WILD-TYPE    49 124 244  93
D1145V4, multiclass
       clus
vv      NOTCH1 MUTATED NOTCH1 WILD-TYPE
  T0+T1              5               49
  T2                11              124
  T3                17              244
  T4                 9               93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  NOTCH1 MUTATED    23  15   1   3
  NOTCH1 WILD-TYPE 172 158  88  82
D1145V5, multiclass
    clus
vv   NOTCH1 MUTATED NOTCH1 WILD-TYPE
  N0             23              172
  N1             15              158
  N2              1               88
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V6, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    38   1
  NOTCH1 WILD-TYPE 444  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     38    1
  NOTCH1 WILD-TYPE  444   37
   clus
vv  NOTCH1 MUTATED NOTCH1 WILD-TYPE
  0             38              444
  1              1               37
[1] 2 2
[1] FALSE
D1145V7, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    16  29
  NOTCH1 WILD-TYPE 156 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     16   29
  NOTCH1 WILD-TYPE  156  377
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  FEMALE             16              156
  MALE               29              377
[1] 2 2
[1] FALSE
D1145V8, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED    30   8
  NOTCH1 WILD-TYPE 386  94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED     30    8
  NOTCH1 WILD-TYPE  386   94
     clus
vv    NOTCH1 MUTATED NOTCH1 WILD-TYPE
  NO              30              386
  YES              8               94
[1] 2 2
[1] FALSE
D1145V9, continuous
D1145V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NOTCH1 MUTATED      15                         2
  NOTCH1 WILD-TYPE   118                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOTCH1 MUTATED                                           0    22
  NOTCH1 WILD-TYPE                                         1   335
D1145V11, multiclass
                                           clus
vv                                          NOTCH1 MUTATED NOTCH1 WILD-TYPE
  ASIAN                                                 15              118
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V12, binary
                  cls
clus                 0   1
  NOTCH1 MUTATED     2  31
  NOTCH1 WILD-TYPE   8 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH1 MUTATED      2   31
  NOTCH1 WILD-TYPE    8  367
                        clus
vv                       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  HISPANIC OR LATINO                  2                8
  NOT HISPANIC OR LATINO             31              367
[1] 2 2
[1] FALSE

Clustering(1146) Variable = C16ORF7 MUTATION ANALYSIS
D1146V1, survival
                   sevent
clus2                 0   1
  C16ORF7 MUTATED     7   8
  C16ORF7 WILD-TYPE 331 208
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
               15               539 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
                8               208 
$`C16ORF7 MUTATED`
TCGA-L5-A43J TCGA-L5-A88Z TCGA-L5-A8NF TCGA-LN-A7HX TCGA-VR-AA7I TCGA-ZR-A9CJ 
        4.31         7.40         2.66        12.23        15.91        19.73 
TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-7716 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 
        9.34         6.61        39.78        31.96        16.14         1.02 
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-VQ-A8P2 
       22.68         6.58        38.14 

$`C16ORF7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
        2.60        25.12         3.75         3.02        55.50        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       33.63        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
             1.02              0.00 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
            39.78            122.30 
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
            12.23             13.58 
[1] "1.0 - 39.8 (12.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1146V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF7 MUTATED         0        0        0        0         2         4
  C16ORF7 WILD-TYPE      10       20       46       31        82        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF7 MUTATED           2          1          1          1        3
  C16ORF7 WILD-TYPE        27         83         61         38       40
                   vv
clus                STAGE IVA
  C16ORF7 MUTATED           1
  C16ORF7 WILD-TYPE         3
D1146V3, multiclass
            clus
vv           C16ORF7 MUTATED C16ORF7 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                4                79
  STAGE III                2                27
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                1                 3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C16ORF7 MUTATED       2   2   7   4
  C16ORF7 WILD-TYPE    52 133 254  98
D1146V4, multiclass
       clus
vv      C16ORF7 MUTATED C16ORF7 WILD-TYPE
  T0+T1               2                52
  T2                  2               133
  T3                  7               254
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C16ORF7 MUTATED     4   7   3   2
  C16ORF7 WILD-TYPE 191 166  86  83
D1146V5, multiclass
    clus
vv   C16ORF7 MUTATED C16ORF7 WILD-TYPE
  N0               4               191
  N1               7               166
  N2               3                86
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V6, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED    11   3
  C16ORF7 WILD-TYPE 471  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED     11    3
  C16ORF7 WILD-TYPE  471   35
   clus
vv  C16ORF7 MUTATED C16ORF7 WILD-TYPE
  0              11               471
  1               3                35
[1] 2 2
[1] FALSE
D1146V7, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED     6  10
  C16ORF7 WILD-TYPE 166 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED      6   10
  C16ORF7 WILD-TYPE  166  396
        clus
vv       C16ORF7 MUTATED C16ORF7 WILD-TYPE
  FEMALE               6               166
  MALE                10               396
[1] 2 2
[1] FALSE
D1146V8, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED    11   2
  C16ORF7 WILD-TYPE 405 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED     11    2
  C16ORF7 WILD-TYPE  405  100
     clus
vv    C16ORF7 MUTATED C16ORF7 WILD-TYPE
  NO               11               405
  YES               2               100
[1] 2 2
[1] FALSE
D1146V9, continuous
[1] "Remove cluster labels:" "C16ORF7 MUTATED"       
clus
  C16ORF7 MUTATED C16ORF7 WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C16ORF7 WILD-TYPE" "C16ORF7 WILD-TYPE" 
D1146V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF7 MUTATED       4                         0
  C16ORF7 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF7 MUTATED                                           0    11
  C16ORF7 WILD-TYPE                                         1   346
D1146V11, multiclass
                                           clus
vv                                          C16ORF7 MUTATED C16ORF7 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V12, binary
                   cls
clus                  0   1
  C16ORF7 MUTATED     0  10
  C16ORF7 WILD-TYPE  10 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C16ORF7 MUTATED      0   10
  C16ORF7 WILD-TYPE   10  388
                        clus
vv                       C16ORF7 MUTATED C16ORF7 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              10               388
[1] 2 2
[1] FALSE

Clustering(1147) Variable = HIVEP3 MUTATION ANALYSIS
D1147V1, survival
                  sevent
clus2                0   1
  HIVEP3 MUTATED    25  10
  HIVEP3 WILD-TYPE 313 206
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              35              519 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              10              206 
$`HIVEP3 MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-CG-4460 TCGA-2H-A9GH TCGA-JY-A93C TCGA-L5-A4OH 
       19.99         5.16        21.99        31.27        23.18        32.61 
TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8361 
        2.10        26.70         9.47        34.68        44.94        31.10 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5800 
        0.26         4.31         1.12        27.12        31.96        13.15 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4449 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5730 
        6.58         1.02        19.07         6.02       105.07         4.01 
TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H0 
        5.92        11.44        24.20        29.98         0.10         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-A6RN TCGA-VQ-A8P2 
       12.95        14.07         3.45        19.53        38.14 

$`HIVEP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15         9.86        25.78        20.05        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56        11.01         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        2.20         7.40         6.18        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        0.99        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.58        20.25         0.26        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       23.80        21.17        15.68        33.40        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
             0.1              0.0 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
          105.07           122.30 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
           14.07            13.55 
[1] "0.1 - 105.1 (14.1)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1147V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP3 MUTATED         1        1        3        3         6         4
  HIVEP3 WILD-TYPE       9       19       43       28        78        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP3 MUTATED           0          3          5          4        5
  HIVEP3 WILD-TYPE        29         81         57         35       38
                  vv
clus               STAGE IVA
  HIVEP3 MUTATED           0
  HIVEP3 WILD-TYPE         4
D1147V3, multiclass
            clus
vv           HIVEP3 MUTATED HIVEP3 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                3               28
  STAGE IIA               6               78
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              5               57
  STAGE IIIC              4               35
  STAGE IV                5               38
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  HIVEP3 MUTATED       5   6  14  11
  HIVEP3 WILD-TYPE    49 129 247  91
D1147V4, multiclass
       clus
vv      HIVEP3 MUTATED HIVEP3 WILD-TYPE
  T0+T1              5               49
  T2                 6              129
  T3                14              247
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  HIVEP3 MUTATED    11  12   7   5
  HIVEP3 WILD-TYPE 184 161  82  80
D1147V5, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  N0             11              184
  N1             12              161
  N2              7               82
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V6, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    30   5
  HIVEP3 WILD-TYPE 452  33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     30    5
  HIVEP3 WILD-TYPE  452   33
   clus
vv  HIVEP3 MUTATED HIVEP3 WILD-TYPE
  0             30              452
  1              5               33
[1] 2 2
[1] FALSE
D1147V7, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    16  20
  HIVEP3 WILD-TYPE 156 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     16   20
  HIVEP3 WILD-TYPE  156  386
        clus
vv       HIVEP3 MUTATED HIVEP3 WILD-TYPE
  FEMALE             16              156
  MALE               20              386
[1] 2 2
[1] FALSE
D1147V8, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    33   1
  HIVEP3 WILD-TYPE 383 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     33    1
  HIVEP3 WILD-TYPE  383  101
     clus
vv    HIVEP3 MUTATED HIVEP3 WILD-TYPE
  NO              33              383
  YES              1              101
[1] 2 2
[1] FALSE
D1147V9, continuous
[1] "Remove cluster labels:" "HIVEP3 MUTATED"        
clus
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JD 
"HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" "HIVEP3 WILD-TYPE" 
D1147V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HIVEP3 MUTATED      10                         0
  HIVEP3 WILD-TYPE   123                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIVEP3 MUTATED                                           0    19
  HIVEP3 WILD-TYPE                                         1   338
D1147V11, multiclass
                                           clus
vv                                          HIVEP3 MUTATED HIVEP3 WILD-TYPE
  ASIAN                                                 10              123
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 19              338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V12, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED     0  25
  HIVEP3 WILD-TYPE  10 373
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED      0   25
  HIVEP3 WILD-TYPE   10  373
                        clus
vv                       HIVEP3 MUTATED HIVEP3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             25              373
[1] 2 2
[1] FALSE

Clustering(1148) Variable = FBXO32 MUTATION ANALYSIS
D1148V1, survival
                  sevent
clus2                0   1
  FBXO32 MUTATED     6   0
  FBXO32 WILD-TYPE 332 216
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               6              548 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               0              216 
$`FBXO32 MUTATED`
TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8680 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P2 
       44.94         1.12        31.96         6.51         6.58        38.14 

$`FBXO32 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  FBXO32 MUTATED FBXO32 WILD-TYPE 
            1.12             0.00 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
           44.94           122.30 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
          19.270           13.565 
[1] "1.1 - 44.9 (19.3)"  "0.0 - 122.3 (13.6)"
[1] "hr="     "9100000"
D1148V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO32 MUTATED         0        0        0        0         3         1
  FBXO32 WILD-TYPE      10       20       46       31        81        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO32 MUTATED           0          2          0          0        1
  FBXO32 WILD-TYPE        29         82         62         39       42
                  vv
clus               STAGE IVA
  FBXO32 MUTATED           0
  FBXO32 WILD-TYPE         4
D1148V3, multiclass
            clus
vv           FBXO32 MUTATED FBXO32 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FBXO32 MUTATED       0   0   4   3
  FBXO32 WILD-TYPE    54 135 257  99
D1148V4, multiclass
       clus
vv      FBXO32 MUTATED FBXO32 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 4              257
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FBXO32 MUTATED     4   2   1   0
  FBXO32 WILD-TYPE 191 171  88  85
D1148V5, multiclass
    clus
vv   FBXO32 MUTATED FBXO32 WILD-TYPE
  N0              4              191
  N1              2              171
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V6, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     6   1
  FBXO32 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      6    1
  FBXO32 WILD-TYPE  476   37
   clus
vv  FBXO32 MUTATED FBXO32 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D1148V7, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     4   3
  FBXO32 WILD-TYPE 168 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      4    3
  FBXO32 WILD-TYPE  168  403
        clus
vv       FBXO32 MUTATED FBXO32 WILD-TYPE
  FEMALE              4              168
  MALE                3              403
[1] 2 2
[1] FALSE
D1148V8, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     5   1
  FBXO32 WILD-TYPE 411 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      5    1
  FBXO32 WILD-TYPE  411  101
     clus
vv    FBXO32 MUTATED FBXO32 WILD-TYPE
  NO               5              411
  YES              1              101
[1] 2 2
[1] FALSE
D1148V9, continuous
D1148V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO32 MUTATED       3                         0
  FBXO32 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO32 MUTATED                                           0     4
  FBXO32 WILD-TYPE                                         1   353
D1148V11, multiclass
                                           clus
vv                                          FBXO32 MUTATED FBXO32 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V12, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     0   6
  FBXO32 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      0    6
  FBXO32 WILD-TYPE   10  392
                        clus
vv                       FBXO32 MUTATED FBXO32 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(1149) Variable = BIRC7 MUTATION ANALYSIS
D1149V1, survival
                 sevent
clus2               0   1
  BIRC7 MUTATED     4   1
  BIRC7 WILD-TYPE 334 215
  BIRC7 MUTATED BIRC7 WILD-TYPE 
              5             549 
  BIRC7 MUTATED BIRC7 WILD-TYPE 
              1             215 
$`BIRC7 MUTATED`
TCGA-L5-A4OH TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-A4PE TCGA-HU-8602 
       32.61         0.26         4.31        20.42        22.32 

$`BIRC7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BIRC7 MUTATED BIRC7 WILD-TYPE 
           0.26            0.00 
  BIRC7 MUTATED BIRC7 WILD-TYPE 
          32.61          122.30 
  BIRC7 MUTATED BIRC7 WILD-TYPE 
          20.42           13.55 
[1] "0.3 - 32.6 (20.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1149V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BIRC7 MUTATED         1        0        3        0         0         1
  BIRC7 WILD-TYPE       9       20       43       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIRC7 MUTATED           0          0          0          0        0         0
  BIRC7 WILD-TYPE        29         84         62         39       43         4
D1149V3, multiclass
            clus
vv           BIRC7 MUTATED BIRC7 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BIRC7 MUTATED       1   4   0   1
  BIRC7 WILD-TYPE    53 131 261 101
D1149V4, multiclass
       clus
vv      BIRC7 MUTATED BIRC7 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                0             261
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BIRC7 MUTATED     5   0   0   0
  BIRC7 WILD-TYPE 190 173  89  85
D1149V5, multiclass
    clus
vv   BIRC7 MUTATED BIRC7 WILD-TYPE
  N0             5             190
  N1             0             173
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V6, binary
                 cls
clus                0   1
  BIRC7 MUTATED     6   0
  BIRC7 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC7 MUTATED      6    0
  BIRC7 WILD-TYPE  476   38
   clus
vv  BIRC7 MUTATED BIRC7 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1149V7, binary
                 cls
clus                0   1
  BIRC7 MUTATED     5   1
  BIRC7 WILD-TYPE 167 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC7 MUTATED      5    1
  BIRC7 WILD-TYPE  167  405
        clus
vv       BIRC7 MUTATED BIRC7 WILD-TYPE
  FEMALE             5             167
  MALE               1             405
[1] 2 2
[1] FALSE
D1149V8, binary
                 cls
clus                0   1
  BIRC7 MUTATED     5   0
  BIRC7 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC7 MUTATED      5    0
  BIRC7 WILD-TYPE  411  102
     clus
vv    BIRC7 MUTATED BIRC7 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D1149V9, continuous
D1149V10, continuous
[1] "Remove cluster labels:" "BIRC7 MUTATED"         
clus
  BIRC7 MUTATED BIRC7 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OM 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" "BIRC7 WILD-TYPE" 
     TCGA-Z6-AAPN 
"BIRC7 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BIRC7 MUTATED       1                         0
  BIRC7 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BIRC7 MUTATED                                           0     5
  BIRC7 WILD-TYPE                                         1   352
D1149V11, multiclass
                                           clus
vv                                          BIRC7 MUTATED BIRC7 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V12, binary
                 cls
clus                0   1
  BIRC7 MUTATED     0   5
  BIRC7 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC7 MUTATED      0    5
  BIRC7 WILD-TYPE   10  393
                        clus
vv                       BIRC7 MUTATED BIRC7 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1150) Variable = AFP MUTATION ANALYSIS
D1150V1, survival
               sevent
clus2             0   1
  AFP MUTATED     0   3
  AFP WILD-TYPE 338 213
  AFP MUTATED AFP WILD-TYPE 
            3           551 
  AFP MUTATED AFP WILD-TYPE 
            3           213 
$`AFP MUTATED`
TCGA-BR-4184 TCGA-CD-A4MI TCGA-R5-A7ZF 
        6.97        11.77         8.52 

$`AFP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  AFP MUTATED AFP WILD-TYPE 
         6.97          0.00 
  AFP MUTATED AFP WILD-TYPE 
        11.77        122.30 
  AFP MUTATED AFP WILD-TYPE 
         8.52         13.68 
[1] "7.0 - 11.8 (8.5)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "5.4"
D1150V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AFP MUTATED         0        0        0        0         0         1
  AFP WILD-TYPE      10       20       46       31        84        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFP MUTATED           0          2          0          0        1         0
  AFP WILD-TYPE        29         82         62         39       42         4
D1150V3, multiclass
            clus
vv           AFP MUTATED AFP WILD-TYPE
  STAGE I              0            10
  STAGE IA             0            20
  STAGE IB             0            46
  STAGE II             0            31
  STAGE IIA            0            84
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           2            82
  STAGE IIIB           0            62
  STAGE IIIC           0            39
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  AFP MUTATED       0   0   2   2
  AFP WILD-TYPE    54 135 259 100
D1150V4, multiclass
       clus
vv      AFP MUTATED AFP WILD-TYPE
  T0+T1           0            54
  T2              0           135
  T3              2           259
  T4              2           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  AFP MUTATED     1   3   0   0
  AFP WILD-TYPE 194 170  89  85
D1150V5, multiclass
    clus
vv   AFP MUTATED AFP WILD-TYPE
  N0           1           194
  N1           3           170
  N2           0            89
  N3           0            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V6, binary
               cls
clus              0   1
  AFP MUTATED     2   1
  AFP WILD-TYPE 480  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      2    1
  AFP WILD-TYPE  480   37
   clus
vv  AFP MUTATED AFP WILD-TYPE
  0           2           480
  1           1            37
[1] 2 2
[1] FALSE
D1150V7, binary
               cls
clus              0   1
  AFP MUTATED     1   3
  AFP WILD-TYPE 171 403
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      1    3
  AFP WILD-TYPE  171  403
        clus
vv       AFP MUTATED AFP WILD-TYPE
  FEMALE           1           171
  MALE             3           403
[1] 2 2
[1] FALSE
D1150V8, binary
               cls
clus              0   1
  AFP MUTATED     4   0
  AFP WILD-TYPE 412 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      4    0
  AFP WILD-TYPE  412  102
     clus
vv    AFP MUTATED AFP WILD-TYPE
  NO            4           412
  YES           0           102
[1] 2 2
[1] FALSE
D1150V9, continuous
D1150V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  AFP MUTATED       1                         1
  AFP WILD-TYPE   132                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AFP MUTATED                                           0     2
  AFP WILD-TYPE                                         1   355
D1150V11, multiclass
                                           clus
vv                                          AFP MUTATED AFP WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               2           355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V12, binary
               cls
clus              0   1
  AFP MUTATED     0   4
  AFP WILD-TYPE  10 394
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      0    4
  AFP WILD-TYPE   10  394
                        clus
vv                       AFP MUTATED AFP WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           4           394
[1] 2 2
[1] FALSE

Clustering(1151) Variable = COL11A1 MUTATION ANALYSIS
D1151V1, survival
                   sevent
clus2                 0   1
  COL11A1 MUTATED    45  14
  COL11A1 WILD-TYPE 293 202
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               59               495 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               14               202 
$`COL11A1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-CG-5727 TCGA-IG-A97I TCGA-JY-A6FA 
       60.39         4.31        19.99        79.07        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A4OJ TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A8NR 
       68.02        41.52        21.01        29.00        25.12         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A4A2 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8WG 
       13.41        52.57        12.49         5.06        38.40        12.69 
TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8EU TCGA-B7-5818 TCGA-B7-A5TN TCGA-BR-4187 
       20.38        27.09        18.31        11.70         9.44         4.64 
TCGA-BR-4201 TCGA-BR-6453 TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8369 
       30.90        15.95        35.24        29.42        31.10        14.04 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-A4J7 TCGA-CD-8536 
       31.27         1.12        12.79        31.96        32.52        12.43 
TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-5723 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY 
       15.95        54.08       105.07        13.78        14.76        11.44 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-A4BE TCGA-HF-7133 TCGA-HU-8602 TCGA-HU-A4GN 
       19.96         7.99        11.08        63.06        22.32        29.98 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IN-A6RP TCGA-IP-7968 TCGA-R5-A7O7 
        8.98         6.58        20.25         6.44         2.53        45.67 
TCGA-R5-A7ZI TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-AA6I 
       74.53        48.79        38.14        22.19        16.14 

$`COL11A1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        9.86        25.78        20.05        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
        4.67        14.50       122.10         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48         2.60         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49        21.37        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         7.59        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43         1.55         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         6.61         6.97         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       29.59         9.60        32.25         8.05         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72        14.17         0.53        28.34         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET 
       20.91        14.27        16.44         5.92        36.43        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GY 
       25.81        11.77        21.37         0.10         6.51         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       43.36        37.41        37.22        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  COL11A1 MUTATED COL11A1 WILD-TYPE 
             1.12              0.00 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
           105.07            122.30 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
            20.25             13.35 
[1] "1.1 - 105.1 (20.2)" "0.0 - 122.3 (13.3)"
[1] "hr=" "2.5"
D1151V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL11A1 MUTATED         2        0        2        6        11        11
  COL11A1 WILD-TYPE       8       20       44       25        73        72
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL11A1 MUTATED           2          3          8          5        6
  COL11A1 WILD-TYPE        27         81         54         34       37
                   vv
clus                STAGE IVA
  COL11A1 MUTATED           0
  COL11A1 WILD-TYPE         4
D1151V3, multiclass
            clus
vv           COL11A1 MUTATED COL11A1 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 6                25
  STAGE IIA               11                73
  STAGE IIB               11                72
  STAGE III                2                27
  STAGE IIIA               3                81
  STAGE IIIB               8                54
  STAGE IIIC               5                34
  STAGE IV                 6                37
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  COL11A1 MUTATED       4  12  28  13
  COL11A1 WILD-TYPE    50 123 233  89
D1151V4, multiclass
       clus
vv      COL11A1 MUTATED COL11A1 WILD-TYPE
  T0+T1               4                50
  T2                 12               123
  T3                 28               233
  T4                 13                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  COL11A1 MUTATED    22  14   8  10
  COL11A1 WILD-TYPE 173 159  81  75
D1151V5, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  N0              22               173
  N1              14               159
  N2               8                81
  N3              10                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V6, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    48   4
  COL11A1 WILD-TYPE 434  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     48    4
  COL11A1 WILD-TYPE  434   34
   clus
vv  COL11A1 MUTATED COL11A1 WILD-TYPE
  0              48               434
  1               4                34
[1] 2 2
[1] FALSE
D1151V7, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    19  42
  COL11A1 WILD-TYPE 153 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     19   42
  COL11A1 WILD-TYPE  153  364
        clus
vv       COL11A1 MUTATED COL11A1 WILD-TYPE
  FEMALE              19               153
  MALE                42               364
[1] 2 2
[1] FALSE
D1151V8, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    44  13
  COL11A1 WILD-TYPE 372  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     44   13
  COL11A1 WILD-TYPE  372   89
     clus
vv    COL11A1 MUTATED COL11A1 WILD-TYPE
  NO               44               372
  YES              13                89
[1] 2 2
[1] FALSE
D1151V9, continuous
D1151V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL11A1 MUTATED      11                         1
  COL11A1 WILD-TYPE   122                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL11A1 MUTATED                                           0    42
  COL11A1 WILD-TYPE                                         1   315
D1151V11, multiclass
                                           clus
vv                                          COL11A1 MUTATED COL11A1 WILD-TYPE
  ASIAN                                                  11               122
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  42               315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V12, binary
                   cls
clus                  0   1
  COL11A1 MUTATED     3  35
  COL11A1 WILD-TYPE   7 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED      3   35
  COL11A1 WILD-TYPE    7  363
                        clus
vv                       COL11A1 MUTATED COL11A1 WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              35               363
[1] 2 2
[1] FALSE

Clustering(1152) Variable = FAM166B MUTATION ANALYSIS
D1152V1, survival
                   sevent
clus2                 0   1
  FAM166B MUTATED     5   4
  FAM166B WILD-TYPE 333 212
  FAM166B MUTATED FAM166B WILD-TYPE 
                9               545 
  FAM166B MUTATED FAM166B WILD-TYPE 
                4               212 
$`FAM166B MUTATED`
TCGA-L5-A43J TCGA-L5-A43C TCGA-L5-A8NM TCGA-XP-A8T6 TCGA-BR-6455 TCGA-BR-8487 
        4.31         3.16         7.76        25.08        13.87         1.12 
TCGA-BR-A4IY TCGA-CG-5723 TCGA-R5-A7ZI 
       12.89       105.07        74.53 

$`FAM166B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  FAM166B MUTATED FAM166B WILD-TYPE 
             1.12              0.00 
  FAM166B MUTATED FAM166B WILD-TYPE 
           105.07            122.30 
  FAM166B MUTATED FAM166B WILD-TYPE 
            12.89             13.58 
[1] "1.1 - 105.1 (12.9)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1152V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM166B MUTATED         0        0        0        1         1         5
  FAM166B WILD-TYPE      10       20       46       30        83        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM166B MUTATED           0          0          0          0        1
  FAM166B WILD-TYPE        29         84         62         39       42
                   vv
clus                STAGE IVA
  FAM166B MUTATED           0
  FAM166B WILD-TYPE         4
D1152V3, multiclass
            clus
vv           FAM166B MUTATED FAM166B WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                5                78
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  FAM166B MUTATED       0   3   3   2
  FAM166B WILD-TYPE    54 132 258 100
D1152V4, multiclass
       clus
vv      FAM166B MUTATED FAM166B WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  3               258
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  FAM166B MUTATED     3   5   0   0
  FAM166B WILD-TYPE 192 168  89  85
D1152V5, multiclass
    clus
vv   FAM166B MUTATED FAM166B WILD-TYPE
  N0               3               192
  N1               5               168
  N2               0                89
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V6, binary
                   cls
clus                  0   1
  FAM166B MUTATED     6   1
  FAM166B WILD-TYPE 476  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM166B MUTATED      6    1
  FAM166B WILD-TYPE  476   37
   clus
vv  FAM166B MUTATED FAM166B WILD-TYPE
  0               6               476
  1               1                37
[1] 2 2
[1] FALSE
D1152V7, binary
                   cls
clus                  0   1
  FAM166B MUTATED     3   6
  FAM166B WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM166B MUTATED      3    6
  FAM166B WILD-TYPE  169  400
        clus
vv       FAM166B MUTATED FAM166B WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D1152V8, binary
                   cls
clus                  0   1
  FAM166B MUTATED     8   0
  FAM166B WILD-TYPE 408 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM166B MUTATED      8    0
  FAM166B WILD-TYPE  408  102
     clus
vv    FAM166B MUTATED FAM166B WILD-TYPE
  NO                8               408
  YES               0               102
[1] 2 2
[1] FALSE
D1152V9, continuous
[1] "Remove cluster labels:" "FAM166B MUTATED"       
clus
  FAM166B MUTATED FAM166B WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-VR-A8EZ        TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-VR-AA7B        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T7 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"FAM166B WILD-TYPE" "FAM166B WILD-TYPE" "FAM166B WILD-TYPE" 
D1152V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM166B MUTATED       1                         1
  FAM166B WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM166B MUTATED                                           0     6
  FAM166B WILD-TYPE                                         1   351
D1152V11, multiclass
                                           clus
vv                                          FAM166B MUTATED FAM166B WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V12, binary
                   cls
clus                  0   1
  FAM166B MUTATED     2   3
  FAM166B WILD-TYPE   8 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM166B MUTATED      2    3
  FAM166B WILD-TYPE    8  395
                        clus
vv                       FAM166B MUTATED FAM166B WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO               3               395
[1] 2 2
[1] FALSE

Clustering(1153) Variable = ARHGEF17 MUTATION ANALYSIS
D1153V1, survival
                    sevent
clus2                  0   1
  ARHGEF17 MUTATED    17   6
  ARHGEF17 WILD-TYPE 321 210
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                23                531 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                 6                210 
$`ARHGEF17 MUTATED`
TCGA-CG-4460 TCGA-IG-A625 TCGA-JY-A93F TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-7707 
       21.99        12.82        24.03         2.66         6.97        35.84 
TCGA-BR-7716 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8381 TCGA-BR-8487 
       39.78        29.59         6.18         4.31         7.36         1.12 
TCGA-BR-8591 TCGA-BR-A4IY TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-8579 TCGA-D7-A6EY 
       28.14        12.89        11.77         6.02        20.91        11.44 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GH TCGA-RD-A7BT TCGA-VQ-A8P2 
       11.08        77.29        11.77         8.61        38.14 

$`ARHGEF17 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        33.63        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27        14.79        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        21.14        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
              1.12               0.00 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
             77.29             122.30 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
             11.77              13.78 
[1] "1.1 - 77.3 (11.8)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.5"
D1153V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF17 MUTATED         0        1        4        1         4         5
  ARHGEF17 WILD-TYPE      10       19       42       30        80        78
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF17 MUTATED           0          3          2          1        4
  ARHGEF17 WILD-TYPE        29         81         60         38       39
                    vv
clus                 STAGE IVA
  ARHGEF17 MUTATED           0
  ARHGEF17 WILD-TYPE         4
D1153V3, multiclass
            clus
vv           ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  4                 42
  STAGE II                  1                 30
  STAGE IIA                 4                 80
  STAGE IIB                 5                 78
  STAGE III                 0                 29
  STAGE IIIA                3                 81
  STAGE IIIB                2                 60
  STAGE IIIC                1                 38
  STAGE IV                  4                 39
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  ARHGEF17 MUTATED       1   6  11   7
  ARHGEF17 WILD-TYPE    53 129 250  95
D1153V4, multiclass
       clus
vv      ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  T0+T1                1                 53
  T2                   6                129
  T3                  11                250
  T4                   7                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  ARHGEF17 MUTATED    11   8   3   3
  ARHGEF17 WILD-TYPE 184 165  86  82
D1153V5, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  N0               11                184
  N1                8                165
  N2                3                 86
  N3                3                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V6, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    23   1
  ARHGEF17 WILD-TYPE 459  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     23    1
  ARHGEF17 WILD-TYPE  459   37
   clus
vv  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  0               23                459
  1                1                 37
[1] 2 2
[1] FALSE
D1153V7, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    10  15
  ARHGEF17 WILD-TYPE 162 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     10   15
  ARHGEF17 WILD-TYPE  162  391
        clus
vv       ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  FEMALE               10                162
  MALE                 15                391
[1] 2 2
[1] FALSE
D1153V8, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    18   4
  ARHGEF17 WILD-TYPE 398  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     18    4
  ARHGEF17 WILD-TYPE  398   98
     clus
vv    ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  NO                18                398
  YES                4                 98
[1] 2 2
[1] FALSE
D1153V9, continuous
D1153V10, continuous
[1] "Remove cluster labels:" "ARHGEF17 MUTATED"      
clus
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                 1                 97 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A4OE         TCGA-L5-A4OG         TCGA-L5-A4OI 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A88T         TCGA-L5-A88Y         TCGA-L5-A8NG 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A8NT         TCGA-Q9-A6FU         TCGA-IC-A6RE 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-IG-A3QL         TCGA-IG-A3Y9         TCGA-IG-A3YA 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-IG-A3YC         TCGA-IG-A4P3         TCGA-IG-A4QT 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-IG-A50L         TCGA-IG-A5B8         TCGA-IG-A6QS 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-IG-A8O2         TCGA-IG-A97H         TCGA-JY-A6FA 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-JY-A6FE         TCGA-JY-A6FG         TCGA-JY-A6FH 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-L5-A43C         TCGA-L5-A43E 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A43H         TCGA-L5-A4OH         TCGA-L5-A4OM 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A4ON         TCGA-L5-A4OO         TCGA-L5-A4OP 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A4OQ         TCGA-L5-A4OT         TCGA-L5-A4OU 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A4OW         TCGA-L5-A4OX         TCGA-L5-A88S 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A88V         TCGA-L5-A893         TCGA-L5-A8NE 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A8NF         TCGA-L5-A8NK         TCGA-L5-A8NN 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A8NQ         TCGA-L5-A8NR         TCGA-L5-A8NS 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-L5-A8NW         TCGA-LN-A49O         TCGA-LN-A49P 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A49R         TCGA-LN-A49S         TCGA-LN-A49U 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A49V         TCGA-LN-A49W         TCGA-LN-A4A3 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A4A6         TCGA-LN-A4A9         TCGA-LN-A5U6 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A5U7         TCGA-LN-A7HV         TCGA-LN-A7HW 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A7HX         TCGA-LN-A7HZ         TCGA-LN-A8HZ 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-LN-A8I0         TCGA-M9-A5M8         TCGA-Q9-A6FW 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-R6-A6DN         TCGA-R6-A6L4         TCGA-R6-A6XQ 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-R6-A6Y2         TCGA-R6-A8W5         TCGA-R6-A8W8 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-R6-A8WC         TCGA-RE-A7BO         TCGA-V5-A7RB 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-AASV         TCGA-VR-A8EP 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-VR-A8ER         TCGA-VR-A8EU         TCGA-VR-A8EW 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EZ         TCGA-VR-A8Q7 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-VR-AA4G         TCGA-VR-AA7D         TCGA-VR-AA7I 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-X8-AAAR         TCGA-XP-A8T6         TCGA-XP-A8T7 
"ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" "ARHGEF17 WILD-TYPE" 
        TCGA-XP-A8T8 
"ARHGEF17 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF17 MUTATED       4                         1
  ARHGEF17 WILD-TYPE   129                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF17 MUTATED                                           1    15
  ARHGEF17 WILD-TYPE                                         0   342
D1153V11, multiclass
                                           clus
vv                                          ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                1                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   15                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V12, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED     0  19
  ARHGEF17 WILD-TYPE  10 379
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED      0   19
  ARHGEF17 WILD-TYPE   10  379
                        clus
vv                       ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               19                379
[1] 2 2
[1] FALSE

Clustering(1154) Variable = RRBP1 MUTATION ANALYSIS
D1154V1, survival
                 sevent
clus2               0   1
  RRBP1 MUTATED    13   5
  RRBP1 WILD-TYPE 325 211
  RRBP1 MUTATED RRBP1 WILD-TYPE 
             18             536 
  RRBP1 MUTATED RRBP1 WILD-TYPE 
              5             211 
$`RRBP1 MUTATED`
TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A8NM TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-VR-A8EQ 
       25.22        47.93         7.76        12.59        12.49        22.82 
TCGA-BR-7717 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-HJ-7597 
       18.15        29.59        32.25        31.27         1.12        26.47 
TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GP TCGA-MX-A5UJ TCGA-SW-A7EA 
        1.51        22.32        29.98         8.98        19.73        19.04 

$`RRBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.62        12.46        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       52.21        30.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  RRBP1 MUTATED RRBP1 WILD-TYPE 
           1.12            0.00 
  RRBP1 MUTATED RRBP1 WILD-TYPE 
          47.93          122.30 
  RRBP1 MUTATED RRBP1 WILD-TYPE 
         21.025          13.495 
[1] "1.1 - 47.9 (21.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1154V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRBP1 MUTATED         1        1        2        0         5         5
  RRBP1 WILD-TYPE       9       19       44       31        79        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRBP1 MUTATED           1          2          0          1        1         0
  RRBP1 WILD-TYPE        28         82         62         38       42         4
D1154V3, multiclass
            clus
vv           RRBP1 MUTATED RRBP1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RRBP1 MUTATED       2   5   7   6
  RRBP1 WILD-TYPE    52 130 254  96
D1154V4, multiclass
       clus
vv      RRBP1 MUTATED RRBP1 WILD-TYPE
  T0+T1             2              52
  T2                5             130
  T3                7             254
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RRBP1 MUTATED    10   7   2   1
  RRBP1 WILD-TYPE 185 166  87  84
D1154V5, multiclass
    clus
vv   RRBP1 MUTATED RRBP1 WILD-TYPE
  N0            10             185
  N1             7             166
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V6, binary
                 cls
clus                0   1
  RRBP1 MUTATED    17   0
  RRBP1 WILD-TYPE 465  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRBP1 MUTATED     17    0
  RRBP1 WILD-TYPE  465   38
   clus
vv  RRBP1 MUTATED RRBP1 WILD-TYPE
  0            17             465
  1             0              38
[1] 2 2
[1] FALSE
D1154V7, binary
                 cls
clus                0   1
  RRBP1 MUTATED    10  10
  RRBP1 WILD-TYPE 162 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRBP1 MUTATED     10   10
  RRBP1 WILD-TYPE  162  396
        clus
vv       RRBP1 MUTATED RRBP1 WILD-TYPE
  FEMALE            10             162
  MALE              10             396
[1] 2 2
[1] FALSE
D1154V8, binary
                 cls
clus                0   1
  RRBP1 MUTATED    18   2
  RRBP1 WILD-TYPE 398 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRBP1 MUTATED     18    2
  RRBP1 WILD-TYPE  398  100
     clus
vv    RRBP1 MUTATED RRBP1 WILD-TYPE
  NO             18             398
  YES             2             100
[1] 2 2
[1] FALSE
D1154V9, continuous
D1154V10, continuous
[1] "Remove cluster labels:" "RRBP1 MUTATED"         
clus
  RRBP1 MUTATED RRBP1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" "RRBP1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"RRBP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RRBP1 MUTATED       6                         1
  RRBP1 WILD-TYPE   127                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRBP1 MUTATED                                           0    13
  RRBP1 WILD-TYPE                                         1   344
D1154V11, multiclass
                                           clus
vv                                          RRBP1 MUTATED RRBP1 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V12, binary
                 cls
clus                0   1
  RRBP1 MUTATED     0  16
  RRBP1 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRBP1 MUTATED      0   16
  RRBP1 WILD-TYPE   10  382
                        clus
vv                       RRBP1 MUTATED RRBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(1155) Variable = PROK2 MUTATION ANALYSIS
D1155V1, survival
                 sevent
clus2               0   1
  PROK2 MUTATED     3   1
  PROK2 WILD-TYPE 335 215
  PROK2 MUTATED PROK2 WILD-TYPE 
              4             550 
  PROK2 MUTATED PROK2 WILD-TYPE 
              1             215 
$`PROK2 MUTATED`
TCGA-BR-4257 TCGA-CG-5721 TCGA-HF-A5NB TCGA-MX-A5UJ 
        9.67         6.02        30.51        19.73 

$`PROK2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PROK2 MUTATED PROK2 WILD-TYPE 
           6.02            0.00 
  PROK2 MUTATED PROK2 WILD-TYPE 
          30.51          122.30 
  PROK2 MUTATED PROK2 WILD-TYPE 
         14.700          13.565 
[1] "6.0 - 30.5 (14.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.5"
D1155V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PROK2 MUTATED         0        0        0        0         0         0
  PROK2 WILD-TYPE      10       20       46       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PROK2 MUTATED           0          1          0          1        1         0
  PROK2 WILD-TYPE        29         83         62         38       42         4
D1155V3, multiclass
            clus
vv           PROK2 MUTATED PROK2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PROK2 MUTATED       0   0   1   2
  PROK2 WILD-TYPE    54 135 260 100
D1155V4, multiclass
       clus
vv      PROK2 MUTATED PROK2 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PROK2 MUTATED     0   1   1   1
  PROK2 WILD-TYPE 195 172  88  84
D1155V5, multiclass
    clus
vv   PROK2 MUTATED PROK2 WILD-TYPE
  N0             0             195
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V6, binary
                 cls
clus                0   1
  PROK2 MUTATED     4   0
  PROK2 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROK2 MUTATED      4    0
  PROK2 WILD-TYPE  478   38
   clus
vv  PROK2 MUTATED PROK2 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D1155V7, binary
                 cls
clus                0   1
  PROK2 MUTATED     3   1
  PROK2 WILD-TYPE 169 405
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROK2 MUTATED      3    1
  PROK2 WILD-TYPE  169  405
        clus
vv       PROK2 MUTATED PROK2 WILD-TYPE
  FEMALE             3             169
  MALE               1             405
[1] 2 2
[1] FALSE
D1155V8, binary
                 cls
clus                0   1
  PROK2 MUTATED     3   1
  PROK2 WILD-TYPE 413 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROK2 MUTATED      3    1
  PROK2 WILD-TYPE  413  101
     clus
vv    PROK2 MUTATED PROK2 WILD-TYPE
  NO              3             413
  YES             1             101
[1] 2 2
[1] FALSE
D1155V9, continuous
D1155V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PROK2 MUTATED       0                         0
  PROK2 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PROK2 MUTATED                                           0     2
  PROK2 WILD-TYPE                                         1   355
D1155V11, multiclass
[1] "Remove cluster labels:" "PROK2 MUTATED"         
clus
  PROK2 MUTATED PROK2 WILD-TYPE 
              2             503 
     TCGA-IC-A6RF      TCGA-JY-A6FB      TCGA-JY-A938      TCGA-L5-A43I 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG      TCGA-L5-A4OI 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG      TCGA-L5-A8NT 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-Q9-A6FU      TCGA-S8-A6BV      TCGA-EQ-A4SO      TCGA-F1-6177 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-KB-A93G      TCGA-MX-A663      TCGA-IC-A6RE 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A4P3      TCGA-IG-A4QS 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A51D      TCGA-IG-A5B8 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IG-A5S3      TCGA-IG-A625      TCGA-IG-A6QS      TCGA-IG-A7DP 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-IG-A97I      TCGA-JY-A6F8 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-JY-A6FA      TCGA-JY-A6FD      TCGA-JY-A6FE      TCGA-JY-A6FG 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-JY-A6FH      TCGA-JY-A939      TCGA-JY-A93C      TCGA-JY-A93D 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-JY-A93E      TCGA-JY-A93F      TCGA-KH-A6WC      TCGA-L5-A43C 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OF      TCGA-L5-A4OH 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A4OJ      TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A4OP      TCGA-L5-A4OQ      TCGA-L5-A4OR      TCGA-L5-A4OS 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OX      TCGA-L5-A88S 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A88V      TCGA-L5-A88W      TCGA-L5-A88Z      TCGA-L5-A891 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A893      TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NH 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A8NI      TCGA-L5-A8NJ      TCGA-L5-A8NK      TCGA-L5-A8NL 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A8NM      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NS 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L5-A8NU      TCGA-L5-A8NV      TCGA-L5-A8NW      TCGA-L7-A56G 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-L7-A6VZ      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-LN-A8I1      TCGA-LN-A9FO 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-LN-A9FP      TCGA-LN-A9FQ      TCGA-LN-A9FR      TCGA-Q9-A6FW 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6DQ      TCGA-R6-A6KZ      TCGA-R6-A6L4 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R6-A6L6      TCGA-R6-A6XG      TCGA-R6-A6XQ      TCGA-R6-A6Y0 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R6-A8WG      TCGA-RE-A7BO      TCGA-S8-A6BW      TCGA-V5-A7RC 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-V5-A7RE      TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VR-A8EO      TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ET 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE      TCGA-Z6-A9VB 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-Z6-AAPN      TCGA-ZR-A9CJ      TCGA-B7-5816      TCGA-B7-5818 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4256      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-D7-5577 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-A6EV      TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-A6F0      TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-D7-A74A      TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IN-A6RJ      TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IN-A6RP      TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IN-A7NT      TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-IP-7968      TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A666 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R5-A7O7      TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-R5-A7ZR      TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-RD-A7BT      TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-RD-A8MW      TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-RD-A8N4      TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-SW-A7EA      TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DU 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-A8P2      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-AA64      TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-AA6B      TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
     TCGA-VQ-AA6J      TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"PROK2 WILD-TYPE" "PROK2 WILD-TYPE" "PROK2 WILD-TYPE" 
D1155V12, binary
                 cls
clus                0   1
  PROK2 MUTATED     0   2
  PROK2 WILD-TYPE  10 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROK2 MUTATED      0    2
  PROK2 WILD-TYPE   10  396
                        clus
vv                       PROK2 MUTATED PROK2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             2             396
[1] 2 2
[1] FALSE

Clustering(1156) Variable = GIGYF2 MUTATION ANALYSIS
D1156V1, survival
                  sevent
clus2                0   1
  GIGYF2 MUTATED    14   4
  GIGYF2 WILD-TYPE 324 212
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              18              536 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              212 
$`GIGYF2 MUTATED`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A88T TCGA-IG-A3I8 TCGA-LN-A7HX TCGA-LN-A8I0 
       15.68        34.85        22.82        33.27        12.23        13.38 
TCGA-V5-AASX TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 
        8.98        11.01         6.97         9.67        34.68        30.90 
TCGA-BR-6852 TCGA-BR-7959 TCGA-BR-8081 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5721 
       44.94        33.21        32.25         0.26         6.58         6.02 

$`GIGYF2 WILD-TYPE`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
            0.26             0.00 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           44.94           122.30 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          14.530           13.565 
[1] "0.3 - 44.9 (14.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2"  
D1156V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GIGYF2 MUTATED         0        2        1        0         6         4
  GIGYF2 WILD-TYPE      10       18       45       31        78        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIGYF2 MUTATED           0          3          0          0        1
  GIGYF2 WILD-TYPE        29         81         62         39       42
                  vv
clus               STAGE IVA
  GIGYF2 MUTATED           0
  GIGYF2 WILD-TYPE         4
D1156V3, multiclass
            clus
vv           GIGYF2 MUTATED GIGYF2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                2               18
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               6               78
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GIGYF2 MUTATED       2   4   7   4
  GIGYF2 WILD-TYPE    52 131 254  98
D1156V4, multiclass
       clus
vv      GIGYF2 MUTATED GIGYF2 WILD-TYPE
  T0+T1              2               52
  T2                 4              131
  T3                 7              254
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GIGYF2 MUTATED    11   4   1   0
  GIGYF2 WILD-TYPE 184 169  88  85
D1156V5, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  N0             11              184
  N1              4              169
  N2              1               88
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V6, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    17   0
  GIGYF2 WILD-TYPE 465  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     17    0
  GIGYF2 WILD-TYPE  465   38
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0             17              465
  1              0               38
[1] 2 2
[1] FALSE
D1156V7, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED     7  12
  GIGYF2 WILD-TYPE 165 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      7   12
  GIGYF2 WILD-TYPE  165  394
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  FEMALE              7              165
  MALE               12              394
[1] 2 2
[1] FALSE
D1156V8, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    16   2
  GIGYF2 WILD-TYPE 400 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     16    2
  GIGYF2 WILD-TYPE  400  100
     clus
vv    GIGYF2 MUTATED GIGYF2 WILD-TYPE
  NO              16              400
  YES              2              100
[1] 2 2
[1] FALSE
D1156V9, continuous
D1156V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GIGYF2 MUTATED       4                         0
  GIGYF2 WILD-TYPE   129                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GIGYF2 MUTATED                                           0    14
  GIGYF2 WILD-TYPE                                         1   343
D1156V11, multiclass
                                           clus
vv                                          GIGYF2 MUTATED GIGYF2 WILD-TYPE
  ASIAN                                                  4              129
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V12, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED     0  16
  GIGYF2 WILD-TYPE  10 382
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      0   16
  GIGYF2 WILD-TYPE   10  382
                        clus
vv                       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             16              382
[1] 2 2
[1] FALSE

Clustering(1157) Variable = PSMC4 MUTATION ANALYSIS
D1157V1, survival
                 sevent
clus2               0   1
  PSMC4 MUTATED    10   5
  PSMC4 WILD-TYPE 328 211
  PSMC4 MUTATED PSMC4 WILD-TYPE 
             15             539 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
              5             211 
$`PSMC4 MUTATED`
TCGA-L5-A4OI TCGA-2H-A9GG TCGA-KH-A6WC TCGA-L5-A43H TCGA-LN-A49M TCGA-LN-A49U 
       19.99        20.05         6.28         0.30        12.66        15.35 
TCGA-LN-A4MR TCGA-R6-A8WC TCGA-BR-4184 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       13.22         2.30         6.97        12.43         6.58        11.77 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       30.51        22.68        29.98 

$`PSMC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        10.45        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        11.54        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        12.43        11.61        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PSMC4 MUTATED PSMC4 WILD-TYPE 
            0.3             0.0 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          30.51          122.30 
  PSMC4 MUTATED PSMC4 WILD-TYPE 
          12.66           13.68 
[1] "0.3 - 30.5 (12.7)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D1157V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSMC4 MUTATED         0        1        0        1         5         1
  PSMC4 WILD-TYPE      10       19       46       30        79        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMC4 MUTATED           2          2          0          2        0         0
  PSMC4 WILD-TYPE        27         82         62         37       43         4
D1157V3, multiclass
            clus
vv           PSMC4 MUTATED PSMC4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PSMC4 MUTATED       2   3   9   1
  PSMC4 WILD-TYPE    52 132 252 101
D1157V4, multiclass
       clus
vv      PSMC4 MUTATED PSMC4 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                9             252
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PSMC4 MUTATED     6   6   0   2
  PSMC4 WILD-TYPE 189 167  89  83
D1157V5, multiclass
    clus
vv   PSMC4 MUTATED PSMC4 WILD-TYPE
  N0             6             189
  N1             6             167
  N2             0              89
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V6, binary
                 cls
clus                0   1
  PSMC4 MUTATED    13   0
  PSMC4 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED     13    0
  PSMC4 WILD-TYPE  469   38
   clus
vv  PSMC4 MUTATED PSMC4 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D1157V7, binary
                 cls
clus                0   1
  PSMC4 MUTATED     3  13
  PSMC4 WILD-TYPE 169 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED      3   13
  PSMC4 WILD-TYPE  169  393
        clus
vv       PSMC4 MUTATED PSMC4 WILD-TYPE
  FEMALE             3             169
  MALE              13             393
[1] 2 2
[1] FALSE
D1157V8, binary
                 cls
clus                0   1
  PSMC4 MUTATED    10   4
  PSMC4 WILD-TYPE 406  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED     10    4
  PSMC4 WILD-TYPE  406   98
     clus
vv    PSMC4 MUTATED PSMC4 WILD-TYPE
  NO             10             406
  YES             4              98
[1] 2 2
[1] FALSE
D1157V9, continuous
D1157V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PSMC4 MUTATED       8                         0
  PSMC4 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSMC4 MUTATED                                           0     6
  PSMC4 WILD-TYPE                                         1   351
D1157V11, multiclass
                                           clus
vv                                          PSMC4 MUTATED PSMC4 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V12, binary
                 cls
clus                0   1
  PSMC4 MUTATED     0  12
  PSMC4 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMC4 MUTATED      0   12
  PSMC4 WILD-TYPE   10  386
                        clus
vv                       PSMC4 MUTATED PSMC4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(1158) Variable = ITGB8 MUTATION ANALYSIS
D1158V1, survival
                 sevent
clus2               0   1
  ITGB8 MUTATED     8   6
  ITGB8 WILD-TYPE 330 210
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             14             540 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
              6             210 
$`ITGB8 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8680 
       21.99        26.70        34.68        29.59        25.05        31.96 
TCGA-CD-A4MG TCGA-CG-5719 TCGA-D7-6527 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8243 
        6.58         1.02        10.26        14.47        26.47         5.92 
TCGA-HU-A4G8 TCGA-MX-A5UJ 
       22.68        19.73 

$`ITGB8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        3.32        11.80        31.27        14.79         7.36         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21        30.51         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ITGB8 MUTATED ITGB8 WILD-TYPE 
           1.02            0.00 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
          34.68          122.30 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
         22.335          13.495 
[1] "1.0 - 34.7 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1158V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGB8 MUTATED         0        0        3        1         2         3
  ITGB8 WILD-TYPE      10       20       43       30        82        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGB8 MUTATED           0          1          0          2        3         0
  ITGB8 WILD-TYPE        29         83         62         37       40         4
D1158V3, multiclass
            clus
vv           ITGB8 MUTATED ITGB8 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ITGB8 MUTATED       0   4   4   7
  ITGB8 WILD-TYPE    54 131 257  95
D1158V4, multiclass
       clus
vv      ITGB8 MUTATED ITGB8 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                4             257
  T4                7              95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ITGB8 MUTATED     8   3   2   2
  ITGB8 WILD-TYPE 187 170  87  83
D1158V5, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  N0             8             187
  N1             3             170
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V6, binary
                 cls
clus                0   1
  ITGB8 MUTATED    11   3
  ITGB8 WILD-TYPE 471  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED     11    3
  ITGB8 WILD-TYPE  471   35
   clus
vv  ITGB8 MUTATED ITGB8 WILD-TYPE
  0            11             471
  1             3              35
[1] 2 2
[1] FALSE
D1158V7, binary
                 cls
clus                0   1
  ITGB8 MUTATED     9   6
  ITGB8 WILD-TYPE 163 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      9    6
  ITGB8 WILD-TYPE  163  400
        clus
vv       ITGB8 MUTATED ITGB8 WILD-TYPE
  FEMALE             9             163
  MALE               6             400
[1] 2 2
[1] FALSE
D1158V8, binary
                 cls
clus                0   1
  ITGB8 MUTATED    12   1
  ITGB8 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED     12    1
  ITGB8 WILD-TYPE  404  101
     clus
vv    ITGB8 MUTATED ITGB8 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D1158V9, continuous
D1158V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGB8 MUTATED       4                         0
  ITGB8 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGB8 MUTATED                                           0     8
  ITGB8 WILD-TYPE                                         1   349
D1158V11, multiclass
                                           clus
vv                                          ITGB8 MUTATED ITGB8 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V12, binary
                 cls
clus                0   1
  ITGB8 MUTATED     0  12
  ITGB8 WILD-TYPE  10 386
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      0   12
  ITGB8 WILD-TYPE   10  386
                        clus
vv                       ITGB8 MUTATED ITGB8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            12             386
[1] 2 2
[1] FALSE

Clustering(1159) Variable = ARHGEF5 MUTATION ANALYSIS
D1159V1, survival
                   sevent
clus2                 0   1
  ARHGEF5 MUTATED     7   1
  ARHGEF5 WILD-TYPE 331 215
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                8               546 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1               215 
$`ARHGEF5 MUTATED`
TCGA-IG-A5S3 TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 
       23.41        26.70        29.59        16.14        12.62         6.02 
TCGA-FP-A4BE TCGA-HF-7132 
       11.08        77.29 

$`ARHGEF5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
             6.02              0.00 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            77.29            122.30 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
           19.775            13.530 
[1] "6.0 - 77.3 (19.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.2"
D1159V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF5 MUTATED         0        0        1        1         1         3
  ARHGEF5 WILD-TYPE      10       20       45       30        83        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF5 MUTATED           0          0          1          0        1
  ARHGEF5 WILD-TYPE        29         84         61         39       42
                   vv
clus                STAGE IVA
  ARHGEF5 MUTATED           0
  ARHGEF5 WILD-TYPE         4
D1159V3, multiclass
            clus
vv           ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ARHGEF5 MUTATED       0   2   3   3
  ARHGEF5 WILD-TYPE    54 133 258  99
D1159V4, multiclass
       clus
vv      ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  3               258
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ARHGEF5 MUTATED     5   2   0   1
  ARHGEF5 WILD-TYPE 190 171  89  84
D1159V5, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  N0               5               190
  N1               2               171
  N2               0                89
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V6, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     8   0
  ARHGEF5 WILD-TYPE 474  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      8    0
  ARHGEF5 WILD-TYPE  474   38
   clus
vv  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  0               8               474
  1               0                38
[1] 2 2
[1] FALSE
D1159V7, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     4   4
  ARHGEF5 WILD-TYPE 168 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      4    4
  ARHGEF5 WILD-TYPE  168  402
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  FEMALE               4               168
  MALE                 4               402
[1] 2 2
[1] FALSE
D1159V8, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     6   2
  ARHGEF5 WILD-TYPE 410 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      6    2
  ARHGEF5 WILD-TYPE  410  100
     clus
vv    ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  NO                6               410
  YES               2               100
[1] 2 2
[1] FALSE
D1159V9, continuous
[1] "Remove cluster labels:" "ARHGEF5 MUTATED"       
clus
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A7DP 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" "ARHGEF5 WILD-TYPE" 
D1159V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF5 MUTATED       1                         1
  ARHGEF5 WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF5 MUTATED                                           0     4
  ARHGEF5 WILD-TYPE                                         1   353
D1159V11, multiclass
                                           clus
vv                                          ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V12, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     0   6
  ARHGEF5 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      0    6
  ARHGEF5 WILD-TYPE   10  392
                        clus
vv                       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1160) Variable = INVS MUTATION ANALYSIS
D1160V1, survival
                sevent
clus2              0   1
  INVS MUTATED    11   9
  INVS WILD-TYPE 327 207
  INVS MUTATED INVS WILD-TYPE 
            20            534 
  INVS MUTATED INVS WILD-TYPE 
             9            207 
$`INVS MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-JY-A6F8 TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-4201 
       14.30         7.63       122.10         7.76        26.70        30.90 
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8382 
        9.34        34.68        19.33         0.95         4.31        25.05 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GD 
       31.96         6.58        30.51        26.47        22.32        22.75 
TCGA-HU-A4GX TCGA-HU-A4H3 
       20.25        29.00 

$`INVS WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       20.05        31.27        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        6.61        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19        17.52        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        63.06        52.21         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  INVS MUTATED INVS WILD-TYPE 
          0.95           0.00 
  INVS MUTATED INVS WILD-TYPE 
         122.1          122.3 
  INVS MUTATED INVS WILD-TYPE 
        22.535         13.445 
[1] "0.9 - 122.1 (22.5)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.1"
D1160V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INVS MUTATED         1        0        2        0         3         5
  INVS WILD-TYPE       9       20       44       31        81        78
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INVS MUTATED           2          0          0          5        2         0
  INVS WILD-TYPE        27         84         62         34       41         4
D1160V3, multiclass
            clus
vv           INVS MUTATED INVS WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             5             78
  STAGE III             2             27
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            5             34
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  INVS MUTATED       2   4   7   9
  INVS WILD-TYPE    52 131 254  93
D1160V4, multiclass
       clus
vv      INVS MUTATED INVS WILD-TYPE
  T0+T1            2             52
  T2               4            131
  T3               7            254
  T4               9             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  INVS MUTATED     8   6   3   4
  INVS WILD-TYPE 187 167  86  81
D1160V5, multiclass
    clus
vv   INVS MUTATED INVS WILD-TYPE
  N0            8            187
  N1            6            167
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V6, binary
                cls
clus               0   1
  INVS MUTATED    21   1
  INVS WILD-TYPE 461  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  INVS MUTATED     21    1
  INVS WILD-TYPE  461   37
   clus
vv  INVS MUTATED INVS WILD-TYPE
  0           21            461
  1            1             37
[1] 2 2
[1] FALSE
D1160V7, binary
                cls
clus               0   1
  INVS MUTATED    15   8
  INVS WILD-TYPE 157 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  INVS MUTATED     15    8
  INVS WILD-TYPE  157  398
        clus
vv       INVS MUTATED INVS WILD-TYPE
  FEMALE           15            157
  MALE              8            398
[1] 2 2
[1] FALSE
D1160V8, binary
                cls
clus               0   1
  INVS MUTATED    19   1
  INVS WILD-TYPE 397 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  INVS MUTATED     19    1
  INVS WILD-TYPE  397  101
     clus
vv    INVS MUTATED INVS WILD-TYPE
  NO            19            397
  YES            1            101
[1] 2 2
[1] FALSE
D1160V9, continuous
D1160V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  INVS MUTATED       6                         0
  INVS WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INVS MUTATED                                           0    14
  INVS WILD-TYPE                                         1   343
D1160V11, multiclass
                                           clus
vv                                          INVS MUTATED INVS WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V12, binary
                cls
clus               0   1
  INVS MUTATED     0  18
  INVS WILD-TYPE  10 380
[1] "tbl2"
                cls
clus             [,1] [,2]
  INVS MUTATED      0   18
  INVS WILD-TYPE   10  380
                        clus
vv                       INVS MUTATED INVS WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           18            380
[1] 2 2
[1] FALSE

Clustering(1161) Variable = E2F5 MUTATION ANALYSIS
D1161V1, survival
                sevent
clus2              0   1
  E2F5 MUTATED     3   1
  E2F5 WILD-TYPE 335 215
  E2F5 MUTATED E2F5 WILD-TYPE 
             4            550 
  E2F5 MUTATED E2F5 WILD-TYPE 
             1            215 
$`E2F5 MUTATED`
TCGA-LN-A49M TCGA-D7-A6EX TCGA-HU-A4GQ TCGA-HU-A4H3 
       12.66        11.31         0.10        29.00 

$`E2F5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  E2F5 MUTATED E2F5 WILD-TYPE 
           0.1            0.0 
  E2F5 MUTATED E2F5 WILD-TYPE 
          29.0          122.3 
  E2F5 MUTATED E2F5 WILD-TYPE 
        11.985         13.630 
[1] "0.1 - 29.0 (12.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1161V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  E2F5 MUTATED         0        0        0        0         1         0
  E2F5 WILD-TYPE      10       20       46       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F5 MUTATED           0          1          0          2        0         0
  E2F5 WILD-TYPE        29         83         62         37       43         4
D1161V3, multiclass
            clus
vv           E2F5 MUTATED E2F5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  E2F5 MUTATED       1   1   1   2
  E2F5 WILD-TYPE    53 134 260 100
D1161V4, multiclass
       clus
vv      E2F5 MUTATED E2F5 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               1            260
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  E2F5 MUTATED     1   0   2   1
  E2F5 WILD-TYPE 194 173  87  84
D1161V5, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  N0            1            194
  N1            0            173
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V6, binary
                cls
clus               0   1
  E2F5 MUTATED     5   0
  E2F5 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      5    0
  E2F5 WILD-TYPE  477   38
   clus
vv  E2F5 MUTATED E2F5 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D1161V7, binary
                cls
clus               0   1
  E2F5 MUTATED     3   2
  E2F5 WILD-TYPE 169 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      3    2
  E2F5 WILD-TYPE  169  404
        clus
vv       E2F5 MUTATED E2F5 WILD-TYPE
  FEMALE            3            169
  MALE              2            404
[1] 2 2
[1] FALSE
D1161V8, binary
                cls
clus               0   1
  E2F5 MUTATED     2   1
  E2F5 WILD-TYPE 414 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      2    1
  E2F5 WILD-TYPE  414  101
     clus
vv    E2F5 MUTATED E2F5 WILD-TYPE
  NO             2            414
  YES            1            101
[1] 2 2
[1] FALSE
D1161V9, continuous
[1] "Remove cluster labels:" "E2F5 MUTATED"          
clus
  E2F5 MUTATED E2F5 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"E2F5 WILD-TYPE" "E2F5 WILD-TYPE" "E2F5 WILD-TYPE" 
D1161V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  E2F5 MUTATED       3                         0
  E2F5 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  E2F5 MUTATED                                           0     2
  E2F5 WILD-TYPE                                         1   355
D1161V11, multiclass
                                           clus
vv                                          E2F5 MUTATED E2F5 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V12, binary
                cls
clus               0   1
  E2F5 MUTATED     0   5
  E2F5 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      0    5
  E2F5 WILD-TYPE   10  393
                        clus
vv                       E2F5 MUTATED E2F5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1162) Variable = MKI67IP MUTATION ANALYSIS
D1162V1, survival
                   sevent
clus2                 0   1
  MKI67IP MUTATED     3   6
  MKI67IP WILD-TYPE 335 210
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                9               545 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                6               210 
$`MKI67IP MUTATED`
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-R6-A6XQ TCGA-BR-4184 TCGA-BR-4256 TCGA-CD-8530 
        7.76        83.24         6.35         6.97         9.34        12.39 
TCGA-CG-4300 TCGA-CG-5721 TCGA-FP-A4BE 
       20.02         6.02        11.08 

$`MKI67IP WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       13.22         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         4.08         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.61         6.58        12.20        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  MKI67IP MUTATED MKI67IP WILD-TYPE 
             6.02              0.00 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
            83.24            122.30 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
             9.34             13.78 
[1] "6.0 - 83.2 (9.3)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "2"  
D1162V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MKI67IP MUTATED         0        0        0        1         2         1
  MKI67IP WILD-TYPE      10       20       46       30        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MKI67IP MUTATED           0          1          1          0        1
  MKI67IP WILD-TYPE        29         83         61         39       42
                   vv
clus                STAGE IVA
  MKI67IP MUTATED           0
  MKI67IP WILD-TYPE         4
D1162V3, multiclass
            clus
vv           MKI67IP MUTATED MKI67IP WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  MKI67IP MUTATED       0   2   4   1
  MKI67IP WILD-TYPE    54 133 257 101
D1162V4, multiclass
       clus
vv      MKI67IP MUTATED MKI67IP WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  4               257
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  MKI67IP MUTATED     3   4   1   0
  MKI67IP WILD-TYPE 192 169  88  85
D1162V5, multiclass
    clus
vv   MKI67IP MUTATED MKI67IP WILD-TYPE
  N0               3               192
  N1               4               169
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V6, binary
                   cls
clus                  0   1
  MKI67IP MUTATED     7   0
  MKI67IP WILD-TYPE 475  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      7    0
  MKI67IP WILD-TYPE  475   38
   clus
vv  MKI67IP MUTATED MKI67IP WILD-TYPE
  0               7               475
  1               0                38
[1] 2 2
[1] FALSE
D1162V7, binary
                   cls
clus                  0   1
  MKI67IP MUTATED     1   8
  MKI67IP WILD-TYPE 171 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      1    8
  MKI67IP WILD-TYPE  171  398
        clus
vv       MKI67IP MUTATED MKI67IP WILD-TYPE
  FEMALE               1               171
  MALE                 8               398
[1] 2 2
[1] FALSE
D1162V8, binary
                   cls
clus                  0   1
  MKI67IP MUTATED     5   2
  MKI67IP WILD-TYPE 411 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      5    2
  MKI67IP WILD-TYPE  411  100
     clus
vv    MKI67IP MUTATED MKI67IP WILD-TYPE
  NO                5               411
  YES               2               100
[1] 2 2
[1] FALSE
D1162V9, continuous
D1162V10, continuous
[1] "Remove cluster labels:" "MKI67IP MUTATED"       
clus
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" "MKI67IP WILD-TYPE" 
       TCGA-Z6-AAPN 
"MKI67IP WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MKI67IP MUTATED       1                         1
  MKI67IP WILD-TYPE   132                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKI67IP MUTATED                                           0     5
  MKI67IP WILD-TYPE                                         1   352
D1162V11, multiclass
                                           clus
vv                                          MKI67IP MUTATED MKI67IP WILD-TYPE
  ASIAN                                                   1               132
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V12, binary
                   cls
clus                  0   1
  MKI67IP MUTATED     0   5
  MKI67IP WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      0    5
  MKI67IP WILD-TYPE   10  393
                        clus
vv                       MKI67IP MUTATED MKI67IP WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(1163) Variable = TMEM63A MUTATION ANALYSIS
D1163V1, survival
                   sevent
clus2                 0   1
  TMEM63A MUTATED     6   6
  TMEM63A WILD-TYPE 332 210
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               12               542 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                6               210 
$`TMEM63A MUTATED`
TCGA-R6-A6L6 TCGA-VR-A8EZ TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-8536 
        7.04        18.18        29.59        25.05        28.14        12.43 
TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       15.95       105.07        21.07         0.10        38.14        18.41 

$`TMEM63A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        42.64        66.81        11.24        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TMEM63A MUTATED TMEM63A WILD-TYPE 
              0.1               0.0 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
           105.07            122.30 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
           19.740            13.495 
[1] "0.1 - 105.1 (19.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1163V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM63A MUTATED         0        0        0        3         0         2
  TMEM63A WILD-TYPE      10       20       46       28        84        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM63A MUTATED           0          2          1          4        1
  TMEM63A WILD-TYPE        29         82         61         35       42
                   vv
clus                STAGE IVA
  TMEM63A MUTATED           0
  TMEM63A WILD-TYPE         4
D1163V3, multiclass
            clus
vv           TMEM63A MUTATED TMEM63A WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 3                28
  STAGE IIA                0                84
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               2                82
  STAGE IIIB               1                61
  STAGE IIIC               4                35
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  TMEM63A MUTATED       0   3   3   7
  TMEM63A WILD-TYPE    54 132 258  95
D1163V4, multiclass
       clus
vv      TMEM63A MUTATED TMEM63A WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                  3               258
  T4                  7                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  TMEM63A MUTATED     3   4   4   3
  TMEM63A WILD-TYPE 192 169  85  82
D1163V5, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  N0               3               192
  N1               4               169
  N2               4                85
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V6, binary
                   cls
clus                  0   1
  TMEM63A MUTATED    14   0
  TMEM63A WILD-TYPE 468  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED     14    0
  TMEM63A WILD-TYPE  468   38
   clus
vv  TMEM63A MUTATED TMEM63A WILD-TYPE
  0              14               468
  1               0                38
[1] 2 2
[1] FALSE
D1163V7, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     5  10
  TMEM63A WILD-TYPE 167 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      5   10
  TMEM63A WILD-TYPE  167  396
        clus
vv       TMEM63A MUTATED TMEM63A WILD-TYPE
  FEMALE               5               167
  MALE                10               396
[1] 2 2
[1] FALSE
D1163V8, binary
                   cls
clus                  0   1
  TMEM63A MUTATED    11   2
  TMEM63A WILD-TYPE 405 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED     11    2
  TMEM63A WILD-TYPE  405  100
     clus
vv    TMEM63A MUTATED TMEM63A WILD-TYPE
  NO               11               405
  YES               2               100
[1] 2 2
[1] FALSE
D1163V9, continuous
[1] "Remove cluster labels:" "TMEM63A MUTATED"       
clus
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-A8EP        TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
D1163V10, continuous
[1] "Remove cluster labels:" "TMEM63A MUTATED"       
clus
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" "TMEM63A WILD-TYPE" 
       TCGA-Z6-AAPN 
"TMEM63A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM63A MUTATED       2                         0
  TMEM63A WILD-TYPE   131                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM63A MUTATED                                           0    10
  TMEM63A WILD-TYPE                                         1   347
D1163V11, multiclass
                                           clus
vv                                          TMEM63A MUTATED TMEM63A WILD-TYPE
  ASIAN                                                   2               131
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V12, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     0   9
  TMEM63A WILD-TYPE  10 389
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      0    9
  TMEM63A WILD-TYPE   10  389
                        clus
vv                       TMEM63A MUTATED TMEM63A WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               9               389
[1] 2 2
[1] FALSE

Clustering(1164) Variable = ZCCHC2 MUTATION ANALYSIS
D1164V1, survival
                  sevent
clus2                0   1
  ZCCHC2 MUTATED     5   3
  ZCCHC2 WILD-TYPE 333 213
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               8              546 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               3              213 
$`ZCCHC2 MUTATED`
TCGA-LN-A4A6 TCGA-VR-AA4G TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8285 
       12.85        18.05         6.97        34.68        36.16         0.56 
TCGA-CD-8536 TCGA-VQ-A8PE 
       12.43        22.19 

$`ZCCHC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PK 
       13.02        43.36        37.41        38.14        37.22        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
            0.56             0.00 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
           36.16           122.30 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
          15.450           13.565 
[1] "0.6 - 36.2 (15.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1164V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC2 MUTATED         0        1        0        2         1         0
  ZCCHC2 WILD-TYPE      10       19       46       29        83        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC2 MUTATED           0          2          1          1        0
  ZCCHC2 WILD-TYPE        29         82         61         38       43
                  vv
clus               STAGE IVA
  ZCCHC2 MUTATED           0
  ZCCHC2 WILD-TYPE         4
D1164V3, multiclass
            clus
vv           ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                2               29
  STAGE IIA               1               83
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZCCHC2 MUTATED       1   2   4   1
  ZCCHC2 WILD-TYPE    53 133 257 101
D1164V4, multiclass
       clus
vv      ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 4              257
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZCCHC2 MUTATED     4   1   1   2
  ZCCHC2 WILD-TYPE 191 172  88  83
D1164V5, multiclass
    clus
vv   ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  N0              4              191
  N1              1              172
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V6, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     7   0
  ZCCHC2 WILD-TYPE 475  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      7    0
  ZCCHC2 WILD-TYPE  475   38
   clus
vv  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  0              7              475
  1              0               38
[1] 2 2
[1] FALSE
D1164V7, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     3   5
  ZCCHC2 WILD-TYPE 169 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      3    5
  ZCCHC2 WILD-TYPE  169  401
        clus
vv       ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  FEMALE              3              169
  MALE                5              401
[1] 2 2
[1] FALSE
D1164V8, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     8   0
  ZCCHC2 WILD-TYPE 408 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      8    0
  ZCCHC2 WILD-TYPE  408  102
     clus
vv    ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  NO               8              408
  YES              0              102
[1] 2 2
[1] FALSE
D1164V9, continuous
[1] "Remove cluster labels:" "ZCCHC2 MUTATED"        
clus
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
D1164V10, continuous
[1] "Remove cluster labels:" "ZCCHC2 MUTATED"        
clus
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" "ZCCHC2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC2 MUTATED       2                         0
  ZCCHC2 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC2 MUTATED                                           0     6
  ZCCHC2 WILD-TYPE                                         1   351
D1164V11, multiclass
                                           clus
vv                                          ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V12, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     0   6
  ZCCHC2 WILD-TYPE  10 392
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      0    6
  ZCCHC2 WILD-TYPE   10  392
                        clus
vv                       ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              6              392
[1] 2 2
[1] FALSE

Clustering(1165) Variable = EPHB6 MUTATION ANALYSIS
D1165V1, survival
                 sevent
clus2               0   1
  EPHB6 MUTATED    13   7
  EPHB6 WILD-TYPE 325 209
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             20             534 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              7             209 
$`EPHB6 MUTATED`
TCGA-2H-A9GR TCGA-JY-A6FE TCGA-JY-A93D TCGA-L5-A88W TCGA-V5-AASV TCGA-BR-4184 
       32.45         3.68        31.56        25.12        15.35         6.97 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 
       34.68        30.90        35.84        29.59        31.10        28.14 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5728 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4H3 
       31.96         6.58        65.10        11.44        14.47        29.00 
TCGA-HU-A4H5 TCGA-VQ-A8P2 
       23.80        38.14 

$`EPHB6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75        68.02        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
       29.00         7.13         7.43        15.48         2.60         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  EPHB6 MUTATED EPHB6 WILD-TYPE 
           3.68            0.00 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
           65.1           122.3 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
         29.295          13.410 
[1] "3.7 - 65.1 (29.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.7"
D1165V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHB6 MUTATED         0        1        4        0         4         2
  EPHB6 WILD-TYPE      10       19       42       31        80        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHB6 MUTATED           1          3          1          4        1         0
  EPHB6 WILD-TYPE        28         81         61         35       42         4
D1165V3, multiclass
            clus
vv           EPHB6 MUTATED EPHB6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               4              42
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             4              35
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  EPHB6 MUTATED       1   5   9   6
  EPHB6 WILD-TYPE    53 130 252  96
D1165V4, multiclass
       clus
vv      EPHB6 MUTATED EPHB6 WILD-TYPE
  T0+T1             1              53
  T2                5             130
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  EPHB6 MUTATED    11   3   3   4
  EPHB6 WILD-TYPE 184 170  86  81
D1165V5, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  N0            11             184
  N1             3             170
  N2             3              86
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V6, binary
                 cls
clus                0   1
  EPHB6 MUTATED    18   1
  EPHB6 WILD-TYPE 464  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED     18    1
  EPHB6 WILD-TYPE  464   37
   clus
vv  EPHB6 MUTATED EPHB6 WILD-TYPE
  0            18             464
  1             1              37
[1] 2 2
[1] FALSE
D1165V7, binary
                 cls
clus                0   1
  EPHB6 MUTATED     8  14
  EPHB6 WILD-TYPE 164 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      8   14
  EPHB6 WILD-TYPE  164  392
        clus
vv       EPHB6 MUTATED EPHB6 WILD-TYPE
  FEMALE             8             164
  MALE              14             392
[1] 2 2
[1] FALSE
D1165V8, binary
                 cls
clus                0   1
  EPHB6 MUTATED    14   5
  EPHB6 WILD-TYPE 402  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED     14    5
  EPHB6 WILD-TYPE  402   97
     clus
vv    EPHB6 MUTATED EPHB6 WILD-TYPE
  NO             14             402
  YES             5              97
[1] 2 2
[1] FALSE
D1165V9, continuous
[1] "Remove cluster labels:" "EPHB6 MUTATED"         
clus
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
D1165V10, continuous
[1] "Remove cluster labels:" "EPHB6 MUTATED"         
clus
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHB6 MUTATED       5                         1
  EPHB6 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHB6 MUTATED                                           0    14
  EPHB6 WILD-TYPE                                         1   343
D1165V11, multiclass
                                           clus
vv                                          EPHB6 MUTATED EPHB6 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V12, binary
                 cls
clus                0   1
  EPHB6 MUTATED     0  16
  EPHB6 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      0   16
  EPHB6 WILD-TYPE   10  382
                        clus
vv                       EPHB6 MUTATED EPHB6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(1166) Variable = GPR1 MUTATION ANALYSIS
D1166V1, survival
                sevent
clus2              0   1
  GPR1 MUTATED     5   2
  GPR1 WILD-TYPE 333 214
  GPR1 MUTATED GPR1 WILD-TYPE 
             7            547 
  GPR1 MUTATED GPR1 WILD-TYPE 
             2            214 
$`GPR1 MUTATED`
TCGA-XP-A8T7 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A6EY TCGA-HU-A4GU 
       41.23        35.84        31.96         6.58        11.44         6.58 
TCGA-MX-A5UJ 
       19.73 

$`GPR1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GPR1 MUTATED GPR1 WILD-TYPE 
          6.58           0.00 
  GPR1 MUTATED GPR1 WILD-TYPE 
         41.23         122.30 
  GPR1 MUTATED GPR1 WILD-TYPE 
         19.73          13.55 
[1] "6.6 - 41.2 (19.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1166V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR1 MUTATED         0        0        1        0         2         1
  GPR1 WILD-TYPE      10       20       45       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR1 MUTATED           0          1          1          0        1         0
  GPR1 WILD-TYPE        29         83         61         39       42         4
D1166V3, multiclass
            clus
vv           GPR1 MUTATED GPR1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GPR1 MUTATED       0   2   4   1
  GPR1 WILD-TYPE    54 133 257 101
D1166V4, multiclass
       clus
vv      GPR1 MUTATED GPR1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               4            257
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GPR1 MUTATED     3   1   2   1
  GPR1 WILD-TYPE 192 172  87  84
D1166V5, multiclass
    clus
vv   GPR1 MUTATED GPR1 WILD-TYPE
  N0            3            192
  N1            1            172
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V6, binary
                cls
clus               0   1
  GPR1 MUTATED     6   1
  GPR1 WILD-TYPE 476  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      6    1
  GPR1 WILD-TYPE  476   37
   clus
vv  GPR1 MUTATED GPR1 WILD-TYPE
  0            6            476
  1            1             37
[1] 2 2
[1] FALSE
D1166V7, binary
                cls
clus               0   1
  GPR1 MUTATED     4   3
  GPR1 WILD-TYPE 168 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      4    3
  GPR1 WILD-TYPE  168  403
        clus
vv       GPR1 MUTATED GPR1 WILD-TYPE
  FEMALE            4            168
  MALE              3            403
[1] 2 2
[1] FALSE
D1166V8, binary
                cls
clus               0   1
  GPR1 MUTATED     7   0
  GPR1 WILD-TYPE 409 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      7    0
  GPR1 WILD-TYPE  409  102
     clus
vv    GPR1 MUTATED GPR1 WILD-TYPE
  NO             7            409
  YES            0            102
[1] 2 2
[1] FALSE
D1166V9, continuous
[1] "Remove cluster labels:" "GPR1 MUTATED"          
clus
  GPR1 MUTATED GPR1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
D1166V10, continuous
[1] "Remove cluster labels:" "GPR1 MUTATED"          
clus
  GPR1 MUTATED GPR1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T8 
"GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" "GPR1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"GPR1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GPR1 MUTATED       3                         0
  GPR1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR1 MUTATED                                           0     4
  GPR1 WILD-TYPE                                         1   353
D1166V11, multiclass
                                           clus
vv                                          GPR1 MUTATED GPR1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V12, binary
                cls
clus               0   1
  GPR1 MUTATED     1   6
  GPR1 WILD-TYPE   9 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      1    6
  GPR1 WILD-TYPE    9  392
                        clus
vv                       GPR1 MUTATED GPR1 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1167) Variable = PCDHGC3 MUTATION ANALYSIS
D1167V1, survival
                   sevent
clus2                 0   1
  PCDHGC3 MUTATED     8   6
  PCDHGC3 WILD-TYPE 330 210
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
               14               540 
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
                6               210 
$`PCDHGC3 MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-JY-A93D TCGA-L5-A8NM TCGA-B7-5816 TCGA-BR-4184 
       19.99         5.16        31.56         7.76        26.70         6.97 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8368 TCGA-CD-8536 TCGA-CD-A4MI 
        9.67        34.68        32.78         4.31        12.43        11.77 
TCGA-HU-A4GU TCGA-HU-A4HD 
        6.58        33.40 

$`PCDHGC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
             4.31              0.00 
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
            34.68            122.30 
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
            12.10             13.63 
[1] "4.3 - 34.7 (12.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1167V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCDHGC3 MUTATED         0        0        1        1         2         3
  PCDHGC3 WILD-TYPE      10       20       45       30        82        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGC3 MUTATED           0          3          1          2        0
  PCDHGC3 WILD-TYPE        29         81         61         37       43
                   vv
clus                STAGE IVA
  PCDHGC3 MUTATED           0
  PCDHGC3 WILD-TYPE         4
D1167V3, multiclass
            clus
vv           PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 1                30
  STAGE IIA                2                82
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               1                61
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  PCDHGC3 MUTATED       0   3  10   1
  PCDHGC3 WILD-TYPE    54 132 251 101
D1167V4, multiclass
       clus
vv      PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  T0+T1               0                54
  T2                  3               132
  T3                 10               251
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  PCDHGC3 MUTATED     5   4   2   2
  PCDHGC3 WILD-TYPE 190 169  87  83
D1167V5, multiclass
    clus
vv   PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  N0               5               190
  N1               4               169
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V6, binary
                   cls
clus                  0   1
  PCDHGC3 MUTATED    12   0
  PCDHGC3 WILD-TYPE 470  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC3 MUTATED     12    0
  PCDHGC3 WILD-TYPE  470   38
   clus
vv  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  0              12               470
  1               0                38
[1] 2 2
[1] FALSE
D1167V7, binary
                   cls
clus                  0   1
  PCDHGC3 MUTATED     8   7
  PCDHGC3 WILD-TYPE 164 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC3 MUTATED      8    7
  PCDHGC3 WILD-TYPE  164  399
        clus
vv       PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  FEMALE               8               164
  MALE                 7               399
[1] 2 2
[1] FALSE
D1167V8, binary
                   cls
clus                  0   1
  PCDHGC3 MUTATED    13   1
  PCDHGC3 WILD-TYPE 403 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC3 MUTATED     13    1
  PCDHGC3 WILD-TYPE  403  101
     clus
vv    PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  NO               13               403
  YES               1               101
[1] 2 2
[1] FALSE
D1167V9, continuous
D1167V10, continuous
[1] "Remove cluster labels:" "PCDHGC3 MUTATED"       
clus
  PCDHGC3 MUTATED PCDHGC3 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-IC-A6RE        TCGA-IG-A3QL        TCGA-IG-A3Y9 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3        TCGA-IG-A4QT 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS        TCGA-IG-A8O2 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE        TCGA-JY-A6FG 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C        TCGA-L5-A43E 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM        TCGA-L5-A4ON 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OT 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" "PCDHGC3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PCDHGC3 MUTATED       4                         0
  PCDHGC3 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCDHGC3 MUTATED                                           0    11
  PCDHGC3 WILD-TYPE                                         1   346
D1167V11, multiclass
                                           clus
vv                                          PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V12, binary
                   cls
clus                  0   1
  PCDHGC3 MUTATED     0  12
  PCDHGC3 WILD-TYPE  10 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC3 MUTATED      0   12
  PCDHGC3 WILD-TYPE   10  386
                        clus
vv                       PCDHGC3 MUTATED PCDHGC3 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              12               386
[1] 2 2
[1] FALSE

Clustering(1168) Variable = CACNA1H MUTATION ANALYSIS
D1168V1, survival
                   sevent
clus2                 0   1
  CACNA1H MUTATED    25  14
  CACNA1H WILD-TYPE 313 202
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               39               515 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
               14               202 
$`CACNA1H MUTATED`
TCGA-L5-A4OI TCGA-IG-A97H TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A8NM TCGA-L5-A8NV 
       19.99        14.50        18.35         7.17         7.76        52.57 
TCGA-LN-A4A4 TCGA-LN-A4MR TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-B7-A5TI TCGA-BR-4201 
       12.59        13.22         5.06         6.35        19.56        30.90 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
        9.67        34.68        32.25        31.27         1.12        31.96 
TCGA-BR-A44U TCGA-BR-A4QL TCGA-CD-8534 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 
       13.87        16.14        12.07         6.58         6.02        28.96 
TCGA-D7-8570 TCGA-D7-A4YY TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HJ-7597 
       24.72        13.78        14.47        19.53        11.08        26.47 
TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-KB-A6F5 TCGA-R5-A7O7 
        3.25        29.98         8.98         2.10         5.56        45.67 
TCGA-RD-A7C1 TCGA-VQ-A8P2 TCGA-VQ-A8PQ 
       16.67        38.14        15.65 

$`CACNA1H WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
        1.32         2.66        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       18.35         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
        1.87        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CACNA1H MUTATED CACNA1H WILD-TYPE 
             1.12              0.00 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
            52.57            122.30 
  CACNA1H MUTATED CACNA1H WILD-TYPE 
            14.50             13.48 
[1] "1.1 - 52.6 (14.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1168V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CACNA1H MUTATED         0        2        3        1         9         4
  CACNA1H WILD-TYPE      10       18       43       30        75        79
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1H MUTATED           1          2          5          4        4
  CACNA1H WILD-TYPE        28         82         57         35       39
                   vv
clus                STAGE IVA
  CACNA1H MUTATED           0
  CACNA1H WILD-TYPE         4
D1168V3, multiclass
            clus
vv           CACNA1H MUTATED CACNA1H WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                18
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                9                75
  STAGE IIB                4                79
  STAGE III                1                28
  STAGE IIIA               2                82
  STAGE IIIB               5                57
  STAGE IIIC               4                35
  STAGE IV                 4                39
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CACNA1H MUTATED       3   8  16   9
  CACNA1H WILD-TYPE    51 127 245  93
D1168V4, multiclass
       clus
vv      CACNA1H MUTATED CACNA1H WILD-TYPE
  T0+T1               3                51
  T2                  8               127
  T3                 16               245
  T4                  9                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CACNA1H MUTATED    13  11   3   8
  CACNA1H WILD-TYPE 182 162  86  77
D1168V5, multiclass
    clus
vv   CACNA1H MUTATED CACNA1H WILD-TYPE
  N0              13               182
  N1              11               162
  N2               3                86
  N3               8                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V6, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    31   3
  CACNA1H WILD-TYPE 451  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     31    3
  CACNA1H WILD-TYPE  451   35
   clus
vv  CACNA1H MUTATED CACNA1H WILD-TYPE
  0              31               451
  1               3                35
[1] 2 2
[1] FALSE
D1168V7, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    12  28
  CACNA1H WILD-TYPE 160 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     12   28
  CACNA1H WILD-TYPE  160  378
        clus
vv       CACNA1H MUTATED CACNA1H WILD-TYPE
  FEMALE              12               160
  MALE                28               378
[1] 2 2
[1] FALSE
D1168V8, binary
                   cls
clus                  0   1
  CACNA1H MUTATED    30   5
  CACNA1H WILD-TYPE 386  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED     30    5
  CACNA1H WILD-TYPE  386   97
     clus
vv    CACNA1H MUTATED CACNA1H WILD-TYPE
  NO               30               386
  YES               5                97
[1] 2 2
[1] FALSE
D1168V9, continuous
[1] "Remove cluster labels:" "CACNA1H MUTATED"       
clus
  CACNA1H MUTATED CACNA1H WILD-TYPE 
                2                66 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A5        TCGA-LN-A4A6 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A5U5 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ        TCGA-V5-A7RB 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV        TCGA-V5-AASW 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP        TCGA-VR-A8EQ 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU        TCGA-VR-A8EW 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B        TCGA-VR-AA7D 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
       TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"CACNA1H WILD-TYPE" "CACNA1H WILD-TYPE" 
D1168V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CACNA1H MUTATED      10                         1
  CACNA1H WILD-TYPE   123                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CACNA1H MUTATED                                           0    26
  CACNA1H WILD-TYPE                                         1   331
D1168V11, multiclass
                                           clus
vv                                          CACNA1H MUTATED CACNA1H WILD-TYPE
  ASIAN                                                  10               123
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V12, binary
                   cls
clus                  0   1
  CACNA1H MUTATED     1  29
  CACNA1H WILD-TYPE   9 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1H MUTATED      1   29
  CACNA1H WILD-TYPE    9  369
                        clus
vv                       CACNA1H MUTATED CACNA1H WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              29               369
[1] 2 2
[1] FALSE

Clustering(1169) Variable = RPS6KA5 MUTATION ANALYSIS
D1169V1, survival
                   sevent
clus2                 0   1
  RPS6KA5 MUTATED     6   3
  RPS6KA5 WILD-TYPE 332 213
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                9               545 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                3               213 
$`RPS6KA5 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-LN-A4MR TCGA-R6-A8WC TCGA-BR-8368 TCGA-D7-A747 
        4.31        24.00        13.22         2.30         4.31         8.38 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-VQ-A8P2 
       22.68         6.51        38.14 

$`RPS6KA5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
              2.3               0.0 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            38.14            122.30 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
             8.38             13.68 
[1] "2.3 - 38.1 (8.4)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "1.1"
D1169V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RPS6KA5 MUTATED         0        0        1        0         2         3
  RPS6KA5 WILD-TYPE      10       20       45       31        82        80
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA5 MUTATED           0          1          1          0        0
  RPS6KA5 WILD-TYPE        29         83         61         39       43
                   vv
clus                STAGE IVA
  RPS6KA5 MUTATED           0
  RPS6KA5 WILD-TYPE         4
D1169V3, multiclass
            clus
vv           RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                3                80
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  RPS6KA5 MUTATED       0   2   5   1
  RPS6KA5 WILD-TYPE    54 133 256 101
D1169V4, multiclass
       clus
vv      RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  T0+T1               0                54
  T2                  2               133
  T3                  5               256
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  RPS6KA5 MUTATED     4   3   1   0
  RPS6KA5 WILD-TYPE 191 170  88  85
D1169V5, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  N0               4               191
  N1               3               170
  N2               1                88
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V6, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     6   0
  RPS6KA5 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      6    0
  RPS6KA5 WILD-TYPE  476   38
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D1169V7, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     3   6
  RPS6KA5 WILD-TYPE 169 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      3    6
  RPS6KA5 WILD-TYPE  169  400
        clus
vv       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  FEMALE               3               169
  MALE                 6               400
[1] 2 2
[1] FALSE
D1169V8, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     6   1
  RPS6KA5 WILD-TYPE 410 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      6    1
  RPS6KA5 WILD-TYPE  410  101
     clus
vv    RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  NO                6               410
  YES               1               101
[1] 2 2
[1] FALSE
D1169V9, continuous
[1] "Remove cluster labels:" "RPS6KA5 MUTATED"       
clus
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
D1169V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RPS6KA5 MUTATED       3                         0
  RPS6KA5 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPS6KA5 MUTATED                                           0     6
  RPS6KA5 WILD-TYPE                                         1   351
D1169V11, multiclass
                                           clus
vv                                          RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V12, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     0   6
  RPS6KA5 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      0    6
  RPS6KA5 WILD-TYPE   10  392
                        clus
vv                       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1170) Variable = NAGPA MUTATION ANALYSIS
D1170V1, survival
                 sevent
clus2               0   1
  NAGPA MUTATED     6   2
  NAGPA WILD-TYPE 332 214
  NAGPA MUTATED NAGPA WILD-TYPE 
              8             546 
  NAGPA MUTATED NAGPA WILD-TYPE 
              2             214 
$`NAGPA MUTATED`
TCGA-JY-A93E TCGA-VR-A8EW TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8487 TCGA-CG-5730 
       25.22         8.12        44.94         8.05         1.12         4.01 
TCGA-HU-A4G3 TCGA-HU-A4GF 
        5.59        25.81 

$`NAGPA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       22.32        22.82        21.07         0.76        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NAGPA MUTATED NAGPA WILD-TYPE 
           1.12            0.00 
  NAGPA MUTATED NAGPA WILD-TYPE 
          44.94          122.30 
  NAGPA MUTATED NAGPA WILD-TYPE 
          8.085          13.630 
[1] "1.1 - 44.9 (8.1)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1170V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAGPA MUTATED         1        0        0        0         3         1
  NAGPA WILD-TYPE       9       20       46       31        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAGPA MUTATED           0          1          1          1        1         0
  NAGPA WILD-TYPE        29         83         61         38       42         4
D1170V3, multiclass
            clus
vv           NAGPA MUTATED NAGPA WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NAGPA MUTATED       1   2   5   1
  NAGPA WILD-TYPE    53 133 256 101
D1170V4, multiclass
       clus
vv      NAGPA MUTATED NAGPA WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                5             256
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NAGPA MUTATED     3   3   2   1
  NAGPA WILD-TYPE 192 170  87  84
D1170V5, multiclass
    clus
vv   NAGPA MUTATED NAGPA WILD-TYPE
  N0             3             192
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V6, binary
                 cls
clus                0   1
  NAGPA MUTATED     7   1
  NAGPA WILD-TYPE 475  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      7    1
  NAGPA WILD-TYPE  475   37
   clus
vv  NAGPA MUTATED NAGPA WILD-TYPE
  0             7             475
  1             1              37
[1] 2 2
[1] FALSE
D1170V7, binary
                 cls
clus                0   1
  NAGPA MUTATED     4   5
  NAGPA WILD-TYPE 168 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      4    5
  NAGPA WILD-TYPE  168  401
        clus
vv       NAGPA MUTATED NAGPA WILD-TYPE
  FEMALE             4             168
  MALE               5             401
[1] 2 2
[1] FALSE
D1170V8, binary
                 cls
clus                0   1
  NAGPA MUTATED     8   0
  NAGPA WILD-TYPE 408 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      8    0
  NAGPA WILD-TYPE  408  102
     clus
vv    NAGPA MUTATED NAGPA WILD-TYPE
  NO              8             408
  YES             0             102
[1] 2 2
[1] FALSE
D1170V9, continuous
[1] "Remove cluster labels:" "NAGPA MUTATED"         
clus
  NAGPA MUTATED NAGPA WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
D1170V10, continuous
[1] "Remove cluster labels:" "NAGPA MUTATED"         
clus
  NAGPA MUTATED NAGPA WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-A8ER      TCGA-VR-A8EU      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" "NAGPA WILD-TYPE" 
     TCGA-Z6-AAPN 
"NAGPA WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAGPA MUTATED       3                         1
  NAGPA WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAGPA MUTATED                                           0     4
  NAGPA WILD-TYPE                                         1   353
D1170V11, multiclass
                                           clus
vv                                          NAGPA MUTATED NAGPA WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V12, binary
                 cls
clus                0   1
  NAGPA MUTATED     0   6
  NAGPA WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      0    6
  NAGPA WILD-TYPE   10  392
                        clus
vv                       NAGPA MUTATED NAGPA WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1171) Variable = KCNJ6 MUTATION ANALYSIS
D1171V1, survival
                 sevent
clus2               0   1
  KCNJ6 MUTATED     8   3
  KCNJ6 WILD-TYPE 330 213
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
             11             543 
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
              3             213 
$`KCNJ6 MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NW TCGA-B7-5816 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       24.00        46.09        26.70         1.12        28.14        31.96 
TCGA-BR-A4QL TCGA-CG-4304 TCGA-CG-5728 TCGA-HU-A4GN TCGA-HU-A4H8 
       16.14        27.02        65.10        29.98        14.07 

$`KCNJ6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
           1.12            0.00 
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
           65.1           122.3 
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
          27.02           13.41 
[1] "1.1 - 65.1 (27.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.2"
D1171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNJ6 MUTATED         0        0        4        0         2         1
  KCNJ6 WILD-TYPE      10       20       42       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNJ6 MUTATED           0          1          2          1        1         0
  KCNJ6 WILD-TYPE        29         83         60         38       42         4
D1171V3, multiclass
            clus
vv           KCNJ6 MUTATED KCNJ6 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               4              42
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNJ6 MUTATED       1   4   3   4
  KCNJ6 WILD-TYPE    53 131 258  98
D1171V4, multiclass
       clus
vv      KCNJ6 MUTATED KCNJ6 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNJ6 MUTATED     5   3   2   2
  KCNJ6 WILD-TYPE 190 170  87  83
D1171V5, multiclass
    clus
vv   KCNJ6 MUTATED KCNJ6 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V6, binary
                 cls
clus                0   1
  KCNJ6 MUTATED    10   1
  KCNJ6 WILD-TYPE 472  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNJ6 MUTATED     10    1
  KCNJ6 WILD-TYPE  472   37
   clus
vv  KCNJ6 MUTATED KCNJ6 WILD-TYPE
  0            10             472
  1             1              37
[1] 2 2
[1] FALSE
D1171V7, binary
                 cls
clus                0   1
  KCNJ6 MUTATED     5   7
  KCNJ6 WILD-TYPE 167 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNJ6 MUTATED      5    7
  KCNJ6 WILD-TYPE  167  399
        clus
vv       KCNJ6 MUTATED KCNJ6 WILD-TYPE
  FEMALE             5             167
  MALE               7             399
[1] 2 2
[1] FALSE
D1171V8, binary
                 cls
clus                0   1
  KCNJ6 MUTATED     9   0
  KCNJ6 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNJ6 MUTATED      9    0
  KCNJ6 WILD-TYPE  407  102
     clus
vv    KCNJ6 MUTATED KCNJ6 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D1171V9, continuous
D1171V10, continuous
[1] "Remove cluster labels:" "KCNJ6 MUTATED"         
clus
  KCNJ6 MUTATED KCNJ6 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OG 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-LN-A49O      TCGA-LN-A49P 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" "KCNJ6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNJ6 MUTATED       3                         0
  KCNJ6 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNJ6 MUTATED                                           0     7
  KCNJ6 WILD-TYPE                                         1   350
D1171V11, multiclass
                                           clus
vv                                          KCNJ6 MUTATED KCNJ6 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V12, binary
                 cls
clus                0   1
  KCNJ6 MUTATED     0   8
  KCNJ6 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNJ6 MUTATED      0    8
  KCNJ6 WILD-TYPE   10  390
                        clus
vv                       KCNJ6 MUTATED KCNJ6 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1172) Variable = PIGZ MUTATION ANALYSIS
D1172V1, survival
                sevent
clus2              0   1
  PIGZ MUTATED     5   4
  PIGZ WILD-TYPE 333 212
  PIGZ MUTATED PIGZ WILD-TYPE 
             9            545 
  PIGZ MUTATED PIGZ WILD-TYPE 
             4            212 
$`PIGZ MUTATED`
TCGA-L5-A8NH TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6452 TCGA-D7-A6EY TCGA-HU-8249 
       12.92         6.97         4.08        34.68        11.44        28.96 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GU 
       22.32        22.68         6.58 

$`PIGZ WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PIGZ MUTATED PIGZ WILD-TYPE 
          4.08           0.00 
  PIGZ MUTATED PIGZ WILD-TYPE 
         34.68         122.30 
  PIGZ MUTATED PIGZ WILD-TYPE 
         12.92          13.58 
[1] "4.1 - 34.7 (12.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1172V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGZ MUTATED         0        0        0        0         1         3
  PIGZ WILD-TYPE      10       20       46       31        83        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGZ MUTATED           0          3          1          0        1         0
  PIGZ WILD-TYPE        29         81         61         39       42         4
D1172V3, multiclass
            clus
vv           PIGZ MUTATED PIGZ WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PIGZ MUTATED       1   0   7   1
  PIGZ WILD-TYPE    53 135 254 101
D1172V4, multiclass
       clus
vv      PIGZ MUTATED PIGZ WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               7            254
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PIGZ MUTATED     3   4   1   1
  PIGZ WILD-TYPE 192 169  88  84
D1172V5, multiclass
    clus
vv   PIGZ MUTATED PIGZ WILD-TYPE
  N0            3            192
  N1            4            169
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V6, binary
                cls
clus               0   1
  PIGZ MUTATED     8   1
  PIGZ WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      8    1
  PIGZ WILD-TYPE  474   37
   clus
vv  PIGZ MUTATED PIGZ WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D1172V7, binary
                cls
clus               0   1
  PIGZ MUTATED     6   4
  PIGZ WILD-TYPE 166 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      6    4
  PIGZ WILD-TYPE  166  402
        clus
vv       PIGZ MUTATED PIGZ WILD-TYPE
  FEMALE            6            166
  MALE              4            402
[1] 2 2
[1] FALSE
D1172V8, binary
                cls
clus               0   1
  PIGZ MUTATED     8   0
  PIGZ WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      8    0
  PIGZ WILD-TYPE  408  102
     clus
vv    PIGZ MUTATED PIGZ WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D1172V9, continuous
D1172V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGZ MUTATED       4                         0
  PIGZ WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGZ MUTATED                                           0     6
  PIGZ WILD-TYPE                                         1   351
D1172V11, multiclass
                                           clus
vv                                          PIGZ MUTATED PIGZ WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V12, binary
                cls
clus               0   1
  PIGZ MUTATED     0   9
  PIGZ WILD-TYPE  10 389
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      0    9
  PIGZ WILD-TYPE   10  389
                        clus
vv                       PIGZ MUTATED PIGZ WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            9            389
[1] 2 2
[1] FALSE

Clustering(1173) Variable = DBF4 MUTATION ANALYSIS
D1173V1, survival
                sevent
clus2              0   1
  DBF4 MUTATED     5   4
  DBF4 WILD-TYPE 333 212
  DBF4 MUTATED DBF4 WILD-TYPE 
             9            545 
  DBF4 MUTATED DBF4 WILD-TYPE 
             4            212 
$`DBF4 MUTATED`
TCGA-L5-A4OM TCGA-R6-A6XG TCGA-VR-AA7B TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 
       47.93        38.40        11.24         6.97        34.68         1.12 
TCGA-CG-5733 TCGA-HU-A4H3 TCGA-VQ-A8DL 
       21.07        29.00         0.92 

$`DBF4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       33.70        18.18        52.27        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DBF4 MUTATED DBF4 WILD-TYPE 
          0.92           0.00 
  DBF4 MUTATED DBF4 WILD-TYPE 
         47.93         122.30 
  DBF4 MUTATED DBF4 WILD-TYPE 
         21.07          13.55 
[1] "0.9 - 47.9 (21.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1173V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DBF4 MUTATED         0        1        0        0         3         0
  DBF4 WILD-TYPE      10       19       46       31        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBF4 MUTATED           0          2          0          1        1         0
  DBF4 WILD-TYPE        29         82         62         38       42         4
D1173V3, multiclass
            clus
vv           DBF4 MUTATED DBF4 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DBF4 MUTATED       1   1   5   1
  DBF4 WILD-TYPE    53 134 256 101
D1173V4, multiclass
       clus
vv      DBF4 MUTATED DBF4 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               5            256
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DBF4 MUTATED     4   1   1   2
  DBF4 WILD-TYPE 191 172  88  83
D1173V5, multiclass
    clus
vv   DBF4 MUTATED DBF4 WILD-TYPE
  N0            4            191
  N1            1            172
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V6, binary
                cls
clus               0   1
  DBF4 MUTATED     5   1
  DBF4 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      5    1
  DBF4 WILD-TYPE  477   37
   clus
vv  DBF4 MUTATED DBF4 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D1173V7, binary
                cls
clus               0   1
  DBF4 MUTATED     7   2
  DBF4 WILD-TYPE 165 404
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      7    2
  DBF4 WILD-TYPE  165  404
        clus
vv       DBF4 MUTATED DBF4 WILD-TYPE
  FEMALE            7            165
  MALE              2            404
[1] 2 2
[1] FALSE
D1173V8, binary
                cls
clus               0   1
  DBF4 MUTATED     8   0
  DBF4 WILD-TYPE 408 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      8    0
  DBF4 WILD-TYPE  408  102
     clus
vv    DBF4 MUTATED DBF4 WILD-TYPE
  NO             8            408
  YES            0            102
[1] 2 2
[1] FALSE
D1173V9, continuous
[1] "Remove cluster labels:" "DBF4 MUTATED"          
clus
  DBF4 MUTATED DBF4 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
D1173V10, continuous
[1] "Remove cluster labels:" "DBF4 MUTATED"          
clus
  DBF4 MUTATED DBF4 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" "DBF4 WILD-TYPE" 
    TCGA-Z6-AAPN 
"DBF4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DBF4 MUTATED       1                         0
  DBF4 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DBF4 MUTATED                                           0     7
  DBF4 WILD-TYPE                                         1   350
D1173V11, multiclass
                                           clus
vv                                          DBF4 MUTATED DBF4 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V12, binary
                cls
clus               0   1
  DBF4 MUTATED     0   5
  DBF4 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBF4 MUTATED      0    5
  DBF4 WILD-TYPE   10  393
                        clus
vv                       DBF4 MUTATED DBF4 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1174) Variable = DOK7 MUTATION ANALYSIS
D1174V1, survival
                sevent
clus2              0   1
  DOK7 MUTATED     4   2
  DOK7 WILD-TYPE 334 214
  DOK7 MUTATED DOK7 WILD-TYPE 
             6            548 
  DOK7 MUTATED DOK7 WILD-TYPE 
             2            214 
$`DOK7 MUTATED`
TCGA-CG-4460 TCGA-BR-8487 TCGA-CD-8527 TCGA-FP-8211 TCGA-HU-A4GN TCGA-HU-A4H4 
       21.99         1.12         7.17        13.58        29.98        23.84 

$`DOK7 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  DOK7 MUTATED DOK7 WILD-TYPE 
          1.12           0.00 
  DOK7 MUTATED DOK7 WILD-TYPE 
         29.98         122.30 
  DOK7 MUTATED DOK7 WILD-TYPE 
        17.785         13.530 
[1] "1.1 - 30.0 (17.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1174V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOK7 MUTATED         0        0        1        1         2         2
  DOK7 WILD-TYPE      10       20       45       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOK7 MUTATED           0          0          0          0        1         0
  DOK7 WILD-TYPE        29         84         62         39       42         4
D1174V3, multiclass
            clus
vv           DOK7 MUTATED DOK7 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  DOK7 MUTATED       0   4   2   1
  DOK7 WILD-TYPE    54 131 259 101
D1174V4, multiclass
       clus
vv      DOK7 MUTATED DOK7 WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  DOK7 MUTATED     2   4   1   0
  DOK7 WILD-TYPE 193 169  88  85
D1174V5, multiclass
    clus
vv   DOK7 MUTATED DOK7 WILD-TYPE
  N0            2            193
  N1            4            169
  N2            1             88
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V6, binary
                cls
clus               0   1
  DOK7 MUTATED     5   1
  DOK7 WILD-TYPE 477  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK7 MUTATED      5    1
  DOK7 WILD-TYPE  477   37
   clus
vv  DOK7 MUTATED DOK7 WILD-TYPE
  0            5            477
  1            1             37
[1] 2 2
[1] FALSE
D1174V7, binary
                cls
clus               0   1
  DOK7 MUTATED     4   3
  DOK7 WILD-TYPE 168 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK7 MUTATED      4    3
  DOK7 WILD-TYPE  168  403
        clus
vv       DOK7 MUTATED DOK7 WILD-TYPE
  FEMALE            4            168
  MALE              3            403
[1] 2 2
[1] FALSE
D1174V8, binary
                cls
clus               0   1
  DOK7 MUTATED     5   1
  DOK7 WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK7 MUTATED      5    1
  DOK7 WILD-TYPE  411  101
     clus
vv    DOK7 MUTATED DOK7 WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D1174V9, continuous
D1174V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DOK7 MUTATED       3                         0
  DOK7 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOK7 MUTATED                                           0     2
  DOK7 WILD-TYPE                                         1   355
D1174V11, multiclass
                                           clus
vv                                          DOK7 MUTATED DOK7 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V12, binary
                cls
clus               0   1
  DOK7 MUTATED     0   5
  DOK7 WILD-TYPE  10 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK7 MUTATED      0    5
  DOK7 WILD-TYPE   10  393
                        clus
vv                       DOK7 MUTATED DOK7 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            5            393
[1] 2 2
[1] FALSE

Clustering(1175) Variable = HECA MUTATION ANALYSIS
D1175V1, survival
                sevent
clus2              0   1
  HECA MUTATED    14   5
  HECA WILD-TYPE 324 211
  HECA MUTATED HECA WILD-TYPE 
            19            535 
  HECA MUTATED HECA WILD-TYPE 
             5            211 
$`HECA MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-LN-A5U6 TCGA-VR-A8EZ TCGA-BR-4201 TCGA-BR-6452 
       21.99         5.92        12.33        18.18        30.90        34.68 
TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8368 TCGA-CD-8531 TCGA-CD-A4MJ TCGA-CG-5721 
       30.90        35.84         4.31        12.59        12.62         6.02 
TCGA-CG-5728 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-A4G3 TCGA-HU-A4G9 
       65.10        26.47         1.51        24.39         5.59        24.20 
TCGA-MX-A5UJ 
       19.73 

$`HECA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.53         7.17        12.33        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HECA MUTATED HECA WILD-TYPE 
          1.51           0.00 
  HECA MUTATED HECA WILD-TYPE 
          65.1          122.3 
  HECA MUTATED HECA WILD-TYPE 
         19.73          13.51 
[1] "1.5 - 65.1 (19.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1175V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HECA MUTATED         0        2        5        0         1         2
  HECA WILD-TYPE      10       18       41       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HECA MUTATED           1          3          0          1        2         0
  HECA WILD-TYPE        28         81         62         38       41         4
D1175V3, multiclass
            clus
vv           HECA MUTATED HECA WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              5             41
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  HECA MUTATED       2   8   7   2
  HECA WILD-TYPE    52 127 254 100
D1175V4, multiclass
       clus
vv      HECA MUTATED HECA WILD-TYPE
  T0+T1            2             52
  T2               8            127
  T3               7            254
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  HECA MUTATED     8   5   4   1
  HECA WILD-TYPE 187 168  85  84
D1175V5, multiclass
    clus
vv   HECA MUTATED HECA WILD-TYPE
  N0            8            187
  N1            5            168
  N2            4             85
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V6, binary
                cls
clus               0   1
  HECA MUTATED    17   1
  HECA WILD-TYPE 465  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED     17    1
  HECA WILD-TYPE  465   37
   clus
vv  HECA MUTATED HECA WILD-TYPE
  0           17            465
  1            1             37
[1] 2 2
[1] FALSE
D1175V7, binary
                cls
clus               0   1
  HECA MUTATED    11   8
  HECA WILD-TYPE 161 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED     11    8
  HECA WILD-TYPE  161  398
        clus
vv       HECA MUTATED HECA WILD-TYPE
  FEMALE           11            161
  MALE              8            398
[1] 2 2
[1] FALSE
D1175V8, binary
                cls
clus               0   1
  HECA MUTATED    16   2
  HECA WILD-TYPE 400 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED     16    2
  HECA WILD-TYPE  400  100
     clus
vv    HECA MUTATED HECA WILD-TYPE
  NO            16            400
  YES            2            100
[1] 2 2
[1] FALSE
D1175V9, continuous
[1] "Remove cluster labels:" "HECA MUTATED"          
clus
  HECA MUTATED HECA WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8Q7 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"HECA WILD-TYPE" "HECA WILD-TYPE" 
D1175V10, continuous
[1] "Remove cluster labels:" "HECA MUTATED"          
clus
  HECA MUTATED HECA WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U7     TCGA-LN-A7HV 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8Q7 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" "HECA WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HECA MUTATED       7                         0
  HECA WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HECA MUTATED                                           0     8
  HECA WILD-TYPE                                         1   349
D1175V11, multiclass
                                           clus
vv                                          HECA MUTATED HECA WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V12, binary
                cls
clus               0   1
  HECA MUTATED     0  14
  HECA WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  HECA MUTATED      0   14
  HECA WILD-TYPE   10  384
                        clus
vv                       HECA MUTATED HECA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(1176) Variable = IGBP1 MUTATION ANALYSIS
D1176V1, survival
                 sevent
clus2               0   1
  IGBP1 MUTATED     4   2
  IGBP1 WILD-TYPE 334 214
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             548 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              2             214 
$`IGBP1 MUTATED`
TCGA-BR-6852 TCGA-BR-8676 TCGA-D7-A6EZ TCGA-D7-A74B TCGA-IN-A7NT TCGA-VQ-AA69 
       44.94         7.53        20.32         7.13        10.62        28.41 

$`IGBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 
       22.29        15.65         8.38         4.34        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  IGBP1 MUTATED IGBP1 WILD-TYPE 
           7.13            0.00 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
          44.94          122.30 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
         15.470          13.565 
[1] "7.1 - 44.9 (15.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1176V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGBP1 MUTATED         0        0        0        0         1         1
  IGBP1 WILD-TYPE      10       20       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGBP1 MUTATED           0          2          2          0        0         0
  IGBP1 WILD-TYPE        29         82         60         39       43         4
D1176V3, multiclass
            clus
vv           IGBP1 MUTATED IGBP1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  IGBP1 MUTATED       0   0   6   0
  IGBP1 WILD-TYPE    54 135 255 102
D1176V4, multiclass
       clus
vv      IGBP1 MUTATED IGBP1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                6             255
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  IGBP1 MUTATED     1   1   2   2
  IGBP1 WILD-TYPE 194 172  87  83
D1176V5, multiclass
    clus
vv   IGBP1 MUTATED IGBP1 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V6, binary
                 cls
clus                0   1
  IGBP1 MUTATED     6   0
  IGBP1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      6    0
  IGBP1 WILD-TYPE  476   38
   clus
vv  IGBP1 MUTATED IGBP1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1176V7, binary
                 cls
clus                0   1
  IGBP1 MUTATED     3   3
  IGBP1 WILD-TYPE 169 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      3    3
  IGBP1 WILD-TYPE  169  403
        clus
vv       IGBP1 MUTATED IGBP1 WILD-TYPE
  FEMALE             3             169
  MALE               3             403
[1] 2 2
[1] FALSE
D1176V8, binary
                 cls
clus                0   1
  IGBP1 MUTATED     5   1
  IGBP1 WILD-TYPE 411 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      5    1
  IGBP1 WILD-TYPE  411  101
     clus
vv    IGBP1 MUTATED IGBP1 WILD-TYPE
  NO              5             411
  YES             1             101
[1] 2 2
[1] FALSE
D1176V9, continuous
D1176V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IGBP1 MUTATED       0                         0
  IGBP1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGBP1 MUTATED                                           0     6
  IGBP1 WILD-TYPE                                         1   351
D1176V11, multiclass
                                           clus
vv                                          IGBP1 MUTATED IGBP1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V12, binary
                 cls
clus                0   1
  IGBP1 MUTATED     0   5
  IGBP1 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      0    5
  IGBP1 WILD-TYPE   10  393
                        clus
vv                       IGBP1 MUTATED IGBP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1177) Variable = INSM2 MUTATION ANALYSIS
D1177V1, survival
                 sevent
clus2               0   1
  INSM2 MUTATED     8   4
  INSM2 WILD-TYPE 330 212
  INSM2 MUTATED INSM2 WILD-TYPE 
             12             542 
  INSM2 MUTATED INSM2 WILD-TYPE 
              4             212 
$`INSM2 MUTATED`
TCGA-L5-A4OI TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-8368 TCGA-BR-8382 
       19.99        26.70         6.61        14.43         4.31        25.05 
TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-MX-A5UJ TCGA-VQ-A8P2 
        6.02        65.10         5.92        30.51        19.73        38.14 

$`INSM2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        4.08         9.34         9.67         6.18         9.57        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  INSM2 MUTATED INSM2 WILD-TYPE 
           4.31            0.00 
  INSM2 MUTATED INSM2 WILD-TYPE 
           65.1           122.3 
  INSM2 MUTATED INSM2 WILD-TYPE 
          19.86           13.51 
[1] "4.3 - 65.1 (19.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1177V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INSM2 MUTATED         1        0        2        0         0         2
  INSM2 WILD-TYPE       9       20       44       31        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSM2 MUTATED           2          2          0          3        1         0
  INSM2 WILD-TYPE        27         82         62         36       42         4
D1177V3, multiclass
            clus
vv           INSM2 MUTATED INSM2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  INSM2 MUTATED       1   3   3   6
  INSM2 WILD-TYPE    53 132 258  96
D1177V4, multiclass
       clus
vv      INSM2 MUTATED INSM2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  INSM2 MUTATED     3   6   1   3
  INSM2 WILD-TYPE 192 167  88  82
D1177V5, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  N0             3             192
  N1             6             167
  N2             1              88
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V6, binary
                 cls
clus                0   1
  INSM2 MUTATED    11   0
  INSM2 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED     11    0
  INSM2 WILD-TYPE  471   38
   clus
vv  INSM2 MUTATED INSM2 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D1177V7, binary
                 cls
clus                0   1
  INSM2 MUTATED     8   5
  INSM2 WILD-TYPE 164 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      8    5
  INSM2 WILD-TYPE  164  401
        clus
vv       INSM2 MUTATED INSM2 WILD-TYPE
  FEMALE             8             164
  MALE               5             401
[1] 2 2
[1] FALSE
D1177V8, binary
                 cls
clus                0   1
  INSM2 MUTATED    10   2
  INSM2 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED     10    2
  INSM2 WILD-TYPE  406  100
     clus
vv    INSM2 MUTATED INSM2 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D1177V9, continuous
D1177V10, continuous
[1] "Remove cluster labels:" "INSM2 MUTATED"         
clus
  INSM2 MUTATED INSM2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" "INSM2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"INSM2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  INSM2 MUTATED       0                         1
  INSM2 WILD-TYPE   133                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INSM2 MUTATED                                           0     9
  INSM2 WILD-TYPE                                         1   348
D1177V11, multiclass
                                           clus
vv                                          INSM2 MUTATED INSM2 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V12, binary
                 cls
clus                0   1
  INSM2 MUTATED     0   8
  INSM2 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      0    8
  INSM2 WILD-TYPE   10  390
                        clus
vv                       INSM2 MUTATED INSM2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1178) Variable = SAE1 MUTATION ANALYSIS
D1178V1, survival
                sevent
clus2              0   1
  SAE1 MUTATED     4   2
  SAE1 WILD-TYPE 334 214
  SAE1 MUTATED SAE1 WILD-TYPE 
             6            548 
  SAE1 MUTATED SAE1 WILD-TYPE 
             2            214 
$`SAE1 MUTATED`
TCGA-L5-A4OU TCGA-L5-A8NM TCGA-BR-8361 TCGA-BR-A4J2 TCGA-D7-8575 TCGA-HU-A4GN 
       29.00         7.76        31.10        14.17        18.21        29.98 

$`SAE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SAE1 MUTATED SAE1 WILD-TYPE 
          7.76           0.00 
  SAE1 MUTATED SAE1 WILD-TYPE 
          31.1          122.3 
  SAE1 MUTATED SAE1 WILD-TYPE 
        23.605         13.510 
[1] "7.8 - 31.1 (23.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D1178V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAE1 MUTATED         0        0        0        0         2         2
  SAE1 WILD-TYPE      10       20       46       31        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAE1 MUTATED           0          1          0          1        0         0
  SAE1 WILD-TYPE        29         83         62         38       43         4
D1178V3, multiclass
            clus
vv           SAE1 MUTATED SAE1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  SAE1 MUTATED       0   2   2   2
  SAE1 WILD-TYPE    54 133 259 100
D1178V4, multiclass
       clus
vv      SAE1 MUTATED SAE1 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               2            259
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  SAE1 MUTATED     2   2   2   0
  SAE1 WILD-TYPE 193 171  87  85
D1178V5, multiclass
    clus
vv   SAE1 MUTATED SAE1 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            2             87
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V6, binary
                cls
clus               0   1
  SAE1 MUTATED     6   0
  SAE1 WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAE1 MUTATED      6    0
  SAE1 WILD-TYPE  476   38
   clus
vv  SAE1 MUTATED SAE1 WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D1178V7, binary
                cls
clus               0   1
  SAE1 MUTATED     2   4
  SAE1 WILD-TYPE 170 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAE1 MUTATED      2    4
  SAE1 WILD-TYPE  170  402
        clus
vv       SAE1 MUTATED SAE1 WILD-TYPE
  FEMALE            2            170
  MALE              4            402
[1] 2 2
[1] FALSE
D1178V8, binary
                cls
clus               0   1
  SAE1 MUTATED     6   0
  SAE1 WILD-TYPE 410 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAE1 MUTATED      6    0
  SAE1 WILD-TYPE  410  102
     clus
vv    SAE1 MUTATED SAE1 WILD-TYPE
  NO             6            410
  YES            0            102
[1] 2 2
[1] FALSE
D1178V9, continuous
D1178V10, continuous
[1] "Remove cluster labels:" "SAE1 MUTATED"          
clus
  SAE1 MUTATED SAE1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OW     TCGA-L5-A4OX 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" "SAE1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"SAE1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SAE1 MUTATED       2                         0
  SAE1 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SAE1 MUTATED                                           0     4
  SAE1 WILD-TYPE                                         1   353
D1178V11, multiclass
                                           clus
vv                                          SAE1 MUTATED SAE1 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V12, binary
                cls
clus               0   1
  SAE1 MUTATED     0   4
  SAE1 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAE1 MUTATED      0    4
  SAE1 WILD-TYPE   10  394
                        clus
vv                       SAE1 MUTATED SAE1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(1179) Variable = SUCLG2 MUTATION ANALYSIS
D1179V1, survival
                  sevent
clus2                0   1
  SUCLG2 MUTATED     3   3
  SUCLG2 WILD-TYPE 335 213
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               6              548 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               3              213 
$`SUCLG2 MUTATED`
TCGA-CG-4460 TCGA-JY-A93C TCGA-BR-A4QL TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4H8 
       21.99        23.18        16.14       105.07        11.44        14.07 

$`SUCLG2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
           11.44             0.00 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
          105.07           122.30 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
          19.065           13.510 
[1] "11.4 - 105.1 (19.1)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "1.2"
D1179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SUCLG2 MUTATED         1        0        1        1         0         0
  SUCLG2 WILD-TYPE       9       20       45       30        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUCLG2 MUTATED           0          1          3          0        1
  SUCLG2 WILD-TYPE        29         83         59         39       42
                  vv
clus               STAGE IVA
  SUCLG2 MUTATED           0
  SUCLG2 WILD-TYPE         4
D1179V3, multiclass
            clus
vv           SUCLG2 MUTATED SUCLG2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              3               59
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SUCLG2 MUTATED       2   1   3   2
  SUCLG2 WILD-TYPE    52 134 258 100
D1179V4, multiclass
       clus
vv      SUCLG2 MUTATED SUCLG2 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 3              258
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SUCLG2 MUTATED     1   4   1   2
  SUCLG2 WILD-TYPE 194 169  88  83
D1179V5, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  N0              1              194
  N1              4              169
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V6, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     6   1
  SUCLG2 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      6    1
  SUCLG2 WILD-TYPE  476   37
   clus
vv  SUCLG2 MUTATED SUCLG2 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D1179V7, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     4   4
  SUCLG2 WILD-TYPE 168 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      4    4
  SUCLG2 WILD-TYPE  168  402
        clus
vv       SUCLG2 MUTATED SUCLG2 WILD-TYPE
  FEMALE              4              168
  MALE                4              402
[1] 2 2
[1] FALSE
D1179V8, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     7   0
  SUCLG2 WILD-TYPE 409 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      7    0
  SUCLG2 WILD-TYPE  409  102
     clus
vv    SUCLG2 MUTATED SUCLG2 WILD-TYPE
  NO               7              409
  YES              0              102
[1] 2 2
[1] FALSE
D1179V9, continuous
D1179V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SUCLG2 MUTATED       2                         1
  SUCLG2 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SUCLG2 MUTATED                                           0     3
  SUCLG2 WILD-TYPE                                         1   354
D1179V11, multiclass
                                           clus
vv                                          SUCLG2 MUTATED SUCLG2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V12, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     0   5
  SUCLG2 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      0    5
  SUCLG2 WILD-TYPE   10  393
                        clus
vv                       SUCLG2 MUTATED SUCLG2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1180) Variable = CDC6 MUTATION ANALYSIS
D1180V1, survival
                sevent
clus2              0   1
  CDC6 MUTATED     7   5
  CDC6 WILD-TYPE 331 211
  CDC6 MUTATED CDC6 WILD-TYPE 
            12            542 
  CDC6 MUTATED CDC6 WILD-TYPE 
             5            211 
$`CDC6 MUTATED`
TCGA-JY-A93D TCGA-KH-A6WC TCGA-L5-A8NR TCGA-LN-A49S TCGA-LN-A9FR TCGA-BR-4184 
       31.56         6.28         8.71        13.15        12.26         6.97 
TCGA-BR-8284 TCGA-CD-8529 TCGA-CD-A487 TCGA-D7-6518 TCGA-EQ-8122 TCGA-HJ-7597 
        8.05        12.30        12.30        19.13         7.99        26.47 

$`CDC6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       47.38        21.70        23.18        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41        12.33        13.38        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        30.51         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CDC6 MUTATED CDC6 WILD-TYPE 
          6.28           0.00 
  CDC6 MUTATED CDC6 WILD-TYPE 
         31.56         122.30 
  CDC6 MUTATED CDC6 WILD-TYPE 
        12.280         13.825 
[1] "6.3 - 31.6 (12.3)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.4"
D1180V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC6 MUTATED         0        1        1        0         1         4
  CDC6 WILD-TYPE      10       19       45       31        83        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC6 MUTATED           1          2          0          2        1         0
  CDC6 WILD-TYPE        28         82         62         37       42         4
D1180V3, multiclass
            clus
vv           CDC6 MUTATED CDC6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             4             79
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CDC6 MUTATED       1   4   5   3
  CDC6 WILD-TYPE    53 131 256  99
D1180V4, multiclass
       clus
vv      CDC6 MUTATED CDC6 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               5            256
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CDC6 MUTATED     5   5   0   3
  CDC6 WILD-TYPE 190 168  89  82
D1180V5, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  N0            5            190
  N1            5            168
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V6, binary
                cls
clus               0   1
  CDC6 MUTATED     9   1
  CDC6 WILD-TYPE 473  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      9    1
  CDC6 WILD-TYPE  473   37
   clus
vv  CDC6 MUTATED CDC6 WILD-TYPE
  0            9            473
  1            1             37
[1] 2 2
[1] FALSE
D1180V7, binary
                cls
clus               0   1
  CDC6 MUTATED     4   9
  CDC6 WILD-TYPE 168 397
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      4    9
  CDC6 WILD-TYPE  168  397
        clus
vv       CDC6 MUTATED CDC6 WILD-TYPE
  FEMALE            4            168
  MALE              9            397
[1] 2 2
[1] FALSE
D1180V8, binary
                cls
clus               0   1
  CDC6 MUTATED     7   6
  CDC6 WILD-TYPE 409  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      7    6
  CDC6 WILD-TYPE  409   96
     clus
vv    CDC6 MUTATED CDC6 WILD-TYPE
  NO             7            409
  YES            6             96
[1] 2 2
[1] FALSE
D1180V9, continuous
[1] "Remove cluster labels:" "CDC6 MUTATED"          
clus
  CDC6 MUTATED CDC6 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-LN-A49K     TCGA-LN-A49L     TCGA-LN-A49M 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A49X 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A49Y     TCGA-LN-A4A1     TCGA-LN-A4A2     TCGA-LN-A4A3 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6     TCGA-LN-A4A8 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR     TCGA-LN-A5U5 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV     TCGA-LN-A7HW 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ     TCGA-V5-A7RB 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV     TCGA-V5-AASW 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
D1180V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CDC6 MUTATED       4                         0
  CDC6 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC6 MUTATED                                           0     8
  CDC6 WILD-TYPE                                         1   349
D1180V11, multiclass
                                           clus
vv                                          CDC6 MUTATED CDC6 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V12, binary
                cls
clus               0   1
  CDC6 MUTATED     0  11
  CDC6 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      0   11
  CDC6 WILD-TYPE   10  387
                        clus
vv                       CDC6 MUTATED CDC6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(1181) Variable = CUL5 MUTATION ANALYSIS
D1181V1, survival
                sevent
clus2              0   1
  CUL5 MUTATED    10   4
  CUL5 WILD-TYPE 328 212
  CUL5 MUTATED CUL5 WILD-TYPE 
            14            540 
  CUL5 MUTATED CUL5 WILD-TYPE 
             4            212 
$`CUL5 MUTATED`
TCGA-L5-A4OF TCGA-L5-A8NJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7722 TCGA-BR-8360 
       26.33        16.47         6.97        34.68        15.32         6.18 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-6528 TCGA-D7-8572 TCGA-FP-A4BE 
        1.12        31.96         6.02        15.22        16.80        11.08 
TCGA-HU-A4GN TCGA-HU-A4GQ 
       29.98         0.10 

$`CUL5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  CUL5 MUTATED CUL5 WILD-TYPE 
           0.1            0.0 
  CUL5 MUTATED CUL5 WILD-TYPE 
         34.68         122.30 
  CUL5 MUTATED CUL5 WILD-TYPE 
         15.27          13.53 
[1] "0.1 - 34.7 (15.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1181V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUL5 MUTATED         0        0        1        0         5         3
  CUL5 WILD-TYPE      10       20       45       31        79        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUL5 MUTATED           1          2          0          1        2         0
  CUL5 WILD-TYPE        28         82         62         38       41         4
D1181V3, multiclass
            clus
vv           CUL5 MUTATED CUL5 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             3             80
  STAGE III             1             28
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CUL5 MUTATED       1   3   7   4
  CUL5 WILD-TYPE    53 132 254  98
D1181V4, multiclass
       clus
vv      CUL5 MUTATED CUL5 WILD-TYPE
  T0+T1            1             53
  T2               3            132
  T3               7            254
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CUL5 MUTATED     6   6   3   0
  CUL5 WILD-TYPE 189 167  86  85
D1181V5, multiclass
    clus
vv   CUL5 MUTATED CUL5 WILD-TYPE
  N0            6            189
  N1            6            167
  N2            3             86
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V6, binary
                cls
clus               0   1
  CUL5 MUTATED    12   1
  CUL5 WILD-TYPE 470  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL5 MUTATED     12    1
  CUL5 WILD-TYPE  470   37
   clus
vv  CUL5 MUTATED CUL5 WILD-TYPE
  0           12            470
  1            1             37
[1] 2 2
[1] FALSE
D1181V7, binary
                cls
clus               0   1
  CUL5 MUTATED     4  11
  CUL5 WILD-TYPE 168 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL5 MUTATED      4   11
  CUL5 WILD-TYPE  168  395
        clus
vv       CUL5 MUTATED CUL5 WILD-TYPE
  FEMALE            4            168
  MALE             11            395
[1] 2 2
[1] FALSE
D1181V8, binary
                cls
clus               0   1
  CUL5 MUTATED    13   1
  CUL5 WILD-TYPE 403 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL5 MUTATED     13    1
  CUL5 WILD-TYPE  403  101
     clus
vv    CUL5 MUTATED CUL5 WILD-TYPE
  NO            13            403
  YES            1            101
[1] 2 2
[1] FALSE
D1181V9, continuous
D1181V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUL5 MUTATED       3                         1
  CUL5 WILD-TYPE   130                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUL5 MUTATED                                           0    10
  CUL5 WILD-TYPE                                         1   347
D1181V11, multiclass
                                           clus
vv                                          CUL5 MUTATED CUL5 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V12, binary
                cls
clus               0   1
  CUL5 MUTATED     0  12
  CUL5 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL5 MUTATED      0   12
  CUL5 WILD-TYPE   10  386
                        clus
vv                       CUL5 MUTATED CUL5 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1182) Variable = SERPINB8 MUTATION ANALYSIS
D1182V1, survival
                    sevent
clus2                  0   1
  SERPINB8 MUTATED     6   1
  SERPINB8 WILD-TYPE 332 215
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 7                547 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 1                215 
$`SERPINB8 MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5732 TCGA-HU-A4H3 
       36.16        35.84       105.07        65.10        69.04        29.00 
TCGA-HU-A4H8 
       14.07 

$`SERPINB8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       30.90        31.20        44.94        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
             14.07               0.00 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
            105.07             122.30 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
             36.16              13.48 
[1] "14.1 - 105.1 (36.2)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "6.5"
D1182V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB8 MUTATED         0        1        4        1         0         0
  SERPINB8 WILD-TYPE      10       19       42       30        84        83
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB8 MUTATED           0          0          0          1        1
  SERPINB8 WILD-TYPE        29         84         62         38       42
                    vv
clus                 STAGE IVA
  SERPINB8 MUTATED           0
  SERPINB8 WILD-TYPE         4
D1182V3, multiclass
            clus
vv           SERPINB8 MUTATED SERPINB8 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  4                 42
  STAGE II                  1                 30
  STAGE IIA                 0                 84
  STAGE IIB                 0                 83
  STAGE III                 0                 29
  STAGE IIIA                0                 84
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SERPINB8 MUTATED       2   5   0   1
  SERPINB8 WILD-TYPE    52 130 261 101
D1182V4, multiclass
       clus
vv      SERPINB8 MUTATED SERPINB8 WILD-TYPE
  T0+T1                2                 52
  T2                   5                130
  T3                   0                261
  T4                   1                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SERPINB8 MUTATED     4   2   0   2
  SERPINB8 WILD-TYPE 191 171  89  83
D1182V5, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  N0                4                191
  N1                2                171
  N2                0                 89
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V6, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     8   0
  SERPINB8 WILD-TYPE 474  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      8    0
  SERPINB8 WILD-TYPE  474   38
   clus
vv  SERPINB8 MUTATED SERPINB8 WILD-TYPE
  0                8                474
  1                0                 38
[1] 2 2
[1] FALSE
D1182V7, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     3   5
  SERPINB8 WILD-TYPE 169 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      3    5
  SERPINB8 WILD-TYPE  169  401
        clus
vv       SERPINB8 MUTATED SERPINB8 WILD-TYPE
  FEMALE                3                169
  MALE                  5                401
[1] 2 2
[1] FALSE
D1182V8, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     5   0
  SERPINB8 WILD-TYPE 411 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      5    0
  SERPINB8 WILD-TYPE  411  102
     clus
vv    SERPINB8 MUTATED SERPINB8 WILD-TYPE
  NO                 5                411
  YES                0                102
[1] 2 2
[1] FALSE
D1182V9, continuous
D1182V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB8 MUTATED       2                         0
  SERPINB8 WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB8 MUTATED                                           0     2
  SERPINB8 WILD-TYPE                                         1   355
D1182V11, multiclass
                                           clus
vv                                          SERPINB8 MUTATED SERPINB8 WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V12, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     0   4
  SERPINB8 WILD-TYPE  10 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      0    4
  SERPINB8 WILD-TYPE   10  394
                        clus
vv                       SERPINB8 MUTATED SERPINB8 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                4                394
[1] 2 2
[1] FALSE

Clustering(1183) Variable = HSP90AB1 MUTATION ANALYSIS
D1183V1, survival
                    sevent
clus2                  0   1
  HSP90AB1 MUTATED     4   9
  HSP90AB1 WILD-TYPE 334 207
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                13                541 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 9                207 
$`HSP90AB1 MUTATED`
TCGA-JY-A6FG TCGA-RE-A7BO TCGA-VR-AA7I TCGA-BR-4201 TCGA-BR-8284 TCGA-BR-8361 
       41.52         7.00        15.91        30.90         8.05        31.10 
TCGA-BR-8487 TCGA-BR-8687 TCGA-CD-A4MG TCGA-D7-5577 TCGA-D7-A6EV TCGA-D7-A6EZ 
        1.12         8.22         6.58        25.71        11.24        20.32 
TCGA-HF-7132 
       77.29 

$`HSP90AB1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        18.35         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       65.10         4.01        69.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
              1.12               0.00 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
             77.29             122.30 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
             15.91              13.55 
[1] "1.1 - 77.3 (15.9)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1183V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSP90AB1 MUTATED         0        0        0        1         2         2
  HSP90AB1 WILD-TYPE      10       20       46       30        82        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90AB1 MUTATED           2          2          0          3        0
  HSP90AB1 WILD-TYPE        27         82         62         36       43
                    vv
clus                 STAGE IVA
  HSP90AB1 MUTATED           0
  HSP90AB1 WILD-TYPE         4
D1183V3, multiclass
            clus
vv           HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  0                 46
  STAGE II                  1                 30
  STAGE IIA                 2                 82
  STAGE IIB                 2                 81
  STAGE III                 2                 27
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                3                 36
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  HSP90AB1 MUTATED       1   4   4   4
  HSP90AB1 WILD-TYPE    53 131 257  98
D1183V4, multiclass
       clus
vv      HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  T0+T1                1                 53
  T2                   4                131
  T3                   4                257
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  HSP90AB1 MUTATED     3   3   4   2
  HSP90AB1 WILD-TYPE 192 170  85  83
D1183V5, multiclass
    clus
vv   HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  N0                3                192
  N1                3                170
  N2                4                 85
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V6, binary
                    cls
clus                   0   1
  HSP90AB1 MUTATED    13   0
  HSP90AB1 WILD-TYPE 469  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED     13    0
  HSP90AB1 WILD-TYPE  469   38
   clus
vv  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  0               13                469
  1                0                 38
[1] 2 2
[1] FALSE
D1183V7, binary
                    cls
clus                   0   1
  HSP90AB1 MUTATED     8   5
  HSP90AB1 WILD-TYPE 164 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      8    5
  HSP90AB1 WILD-TYPE  164  401
        clus
vv       HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  FEMALE                8                164
  MALE                  5                401
[1] 2 2
[1] FALSE
D1183V8, binary
                    cls
clus                   0   1
  HSP90AB1 MUTATED    12   1
  HSP90AB1 WILD-TYPE 404 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED     12    1
  HSP90AB1 WILD-TYPE  404  101
     clus
vv    HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  NO                12                404
  YES                1                101
[1] 2 2
[1] FALSE
D1183V9, continuous
[1] "Remove cluster labels:" "HSP90AB1 MUTATED"      
clus
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 1                 67 
        TCGA-IG-A3I8         TCGA-IG-A3QL         TCGA-IG-A3Y9 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-IG-A3YA         TCGA-IG-A3YB         TCGA-IG-A3YC 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-IG-A51D         TCGA-IG-A5S3         TCGA-IG-A7DP 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-KH-A6WC         TCGA-LN-A49K         TCGA-LN-A49L 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A49M         TCGA-LN-A49N         TCGA-LN-A49O 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A49X         TCGA-LN-A49Y         TCGA-LN-A4A1 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A4A2         TCGA-LN-A4A3         TCGA-LN-A4A4 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A4A5         TCGA-LN-A4A6         TCGA-LN-A4A8 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A4A9         TCGA-LN-A4MQ         TCGA-LN-A4MR 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A5U5         TCGA-LN-A5U6         TCGA-LN-A5U7 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A7HV         TCGA-LN-A7HW         TCGA-LN-A7HX 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-LN-A7HY         TCGA-LN-A7HZ         TCGA-V5-A7RB 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-V5-A7RC         TCGA-V5-A7RE         TCGA-V5-AASV 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-V5-AASW         TCGA-V5-AASX         TCGA-VR-A8EO 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8EQ         TCGA-VR-A8ER 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-VR-A8ET         TCGA-VR-A8EU         TCGA-VR-A8EW 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-VR-A8EX         TCGA-VR-A8EY         TCGA-VR-A8EZ 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4D         TCGA-VR-AA4G 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-VR-AA7B         TCGA-VR-AA7D         TCGA-XP-A8T6 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-A8JD 
"HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" "HSP90AB1 WILD-TYPE" 
        TCGA-Z6-A8JE 
"HSP90AB1 WILD-TYPE" 
D1183V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HSP90AB1 MUTATED       1                         0
  HSP90AB1 WILD-TYPE   132                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSP90AB1 MUTATED                                           0    11
  HSP90AB1 WILD-TYPE                                         1   346
D1183V11, multiclass
                                           clus
vv                                          HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  ASIAN                                                    1                132
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V12, binary
                    cls
clus                   0   1
  HSP90AB1 MUTATED     0  10
  HSP90AB1 WILD-TYPE  10 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      0   10
  HSP90AB1 WILD-TYPE   10  388
                        clus
vv                       HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               10                388
[1] 2 2
[1] FALSE

Clustering(1184) Variable = SMARCA4 MUTATION ANALYSIS
D1184V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    27   9
  SMARCA4 WILD-TYPE 311 207
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               36               518 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                9               207 
$`SMARCA4 MUTATED`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A4OI TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IG-A6QS 
       15.68        60.39        19.99        58.55         7.69         9.96 
TCGA-JY-A6FG TCGA-JY-A93F TCGA-L5-A88W TCGA-L5-A8NW TCGA-LN-A7HX TCGA-V5-AASV 
       41.52        24.03        25.12        46.09        12.23        15.35 
TCGA-VR-A8Q7 TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8078 
       52.27        26.70        30.90        34.68        35.24        29.59 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-8536 TCGA-CG-5728 TCGA-F1-6874 
        0.26         4.31         1.12        12.43        65.10        14.47 
TCGA-FP-8099 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H8 
       17.06        22.68         6.51        20.25        23.84        14.07 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-SW-A7EB TCGA-VQ-A8DZ TCGA-VQ-A8P2 
        6.44         6.74        10.62         5.79        13.02        38.14 

$`SMARCA4 WILD-TYPE`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       34.85        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       12.16       122.10        44.75        68.02         3.68        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        25.22         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       22.29        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        29.00        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35        19.53        12.59         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       48.79         5.46        13.25        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             0.26              0.00 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             65.1             122.3 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           18.525            13.410 
[1] "0.3 - 65.1 (18.5)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D1184V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCA4 MUTATED         2        1        7        2         6         8
  SMARCA4 WILD-TYPE       8       19       39       29        78        75
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA4 MUTATED           1          4          0          3        2
  SMARCA4 WILD-TYPE        28         80         62         36       41
                   vv
clus                STAGE IVA
  SMARCA4 MUTATED           0
  SMARCA4 WILD-TYPE         4
D1184V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  2                 8
  STAGE IA                 1                19
  STAGE IB                 7                39
  STAGE II                 2                29
  STAGE IIA                6                78
  STAGE IIB                8                75
  STAGE III                1                28
  STAGE IIIA               4                80
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SMARCA4 MUTATED       6  10  15   6
  SMARCA4 WILD-TYPE    48 125 246  96
D1184V4, multiclass
       clus
vv      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T0+T1               6                48
  T2                 10               125
  T3                 15               246
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SMARCA4 MUTATED    19  10   4   3
  SMARCA4 WILD-TYPE 176 163  85  82
D1184V5, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0              19               176
  N1              10               163
  N2               4                85
  N3               3                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    32   2
  SMARCA4 WILD-TYPE 450  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     32    2
  SMARCA4 WILD-TYPE  450   36
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              32               450
  1               2                36
[1] 2 2
[1] FALSE
D1184V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    18  20
  SMARCA4 WILD-TYPE 154 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     18   20
  SMARCA4 WILD-TYPE  154  386
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              18               154
  MALE                20               386
[1] 2 2
[1] FALSE
D1184V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    30   5
  SMARCA4 WILD-TYPE 386  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     30    5
  SMARCA4 WILD-TYPE  386   97
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               30               386
  YES               5                97
[1] 2 2
[1] FALSE
D1184V9, continuous
D1184V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SMARCA4 MUTATED       7                         2
  SMARCA4 WILD-TYPE   126                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMARCA4 MUTATED                                           0    26
  SMARCA4 WILD-TYPE                                         1   331
D1184V11, multiclass
                                           clus
vv                                          SMARCA4 MUTATED SMARCA4 WILD-TYPE
  ASIAN                                                   7               126
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V12, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     0  26
  SMARCA4 WILD-TYPE  10 372
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      0   26
  SMARCA4 WILD-TYPE   10  372
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              26               372
[1] 2 2
[1] FALSE

Clustering(1185) Variable = SETD2 MUTATION ANALYSIS
D1185V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    14   8
  SETD2 WILD-TYPE 324 208
  SETD2 MUTATED SETD2 WILD-TYPE 
             22             532 
  SETD2 MUTATED SETD2 WILD-TYPE 
              8             208 
$`SETD2 MUTATED`
TCGA-IC-A6RF TCGA-L5-A88Z TCGA-LN-A49W TCGA-LN-A8I1 TCGA-R6-A6Y2 TCGA-V5-AASV 
       15.68         7.40        13.25        13.18         9.30        15.35 
TCGA-VR-AA7D TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8589 
        9.17         6.97        18.35         6.61        32.78        27.12 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-6518 
       31.96        16.14        12.62         6.02        28.96        19.13 
TCGA-HF-7134 TCGA-HU-8604 TCGA-R5-A7ZE TCGA-VQ-A8P2 
       52.21        22.82        18.21        38.14 

$`SETD2 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       12.23        12.03        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 
        9.34         9.67         6.18         9.57        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
       11.08         5.52         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SETD2 MUTATED SETD2 WILD-TYPE 
           6.02            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
          52.21          122.30 
  SETD2 MUTATED SETD2 WILD-TYPE 
          15.91           13.51 
[1] "6.0 - 52.2 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1185V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETD2 MUTATED         1        3        1        0         4         1
  SETD2 WILD-TYPE       9       17       45       31        80        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD2 MUTATED           2          4          2          1        3         0
  SETD2 WILD-TYPE        27         80         60         38       40         4
D1185V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               3              17
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SETD2 MUTATED       5   4   8   5
  SETD2 WILD-TYPE    49 131 253  97
D1185V4, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  T0+T1             5              49
  T2                4             131
  T3                8             253
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SETD2 MUTATED     8   9   3   3
  SETD2 WILD-TYPE 187 164  86  82
D1185V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0             8             187
  N1             9             164
  N2             3              86
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    19   1
  SETD2 WILD-TYPE 463  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     19    1
  SETD2 WILD-TYPE  463   37
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            19             463
  1             1              37
[1] 2 2
[1] FALSE
D1185V7, binary
                 cls
clus                0   1
  SETD2 MUTATED     9  15
  SETD2 WILD-TYPE 163 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      9   15
  SETD2 WILD-TYPE  163  391
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE             9             163
  MALE              15             391
[1] 2 2
[1] FALSE
D1185V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    17   5
  SETD2 WILD-TYPE 399  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     17    5
  SETD2 WILD-TYPE  399   97
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             17             399
  YES             5              97
[1] 2 2
[1] FALSE
D1185V9, continuous
D1185V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SETD2 MUTATED       5                         2
  SETD2 WILD-TYPE   128                        12
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SETD2 MUTATED                                           0    13
  SETD2 WILD-TYPE                                         1   344
D1185V11, multiclass
                                           clus
vv                                          SETD2 MUTATED SETD2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             2              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V12, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  16
  SETD2 WILD-TYPE   9 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   16
  SETD2 WILD-TYPE    9  382
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(1186) Variable = ZC3H8 MUTATION ANALYSIS
D1186V1, survival
                 sevent
clus2               0   1
  ZC3H8 MUTATED     1   4
  ZC3H8 WILD-TYPE 337 212
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              5             549 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              4             212 
$`ZC3H8 MUTATED`
TCGA-CG-4460 TCGA-L7-A56G TCGA-BR-8683 TCGA-D7-A4YY TCGA-RD-A7C1 
       21.99        10.85         9.86        13.78        16.67 

$`ZC3H8 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
           9.86            0.00 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
          21.99          122.30 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
          13.78           13.55 
[1] "9.9 - 22.0 (13.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.4"
D1186V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H8 MUTATED         0        0        1        0         0         0
  ZC3H8 WILD-TYPE      10       20       45       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZC3H8 MUTATED           0          0          2          0        1         0
  ZC3H8 WILD-TYPE        29         84         60         39       42         4
D1186V3, multiclass
            clus
vv           ZC3H8 MUTATED ZC3H8 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZC3H8 MUTATED       0   1   1   2
  ZC3H8 WILD-TYPE    54 134 260 100
D1186V4, multiclass
       clus
vv      ZC3H8 MUTATED ZC3H8 WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                1             260
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZC3H8 MUTATED     1   1   1   1
  ZC3H8 WILD-TYPE 194 172  88  84
D1186V5, multiclass
    clus
vv   ZC3H8 MUTATED ZC3H8 WILD-TYPE
  N0             1             194
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V6, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     3   1
  ZC3H8 WILD-TYPE 479  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      3    1
  ZC3H8 WILD-TYPE  479   37
   clus
vv  ZC3H8 MUTATED ZC3H8 WILD-TYPE
  0             3             479
  1             1              37
[1] 2 2
[1] FALSE
D1186V7, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     1   4
  ZC3H8 WILD-TYPE 171 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      1    4
  ZC3H8 WILD-TYPE  171  402
        clus
vv       ZC3H8 MUTATED ZC3H8 WILD-TYPE
  FEMALE             1             171
  MALE               4             402
[1] 2 2
[1] FALSE
D1186V8, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     3   2
  ZC3H8 WILD-TYPE 413 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      3    2
  ZC3H8 WILD-TYPE  413  100
     clus
vv    ZC3H8 MUTATED ZC3H8 WILD-TYPE
  NO              3             413
  YES             2             100
[1] 2 2
[1] FALSE
D1186V9, continuous
D1186V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H8 MUTATED       1                         1
  ZC3H8 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H8 MUTATED                                           0     2
  ZC3H8 WILD-TYPE                                         1   355
D1186V11, multiclass
                                           clus
vv                                          ZC3H8 MUTATED ZC3H8 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V12, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     0   4
  ZC3H8 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      0    4
  ZC3H8 WILD-TYPE   10  394
                        clus
vv                       ZC3H8 MUTATED ZC3H8 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1187) Variable = NARG2 MUTATION ANALYSIS
D1187V1, survival
                 sevent
clus2               0   1
  NARG2 MUTATED    10   4
  NARG2 WILD-TYPE 328 212
  NARG2 MUTATED NARG2 WILD-TYPE 
             14             540 
  NARG2 MUTATED NARG2 WILD-TYPE 
              4             212 
$`NARG2 MUTATED`
TCGA-L5-A8NK TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-A4QL 
       13.55         6.61        34.68        25.05        28.14        16.14 
TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-5721 TCGA-D7-A4YU TCGA-HJ-7597 TCGA-HU-A4GX 
       12.43        12.62         6.02        16.44        26.47        20.25 
TCGA-HU-A4H4 TCGA-VQ-A8P2 
       23.84        38.14 

$`NARG2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  NARG2 MUTATED NARG2 WILD-TYPE 
           6.02            0.00 
  NARG2 MUTATED NARG2 WILD-TYPE 
          38.14          122.30 
  NARG2 MUTATED NARG2 WILD-TYPE 
         18.345          13.495 
[1] "6.0 - 38.1 (18.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1187V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NARG2 MUTATED         0        0        2        1         2         1
  NARG2 WILD-TYPE      10       20       44       30        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NARG2 MUTATED           1          1          2          3        1         0
  NARG2 WILD-TYPE        28         83         60         36       42         4
D1187V3, multiclass
            clus
vv           NARG2 MUTATED NARG2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             3              36
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NARG2 MUTATED       0   4   5   5
  NARG2 WILD-TYPE    54 131 256  97
D1187V4, multiclass
       clus
vv      NARG2 MUTATED NARG2 WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3                5             256
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NARG2 MUTATED     5   3   2   4
  NARG2 WILD-TYPE 190 170  87  81
D1187V5, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  N0             5             190
  N1             3             170
  N2             2              87
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V6, binary
                 cls
clus                0   1
  NARG2 MUTATED    13   0
  NARG2 WILD-TYPE 469  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED     13    0
  NARG2 WILD-TYPE  469   38
   clus
vv  NARG2 MUTATED NARG2 WILD-TYPE
  0            13             469
  1             0              38
[1] 2 2
[1] FALSE
D1187V7, binary
                 cls
clus                0   1
  NARG2 MUTATED     8   6
  NARG2 WILD-TYPE 164 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      8    6
  NARG2 WILD-TYPE  164  400
        clus
vv       NARG2 MUTATED NARG2 WILD-TYPE
  FEMALE             8             164
  MALE               6             400
[1] 2 2
[1] FALSE
D1187V8, binary
                 cls
clus                0   1
  NARG2 MUTATED    12   1
  NARG2 WILD-TYPE 404 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED     12    1
  NARG2 WILD-TYPE  404  101
     clus
vv    NARG2 MUTATED NARG2 WILD-TYPE
  NO             12             404
  YES             1             101
[1] 2 2
[1] FALSE
D1187V9, continuous
D1187V10, continuous
[1] "Remove cluster labels:" "NARG2 MUTATED"         
clus
  NARG2 MUTATED NARG2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" "NARG2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"NARG2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NARG2 MUTATED       4                         0
  NARG2 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NARG2 MUTATED                                           0     9
  NARG2 WILD-TYPE                                         1   348
D1187V11, multiclass
                                           clus
vv                                          NARG2 MUTATED NARG2 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V12, binary
                 cls
clus                0   1
  NARG2 MUTATED     0  11
  NARG2 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      0   11
  NARG2 WILD-TYPE   10  387
                        clus
vv                       NARG2 MUTATED NARG2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1188) Variable = C3ORF33 MUTATION ANALYSIS
D1188V1, survival
                   sevent
clus2                 0   1
  C3ORF33 MUTATED     5   2
  C3ORF33 WILD-TYPE 333 214
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                7               547 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                2               214 
$`C3ORF33 MUTATED`
TCGA-L5-A4OE TCGA-B7-5818 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8060 TCGA-BR-8591 
       24.00        11.70        32.78        35.84        11.44        28.14 
TCGA-FP-A4BE 
       11.08 

$`C3ORF33 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            11.08              0.00 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            35.84            122.30 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            24.00             13.55 
[1] "11.1 - 35.8 (24.0)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.7"
D1188V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C3ORF33 MUTATED         1        0        2        0         2         1
  C3ORF33 WILD-TYPE       9       20       44       31        82        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF33 MUTATED           0          0          1          1        0
  C3ORF33 WILD-TYPE        29         84         61         38       43
                   vv
clus                STAGE IVA
  C3ORF33 MUTATED           0
  C3ORF33 WILD-TYPE         4
D1188V3, multiclass
            clus
vv           C3ORF33 MUTATED C3ORF33 WILD-TYPE
  STAGE I                  1                 9
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                1                82
  STAGE III                0                29
  STAGE IIIA               0                84
  STAGE IIIB               1                61
  STAGE IIIC               1                38
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C3ORF33 MUTATED       1   3   3   1
  C3ORF33 WILD-TYPE    53 132 258 101
D1188V4, multiclass
       clus
vv      C3ORF33 MUTATED C3ORF33 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  3               258
  T4                  1               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C3ORF33 MUTATED     4   1   2   1
  C3ORF33 WILD-TYPE 191 172  87  84
D1188V5, multiclass
    clus
vv   C3ORF33 MUTATED C3ORF33 WILD-TYPE
  N0               4               191
  N1               1               172
  N2               2                87
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V6, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     6   0
  C3ORF33 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      6    0
  C3ORF33 WILD-TYPE  476   38
   clus
vv  C3ORF33 MUTATED C3ORF33 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D1188V7, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     3   5
  C3ORF33 WILD-TYPE 169 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      3    5
  C3ORF33 WILD-TYPE  169  401
        clus
vv       C3ORF33 MUTATED C3ORF33 WILD-TYPE
  FEMALE               3               169
  MALE                 5               401
[1] 2 2
[1] FALSE
D1188V8, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     7   1
  C3ORF33 WILD-TYPE 409 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      7    1
  C3ORF33 WILD-TYPE  409  101
     clus
vv    C3ORF33 MUTATED C3ORF33 WILD-TYPE
  NO                7               409
  YES               1               101
[1] 2 2
[1] FALSE
D1188V9, continuous
D1188V10, continuous
[1] "Remove cluster labels:" "C3ORF33 MUTATED"       
clus
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OG 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y        TCGA-L5-A8NG 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE        TCGA-IG-A3QL 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC        TCGA-IG-A4P3 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8        TCGA-IG-A6QS 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA        TCGA-JY-A6FE 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" "C3ORF33 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C3ORF33 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C3ORF33 MUTATED       0                         2
  C3ORF33 WILD-TYPE   133                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C3ORF33 MUTATED                                           0     6
  C3ORF33 WILD-TYPE                                         1   351
D1188V11, multiclass
                                           clus
vv                                          C3ORF33 MUTATED C3ORF33 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               2                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V12, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     0   7
  C3ORF33 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      0    7
  C3ORF33 WILD-TYPE   10  391
                        clus
vv                       C3ORF33 MUTATED C3ORF33 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(1189) Variable = ZNF2 MUTATION ANALYSIS
D1189V1, survival
                sevent
clus2              0   1
  ZNF2 MUTATED     5   3
  ZNF2 WILD-TYPE 333 213
  ZNF2 MUTATED ZNF2 WILD-TYPE 
             8            546 
  ZNF2 MUTATED ZNF2 WILD-TYPE 
             3            213 
$`ZNF2 MUTATED`
TCGA-CG-4460 TCGA-L5-A8NU TCGA-BR-6452 TCGA-BR-7707 TCGA-CD-A48C TCGA-HU-A4GF 
       21.99        83.24        34.68        35.84        11.61        25.81 
TCGA-IN-A6RI TCGA-VQ-A8P2 
       18.38        38.14 

$`ZNF2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF2 MUTATED ZNF2 WILD-TYPE 
         11.61           0.00 
  ZNF2 MUTATED ZNF2 WILD-TYPE 
         83.24         122.30 
  ZNF2 MUTATED ZNF2 WILD-TYPE 
        30.245         13.495 
[1] "11.6 - 83.2 (30.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D1189V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF2 MUTATED         1        0        1        0         3         2
  ZNF2 WILD-TYPE       9       20       45       31        81        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF2 MUTATED           0          1          0          0        1         0
  ZNF2 WILD-TYPE        29         83         62         39       42         4
D1189V3, multiclass
            clus
vv           ZNF2 MUTATED ZNF2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ZNF2 MUTATED       1   2   3   3
  ZNF2 WILD-TYPE    53 133 258  99
D1189V4, multiclass
       clus
vv      ZNF2 MUTATED ZNF2 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               3            258
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ZNF2 MUTATED     6   3   0   0
  ZNF2 WILD-TYPE 189 170  89  85
D1189V5, multiclass
    clus
vv   ZNF2 MUTATED ZNF2 WILD-TYPE
  N0            6            189
  N1            3            170
  N2            0             89
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V6, binary
                cls
clus               0   1
  ZNF2 MUTATED     8   1
  ZNF2 WILD-TYPE 474  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF2 MUTATED      8    1
  ZNF2 WILD-TYPE  474   37
   clus
vv  ZNF2 MUTATED ZNF2 WILD-TYPE
  0            8            474
  1            1             37
[1] 2 2
[1] FALSE
D1189V7, binary
                cls
clus               0   1
  ZNF2 MUTATED     4   5
  ZNF2 WILD-TYPE 168 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF2 MUTATED      4    5
  ZNF2 WILD-TYPE  168  401
        clus
vv       ZNF2 MUTATED ZNF2 WILD-TYPE
  FEMALE            4            168
  MALE              5            401
[1] 2 2
[1] FALSE
D1189V8, binary
                cls
clus               0   1
  ZNF2 MUTATED     7   1
  ZNF2 WILD-TYPE 409 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF2 MUTATED      7    1
  ZNF2 WILD-TYPE  409  101
     clus
vv    ZNF2 MUTATED ZNF2 WILD-TYPE
  NO             7            409
  YES            1            101
[1] 2 2
[1] FALSE
D1189V9, continuous
D1189V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ZNF2 MUTATED       2                         0
  ZNF2 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF2 MUTATED                                           0     6
  ZNF2 WILD-TYPE                                         1   351
D1189V11, multiclass
                                           clus
vv                                          ZNF2 MUTATED ZNF2 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V12, binary
                cls
clus               0   1
  ZNF2 MUTATED     0   6
  ZNF2 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF2 MUTATED      0    6
  ZNF2 WILD-TYPE   10  392
                        clus
vv                       ZNF2 MUTATED ZNF2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1190) Variable = ETV1 MUTATION ANALYSIS
D1190V1, survival
                sevent
clus2              0   1
  ETV1 MUTATED     7   1
  ETV1 WILD-TYPE 331 215
  ETV1 MUTATED ETV1 WILD-TYPE 
             8            546 
  ETV1 MUTATED ETV1 WILD-TYPE 
             1            215 
$`ETV1 MUTATED`
TCGA-V5-AASW TCGA-BR-4201 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8680 TCGA-D7-6815 
        9.27        30.90         6.18        31.27        31.96        15.98 
TCGA-D7-6822 TCGA-VQ-A8P2 
       12.33        38.14 

$`ETV1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        18.35         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
       29.42         2.66        19.96         2.20         7.40        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        12.36 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ETV1 MUTATED ETV1 WILD-TYPE 
          6.18           0.00 
  ETV1 MUTATED ETV1 WILD-TYPE 
         38.14         122.30 
  ETV1 MUTATED ETV1 WILD-TYPE 
         23.44          13.53 
[1] "6.2 - 38.1 (23.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "3.9"
D1190V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ETV1 MUTATED         0        0        1        0         1         1
  ETV1 WILD-TYPE      10       20       45       31        83        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETV1 MUTATED           0          1          0          1        1         0
  ETV1 WILD-TYPE        29         83         62         38       42         4
D1190V3, multiclass
            clus
vv           ETV1 MUTATED ETV1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ETV1 MUTATED       0   3   1   3
  ETV1 WILD-TYPE    54 132 260  99
D1190V4, multiclass
       clus
vv      ETV1 MUTATED ETV1 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               1            260
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ETV1 MUTATED     2   2   2   1
  ETV1 WILD-TYPE 193 171  87  84
D1190V5, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V6, binary
                cls
clus               0   1
  ETV1 MUTATED     7   1
  ETV1 WILD-TYPE 475  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      7    1
  ETV1 WILD-TYPE  475   37
   clus
vv  ETV1 MUTATED ETV1 WILD-TYPE
  0            7            475
  1            1             37
[1] 2 2
[1] FALSE
D1190V7, binary
                cls
clus               0   1
  ETV1 MUTATED     3   6
  ETV1 WILD-TYPE 169 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      3    6
  ETV1 WILD-TYPE  169  400
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  FEMALE            3            169
  MALE              6            400
[1] 2 2
[1] FALSE
D1190V8, binary
                cls
clus               0   1
  ETV1 MUTATED     6   2
  ETV1 WILD-TYPE 410 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      6    2
  ETV1 WILD-TYPE  410  100
     clus
vv    ETV1 MUTATED ETV1 WILD-TYPE
  NO             6            410
  YES            2            100
[1] 2 2
[1] FALSE
D1190V9, continuous
[1] "Remove cluster labels:" "ETV1 MUTATED"          
clus
  ETV1 MUTATED ETV1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ETV1 WILD-TYPE" "ETV1 WILD-TYPE" "ETV1 WILD-TYPE" 
D1190V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ETV1 MUTATED       1                         0
  ETV1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ETV1 MUTATED                                           0     8
  ETV1 WILD-TYPE                                         1   349
D1190V11, multiclass
                                           clus
vv                                          ETV1 MUTATED ETV1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V12, binary
                cls
clus               0   1
  ETV1 MUTATED     0   8
  ETV1 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      0    8
  ETV1 WILD-TYPE   10  390
                        clus
vv                       ETV1 MUTATED ETV1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(1191) Variable = TAF6 MUTATION ANALYSIS
D1191V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     8   4
  TAF6 WILD-TYPE 330 212
  TAF6 MUTATED TAF6 WILD-TYPE 
            12            542 
  TAF6 MUTATED TAF6 WILD-TYPE 
             4            212 
$`TAF6 MUTATED`
TCGA-L5-A4OI TCGA-B7-5816 TCGA-BR-8683 TCGA-BR-A4J1 TCGA-CD-8536 TCGA-CG-5721 
       19.99        26.70         9.86         0.72        12.43         6.02 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-VQ-A8P2 
        5.92        13.78        11.44        22.32        24.20        38.14 

$`TAF6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TAF6 MUTATED TAF6 WILD-TYPE 
          0.72           0.00 
  TAF6 MUTATED TAF6 WILD-TYPE 
         38.14         122.30 
  TAF6 MUTATED TAF6 WILD-TYPE 
        13.105         13.565 
[1] "0.7 - 38.1 (13.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1191V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF6 MUTATED         0        1        0        1         0         4
  TAF6 WILD-TYPE      10       19       46       30        84        79
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF6 MUTATED           0          3          3          1        1         0
  TAF6 WILD-TYPE        29         81         59         38       42         4
D1191V3, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              0             46
  STAGE II              1             30
  STAGE IIA             0             84
  STAGE IIB             4             79
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            3             59
  STAGE IIIC            1             38
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TAF6 MUTATED       1   0   5   8
  TAF6 WILD-TYPE    53 135 256  94
D1191V4, multiclass
       clus
vv      TAF6 MUTATED TAF6 WILD-TYPE
  T0+T1            1             53
  T2               0            135
  T3               5            256
  T4               8             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TAF6 MUTATED     6   5   1   3
  TAF6 WILD-TYPE 189 168  88  82
D1191V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            6            189
  N1            5            168
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V6, binary
                cls
clus               0   1
  TAF6 MUTATED    14   0
  TAF6 WILD-TYPE 468  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED     14    0
  TAF6 WILD-TYPE  468   38
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0           14            468
  1            0             38
[1] 2 2
[1] FALSE
D1191V7, binary
                cls
clus               0   1
  TAF6 MUTATED     7   8
  TAF6 WILD-TYPE 165 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      7    8
  TAF6 WILD-TYPE  165  398
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            7            165
  MALE              8            398
[1] 2 2
[1] FALSE
D1191V8, binary
                cls
clus               0   1
  TAF6 MUTATED    10   2
  TAF6 WILD-TYPE 406 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED     10    2
  TAF6 WILD-TYPE  406  100
     clus
vv    TAF6 MUTATED TAF6 WILD-TYPE
  NO            10            406
  YES            2            100
[1] 2 2
[1] FALSE
D1191V9, continuous
D1191V10, continuous
[1] "Remove cluster labels:" "TAF6 MUTATED"          
clus
  TAF6 MUTATED TAF6 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" "TAF6 WILD-TYPE" 
    TCGA-Z6-AAPN 
"TAF6 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TAF6 MUTATED       5                         0
  TAF6 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF6 MUTATED                                           0     9
  TAF6 WILD-TYPE                                         1   348
D1191V11, multiclass
                                           clus
vv                                          TAF6 MUTATED TAF6 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V12, binary
                cls
clus               0   1
  TAF6 MUTATED     0  12
  TAF6 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      0   12
  TAF6 WILD-TYPE   10  386
                        clus
vv                       TAF6 MUTATED TAF6 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1192) Variable = BCL2L2 MUTATION ANALYSIS
D1192V1, survival
                  sevent
clus2                0   1
  BCL2L2 MUTATED     3   1
  BCL2L2 WILD-TYPE 335 215
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
               4              550 
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
               1              215 
$`BCL2L2 MUTATED`
TCGA-L5-A4OI TCGA-BR-4280 TCGA-BR-8487 TCGA-HU-A4GU 
       19.99         6.61         1.12         6.58 

$`BCL2L2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
            1.12             0.00 
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
           19.99           122.30 
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
           6.595           13.630 
[1] "1.1 - 20.0 (6.6)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1192V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL2L2 MUTATED         0        0        0        0         1         1
  BCL2L2 WILD-TYPE      10       20       46       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCL2L2 MUTATED           1          1          0          1        0
  BCL2L2 WILD-TYPE        28         83         62         38       43
                  vv
clus               STAGE IVA
  BCL2L2 MUTATED           0
  BCL2L2 WILD-TYPE         4
D1192V3, multiclass
            clus
vv           BCL2L2 MUTATED BCL2L2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  BCL2L2 MUTATED       0   1   3   1
  BCL2L2 WILD-TYPE    54 134 258 101
D1192V4, multiclass
       clus
vv      BCL2L2 MUTATED BCL2L2 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 3              258
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  BCL2L2 MUTATED     2   2   0   1
  BCL2L2 WILD-TYPE 193 171  89  84
D1192V5, multiclass
    clus
vv   BCL2L2 MUTATED BCL2L2 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V6, binary
                  cls
clus                 0   1
  BCL2L2 MUTATED     4   0
  BCL2L2 WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L2 MUTATED      4    0
  BCL2L2 WILD-TYPE  478   38
   clus
vv  BCL2L2 MUTATED BCL2L2 WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D1192V7, binary
                  cls
clus                 0   1
  BCL2L2 MUTATED     3   2
  BCL2L2 WILD-TYPE 169 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L2 MUTATED      3    2
  BCL2L2 WILD-TYPE  169  404
        clus
vv       BCL2L2 MUTATED BCL2L2 WILD-TYPE
  FEMALE              3              169
  MALE                2              404
[1] 2 2
[1] FALSE
D1192V8, binary
                  cls
clus                 0   1
  BCL2L2 MUTATED     4   0
  BCL2L2 WILD-TYPE 412 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L2 MUTATED      4    0
  BCL2L2 WILD-TYPE  412  102
     clus
vv    BCL2L2 MUTATED BCL2L2 WILD-TYPE
  NO               4              412
  YES              0              102
[1] 2 2
[1] FALSE
D1192V9, continuous
D1192V10, continuous
[1] "Remove cluster labels:" "BCL2L2 MUTATED"        
clus
  BCL2L2 MUTATED BCL2L2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" "BCL2L2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"BCL2L2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCL2L2 MUTATED       1                         0
  BCL2L2 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCL2L2 MUTATED                                           0     4
  BCL2L2 WILD-TYPE                                         1   353
D1192V11, multiclass
                                           clus
vv                                          BCL2L2 MUTATED BCL2L2 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V12, binary
                  cls
clus                 0   1
  BCL2L2 MUTATED     0   4
  BCL2L2 WILD-TYPE  10 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL2L2 MUTATED      0    4
  BCL2L2 WILD-TYPE   10  394
                        clus
vv                       BCL2L2 MUTATED BCL2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(1193) Variable = SPTLC3 MUTATION ANALYSIS
D1193V1, survival
                  sevent
clus2                0   1
  SPTLC3 MUTATED    11   3
  SPTLC3 WILD-TYPE 327 213
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
              14              540 
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
               3              213 
$`SPTLC3 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-IG-A4QS TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8485 
       21.99        79.07         3.88        34.68        33.63         9.21 
TCGA-BR-8589 TCGA-CD-A487 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6822 TCGA-FP-8631 
       27.12        12.30       105.07        65.10        12.33         0.56 
TCGA-HJ-7597 TCGA-HU-A4G9 
       26.47        24.20 

$`SPTLC3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO 
       27.12         5.16        20.02        47.05        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
        5.39        25.18        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        12.36        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
            0.56             0.00 
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
          105.07           122.30 
  SPTLC3 MUTATED SPTLC3 WILD-TYPE 
          25.335           13.510 
[1] "0.6 - 105.1 (25.3)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.9"
D1193V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTLC3 MUTATED         0        1        3        2         2         1
  SPTLC3 WILD-TYPE      10       19       43       29        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPTLC3 MUTATED           0          1          2          1        1
  SPTLC3 WILD-TYPE        29         83         60         38       42
                  vv
clus               STAGE IVA
  SPTLC3 MUTATED           0
  SPTLC3 WILD-TYPE         4
D1193V3, multiclass
            clus
vv           SPTLC3 MUTATED SPTLC3 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SPTLC3 MUTATED       1   4   6   3
  SPTLC3 WILD-TYPE    53 131 255  99
D1193V4, multiclass
       clus
vv      SPTLC3 MUTATED SPTLC3 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 6              255
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SPTLC3 MUTATED     7   4   2   1
  SPTLC3 WILD-TYPE 188 169  87  84
D1193V5, multiclass
    clus
vv   SPTLC3 MUTATED SPTLC3 WILD-TYPE
  N0              7              188
  N1              4              169
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V6, binary
                  cls
clus                 0   1
  SPTLC3 MUTATED    12   1
  SPTLC3 WILD-TYPE 470  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTLC3 MUTATED     12    1
  SPTLC3 WILD-TYPE  470   37
   clus
vv  SPTLC3 MUTATED SPTLC3 WILD-TYPE
  0             12              470
  1              1               37
[1] 2 2
[1] FALSE
D1193V7, binary
                  cls
clus                 0   1
  SPTLC3 MUTATED     7   8
  SPTLC3 WILD-TYPE 165 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTLC3 MUTATED      7    8
  SPTLC3 WILD-TYPE  165  398
        clus
vv       SPTLC3 MUTATED SPTLC3 WILD-TYPE
  FEMALE              7              165
  MALE                8              398
[1] 2 2
[1] FALSE
D1193V8, binary
                  cls
clus                 0   1
  SPTLC3 MUTATED    12   0
  SPTLC3 WILD-TYPE 404 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTLC3 MUTATED     12    0
  SPTLC3 WILD-TYPE  404  102
     clus
vv    SPTLC3 MUTATED SPTLC3 WILD-TYPE
  NO              12              404
  YES              0              102
[1] 2 2
[1] FALSE
D1193V9, continuous
D1193V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPTLC3 MUTATED       2                         0
  SPTLC3 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPTLC3 MUTATED                                           0     9
  SPTLC3 WILD-TYPE                                         1   348
D1193V11, multiclass
                                           clus
vv                                          SPTLC3 MUTATED SPTLC3 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V12, binary
                  cls
clus                 0   1
  SPTLC3 MUTATED     0  11
  SPTLC3 WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPTLC3 MUTATED      0   11
  SPTLC3 WILD-TYPE   10  387
                        clus
vv                       SPTLC3 MUTATED SPTLC3 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(1194) Variable = PPRC1 MUTATION ANALYSIS
D1194V1, survival
                 sevent
clus2               0   1
  PPRC1 MUTATED    13   6
  PPRC1 WILD-TYPE 325 210
  PPRC1 MUTATED PPRC1 WILD-TYPE 
             19             535 
  PPRC1 MUTATED PPRC1 WILD-TYPE 
              6             210 
$`PPRC1 MUTATED`
TCGA-2H-A9GR TCGA-L5-A8NR TCGA-LN-A8I1 TCGA-R6-A6Y2 TCGA-Z6-A9VB TCGA-BR-6452 
       32.45         8.71        13.18         9.30         1.32        34.68 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-A4IY TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-5733 
       31.10         0.26        12.89        12.30         6.58        21.07 
TCGA-D7-5577 TCGA-D7-A4YT TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-SW-A7EA 
       25.71        14.27        22.32        22.68         6.58        19.04 
TCGA-VQ-AA6A 
       38.93 

$`PPRC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        7.40         6.18        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       69.04         7.99        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PPRC1 MUTATED PPRC1 WILD-TYPE 
           0.26            0.00 
  PPRC1 MUTATED PPRC1 WILD-TYPE 
          38.93          122.30 
  PPRC1 MUTATED PPRC1 WILD-TYPE 
          14.27           13.55 
[1] "0.3 - 38.9 (14.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPRC1 MUTATED         0        0        2        0         4         5
  PPRC1 WILD-TYPE      10       20       44       31        80        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPRC1 MUTATED           1          5          0          2        0         0
  PPRC1 WILD-TYPE        28         79         62         37       43         4
D1194V3, multiclass
            clus
vv           PPRC1 MUTATED PPRC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              5              78
  STAGE III              1              28
  STAGE IIIA             5              79
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PPRC1 MUTATED       0   6   8   5
  PPRC1 WILD-TYPE    54 129 253  97
D1194V4, multiclass
       clus
vv      PPRC1 MUTATED PPRC1 WILD-TYPE
  T0+T1             0              54
  T2                6             129
  T3                8             253
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PPRC1 MUTATED     9   5   2   3
  PPRC1 WILD-TYPE 186 168  87  82
D1194V5, multiclass
    clus
vv   PPRC1 MUTATED PPRC1 WILD-TYPE
  N0             9             186
  N1             5             168
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1194V6, binary
                 cls
clus                0   1
  PPRC1 MUTATED    19   0
  PPRC1 WILD-TYPE 463  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPRC1 MUTATED     19    0
  PPRC1 WILD-TYPE  463   38
   clus
vv  PPRC1 MUTATED PPRC1 WILD-TYPE
  0            19             463
  1             0              38
[1] 2 2
[1] FALSE
D1194V7, binary
                 cls
clus                0   1
  PPRC1 MUTATED    11   9
  PPRC1 WILD-TYPE 161 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPRC1 MUTATED     11    9
  PPRC1 WILD-TYPE  161  397
        clus
vv       PPRC1 MUTATED PPRC1 WILD-TYPE
  FEMALE            11             161
  MALE               9             397
[1] 2 2
[1] FALSE
D1194V8, binary
                 cls
clus                0   1
  PPRC1 MUTATED    17   2
  PPRC1 WILD-TYPE 399 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPRC1 MUTATED     17    2
  PPRC1 WILD-TYPE  399  100
     clus
vv    PPRC1 MUTATED PPRC1 WILD-TYPE
  NO             17             399
  YES             2             100
[1] 2 2
[1] FALSE
D1194V9, continuous
D1194V10, continuous
[1] "Remove cluster labels:" "PPRC1 MUTATED"         
clus
  PPRC1 MUTATED PPRC1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A8W5      TCGA-R6-A8W8 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" "PPRC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PPRC1 MUTATED       7                         0
  PPRC1 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPRC1 MUTATED                                           0    10
  PPRC1 WILD-TYPE                                         1   347
D1194V11, multiclass
                                           clus
vv                                          PPRC1 MUTATED PPRC1 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1194V12, binary
                 cls
clus                0   1
  PPRC1 MUTATED     1  15
  PPRC1 WILD-TYPE   9 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPRC1 MUTATED      1   15
  PPRC1 WILD-TYPE    9  383
                        clus
vv                       PPRC1 MUTATED PPRC1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            15             383
[1] 2 2
[1] FALSE

Clustering(1195) Variable = KCNT2 MUTATION ANALYSIS
D1195V1, survival
                 sevent
clus2               0   1
  KCNT2 MUTATED    16  24
  KCNT2 WILD-TYPE 322 192
  KCNT2 MUTATED KCNT2 WILD-TYPE 
             40             514 
  KCNT2 MUTATED KCNT2 WILD-TYPE 
             24             192 
$`KCNT2 MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-CG-4460 TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
        4.31        35.97        21.99         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-JY-A93D TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A8NH 
       32.45        33.27        31.56        32.61        18.35        12.92 
TCGA-VR-A8EU TCGA-B7-A5TJ TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8485 
       18.31        11.01         9.34        35.84         0.26         9.21 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-CD-8535 TCGA-CD-A48C 
        9.86        10.68         7.53        34.98        12.82        11.61 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-5718 TCGA-D7-6527 TCGA-D7-6822 
       11.77        20.02         7.99        36.00        10.26        12.33 
TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       30.51        23.84        14.07        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-R5-A805 TCGA-VQ-A8DL TCGA-VQ-A91U 
        6.74         9.24         0.92         1.71 

$`KCNT2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
       58.55         7.63        13.94         4.21         7.69        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30        26.33        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
       25.81        27.09        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        12.20        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        3.39        18.38        19.53        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52        74.53         6.08         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  KCNT2 MUTATED KCNT2 WILD-TYPE 
           0.26            0.00 
  KCNT2 MUTATED KCNT2 WILD-TYPE 
           36.0           122.3 
  KCNT2 MUTATED KCNT2 WILD-TYPE 
         12.395          13.870 
[1] "0.3 - 36.0 (12.4)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1.8"
D1195V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNT2 MUTATED         1        1        5        2         3         5
  KCNT2 WILD-TYPE       9       19       41       29        81        78
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNT2 MUTATED           3          8          4          4        3         1
  KCNT2 WILD-TYPE        26         76         58         35       40         3
D1195V3, multiclass
            clus
vv           KCNT2 MUTATED KCNT2 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               5              41
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              5              78
  STAGE III              3              26
  STAGE IIIA             8              76
  STAGE IIIB             4              58
  STAGE IIIC             4              35
  STAGE IV               3              40
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  KCNT2 MUTATED       7   9  16   8
  KCNT2 WILD-TYPE    47 126 245  94
D1195V4, multiclass
       clus
vv      KCNT2 MUTATED KCNT2 WILD-TYPE
  T0+T1             7              47
  T2                9             126
  T3               16             245
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  KCNT2 MUTATED    12  19   4   5
  KCNT2 WILD-TYPE 183 154  85  80
D1195V5, multiclass
    clus
vv   KCNT2 MUTATED KCNT2 WILD-TYPE
  N0            12             183
  N1            19             154
  N2             4              85
  N3             5              80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1195V6, binary
                 cls
clus                0   1
  KCNT2 MUTATED    35   4
  KCNT2 WILD-TYPE 447  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNT2 MUTATED     35    4
  KCNT2 WILD-TYPE  447   34
   clus
vv  KCNT2 MUTATED KCNT2 WILD-TYPE
  0            35             447
  1             4              34
[1] 2 2
[1] FALSE
D1195V7, binary
                 cls
clus                0   1
  KCNT2 MUTATED    12  29
  KCNT2 WILD-TYPE 160 377
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNT2 MUTATED     12   29
  KCNT2 WILD-TYPE  160  377
        clus
vv       KCNT2 MUTATED KCNT2 WILD-TYPE
  FEMALE            12             160
  MALE              29             377
[1] 2 2
[1] FALSE
D1195V8, binary
                 cls
clus                0   1
  KCNT2 MUTATED    30   5
  KCNT2 WILD-TYPE 386  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNT2 MUTATED     30    5
  KCNT2 WILD-TYPE  386   97
     clus
vv    KCNT2 MUTATED KCNT2 WILD-TYPE
  NO             30             386
  YES             5              97
[1] 2 2
[1] FALSE
D1195V9, continuous
[1] "Remove cluster labels:" "KCNT2 MUTATED"         
clus
  KCNT2 MUTATED KCNT2 WILD-TYPE 
              2              66 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EW 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"KCNT2 WILD-TYPE" "KCNT2 WILD-TYPE" 
D1195V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNT2 MUTATED       8                         0
  KCNT2 WILD-TYPE   125                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNT2 MUTATED                                           0    24
  KCNT2 WILD-TYPE                                         1   333
D1195V11, multiclass
                                           clus
vv                                          KCNT2 MUTATED KCNT2 WILD-TYPE
  ASIAN                                                 8             125
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                24             333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1195V12, binary
                 cls
clus                0   1
  KCNT2 MUTATED     0  23
  KCNT2 WILD-TYPE  10 375
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNT2 MUTATED      0   23
  KCNT2 WILD-TYPE   10  375
                        clus
vv                       KCNT2 MUTATED KCNT2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            23             375
[1] 2 2
[1] FALSE

Clustering(1196) Variable = CLSTN1 MUTATION ANALYSIS
D1196V1, survival
                  sevent
clus2                0   1
  CLSTN1 MUTATED     7   6
  CLSTN1 WILD-TYPE 331 210
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              13              541 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               6              210 
$`CLSTN1 MUTATED`
TCGA-L5-A43J TCGA-2H-A9GJ TCGA-L5-A4OM TCGA-Z6-AAPN TCGA-BR-6566 TCGA-BR-7723 
        4.31        58.55        47.93         2.66        32.78        28.73 
TCGA-BR-8363 TCGA-CD-8536 TCGA-CG-5733 TCGA-D7-8570 TCGA-FP-A4BE TCGA-HU-8602 
        0.26        12.43        21.07        24.72        11.08        22.32 
TCGA-VQ-A8P2 
       38.14 

$`CLSTN1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
       30.25         0.30        26.33        32.61        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
            0.26             0.00 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           58.55           122.30 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           22.32            13.51 
[1] "0.3 - 58.5 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1196V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLSTN1 MUTATED         1        1        1        1         3         2
  CLSTN1 WILD-TYPE       9       19       45       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLSTN1 MUTATED           0          2          2          0        1
  CLSTN1 WILD-TYPE        29         82         60         39       42
                  vv
clus               STAGE IVA
  CLSTN1 MUTATED           0
  CLSTN1 WILD-TYPE         4
D1196V3, multiclass
            clus
vv           CLSTN1 MUTATED CLSTN1 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CLSTN1 MUTATED       2   2   7   3
  CLSTN1 WILD-TYPE    52 133 254  99
D1196V4, multiclass
       clus
vv      CLSTN1 MUTATED CLSTN1 WILD-TYPE
  T0+T1              2               52
  T2                 2              133
  T3                 7              254
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CLSTN1 MUTATED     9   1   2   2
  CLSTN1 WILD-TYPE 186 172  87  83
D1196V5, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  N0              9              186
  N1              1              172
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1196V6, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    12   0
  CLSTN1 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     12    0
  CLSTN1 WILD-TYPE  470   38
   clus
vv  CLSTN1 MUTATED CLSTN1 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D1196V7, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     6   8
  CLSTN1 WILD-TYPE 166 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      6    8
  CLSTN1 WILD-TYPE  166  398
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  FEMALE              6              166
  MALE                8              398
[1] 2 2
[1] FALSE
D1196V8, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    10   2
  CLSTN1 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     10    2
  CLSTN1 WILD-TYPE  406  100
     clus
vv    CLSTN1 MUTATED CLSTN1 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D1196V9, continuous
D1196V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CLSTN1 MUTATED       2                         1
  CLSTN1 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLSTN1 MUTATED                                           0     9
  CLSTN1 WILD-TYPE                                         1   348
D1196V11, multiclass
                                           clus
vv                                          CLSTN1 MUTATED CLSTN1 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1196V12, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     0   9
  CLSTN1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      0    9
  CLSTN1 WILD-TYPE   10  389
                        clus
vv                       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1197) Variable = PCDH19 MUTATION ANALYSIS
D1197V1, survival
                  sevent
clus2                0   1
  PCDH19 MUTATED    20   7
  PCDH19 WILD-TYPE 318 209
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              27              527 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               7              209 
$`PCDH19 MUTATED`
TCGA-L5-A4OI TCGA-JY-A6FD TCGA-LN-A4A2 TCGA-R6-A6KZ TCGA-B7-5816 TCGA-BR-6452 
       19.99        68.02        12.49         5.06        26.70        34.68 
TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7957 TCGA-BR-8361 TCGA-BR-8369 
       19.33        44.94        35.84         9.07        31.10        14.04 
TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4465 TCGA-D7-8574 
       31.27        31.96        15.95         1.02         9.01        17.19 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G9 
       14.76        11.44        14.47        77.29        30.51        24.20 
TCGA-HU-A4H4 TCGA-RD-A7BS TCGA-VQ-A8P3 
       23.84        11.05        37.22 

$`PCDH19 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        44.75         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       31.20        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         3.45        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
        8.52        74.53         6.08         4.60         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        38.14        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PCDH19 MUTATED PCDH19 WILD-TYPE 
            1.02             0.00 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           77.29           122.30 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           19.99            13.41 
[1] "1.0 - 77.3 (20.0)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.1"
D1197V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCDH19 MUTATED         0        1        3        2         4         4
  PCDH19 WILD-TYPE      10       19       43       29        80        79
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH19 MUTATED           0          3          2          4        4
  PCDH19 WILD-TYPE        29         81         60         35       39
                  vv
clus               STAGE IVA
  PCDH19 MUTATED           0
  PCDH19 WILD-TYPE         4
D1197V3, multiclass
            clus
vv           PCDH19 MUTATED PCDH19 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                2               29
  STAGE IIA               4               80
  STAGE IIB               4               79
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              4               35
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PCDH19 MUTATED       1   8  12   7
  PCDH19 WILD-TYPE    53 127 249  95
D1197V4, multiclass
       clus
vv      PCDH19 MUTATED PCDH19 WILD-TYPE
  T0+T1              1               53
  T2                 8              127
  T3                12              249
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PCDH19 MUTATED     9   6   5   8
  PCDH19 WILD-TYPE 186 167  84  77
D1197V5, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  N0              9              186
  N1              6              167
  N2              5               84
  N3              8               77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1197V6, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    23   4
  PCDH19 WILD-TYPE 459  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     23    4
  PCDH19 WILD-TYPE  459   34
   clus
vv  PCDH19 MUTATED PCDH19 WILD-TYPE
  0             23              459
  1              4               34
[1] 2 2
[1] FALSE
D1197V7, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    17  13
  PCDH19 WILD-TYPE 155 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     17   13
  PCDH19 WILD-TYPE  155  393
        clus
vv       PCDH19 MUTATED PCDH19 WILD-TYPE
  FEMALE             17              155
  MALE               13              393
[1] 2 2
[1] FALSE
D1197V8, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    19   6
  PCDH19 WILD-TYPE 397  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     19    6
  PCDH19 WILD-TYPE  397   96
     clus
vv    PCDH19 MUTATED PCDH19 WILD-TYPE
  NO              19              397
  YES              6               96
[1] 2 2
[1] FALSE
D1197V9, continuous
[1] "Remove cluster labels:" "PCDH19 MUTATED"        
clus
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
D1197V10, continuous
[1] "Remove cluster labels:" "PCDH19 MUTATED"        
clus
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" "PCDH19 WILD-TYPE" 
      TCGA-Z6-AAPN 
"PCDH19 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PCDH19 MUTATED       5                         0
  PCDH19 WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCDH19 MUTATED                                           0    19
  PCDH19 WILD-TYPE                                         1   338
D1197V11, multiclass
                                           clus
vv                                          PCDH19 MUTATED PCDH19 WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 19              338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1197V12, binary
                  cls
clus                 0   1
  PCDH19 MUTATED     0  21
  PCDH19 WILD-TYPE  10 377
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED      0   21
  PCDH19 WILD-TYPE   10  377
                        clus
vv                       PCDH19 MUTATED PCDH19 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             21              377
[1] 2 2
[1] FALSE

Clustering(1198) Variable = LRRC4 MUTATION ANALYSIS
D1198V1, survival
                 sevent
clus2               0   1
  LRRC4 MUTATED    11   8
  LRRC4 WILD-TYPE 327 208
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             19             535 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
              8             208 
$`LRRC4 MUTATED`
TCGA-IG-A8O2 TCGA-BR-4184 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 
        4.67         6.97        14.43        29.59        32.25         6.18 
TCGA-BR-8372 TCGA-BR-A44U TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-8525 TCGA-CD-8528 
       31.27        13.87         1.48        16.14        12.59        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CG-4306 TCGA-CG-5719 TCGA-HF-A5NB TCGA-HU-8243 
       12.30        12.59         1.02         1.02        30.51         5.92 
TCGA-HU-A4GU 
        6.58 

$`LRRC4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.39        12.76        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
       63.06        52.21        26.47         1.51        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  LRRC4 MUTATED LRRC4 WILD-TYPE 
           1.02            0.00 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
          32.25          122.30 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
          12.33           13.78 
[1] "1.0 - 32.2 (12.3)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.5"
D1198V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRC4 MUTATED         0        0        0        0         1         4
  LRRC4 WILD-TYPE      10       20       46       31        83        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRC4 MUTATED           1          4          3          4        3         0
  LRRC4 WILD-TYPE        28         80         59         35       40         4
D1198V3, multiclass
            clus
vv           LRRC4 MUTATED LRRC4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              4              79
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             3              59
  STAGE IIIC             4              35
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  LRRC4 MUTATED       1   0   9  11
  LRRC4 WILD-TYPE    53 135 252  91
D1198V4, multiclass
       clus
vv      LRRC4 MUTATED LRRC4 WILD-TYPE
  T0+T1             1              53
  T2                0             135
  T3                9             252
  T4               11              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  LRRC4 MUTATED     7   6   2   6
  LRRC4 WILD-TYPE 188 167  87  79
D1198V5, multiclass
    clus
vv   LRRC4 MUTATED LRRC4 WILD-TYPE
  N0             7             188
  N1             6             167
  N2             2              87
  N3             6              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1198V6, binary
                 cls
clus                0   1
  LRRC4 MUTATED    18   3
  LRRC4 WILD-TYPE 464  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     18    3
  LRRC4 WILD-TYPE  464   35
   clus
vv  LRRC4 MUTATED LRRC4 WILD-TYPE
  0            18             464
  1             3              35
[1] 2 2
[1] FALSE
D1198V7, binary
                 cls
clus                0   1
  LRRC4 MUTATED    10  12
  LRRC4 WILD-TYPE 162 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     10   12
  LRRC4 WILD-TYPE  162  394
        clus
vv       LRRC4 MUTATED LRRC4 WILD-TYPE
  FEMALE            10             162
  MALE              12             394
[1] 2 2
[1] FALSE
D1198V8, binary
                 cls
clus                0   1
  LRRC4 MUTATED    12   5
  LRRC4 WILD-TYPE 404  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     12    5
  LRRC4 WILD-TYPE  404   97
     clus
vv    LRRC4 MUTATED LRRC4 WILD-TYPE
  NO             12             404
  YES             5              97
[1] 2 2
[1] FALSE
D1198V9, continuous
D1198V10, continuous
[1] "Remove cluster labels:" "LRRC4 MUTATED"         
clus
  LRRC4 MUTATED LRRC4 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" "LRRC4 WILD-TYPE" 
     TCGA-Z6-AAPN 
"LRRC4 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRRC4 MUTATED       7                         0
  LRRC4 WILD-TYPE   126                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRC4 MUTATED                                           0    12
  LRRC4 WILD-TYPE                                         1   345
D1198V11, multiclass
                                           clus
vv                                          LRRC4 MUTATED LRRC4 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1198V12, binary
                 cls
clus                0   1
  LRRC4 MUTATED     0  19
  LRRC4 WILD-TYPE  10 379
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED      0   19
  LRRC4 WILD-TYPE   10  379
                        clus
vv                       LRRC4 MUTATED LRRC4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            19             379
[1] 2 2
[1] FALSE

Clustering(1199) Variable = THYN1 MUTATION ANALYSIS
D1199V1, survival
                 sevent
clus2               0   1
  THYN1 MUTATED     5   5
  THYN1 WILD-TYPE 333 211
  THYN1 MUTATED THYN1 WILD-TYPE 
             10             544 
  THYN1 MUTATED THYN1 WILD-TYPE 
              5             211 
$`THYN1 MUTATED`
TCGA-IC-A6RF TCGA-CG-4460 TCGA-L5-A893 TCGA-BR-4257 TCGA-BR-7707 TCGA-CD-8535 
       15.68        21.99         3.02         9.67        35.84        12.82 
TCGA-CD-A48C TCGA-CG-5726 TCGA-F1-6874 TCGA-HJ-7597 
       11.61        28.96        14.47        26.47 

$`THYN1 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  THYN1 MUTATED THYN1 WILD-TYPE 
           3.02            0.00 
  THYN1 MUTATED THYN1 WILD-TYPE 
          35.84          122.30 
  THYN1 MUTATED THYN1 WILD-TYPE 
         15.075          13.530 
[1] "3.0 - 35.8 (15.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1199V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THYN1 MUTATED         1        2        3        0         0         1
  THYN1 WILD-TYPE       9       18       43       31        84        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THYN1 MUTATED           0          1          0          0        1         0
  THYN1 WILD-TYPE        29         83         62         39       42         4
D1199V3, multiclass
            clus
vv           THYN1 MUTATED THYN1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               2              18
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  THYN1 MUTATED       3   3   2   1
  THYN1 WILD-TYPE    51 132 259 101
D1199V4, multiclass
       clus
vv      THYN1 MUTATED THYN1 WILD-TYPE
  T0+T1             3              51
  T2                3             132
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  THYN1 MUTATED     6   3   0   0
  THYN1 WILD-TYPE 189 170  89  85
D1199V5, multiclass
    clus
vv   THYN1 MUTATED THYN1 WILD-TYPE
  N0             6             189
  N1             3             170
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1199V6, binary
                 cls
clus                0   1
  THYN1 MUTATED     8   1
  THYN1 WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      8    1
  THYN1 WILD-TYPE  474   37
   clus
vv  THYN1 MUTATED THYN1 WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D1199V7, binary
                 cls
clus                0   1
  THYN1 MUTATED     7   3
  THYN1 WILD-TYPE 165 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      7    3
  THYN1 WILD-TYPE  165  403
        clus
vv       THYN1 MUTATED THYN1 WILD-TYPE
  FEMALE             7             165
  MALE               3             403
[1] 2 2
[1] FALSE
D1199V8, binary
                 cls
clus                0   1
  THYN1 MUTATED     9   0
  THYN1 WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      9    0
  THYN1 WILD-TYPE  407  102
     clus
vv    THYN1 MUTATED THYN1 WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D1199V9, continuous
D1199V10, continuous
[1] "Remove cluster labels:" "THYN1 MUTATED"         
clus
  THYN1 MUTATED THYN1 WILD-TYPE 
              2              96 
     TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE      TCGA-L5-A4OG 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A8NE      TCGA-L5-A8NF 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ      TCGA-L5-A8NR 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O      TCGA-LN-A49P 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6      TCGA-LN-A4A9 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV      TCGA-LN-A7HW 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ      TCGA-LN-A8I0 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN      TCGA-R6-A6L4 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5      TCGA-R6-A8W8 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" "THYN1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  THYN1 MUTATED       2                         0
  THYN1 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THYN1 MUTATED                                           0     6
  THYN1 WILD-TYPE                                         1   351
D1199V11, multiclass
                                           clus
vv                                          THYN1 MUTATED THYN1 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1199V12, binary
                 cls
clus                0   1
  THYN1 MUTATED     0   7
  THYN1 WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      0    7
  THYN1 WILD-TYPE   10  391
                        clus
vv                       THYN1 MUTATED THYN1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1200) Variable = BZW1 MUTATION ANALYSIS
D1200V1, survival
                sevent
clus2              0   1
  BZW1 MUTATED     5   4
  BZW1 WILD-TYPE 333 212
  BZW1 MUTATED BZW1 WILD-TYPE 
             9            545 
  BZW1 MUTATED BZW1 WILD-TYPE 
             4            212 
$`BZW1 MUTATED`
TCGA-2H-A9GH TCGA-IG-A4P3 TCGA-L5-A8NH TCGA-BR-6452 TCGA-BR-8487 TCGA-CG-4465 
       31.27        18.64        12.92        34.68         1.12         9.01 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H8 
       22.68         6.51        14.07 

$`BZW1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  BZW1 MUTATED BZW1 WILD-TYPE 
          1.12           0.00 
  BZW1 MUTATED BZW1 WILD-TYPE 
         34.68         122.30 
  BZW1 MUTATED BZW1 WILD-TYPE 
         14.07          13.55 
[1] "1.1 - 34.7 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1200V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BZW1 MUTATED         0        0        1        0         3         3
  BZW1 WILD-TYPE      10       20       45       31        81        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BZW1 MUTATED           0          0          0          0        2         0
  BZW1 WILD-TYPE        29         84         62         39       41         4
D1200V3, multiclass
            clus
vv           BZW1 MUTATED BZW1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            0             84
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  BZW1 MUTATED       3   1   4   1
  BZW1 WILD-TYPE    51 134 257 101
D1200V4, multiclass
       clus
vv      BZW1 MUTATED BZW1 WILD-TYPE
  T0+T1            3             51
  T2               1            134
  T3               4            257
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  BZW1 MUTATED     4   4   0   1
  BZW1 WILD-TYPE 191 169  89  84
D1200V5, multiclass
    clus
vv   BZW1 MUTATED BZW1 WILD-TYPE
  N0            4            191
  N1            4            169
  N2            0             89
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1200V6, binary
                cls
clus               0   1
  BZW1 MUTATED     7   2
  BZW1 WILD-TYPE 475  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BZW1 MUTATED      7    2
  BZW1 WILD-TYPE  475   36
   clus
vv  BZW1 MUTATED BZW1 WILD-TYPE
  0            7            475
  1            2             36
[1] 2 2
[1] FALSE
D1200V7, binary
                cls
clus               0   1
  BZW1 MUTATED     5   4
  BZW1 WILD-TYPE 167 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  BZW1 MUTATED      5    4
  BZW1 WILD-TYPE  167  402
        clus
vv       BZW1 MUTATED BZW1 WILD-TYPE
  FEMALE            5            167
  MALE              4            402
[1] 2 2
[1] FALSE
D1200V8, binary
                cls
clus               0   1
  BZW1 MUTATED     6   1
  BZW1 WILD-TYPE 410 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  BZW1 MUTATED      6    1
  BZW1 WILD-TYPE  410  101
     clus
vv    BZW1 MUTATED BZW1 WILD-TYPE
  NO             6            410
  YES            1            101
[1] 2 2
[1] FALSE
D1200V9, continuous
D1200V10, continuous
[1] "Remove cluster labels:" "BZW1 MUTATED"          
clus
  BZW1 MUTATED BZW1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" "BZW1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"BZW1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BZW1 MUTATED       3                         0
  BZW1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BZW1 MUTATED                                           0     4
  BZW1 WILD-TYPE                                         1   353
D1200V11, multiclass
                                           clus
vv                                          BZW1 MUTATED BZW1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1200V12, binary
                cls
clus               0   1
  BZW1 MUTATED     0   6
  BZW1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  BZW1 MUTATED      0    6
  BZW1 WILD-TYPE   10  392
                        clus
vv                       BZW1 MUTATED BZW1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1201) Variable = CEP110 MUTATION ANALYSIS
D1201V1, survival
                  sevent
clus2                0   1
  CEP110 MUTATED    10   9
  CEP110 WILD-TYPE 328 207
  CEP110 MUTATED CEP110 WILD-TYPE 
              19              535 
  CEP110 MUTATED CEP110 WILD-TYPE 
               9              207 
$`CEP110 MUTATED`
TCGA-L5-A4OI TCGA-Q9-A6FU TCGA-CG-4460 TCGA-L5-A4OJ TCGA-Z6-A8JD TCGA-BR-6566 
       19.99         5.16        21.99        21.01         3.42        32.78 
TCGA-BR-6705 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MI 
       25.61         6.18         0.26        31.96        16.14        11.77 
TCGA-CG-5726 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-SW-A7EA 
       28.96         5.52        77.29        14.07        13.35        19.04 
TCGA-VQ-A8P2 
       38.14 

$`CEP110 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CEP110 MUTATED CEP110 WILD-TYPE 
            0.26             0.00 
  CEP110 MUTATED CEP110 WILD-TYPE 
           77.29           122.30 
  CEP110 MUTATED CEP110 WILD-TYPE 
           19.04            13.51 
[1] "0.3 - 77.3 (19.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1201V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP110 MUTATED         1        1        3        1         2         1
  CEP110 WILD-TYPE       9       19       43       30        82        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP110 MUTATED           0          4          3          1        2
  CEP110 WILD-TYPE        29         80         59         38       41
                  vv
clus               STAGE IVA
  CEP110 MUTATED           0
  CEP110 WILD-TYPE         4
D1201V3, multiclass
            clus
vv           CEP110 MUTATED CEP110 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                3               43
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              3               59
  STAGE IIIC              1               38
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CEP110 MUTATED       3   4   9   3
  CEP110 WILD-TYPE    51 131 252  99
D1201V4, multiclass
       clus
vv      CEP110 MUTATED CEP110 WILD-TYPE
  T0+T1              3               51
  T2                 4              131
  T3                 9              252
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CEP110 MUTATED     7   6   3   3
  CEP110 WILD-TYPE 188 167  86  82
D1201V5, multiclass
    clus
vv   CEP110 MUTATED CEP110 WILD-TYPE
  N0              7              188
  N1              6              167
  N2              3               86
  N3              3               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1201V6, binary
                  cls
clus                 0   1
  CEP110 MUTATED    16   2
  CEP110 WILD-TYPE 466  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED     16    2
  CEP110 WILD-TYPE  466   36
   clus
vv  CEP110 MUTATED CEP110 WILD-TYPE
  0             16              466
  1              2               36
[1] 2 2
[1] FALSE
D1201V7, binary
                  cls
clus                 0   1
  CEP110 MUTATED     8  11
  CEP110 WILD-TYPE 164 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED      8   11
  CEP110 WILD-TYPE  164  395
        clus
vv       CEP110 MUTATED CEP110 WILD-TYPE
  FEMALE              8              164
  MALE               11              395
[1] 2 2
[1] FALSE
D1201V8, binary
                  cls
clus                 0   1
  CEP110 MUTATED    16   2
  CEP110 WILD-TYPE 400 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED     16    2
  CEP110 WILD-TYPE  400  100
     clus
vv    CEP110 MUTATED CEP110 WILD-TYPE
  NO              16              400
  YES              2              100
[1] 2 2
[1] FALSE
D1201V9, continuous
[1] "Remove cluster labels:" "CEP110 MUTATED"        
clus
  CEP110 MUTATED CEP110 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-A8JE 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
D1201V10, continuous
[1] "Remove cluster labels:" "CEP110 MUTATED"        
clus
  CEP110 MUTATED CEP110 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A8NT       TCGA-IC-A6RE       TCGA-IG-A3QL       TCGA-IG-A3Y9 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3       TCGA-IG-A4QT 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS       TCGA-IG-A8O2 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE       TCGA-JY-A6FG 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C       TCGA-L5-A43E 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM       TCGA-L5-A4ON 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OT 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX       TCGA-L5-A88S 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" "CEP110 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP110 MUTATED       3                         0
  CEP110 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP110 MUTATED                                           0    13
  CEP110 WILD-TYPE                                         1   344
D1201V11, multiclass
                                           clus
vv                                          CEP110 MUTATED CEP110 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1201V12, binary
                  cls
clus                 0   1
  CEP110 MUTATED     0  13
  CEP110 WILD-TYPE  10 385
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED      0   13
  CEP110 WILD-TYPE   10  385
                        clus
vv                       CEP110 MUTATED CEP110 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             13              385
[1] 2 2
[1] FALSE

Clustering(1202) Variable = UACA MUTATION ANALYSIS
D1202V1, survival
                sevent
clus2              0   1
  UACA MUTATED    11   3
  UACA WILD-TYPE 327 213
  UACA MUTATED UACA WILD-TYPE 
            14            540 
  UACA MUTATED UACA WILD-TYPE 
             3            213 
$`UACA MUTATED`
TCGA-L5-A4OI TCGA-LN-A4A2 TCGA-LN-A8HZ TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8680 
       19.99        12.49        12.33        44.94         1.12        31.96 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4469 TCGA-CG-5719 TCGA-D7-A4YY TCGA-HU-A4GT 
        6.58         1.02         7.07         1.02        13.78         6.51 
TCGA-HU-A4GU TCGA-HU-A4H8 
        6.58        14.07 

$`UACA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       18.97        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27        16.44         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  UACA MUTATED UACA WILD-TYPE 
          1.02           0.00 
  UACA MUTATED UACA WILD-TYPE 
         44.94         122.30 
  UACA MUTATED UACA WILD-TYPE 
         9.700         13.775 
[1] "1.0 - 44.9 (9.7)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "1.3"
D1202V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UACA MUTATED         0        0        1        0         6         2
  UACA WILD-TYPE      10       20       45       31        78        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UACA MUTATED           0          1          1          1        4         0
  UACA WILD-TYPE        29         83         61         38       39         4
D1202V3, multiclass
            clus
vv           UACA MUTATED UACA WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             6             78
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            1             61
  STAGE IIIC            1             38
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  UACA MUTATED       2   1  10   4
  UACA WILD-TYPE    52 134 251  98
D1202V4, multiclass
       clus
vv      UACA MUTATED UACA WILD-TYPE
  T0+T1            2             52
  T2               1            134
  T3              10            251
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  UACA MUTATED     9   2   2   3
  UACA WILD-TYPE 186 171  87  82
D1202V5, multiclass
    clus
vv   UACA MUTATED UACA WILD-TYPE
  N0            9            186
  N1            2            171
  N2            2             87
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1202V6, binary
                cls
clus               0   1
  UACA MUTATED    13   3
  UACA WILD-TYPE 469  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED     13    3
  UACA WILD-TYPE  469   35
   clus
vv  UACA MUTATED UACA WILD-TYPE
  0           13            469
  1            3             35
[1] 2 2
[1] FALSE
D1202V7, binary
                cls
clus               0   1
  UACA MUTATED     6  11
  UACA WILD-TYPE 166 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      6   11
  UACA WILD-TYPE  166  395
        clus
vv       UACA MUTATED UACA WILD-TYPE
  FEMALE            6            166
  MALE             11            395
[1] 2 2
[1] FALSE
D1202V8, binary
                cls
clus               0   1
  UACA MUTATED     9   3
  UACA WILD-TYPE 407  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      9    3
  UACA WILD-TYPE  407   99
     clus
vv    UACA MUTATED UACA WILD-TYPE
  NO             9            407
  YES            3             99
[1] 2 2
[1] FALSE
D1202V9, continuous
[1] "Remove cluster labels:" "UACA MUTATED"          
clus
  UACA MUTATED UACA WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5     TCGA-LN-A4A6 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
D1202V10, continuous
[1] "Remove cluster labels:" "UACA MUTATED"          
clus
  UACA MUTATED UACA WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8I0 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" "UACA WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UACA MUTATED       7                         0
  UACA WILD-TYPE   126                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UACA MUTATED                                           0     7
  UACA WILD-TYPE                                         1   350
D1202V11, multiclass
                                           clus
vv                                          UACA MUTATED UACA WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1202V12, binary
                cls
clus               0   1
  UACA MUTATED     0  13
  UACA WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      0   13
  UACA WILD-TYPE   10  385
                        clus
vv                       UACA MUTATED UACA WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(1203) Variable = PAPOLB MUTATION ANALYSIS
D1203V1, survival
                  sevent
clus2                0   1
  PAPOLB MUTATED     7   7
  PAPOLB WILD-TYPE 331 209
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              14              540 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
               7              209 
$`PAPOLB MUTATED`
TCGA-VR-A8EY TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-A4J1 TCGA-CG-4441 TCGA-CG-5726 
       33.70        32.78        30.90         0.72        14.01        28.96 
TCGA-D7-6524 TCGA-D7-A6EY TCGA-D7-A747 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-IN-AB1X 
       17.85        11.44         8.38        22.68         0.10        13.51 
TCGA-SW-A7EB TCGA-VQ-A91Q 
        5.79        20.81 

$`PAPOLB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        40.21        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29        15.65         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        15.75         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        19.04         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
       17.85         1.87        15.65         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  PAPOLB MUTATED PAPOLB WILD-TYPE 
             0.1              0.0 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
            33.7            122.3 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
           15.93            13.53 
[1] "0.1 - 33.7 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1203V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAPOLB MUTATED         0        1        0        1         3         2
  PAPOLB WILD-TYPE      10       19       46       30        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAPOLB MUTATED           0          4          1          1        1
  PAPOLB WILD-TYPE        29         80         61         38       42
                  vv
clus               STAGE IVA
  PAPOLB MUTATED           0
  PAPOLB WILD-TYPE         4
D1203V3, multiclass
            clus
vv           PAPOLB MUTATED PAPOLB WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  PAPOLB MUTATED       1   2   9   2
  PAPOLB WILD-TYPE    53 133 252 100
D1203V4, multiclass
       clus
vv      PAPOLB MUTATED PAPOLB WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 9              252
  T4                 2              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  PAPOLB MUTATED     4   4   4   2
  PAPOLB WILD-TYPE 191 169  85  83
D1203V5, multiclass
    clus
vv   PAPOLB MUTATED PAPOLB WILD-TYPE
  N0              4              191
  N1              4              169
  N2              4               85
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1203V6, binary
                  cls
clus                 0   1
  PAPOLB MUTATED    15   0
  PAPOLB WILD-TYPE 467  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED     15    0
  PAPOLB WILD-TYPE  467   38
   clus
vv  PAPOLB MUTATED PAPOLB WILD-TYPE
  0             15              467
  1              0               38
[1] 2 2
[1] FALSE
D1203V7, binary
                  cls
clus                 0   1
  PAPOLB MUTATED     6   9
  PAPOLB WILD-TYPE 166 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED      6    9
  PAPOLB WILD-TYPE  166  397
        clus
vv       PAPOLB MUTATED PAPOLB WILD-TYPE
  FEMALE              6              166
  MALE                9              397
[1] 2 2
[1] FALSE
D1203V8, binary
                  cls
clus                 0   1
  PAPOLB MUTATED    10   1
  PAPOLB WILD-TYPE 406 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED     10    1
  PAPOLB WILD-TYPE  406  101
     clus
vv    PAPOLB MUTATED PAPOLB WILD-TYPE
  NO              10              406
  YES              1              101
[1] 2 2
[1] FALSE
D1203V9, continuous
[1] "Remove cluster labels:" "PAPOLB MUTATED"        
clus
  PAPOLB MUTATED PAPOLB WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" "PAPOLB WILD-TYPE" 
D1203V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PAPOLB MUTATED       3                         0
  PAPOLB WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAPOLB MUTATED                                           0     9
  PAPOLB WILD-TYPE                                         1   348
D1203V11, multiclass
                                           clus
vv                                          PAPOLB MUTATED PAPOLB WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1203V12, binary
                  cls
clus                 0   1
  PAPOLB MUTATED     0  11
  PAPOLB WILD-TYPE  10 387
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED      0   11
  PAPOLB WILD-TYPE   10  387
                        clus
vv                       PAPOLB MUTATED PAPOLB WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             11              387
[1] 2 2
[1] FALSE

Clustering(1204) Variable = TBC1D22B MUTATION ANALYSIS
D1204V1, survival
                    sevent
clus2                  0   1
  TBC1D22B MUTATED     6   2
  TBC1D22B WILD-TYPE 332 214
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 8                546 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 2                214 
$`TBC1D22B MUTATED`
TCGA-JY-A93E TCGA-R6-A6L6 TCGA-BR-8487 TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GQ 
       25.22         7.04         1.12        52.21        22.32         0.10 
TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.58        38.14 

$`TBC1D22B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
               0.1                0.0 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
             52.21             122.30 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
            14.680             13.565 
[1] "0.1 - 52.2 (14.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.6"
D1204V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D22B MUTATED         0        1        0        0         1         2
  TBC1D22B WILD-TYPE      10       19       46       31        83        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D22B MUTATED           0          2          0          1        0
  TBC1D22B WILD-TYPE        29         82         62         38       43
                    vv
clus                 STAGE IVA
  TBC1D22B MUTATED           0
  TBC1D22B WILD-TYPE         4
D1204V3, multiclass
            clus
vv           TBC1D22B MUTATED TBC1D22B WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  0                 43
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  TBC1D22B MUTATED       1   0   4   3
  TBC1D22B WILD-TYPE    53 135 257  99
D1204V4, multiclass
       clus
vv      TBC1D22B MUTATED TBC1D22B WILD-TYPE
  T0+T1                1                 53
  T2                   0                135
  T3                   4                257
  T4                   3                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  TBC1D22B MUTATED     3   3   1   0
  TBC1D22B WILD-TYPE 192 170  88  85
D1204V5, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  N0                3                192
  N1                3                170
  N2                1                 88
  N3                0                 85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1204V6, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     7   0
  TBC1D22B WILD-TYPE 475  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      7    0
  TBC1D22B WILD-TYPE  475   38
   clus
vv  TBC1D22B MUTATED TBC1D22B WILD-TYPE
  0                7                475
  1                0                 38
[1] 2 2
[1] FALSE
D1204V7, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     3   6
  TBC1D22B WILD-TYPE 169 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      3    6
  TBC1D22B WILD-TYPE  169  400
        clus
vv       TBC1D22B MUTATED TBC1D22B WILD-TYPE
  FEMALE                3                169
  MALE                  6                400
[1] 2 2
[1] FALSE
D1204V8, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     7   1
  TBC1D22B WILD-TYPE 409 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      7    1
  TBC1D22B WILD-TYPE  409  101
     clus
vv    TBC1D22B MUTATED TBC1D22B WILD-TYPE
  NO                 7                409
  YES                1                101
[1] 2 2
[1] FALSE
D1204V9, continuous
D1204V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D22B MUTATED       3                         0
  TBC1D22B WILD-TYPE   130                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D22B MUTATED                                           0     5
  TBC1D22B WILD-TYPE                                         1   352
D1204V11, multiclass
                                           clus
vv                                          TBC1D22B MUTATED TBC1D22B WILD-TYPE
  ASIAN                                                    3                130
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1204V12, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     0   6
  TBC1D22B WILD-TYPE  10 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      0    6
  TBC1D22B WILD-TYPE   10  392
                        clus
vv                       TBC1D22B MUTATED TBC1D22B WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                6                392
[1] 2 2
[1] FALSE

Clustering(1205) Variable = HTR1E MUTATION ANALYSIS
D1205V1, survival
                 sevent
clus2               0   1
  HTR1E MUTATED     8   9
  HTR1E WILD-TYPE 330 207
  HTR1E MUTATED HTR1E WILD-TYPE 
             17             537 
  HTR1E MUTATED HTR1E WILD-TYPE 
              9             207 
$`HTR1E MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A625 TCGA-BR-4184 
        7.63         5.92        16.24        33.27        12.82         6.97 
TCGA-BR-7704 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-8527 TCGA-CG-5733 TCGA-F1-A448 
       35.24         6.18        31.96         7.17        21.07        21.27 
TCGA-HF-7132 TCGA-HU-A4GX TCGA-IN-8663 TCGA-VQ-A8P3 TCGA-VQ-AA6G 
       77.29        20.25         3.39        37.22        26.04 

$`HTR1E WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       20.05        31.27        14.30        58.55        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       43.66        28.41        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  HTR1E MUTATED HTR1E WILD-TYPE 
           3.39            0.00 
  HTR1E MUTATED HTR1E WILD-TYPE 
          77.29          122.30 
  HTR1E MUTATED HTR1E WILD-TYPE 
          20.25           13.51 
[1] "3.4 - 77.3 (20.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1205V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTR1E MUTATED         0        0        0        3         3         1
  HTR1E WILD-TYPE      10       20       46       28        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR1E MUTATED           2          3          2          1        1         1
  HTR1E WILD-TYPE        27         81         60         38       42         3
D1205V3, multiclass
            clus
vv           HTR1E MUTATED HTR1E WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               3              28
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  HTR1E MUTATED       0   4  10   3
  HTR1E WILD-TYPE    54 131 251  99
D1205V4, multiclass
       clus
vv      HTR1E MUTATED HTR1E WILD-TYPE
  T0+T1             0              54
  T2                4             131
  T3               10             251
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  HTR1E MUTATED     4   7   5   1
  HTR1E WILD-TYPE 191 166  84  84
D1205V5, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  N0             4             191
  N1             7             166
  N2             5              84
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1205V6, binary
                 cls
clus                0   1
  HTR1E MUTATED    14   2
  HTR1E WILD-TYPE 468  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED     14    2
  HTR1E WILD-TYPE  468   36
   clus
vv  HTR1E MUTATED HTR1E WILD-TYPE
  0            14             468
  1             2              36
[1] 2 2
[1] FALSE
D1205V7, binary
                 cls
clus                0   1
  HTR1E MUTATED     5  12
  HTR1E WILD-TYPE 167 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      5   12
  HTR1E WILD-TYPE  167  394
        clus
vv       HTR1E MUTATED HTR1E WILD-TYPE
  FEMALE             5             167
  MALE              12             394
[1] 2 2
[1] FALSE
D1205V8, binary
                 cls
clus                0   1
  HTR1E MUTATED    13   3
  HTR1E WILD-TYPE 403  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED     13    3
  HTR1E WILD-TYPE  403   99
     clus
vv    HTR1E MUTATED HTR1E WILD-TYPE
  NO             13             403
  YES             3              99
[1] 2 2
[1] FALSE
D1205V9, continuous
[1] "Remove cluster labels:" "HTR1E MUTATED"         
clus
  HTR1E MUTATED HTR1E WILD-TYPE 
              1              67 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YB 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3      TCGA-IG-A7DP 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L      TCGA-LN-A49M 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"HTR1E WILD-TYPE" "HTR1E WILD-TYPE" "HTR1E WILD-TYPE" 
D1205V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HTR1E MUTATED       4                         0
  HTR1E WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTR1E MUTATED                                           0     8
  HTR1E WILD-TYPE                                         1   349
D1205V11, multiclass
                                           clus
vv                                          HTR1E MUTATED HTR1E WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1205V12, binary
                 cls
clus                0   1
  HTR1E MUTATED     1   9
  HTR1E WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      1    9
  HTR1E WILD-TYPE    9  389
                        clus
vv                       HTR1E MUTATED HTR1E WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1206) Variable = SALL2 MUTATION ANALYSIS
D1206V1, survival
                 sevent
clus2               0   1
  SALL2 MUTATED     9   7
  SALL2 WILD-TYPE 329 209
  SALL2 MUTATED SALL2 WILD-TYPE 
             16             538 
  SALL2 MUTATED SALL2 WILD-TYPE 
              7             209 
$`SALL2 MUTATED`
TCGA-LN-A9FP TCGA-R6-A6KZ TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-8687 
       12.03         5.06        31.10        31.27        31.96         8.22 
TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-A4MI TCGA-D7-5578 TCGA-HF-7132 TCGA-HU-A4G9 
        1.48        16.14        11.77        12.66        77.29        24.20 
TCGA-HU-A4GQ TCGA-IN-A6RL TCGA-VQ-A8P2 TCGA-VQ-AA6A 
        0.10        13.35        38.14        38.93 

$`SALL2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       26.73        24.79        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08        34.98        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       13.58         0.56        11.08         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        22.68         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SALL2 MUTATED SALL2 WILD-TYPE 
            0.1             0.0 
  SALL2 MUTATED SALL2 WILD-TYPE 
          77.29          122.30 
  SALL2 MUTATED SALL2 WILD-TYPE 
         14.745          13.565 
[1] "0.1 - 77.3 (14.7)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1206V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SALL2 MUTATED         0        1        0        1         1         0
  SALL2 WILD-TYPE      10       19       46       30        83        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SALL2 MUTATED           0          4          1          6        1         0
  SALL2 WILD-TYPE        29         80         61         33       42         4
D1206V3, multiclass
            clus
vv           SALL2 MUTATED SALL2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             4              80
  STAGE IIIB             1              61
  STAGE IIIC             6              33
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SALL2 MUTATED       1   3   3   8
  SALL2 WILD-TYPE    53 132 258  94
D1206V4, multiclass
       clus
vv      SALL2 MUTATED SALL2 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SALL2 MUTATED     2   4   5   4
  SALL2 WILD-TYPE 193 169  84  81
D1206V5, multiclass
    clus
vv   SALL2 MUTATED SALL2 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             5              84
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1206V6, binary
                 cls
clus                0   1
  SALL2 MUTATED    14   1
  SALL2 WILD-TYPE 468  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED     14    1
  SALL2 WILD-TYPE  468   37
   clus
vv  SALL2 MUTATED SALL2 WILD-TYPE
  0            14             468
  1             1              37
[1] 2 2
[1] FALSE
D1206V7, binary
                 cls
clus                0   1
  SALL2 MUTATED     5  11
  SALL2 WILD-TYPE 167 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      5   11
  SALL2 WILD-TYPE  167  395
        clus
vv       SALL2 MUTATED SALL2 WILD-TYPE
  FEMALE             5             167
  MALE              11             395
[1] 2 2
[1] FALSE
D1206V8, binary
                 cls
clus                0   1
  SALL2 MUTATED    12   4
  SALL2 WILD-TYPE 404  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED     12    4
  SALL2 WILD-TYPE  404   98
     clus
vv    SALL2 MUTATED SALL2 WILD-TYPE
  NO             12             404
  YES             4              98
[1] 2 2
[1] FALSE
D1206V9, continuous
D1206V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SALL2 MUTATED       5                         0
  SALL2 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SALL2 MUTATED                                           0    10
  SALL2 WILD-TYPE                                         1   347
D1206V11, multiclass
                                           clus
vv                                          SALL2 MUTATED SALL2 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1206V12, binary
                 cls
clus                0   1
  SALL2 MUTATED     0  13
  SALL2 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      0   13
  SALL2 WILD-TYPE   10  385
                        clus
vv                       SALL2 MUTATED SALL2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(1207) Variable = BTAF1 MUTATION ANALYSIS
D1207V1, survival
                 sevent
clus2               0   1
  BTAF1 MUTATED    17   6
  BTAF1 WILD-TYPE 321 210
  BTAF1 MUTATED BTAF1 WILD-TYPE 
             23             531 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
              6             210 
$`BTAF1 MUTATED`
TCGA-L5-A4OJ TCGA-L5-A8NF TCGA-L5-A8NM TCGA-L5-A8NN TCGA-R6-A8W5 TCGA-VR-AA4G 
       21.01         2.66         7.76         5.49        15.78        18.05 
TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 
        2.66         6.97        34.68        32.78        35.84        29.59 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8589 TCGA-CG-5717 TCGA-CG-5721 TCGA-D7-8570 
        4.31        25.05        27.12         6.97         6.02        24.72 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       77.29        30.51        23.84        74.53        38.14 

$`BTAF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55        13.22        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       46.19        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
        7.07        30.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 
       11.08         5.52         6.21        63.06        52.21        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  BTAF1 MUTATED BTAF1 WILD-TYPE 
           2.66            0.00 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
          77.29          122.30 
  BTAF1 MUTATED BTAF1 WILD-TYPE 
          23.84           13.48 
[1] "2.7 - 77.3 (23.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.9"
D1207V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTAF1 MUTATED         1        0        2        2         3         3
  BTAF1 WILD-TYPE       9       20       44       29        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTAF1 MUTATED           1          4          2          2        2         2
  BTAF1 WILD-TYPE        28         80         60         37       41         2
D1207V3, multiclass
            clus
vv           BTAF1 MUTATED BTAF1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               2              29
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              1              28
  STAGE IIIA             4              80
  STAGE IIIB             2              60
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              2               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  BTAF1 MUTATED       2   7   7   8
  BTAF1 WILD-TYPE    52 128 254  94
D1207V4, multiclass
       clus
vv      BTAF1 MUTATED BTAF1 WILD-TYPE
  T0+T1             2              52
  T2                7             128
  T3                7             254
  T4                8              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  BTAF1 MUTATED     9  10   2   3
  BTAF1 WILD-TYPE 186 163  87  82
D1207V5, multiclass
    clus
vv   BTAF1 MUTATED BTAF1 WILD-TYPE
  N0             9             186
  N1            10             163
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1207V6, binary
                 cls
clus                0   1
  BTAF1 MUTATED    21   3
  BTAF1 WILD-TYPE 461  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED     21    3
  BTAF1 WILD-TYPE  461   35
   clus
vv  BTAF1 MUTATED BTAF1 WILD-TYPE
  0            21             461
  1             3              35
[1] 2 2
[1] FALSE
D1207V7, binary
                 cls
clus                0   1
  BTAF1 MUTATED    13  12
  BTAF1 WILD-TYPE 159 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED     13   12
  BTAF1 WILD-TYPE  159  394
        clus
vv       BTAF1 MUTATED BTAF1 WILD-TYPE
  FEMALE            13             159
  MALE              12             394
[1] 2 2
[1] FALSE
D1207V8, binary
                 cls
clus                0   1
  BTAF1 MUTATED    20   3
  BTAF1 WILD-TYPE 396  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED     20    3
  BTAF1 WILD-TYPE  396   99
     clus
vv    BTAF1 MUTATED BTAF1 WILD-TYPE
  NO             20             396
  YES             3              99
[1] 2 2
[1] FALSE
D1207V9, continuous
[1] "Remove cluster labels:" "BTAF1 MUTATED"         
clus
  BTAF1 MUTATED BTAF1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA7B 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" "BTAF1 WILD-TYPE" 
D1207V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BTAF1 MUTATED       1                         0
  BTAF1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTAF1 MUTATED                                           0    20
  BTAF1 WILD-TYPE                                         1   337
D1207V11, multiclass
                                           clus
vv                                          BTAF1 MUTATED BTAF1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                20             337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1207V12, binary
                 cls
clus                0   1
  BTAF1 MUTATED     1  14
  BTAF1 WILD-TYPE   9 384
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTAF1 MUTATED      1   14
  BTAF1 WILD-TYPE    9  384
                        clus
vv                       BTAF1 MUTATED BTAF1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            14             384
[1] 2 2
[1] FALSE

Clustering(1208) Variable = ARV1 MUTATION ANALYSIS
D1208V1, survival
                sevent
clus2              0   1
  ARV1 MUTATED     6   1
  ARV1 WILD-TYPE 332 215
  ARV1 MUTATED ARV1 WILD-TYPE 
             7            547 
  ARV1 MUTATED ARV1 WILD-TYPE 
             1            215 
$`ARV1 MUTATED`
TCGA-IC-A6RE TCGA-LN-A7HX TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-5734 TCGA-HU-A4G8 
        7.69        12.23        31.27        12.62         7.99        22.68 
TCGA-MX-A5UJ 
       19.73 

$`ARV1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04        21.07        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        24.26        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ARV1 MUTATED ARV1 WILD-TYPE 
          7.69           0.00 
  ARV1 MUTATED ARV1 WILD-TYPE 
         31.27         122.30 
  ARV1 MUTATED ARV1 WILD-TYPE 
         12.62          13.58 
[1] "7.7 - 31.3 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "2.6"
D1208V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARV1 MUTATED         0        0        1        0         1         2
  ARV1 WILD-TYPE      10       20       45       31        83        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARV1 MUTATED           0          2          0          1        0         0
  ARV1 WILD-TYPE        29         82         62         38       43         4
D1208V3, multiclass
            clus
vv           ARV1 MUTATED ARV1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  ARV1 MUTATED       1   2   3   1
  ARV1 WILD-TYPE    53 133 258 101
D1208V4, multiclass
       clus
vv      ARV1 MUTATED ARV1 WILD-TYPE
  T0+T1            1             53
  T2               2            133
  T3               3            258
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  ARV1 MUTATED     2   3   1   1
  ARV1 WILD-TYPE 193 170  88  84
D1208V5, multiclass
    clus
vv   ARV1 MUTATED ARV1 WILD-TYPE
  N0            2            193
  N1            3            170
  N2            1             88
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1208V6, binary
                cls
clus               0   1
  ARV1 MUTATED     7   0
  ARV1 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      7    0
  ARV1 WILD-TYPE  475   38
   clus
vv  ARV1 MUTATED ARV1 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D1208V7, binary
                cls
clus               0   1
  ARV1 MUTATED     2   5
  ARV1 WILD-TYPE 170 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      2    5
  ARV1 WILD-TYPE  170  401
        clus
vv       ARV1 MUTATED ARV1 WILD-TYPE
  FEMALE            2            170
  MALE              5            401
[1] 2 2
[1] FALSE
D1208V8, binary
                cls
clus               0   1
  ARV1 MUTATED     5   1
  ARV1 WILD-TYPE 411 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      5    1
  ARV1 WILD-TYPE  411  101
     clus
vv    ARV1 MUTATED ARV1 WILD-TYPE
  NO             5            411
  YES            1            101
[1] 2 2
[1] FALSE
D1208V9, continuous
[1] "Remove cluster labels:" "ARV1 MUTATED"          
clus
  ARV1 MUTATED ARV1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
D1208V10, continuous
[1] "Remove cluster labels:" "ARV1 MUTATED"          
clus
  ARV1 MUTATED ARV1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IG-A3QL 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HZ     TCGA-LN-A8HZ     TCGA-LN-A8I0 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN     TCGA-R6-A6L4 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5     TCGA-R6-A8W8 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB     TCGA-V5-A7RC 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" "ARV1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARV1 MUTATED       3                         0
  ARV1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARV1 MUTATED                                           0     3
  ARV1 WILD-TYPE                                         1   354
D1208V11, multiclass
                                           clus
vv                                          ARV1 MUTATED ARV1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1208V12, binary
                cls
clus               0   1
  ARV1 MUTATED     0   6
  ARV1 WILD-TYPE  10 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      0    6
  ARV1 WILD-TYPE   10  392
                        clus
vv                       ARV1 MUTATED ARV1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            6            392
[1] 2 2
[1] FALSE

Clustering(1209) Variable = DOPEY2 MUTATION ANALYSIS
D1209V1, survival
                  sevent
clus2                0   1
  DOPEY2 MUTATED    17  15
  DOPEY2 WILD-TYPE 321 201
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              32              522 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              15              201 
$`DOPEY2 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-JY-A6F8 TCGA-L5-A8NM 
       21.99         5.92        32.45        18.64       122.10         7.76 
TCGA-VR-A8EZ TCGA-ZR-A9CJ TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 
       18.18        19.73         6.97         6.61        34.68        30.90 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8687 TCGA-CD-5813 TCGA-CG-5723 TCGA-CG-5733 
        1.12        31.96         8.22        12.39       105.07        21.07 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8244 TCGA-HU-8602 
       14.27         5.92        11.08        77.29        24.39        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-IN-AB1X TCGA-VQ-A8P2 
       22.68         0.10         6.51         6.58        13.51        38.14 
TCGA-VQ-AA6A TCGA-VQ-AA6K 
       38.93        12.43 

$`DOPEY2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        33.70        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.18         9.57        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        21.14        20.91        16.44        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         8.98        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
       12.59         6.51        10.62        11.70        15.75         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       32.94        54.12        26.04        16.14        27.55        17.26 

  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
             0.1              0.0 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
           122.1            122.3 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
          18.410           13.495 
[1] "0.1 - 122.1 (18.4)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1209V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOPEY2 MUTATED         1        1        0        3         6         7
  DOPEY2 WILD-TYPE       9       19       46       28        78        76
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOPEY2 MUTATED           2          6          0          6        3
  DOPEY2 WILD-TYPE        27         78         62         33       40
                  vv
clus               STAGE IVA
  DOPEY2 MUTATED           0
  DOPEY2 WILD-TYPE         4
D1209V3, multiclass
            clus
vv           DOPEY2 MUTATED DOPEY2 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                3               28
  STAGE IIA               6               78
  STAGE IIB               7               76
  STAGE III               2               27
  STAGE IIIA              6               78
  STAGE IIIB              0               62
  STAGE IIIC              6               33
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  DOPEY2 MUTATED       2   7  15  11
  DOPEY2 WILD-TYPE    52 128 246  91
D1209V4, multiclass
       clus
vv      DOPEY2 MUTATED DOPEY2 WILD-TYPE
  T0+T1              2               52
  T2                 7              128
  T3                15              246
  T4                11               91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  DOPEY2 MUTATED    12  12   6   5
  DOPEY2 WILD-TYPE 183 161  83  80
D1209V5, multiclass
    clus
vv   DOPEY2 MUTATED DOPEY2 WILD-TYPE
  N0             12              183
  N1             12              161
  N2              6               83
  N3              5               80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1209V6, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    31   2
  DOPEY2 WILD-TYPE 451  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     31    2
  DOPEY2 WILD-TYPE  451   36
   clus
vv  DOPEY2 MUTATED DOPEY2 WILD-TYPE
  0             31              451
  1              2               36
[1] 2 2
[1] FALSE
D1209V7, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    15  20
  DOPEY2 WILD-TYPE 157 386
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     15   20
  DOPEY2 WILD-TYPE  157  386
        clus
vv       DOPEY2 MUTATED DOPEY2 WILD-TYPE
  FEMALE             15              157
  MALE               20              386
[1] 2 2
[1] FALSE
D1209V8, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    27   6
  DOPEY2 WILD-TYPE 389  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     27    6
  DOPEY2 WILD-TYPE  389   96
     clus
vv    DOPEY2 MUTATED DOPEY2 WILD-TYPE
  NO              27              389
  YES              6               96
[1] 2 2
[1] FALSE
D1209V9, continuous
[1] "Remove cluster labels:" "DOPEY2 MUTATED"        
clus
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
D1209V10, continuous
[1] "Remove cluster labels:" "DOPEY2 MUTATED"        
clus
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8Q7 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" "DOPEY2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DOPEY2 MUTATED       8                         1
  DOPEY2 WILD-TYPE   125                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOPEY2 MUTATED                                           0    20
  DOPEY2 WILD-TYPE                                         1   337
D1209V11, multiclass
                                           clus
vv                                          DOPEY2 MUTATED DOPEY2 WILD-TYPE
  ASIAN                                                  8              125
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1209V12, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED     0  23
  DOPEY2 WILD-TYPE  10 375
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED      0   23
  DOPEY2 WILD-TYPE   10  375
                        clus
vv                       DOPEY2 MUTATED DOPEY2 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             23              375
[1] 2 2
[1] FALSE

Clustering(1210) Variable = ZNF800 MUTATION ANALYSIS
D1210V1, survival
                  sevent
clus2                0   1
  ZNF800 MUTATED     7   4
  ZNF800 WILD-TYPE 331 212
  ZNF800 MUTATED ZNF800 WILD-TYPE 
              11              543 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
               4              212 
$`ZNF800 MUTATED`
TCGA-L5-A8NW TCGA-ZR-A9CJ TCGA-BR-4184 TCGA-BR-8081 TCGA-CG-4305 TCGA-CG-5723 
       46.09        19.73         6.97        32.25        15.95       105.07 
TCGA-CG-5726 TCGA-D7-A6F0 TCGA-HU-A4G8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       28.96        22.29        22.68        19.73        38.14 

$`ZNF800 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  ZNF800 MUTATED ZNF800 WILD-TYPE 
            6.97             0.00 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
          105.07           122.30 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
           22.68            13.41 
[1] "7.0 - 105.1 (22.7)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.8"
D1210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF800 MUTATED         0        1        2        2         0         2
  ZNF800 WILD-TYPE      10       19       44       29        84        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF800 MUTATED           0          4          0          1        1
  ZNF800 WILD-TYPE        29         80         62         38       42
                  vv
clus               STAGE IVA
  ZNF800 MUTATED           0
  ZNF800 WILD-TYPE         4
D1210V3, multiclass
            clus
vv           ZNF800 MUTATED ZNF800 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                2               29
  STAGE IIA               0               84
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              4               80
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF800 MUTATED       1   4   4   4
  ZNF800 WILD-TYPE    53 131 257  98
D1210V4, multiclass
       clus
vv      ZNF800 MUTATED ZNF800 WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 4              257
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF800 MUTATED     4   6   2   1
  ZNF800 WILD-TYPE 191 167  87  84
D1210V5, multiclass
    clus
vv   ZNF800 MUTATED ZNF800 WILD-TYPE
  N0              4              191
  N1              6              167
  N2              2               87
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1210V6, binary
                  cls
clus                 0   1
  ZNF800 MUTATED    12   0
  ZNF800 WILD-TYPE 470  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED     12    0
  ZNF800 WILD-TYPE  470   38
   clus
vv  ZNF800 MUTATED ZNF800 WILD-TYPE
  0             12              470
  1              0               38
[1] 2 2
[1] FALSE
D1210V7, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     7   7
  ZNF800 WILD-TYPE 165 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      7    7
  ZNF800 WILD-TYPE  165  399
        clus
vv       ZNF800 MUTATED ZNF800 WILD-TYPE
  FEMALE              7              165
  MALE                7              399
[1] 2 2
[1] FALSE
D1210V8, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     9   1
  ZNF800 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      9    1
  ZNF800 WILD-TYPE  407  101
     clus
vv    ZNF800 MUTATED ZNF800 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D1210V9, continuous
D1210V10, continuous
[1] "Remove cluster labels:" "ZNF800 MUTATED"        
clus
  ZNF800 MUTATED ZNF800 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-LN-A49O 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" "ZNF800 WILD-TYPE" 
      TCGA-Z6-AAPN 
"ZNF800 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF800 MUTATED       1                         0
  ZNF800 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF800 MUTATED                                           0    10
  ZNF800 WILD-TYPE                                         1   347
D1210V11, multiclass
                                           clus
vv                                          ZNF800 MUTATED ZNF800 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1210V12, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     0   9
  ZNF800 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      0    9
  ZNF800 WILD-TYPE   10  389
                        clus
vv                       ZNF800 MUTATED ZNF800 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1211) Variable = SRPK3 MUTATION ANALYSIS
D1211V1, survival
                 sevent
clus2               0   1
  SRPK3 MUTATED     8   2
  SRPK3 WILD-TYPE 330 214
  SRPK3 MUTATED SRPK3 WILD-TYPE 
             10             544 
  SRPK3 MUTATED SRPK3 WILD-TYPE 
              2             214 
$`SRPK3 MUTATED`
TCGA-LN-A7HW TCGA-R6-A6Y0 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8361 
       12.00        53.95        30.90        34.68        35.84        31.10 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A489 
        1.12        28.14        31.96        11.31 

$`SRPK3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  SRPK3 MUTATED SRPK3 WILD-TYPE 
           1.12            0.00 
  SRPK3 MUTATED SRPK3 WILD-TYPE 
          53.95          122.30 
  SRPK3 MUTATED SRPK3 WILD-TYPE 
          31.00           13.51 
[1] "1.1 - 54.0 (31.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.9"
D1211V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRPK3 MUTATED         0        0        1        0         4         0
  SRPK3 WILD-TYPE      10       20       45       31        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRPK3 MUTATED           0          0          0          2        2         0
  SRPK3 WILD-TYPE        29         84         62         37       41         4
D1211V3, multiclass
            clus
vv           SRPK3 MUTATED SRPK3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SRPK3 MUTATED       1   3   3   4
  SRPK3 WILD-TYPE    53 132 258  98
D1211V4, multiclass
       clus
vv      SRPK3 MUTATED SRPK3 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                3             258
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SRPK3 MUTATED     5   1   3   1
  SRPK3 WILD-TYPE 190 172  86  84
D1211V5, multiclass
    clus
vv   SRPK3 MUTATED SRPK3 WILD-TYPE
  N0             5             190
  N1             1             172
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1211V6, binary
                 cls
clus                0   1
  SRPK3 MUTATED    11   1
  SRPK3 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRPK3 MUTATED     11    1
  SRPK3 WILD-TYPE  471   37
   clus
vv  SRPK3 MUTATED SRPK3 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D1211V7, binary
                 cls
clus                0   1
  SRPK3 MUTATED     8   5
  SRPK3 WILD-TYPE 164 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRPK3 MUTATED      8    5
  SRPK3 WILD-TYPE  164  401
        clus
vv       SRPK3 MUTATED SRPK3 WILD-TYPE
  FEMALE             8             164
  MALE               5             401
[1] 2 2
[1] FALSE
D1211V8, binary
                 cls
clus                0   1
  SRPK3 MUTATED    10   0
  SRPK3 WILD-TYPE 406 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRPK3 MUTATED     10    0
  SRPK3 WILD-TYPE  406  102
     clus
vv    SRPK3 MUTATED SRPK3 WILD-TYPE
  NO             10             406
  YES             0             102
[1] 2 2
[1] FALSE
D1211V9, continuous
[1] "Remove cluster labels:" "SRPK3 MUTATED"         
clus
  SRPK3 MUTATED SRPK3 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
D1211V10, continuous
[1] "Remove cluster labels:" "SRPK3 MUTATED"         
clus
  SRPK3 MUTATED SRPK3 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" "SRPK3 WILD-TYPE" 
     TCGA-Z6-AAPN 
"SRPK3 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SRPK3 MUTATED       3                         0
  SRPK3 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRPK3 MUTATED                                           0    10
  SRPK3 WILD-TYPE                                         1   347
D1211V11, multiclass
                                           clus
vv                                          SRPK3 MUTATED SRPK3 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1211V12, binary
                 cls
clus                0   1
  SRPK3 MUTATED     0  13
  SRPK3 WILD-TYPE  10 385
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRPK3 MUTATED      0   13
  SRPK3 WILD-TYPE   10  385
                        clus
vv                       SRPK3 MUTATED SRPK3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            13             385
[1] 2 2
[1] FALSE

Clustering(1212) Variable = CIB3 MUTATION ANALYSIS
D1212V1, survival
                sevent
clus2              0   1
  CIB3 MUTATED     2   2
  CIB3 WILD-TYPE 336 214
  CIB3 MUTATED CIB3 WILD-TYPE 
             4            550 
  CIB3 MUTATED CIB3 WILD-TYPE 
             2            214 
$`CIB3 MUTATED`
TCGA-BR-6802 TCGA-BR-8382 TCGA-CG-5733 TCGA-FP-A4BE 
       30.90        25.05        21.07        11.08 

$`CIB3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CIB3 MUTATED CIB3 WILD-TYPE 
         11.08           0.00 
  CIB3 MUTATED CIB3 WILD-TYPE 
          30.9          122.3 
  CIB3 MUTATED CIB3 WILD-TYPE 
         23.06          13.53 
[1] "11.1 - 30.9 (23.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1212V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CIB3 MUTATED         0        0        1        0         1         0
  CIB3 WILD-TYPE      10       20       45       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIB3 MUTATED           0          2          0          1        0         0
  CIB3 WILD-TYPE        29         82         62         38       43         4
D1212V3, multiclass
            clus
vv           CIB3 MUTATED CIB3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            0             62
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  CIB3 MUTATED       0   2   2   1
  CIB3 WILD-TYPE    54 133 259 101
D1212V4, multiclass
       clus
vv      CIB3 MUTATED CIB3 WILD-TYPE
  T0+T1            0             54
  T2               2            133
  T3               2            259
  T4               1            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  CIB3 MUTATED     2   0   2   1
  CIB3 WILD-TYPE 193 173  87  84
D1212V5, multiclass
    clus
vv   CIB3 MUTATED CIB3 WILD-TYPE
  N0            2            193
  N1            0            173
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1212V6, binary
                cls
clus               0   1
  CIB3 MUTATED     5   0
  CIB3 WILD-TYPE 477  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      5    0
  CIB3 WILD-TYPE  477   38
   clus
vv  CIB3 MUTATED CIB3 WILD-TYPE
  0            5            477
  1            0             38
[1] 2 2
[1] FALSE
D1212V7, binary
                cls
clus               0   1
  CIB3 MUTATED     2   3
  CIB3 WILD-TYPE 170 403
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      2    3
  CIB3 WILD-TYPE  170  403
        clus
vv       CIB3 MUTATED CIB3 WILD-TYPE
  FEMALE            2            170
  MALE              3            403
[1] 2 2
[1] FALSE
D1212V8, binary
                cls
clus               0   1
  CIB3 MUTATED     3   1
  CIB3 WILD-TYPE 413 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      3    1
  CIB3 WILD-TYPE  413  101
     clus
vv    CIB3 MUTATED CIB3 WILD-TYPE
  NO             3            413
  YES            1            101
[1] 2 2
[1] FALSE
D1212V9, continuous
D1212V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CIB3 MUTATED       0                         1
  CIB3 WILD-TYPE   133                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CIB3 MUTATED                                           0     2
  CIB3 WILD-TYPE                                         1   355
D1212V11, multiclass
                                           clus
vv                                          CIB3 MUTATED CIB3 WILD-TYPE
  ASIAN                                                0            133
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1212V12, binary
                cls
clus               0   1
  CIB3 MUTATED     0   3
  CIB3 WILD-TYPE  10 395
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      0    3
  CIB3 WILD-TYPE   10  395
                        clus
vv                       CIB3 MUTATED CIB3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            3            395
[1] 2 2
[1] FALSE

Clustering(1213) Variable = PDK3 MUTATION ANALYSIS
D1213V1, survival
                sevent
clus2              0   1
  PDK3 MUTATED     5   2
  PDK3 WILD-TYPE 333 214
  PDK3 MUTATED PDK3 WILD-TYPE 
             7            547 
  PDK3 MUTATED PDK3 WILD-TYPE 
             2            214 
$`PDK3 MUTATED`
TCGA-VR-A8EP TCGA-ZR-A9CJ TCGA-BR-4184 TCGA-BR-8368 TCGA-D7-8578 TCGA-HU-A4GN 
       27.09        19.73         6.97         4.31        21.14        29.98 
TCGA-HU-A4H3 
       29.00 

$`PDK3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       14.37         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  PDK3 MUTATED PDK3 WILD-TYPE 
          4.31           0.00 
  PDK3 MUTATED PDK3 WILD-TYPE 
         29.98         122.30 
  PDK3 MUTATED PDK3 WILD-TYPE 
         21.14          13.51 
[1] "4.3 - 30.0 (21.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1213V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDK3 MUTATED         0        0        2        0         1         0
  PDK3 WILD-TYPE      10       20       44       31        83        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDK3 MUTATED           0          2          1          2        0         0
  PDK3 WILD-TYPE        29         82         61         37       43         4
D1213V3, multiclass
            clus
vv           PDK3 MUTATED PDK3 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              2             44
  STAGE II              0             31
  STAGE IIA             1             83
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            2             82
  STAGE IIIB            1             61
  STAGE IIIC            2             37
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PDK3 MUTATED       0   3   3   2
  PDK3 WILD-TYPE    54 132 258 100
D1213V4, multiclass
       clus
vv      PDK3 MUTATED PDK3 WILD-TYPE
  T0+T1            0             54
  T2               3            132
  T3               3            258
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PDK3 MUTATED     3   2   1   2
  PDK3 WILD-TYPE 192 171  88  83
D1213V5, multiclass
    clus
vv   PDK3 MUTATED PDK3 WILD-TYPE
  N0            3            192
  N1            2            171
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1213V6, binary
                cls
clus               0   1
  PDK3 MUTATED     6   0
  PDK3 WILD-TYPE 476  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK3 MUTATED      6    0
  PDK3 WILD-TYPE  476   38
   clus
vv  PDK3 MUTATED PDK3 WILD-TYPE
  0            6            476
  1            0             38
[1] 2 2
[1] FALSE
D1213V7, binary
                cls
clus               0   1
  PDK3 MUTATED     3   5
  PDK3 WILD-TYPE 169 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK3 MUTATED      3    5
  PDK3 WILD-TYPE  169  401
        clus
vv       PDK3 MUTATED PDK3 WILD-TYPE
  FEMALE            3            169
  MALE              5            401
[1] 2 2
[1] FALSE
D1213V8, binary
                cls
clus               0   1
  PDK3 MUTATED     6   0
  PDK3 WILD-TYPE 410 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK3 MUTATED      6    0
  PDK3 WILD-TYPE  410  102
     clus
vv    PDK3 MUTATED PDK3 WILD-TYPE
  NO             6            410
  YES            0            102
[1] 2 2
[1] FALSE
D1213V9, continuous
[1] "Remove cluster labels:" "PDK3 MUTATED"          
clus
  PDK3 MUTATED PDK3 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
D1213V10, continuous
[1] "Remove cluster labels:" "PDK3 MUTATED"          
clus
  PDK3 MUTATED PDK3 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8ER 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" "PDK3 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PDK3 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PDK3 MUTATED       2                         0
  PDK3 WILD-TYPE   131                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDK3 MUTATED                                           0     6
  PDK3 WILD-TYPE                                         1   351
D1213V11, multiclass
                                           clus
vv                                          PDK3 MUTATED PDK3 WILD-TYPE
  ASIAN                                                2            131
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1213V12, binary
                cls
clus               0   1
  PDK3 MUTATED     0   7
  PDK3 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK3 MUTATED      0    7
  PDK3 WILD-TYPE   10  391
                        clus
vv                       PDK3 MUTATED PDK3 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(1214) Variable = NRIP3 MUTATION ANALYSIS
D1214V1, survival
                 sevent
clus2               0   1
  NRIP3 MUTATED     2   2
  NRIP3 WILD-TYPE 336 214
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              4             550 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              2             214 
$`NRIP3 MUTATED`
TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-5726 
        8.05        31.27        31.96        28.96 

$`NRIP3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
       26.33         4.31        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NRIP3 MUTATED NRIP3 WILD-TYPE 
           8.05            0.00 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
          31.96          122.30 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
         30.115          13.530 
[1] "8.1 - 32.0 (30.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1214V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRIP3 MUTATED         0        1        1        0         0         0
  NRIP3 WILD-TYPE      10       19       45       31        84        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRIP3 MUTATED           0          0          0          2        1         0
  NRIP3 WILD-TYPE        29         84         62         37       42         4
D1214V3, multiclass
            clus
vv           NRIP3 MUTATED NRIP3 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              0              84
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NRIP3 MUTATED       2   1   0   3
  NRIP3 WILD-TYPE    52 134 261  99
D1214V4, multiclass
       clus
vv      NRIP3 MUTATED NRIP3 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                0             261
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NRIP3 MUTATED     2   0   1   2
  NRIP3 WILD-TYPE 193 173  88  83
D1214V5, multiclass
    clus
vv   NRIP3 MUTATED NRIP3 WILD-TYPE
  N0             2             193
  N1             0             173
  N2             1              88
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1214V6, binary
                 cls
clus                0   1
  NRIP3 MUTATED     6   1
  NRIP3 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      6    1
  NRIP3 WILD-TYPE  476   37
   clus
vv  NRIP3 MUTATED NRIP3 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D1214V7, binary
                 cls
clus                0   1
  NRIP3 MUTATED     3   4
  NRIP3 WILD-TYPE 169 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      3    4
  NRIP3 WILD-TYPE  169  402
        clus
vv       NRIP3 MUTATED NRIP3 WILD-TYPE
  FEMALE             3             169
  MALE               4             402
[1] 2 2
[1] FALSE
D1214V8, binary
                 cls
clus                0   1
  NRIP3 MUTATED     3   0
  NRIP3 WILD-TYPE 413 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      3    0
  NRIP3 WILD-TYPE  413  102
     clus
vv    NRIP3 MUTATED NRIP3 WILD-TYPE
  NO              3             413
  YES             0             102
[1] 2 2
[1] FALSE
D1214V9, continuous
D1214V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NRIP3 MUTATED       1                         0
  NRIP3 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRIP3 MUTATED                                           0     4
  NRIP3 WILD-TYPE                                         1   353
D1214V11, multiclass
                                           clus
vv                                          NRIP3 MUTATED NRIP3 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1214V12, binary
                 cls
clus                0   1
  NRIP3 MUTATED     0   5
  NRIP3 WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      0    5
  NRIP3 WILD-TYPE   10  393
                        clus
vv                       NRIP3 MUTATED NRIP3 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1215) Variable = ZKSCAN3 MUTATION ANALYSIS
D1215V1, survival
                   sevent
clus2                 0   1
  ZKSCAN3 MUTATED     9   4
  ZKSCAN3 WILD-TYPE 329 212
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
               13               541 
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
                4               212 
$`ZKSCAN3 MUTATED`
TCGA-LN-A9FP TCGA-R6-A8WC TCGA-RE-A7BO TCGA-VR-A8EO TCGA-BR-6452 TCGA-BR-8487 
       12.03         2.30         7.00        25.81        34.68         1.12 
TCGA-CD-8536 TCGA-CG-5723 TCGA-HU-A4G8 TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PM 
       12.43       105.07        22.68        13.25        38.14         1.87 
TCGA-VQ-AA64 
       18.41 

$`ZKSCAN3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         0.99        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       37.22        22.19        17.85        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
             1.12              0.00 
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
           105.07            122.30 
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
            13.25             13.58 
[1] "1.1 - 105.1 (13.2)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1215V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZKSCAN3 MUTATED         0        0        1        2         4         2
  ZKSCAN3 WILD-TYPE      10       20       45       29        80        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN3 MUTATED           0          1          1          0        1
  ZKSCAN3 WILD-TYPE        29         83         61         39       42
                   vv
clus                STAGE IVA
  ZKSCAN3 MUTATED           0
  ZKSCAN3 WILD-TYPE         4
D1215V3, multiclass
            clus
vv           ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 2                29
  STAGE IIA                4                80
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ZKSCAN3 MUTATED       1   3   6   2
  ZKSCAN3 WILD-TYPE    53 132 255 100
D1215V4, multiclass
       clus
vv      ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  T0+T1               1                53
  T2                  3               132
  T3                  6               255
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ZKSCAN3 MUTATED     6   4   1   1
  ZKSCAN3 WILD-TYPE 189 169  88  84
D1215V5, multiclass
    clus
vv   ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  N0               6               189
  N1               4               169
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1215V6, binary
                   cls
clus                  0   1
  ZKSCAN3 MUTATED    12   0
  ZKSCAN3 WILD-TYPE 470  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN3 MUTATED     12    0
  ZKSCAN3 WILD-TYPE  470   38
   clus
vv  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  0              12               470
  1               0                38
[1] 2 2
[1] FALSE
D1215V7, binary
                   cls
clus                  0   1
  ZKSCAN3 MUTATED     5   8
  ZKSCAN3 WILD-TYPE 167 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN3 MUTATED      5    8
  ZKSCAN3 WILD-TYPE  167  398
        clus
vv       ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  FEMALE               5               167
  MALE                 8               398
[1] 2 2
[1] FALSE
D1215V8, binary
                   cls
clus                  0   1
  ZKSCAN3 MUTATED     8   4
  ZKSCAN3 WILD-TYPE 408  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN3 MUTATED      8    4
  ZKSCAN3 WILD-TYPE  408   98
     clus
vv    ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  NO                8               408
  YES               4                98
[1] 2 2
[1] FALSE
D1215V9, continuous
[1] "Remove cluster labels:" "ZKSCAN3 MUTATED"       
clus
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A4MR        TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A7HZ        TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EP 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
D1215V10, continuous
[1] "Remove cluster labels:" "ZKSCAN3 MUTATED"       
clus
  ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A7HV        TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-LN-A8HZ        TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-R6-A6DN        TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-R6-A8W5        TCGA-R6-A8W8        TCGA-V5-A7RB        TCGA-V5-A7RC 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" "ZKSCAN3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZKSCAN3 MUTATED       3                         0
  ZKSCAN3 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZKSCAN3 MUTATED                                           0     9
  ZKSCAN3 WILD-TYPE                                         1   348
D1215V11, multiclass
                                           clus
vv                                          ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1215V12, binary
                   cls
clus                  0   1
  ZKSCAN3 MUTATED     0   7
  ZKSCAN3 WILD-TYPE  10 391
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN3 MUTATED      0    7
  ZKSCAN3 WILD-TYPE   10  391
                        clus
vv                       ZKSCAN3 MUTATED ZKSCAN3 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               7               391
[1] 2 2
[1] FALSE

Clustering(1216) Variable = ZNF167 MUTATION ANALYSIS
D1216V1, survival
                  sevent
clus2                0   1
  ZNF167 MUTATED    11   3
  ZNF167 WILD-TYPE 327 213
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              14              540 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
               3              213 
$`ZNF167 MUTATED`
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-BR-6852 TCGA-BR-8366 TCGA-BR-8591 TCGA-BR-8680 
       29.00         7.43        44.94         0.95        28.14        31.96 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-A4H4 
        6.02        65.10         4.01        21.07        30.51        23.84 
TCGA-IN-A6RL TCGA-R5-A7O7 
       13.35        45.67 

$`ZNF167 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59         4.90         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19        17.52        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        27.12         9.34         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       15.02        28.96        69.04         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ZNF167 MUTATED ZNF167 WILD-TYPE 
            0.95             0.00 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
            65.1            122.3 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
           25.99            13.51 
[1] "0.9 - 65.1 (26.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.5"
D1216V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF167 MUTATED         0        0        1        0         3         2
  ZNF167 WILD-TYPE      10       20       45       31        81        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF167 MUTATED           0          2          0          2        4
  ZNF167 WILD-TYPE        29         82         62         37       39
                  vv
clus               STAGE IVA
  ZNF167 MUTATED           0
  ZNF167 WILD-TYPE         4
D1216V3, multiclass
            clus
vv           ZNF167 MUTATED ZNF167 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               2               81
  STAGE III               0               29
  STAGE IIIA              2               82
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                4               39
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF167 MUTATED       1   6   4   4
  ZNF167 WILD-TYPE    53 129 257  98
D1216V4, multiclass
       clus
vv      ZNF167 MUTATED ZNF167 WILD-TYPE
  T0+T1              1               53
  T2                 6              129
  T3                 4              257
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF167 MUTATED     4   5   3   2
  ZNF167 WILD-TYPE 191 168  86  83
D1216V5, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  N0              4              191
  N1              5              168
  N2              3               86
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1216V6, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    12   3
  ZNF167 WILD-TYPE 470  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     12    3
  ZNF167 WILD-TYPE  470   35
   clus
vv  ZNF167 MUTATED ZNF167 WILD-TYPE
  0             12              470
  1              3               35
[1] 2 2
[1] FALSE
D1216V7, binary
                  cls
clus                 0   1
  ZNF167 MUTATED     8   7
  ZNF167 WILD-TYPE 164 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED      8    7
  ZNF167 WILD-TYPE  164  399
        clus
vv       ZNF167 MUTATED ZNF167 WILD-TYPE
  FEMALE              8              164
  MALE                7              399
[1] 2 2
[1] FALSE
D1216V8, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    11   1
  ZNF167 WILD-TYPE 405 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     11    1
  ZNF167 WILD-TYPE  405  101
     clus
vv    ZNF167 MUTATED ZNF167 WILD-TYPE
  NO              11              405
  YES              1              101
[1] 2 2
[1] FALSE
D1216V9, continuous
D1216V10, continuous
[1] "Remove cluster labels:" "ZNF167 MUTATED"        
clus
  ZNF167 MUTATED ZNF167 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OW       TCGA-L5-A88S 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NR 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6       TCGA-LN-A4A9 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" "ZNF167 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF167 MUTATED       2                         0
  ZNF167 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF167 MUTATED                                           0     8
  ZNF167 WILD-TYPE                                         1   349
D1216V11, multiclass
                                           clus
vv                                          ZNF167 MUTATED ZNF167 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1216V12, binary
                  cls
clus                 0   1
  ZNF167 MUTATED     1   7
  ZNF167 WILD-TYPE   9 391
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED      1    7
  ZNF167 WILD-TYPE    9  391
                        clus
vv                       ZNF167 MUTATED ZNF167 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              7              391
[1] 2 2
[1] FALSE

Clustering(1217) Variable = ABCA5 MUTATION ANALYSIS
D1217V1, survival
                 sevent
clus2               0   1
  ABCA5 MUTATED    15   5
  ABCA5 WILD-TYPE 323 211
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             20             534 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
              5             211 
$`ABCA5 MUTATED`
TCGA-L5-A4OF TCGA-L5-A8NW TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-7703 
       26.33        46.09         6.97        34.68        15.95        36.16 
TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-A4MH TCGA-D7-5579 TCGA-HF-A5NB 
        4.31        31.96        20.42        12.20        20.91        30.51 
TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-VQ-A8P2 
       26.47        22.68         6.51         6.58        14.07        38.14 
TCGA-VQ-A8P3 TCGA-VQ-AA6G 
       37.22        26.04 

$`ABCA5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25         0.30        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6455 
        9.34         9.67         6.18         9.57         6.61        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.65         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE 
        5.46        13.25        13.02        43.36        37.41        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        16.14        27.55        12.43        17.26 

  ABCA5 MUTATED ABCA5 WILD-TYPE 
           4.31            0.00 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
          46.09          122.30 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
          24.36           13.41 
[1] "4.3 - 46.1 (24.4)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "2.1"
D1217V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA5 MUTATED         0        1        6        0         5         3
  ABCA5 WILD-TYPE      10       19       40       31        79        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCA5 MUTATED           0          5          0          1        2         0
  ABCA5 WILD-TYPE        29         79         62         38       41         4
D1217V3, multiclass
            clus
vv           ABCA5 MUTATED ABCA5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               6              40
  STAGE II               0              31
  STAGE IIA              5              79
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             5              79
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCA5 MUTATED       3   6   8   6
  ABCA5 WILD-TYPE    51 129 253  96
D1217V4, multiclass
       clus
vv      ABCA5 MUTATED ABCA5 WILD-TYPE
  T0+T1             3              51
  T2                6             129
  T3                8             253
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCA5 MUTATED    10   9   3   1
  ABCA5 WILD-TYPE 185 164  86  84
D1217V5, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  N0            10             185
  N1             9             164
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1217V6, binary
                 cls
clus                0   1
  ABCA5 MUTATED    19   1
  ABCA5 WILD-TYPE 463  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     19    1
  ABCA5 WILD-TYPE  463   37
   clus
vv  ABCA5 MUTATED ABCA5 WILD-TYPE
  0            19             463
  1             1              37
[1] 2 2
[1] FALSE
D1217V7, binary
                 cls
clus                0   1
  ABCA5 MUTATED    10  13
  ABCA5 WILD-TYPE 162 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     10   13
  ABCA5 WILD-TYPE  162  393
        clus
vv       ABCA5 MUTATED ABCA5 WILD-TYPE
  FEMALE            10             162
  MALE              13             393
[1] 2 2
[1] FALSE
D1217V8, binary
                 cls
clus                0   1
  ABCA5 MUTATED    16   4
  ABCA5 WILD-TYPE 400  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     16    4
  ABCA5 WILD-TYPE  400   98
     clus
vv    ABCA5 MUTATED ABCA5 WILD-TYPE
  NO             16             400
  YES             4              98
[1] 2 2
[1] FALSE
D1217V9, continuous
D1217V10, continuous
[1] "Remove cluster labels:" "ABCA5 MUTATED"         
clus
  ABCA5 MUTATED ABCA5 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-LN-A49O 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" "ABCA5 WILD-TYPE" 
     TCGA-Z6-AAPN 
"ABCA5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA5 MUTATED       6                         0
  ABCA5 WILD-TYPE   127                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA5 MUTATED                                           0    15
  ABCA5 WILD-TYPE                                         1   342
D1217V11, multiclass
                                           clus
vv                                          ABCA5 MUTATED ABCA5 WILD-TYPE
  ASIAN                                                 6             127
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1217V12, binary
                 cls
clus                0   1
  ABCA5 MUTATED     0  16
  ABCA5 WILD-TYPE  10 382
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED      0   16
  ABCA5 WILD-TYPE   10  382
                        clus
vv                       ABCA5 MUTATED ABCA5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            16             382
[1] 2 2
[1] FALSE

Clustering(1218) Variable = PPM1D MUTATION ANALYSIS
D1218V1, survival
                 sevent
clus2               0   1
  PPM1D MUTATED     6   3
  PPM1D WILD-TYPE 332 213
  PPM1D MUTATED PPM1D WILD-TYPE 
              9             545 
  PPM1D MUTATED PPM1D WILD-TYPE 
              3             213 
$`PPM1D MUTATED`
TCGA-2H-A9GI TCGA-L5-A8NK TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-8360 TCGA-BR-8487 
       14.30        13.55         6.97         7.43         6.18         1.12 
TCGA-BR-8680 TCGA-CG-5721 TCGA-SW-A7EB 
       31.96         6.02         5.79 

$`PPM1D WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       19.96         2.20         7.40        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  PPM1D MUTATED PPM1D WILD-TYPE 
           1.12            0.00 
  PPM1D MUTATED PPM1D WILD-TYPE 
          31.96          122.30 
  PPM1D MUTATED PPM1D WILD-TYPE 
           6.97           13.78 
[1] "1.1 - 32.0 (7.0)"   "0.0 - 122.3 (13.8)"
[1] "hr=" "1.5"
D1218V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPM1D MUTATED         0        0        1        0         3         0
  PPM1D WILD-TYPE      10       20       45       31        81        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPM1D MUTATED           1          2          0          0        2         0
  PPM1D WILD-TYPE        28         82         62         39       41         4
D1218V3, multiclass
            clus
vv           PPM1D MUTATED PPM1D WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              3              81
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PPM1D MUTATED       0   1   6   2
  PPM1D WILD-TYPE    54 134 255 100
D1218V4, multiclass
       clus
vv      PPM1D MUTATED PPM1D WILD-TYPE
  T0+T1             0              54
  T2                1             134
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PPM1D MUTATED     4   4   2   0
  PPM1D WILD-TYPE 191 169  87  85
D1218V5, multiclass
    clus
vv   PPM1D MUTATED PPM1D WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1218V6, binary
                 cls
clus                0   1
  PPM1D MUTATED     8   1
  PPM1D WILD-TYPE 474  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      8    1
  PPM1D WILD-TYPE  474   37
   clus
vv  PPM1D MUTATED PPM1D WILD-TYPE
  0             8             474
  1             1              37
[1] 2 2
[1] FALSE
D1218V7, binary
                 cls
clus                0   1
  PPM1D MUTATED     4   6
  PPM1D WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      4    6
  PPM1D WILD-TYPE  168  400
        clus
vv       PPM1D MUTATED PPM1D WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D1218V8, binary
                 cls
clus                0   1
  PPM1D MUTATED     9   0
  PPM1D WILD-TYPE 407 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      9    0
  PPM1D WILD-TYPE  407  102
     clus
vv    PPM1D MUTATED PPM1D WILD-TYPE
  NO              9             407
  YES             0             102
[1] 2 2
[1] FALSE
D1218V9, continuous
D1218V10, continuous
[1] "Remove cluster labels:" "PPM1D MUTATED"         
clus
  PPM1D MUTATED PPM1D WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" "PPM1D WILD-TYPE" 
     TCGA-Z6-AAPN 
"PPM1D WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PPM1D MUTATED       1                         0
  PPM1D WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPM1D MUTATED                                           0     7
  PPM1D WILD-TYPE                                         1   350
D1218V11, multiclass
                                           clus
vv                                          PPM1D MUTATED PPM1D WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1218V12, binary
                 cls
clus                0   1
  PPM1D MUTATED     0   7
  PPM1D WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPM1D MUTATED      0    7
  PPM1D WILD-TYPE   10  391
                        clus
vv                       PPM1D MUTATED PPM1D WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1219) Variable = CSNK1G1 MUTATION ANALYSIS
D1219V1, survival
                   sevent
clus2                 0   1
  CSNK1G1 MUTATED     5   1
  CSNK1G1 WILD-TYPE 333 215
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                6               548 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                1               215 
$`CSNK1G1 MUTATED`
TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-CG-4306 TCGA-FP-A4BE TCGA-VQ-A8P2 
       31.10         4.31         1.12         1.02        11.08        38.14 

$`CSNK1G1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
             1.02              0.00 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
            38.14            122.30 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
            7.695            13.630 
[1] "1.0 - 38.1 (7.7)"   "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1219V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSNK1G1 MUTATED         0        0        1        0         2         0
  CSNK1G1 WILD-TYPE      10       20       45       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1G1 MUTATED           0          1          0          1        1
  CSNK1G1 WILD-TYPE        29         83         62         38       42
                   vv
clus                STAGE IVA
  CSNK1G1 MUTATED           0
  CSNK1G1 WILD-TYPE         4
D1219V3, multiclass
            clus
vv           CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 1                45
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                0                29
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  CSNK1G1 MUTATED       0   1   4   2
  CSNK1G1 WILD-TYPE    54 134 257 100
D1219V4, multiclass
       clus
vv      CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  4               257
  T4                  2               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  CSNK1G1 MUTATED     3   1   2   0
  CSNK1G1 WILD-TYPE 192 172  87  85
D1219V5, multiclass
    clus
vv   CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  N0               3               192
  N1               1               172
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1219V6, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     5   1
  CSNK1G1 WILD-TYPE 477  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      5    1
  CSNK1G1 WILD-TYPE  477   37
   clus
vv  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  0               5               477
  1               1                37
[1] 2 2
[1] FALSE
D1219V7, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     4   3
  CSNK1G1 WILD-TYPE 168 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      4    3
  CSNK1G1 WILD-TYPE  168  403
        clus
vv       CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  FEMALE               4               168
  MALE                 3               403
[1] 2 2
[1] FALSE
D1219V8, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     3   2
  CSNK1G1 WILD-TYPE 413 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      3    2
  CSNK1G1 WILD-TYPE  413  100
     clus
vv    CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  NO                3               413
  YES               2               100
[1] 2 2
[1] FALSE
D1219V9, continuous
D1219V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK1G1 MUTATED       0                         1
  CSNK1G1 WILD-TYPE   133                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK1G1 MUTATED                                           0     5
  CSNK1G1 WILD-TYPE                                         1   352
D1219V11, multiclass
                                           clus
vv                                          CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1219V12, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     0   5
  CSNK1G1 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      0    5
  CSNK1G1 WILD-TYPE   10  393
                        clus
vv                       CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(1220) Variable = TMC2 MUTATION ANALYSIS
D1220V1, survival
                sevent
clus2              0   1
  TMC2 MUTATED    12   5
  TMC2 WILD-TYPE 326 211
  TMC2 MUTATED TMC2 WILD-TYPE 
            17            537 
  TMC2 MUTATED TMC2 WILD-TYPE 
             5            211 
$`TMC2 MUTATED`
TCGA-L5-A8NM TCGA-Z6-AAPN TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-8370 TCGA-BR-8680 
        7.76         2.66         6.97        36.16         3.32        31.96 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5721 TCGA-FP-8631 TCGA-HU-8602 TCGA-HU-A4GN 
        0.00         9.01         6.02         0.56        22.32        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-AB1V TCGA-VQ-A8P2 
        0.10         6.58        12.95        15.75        38.14 

$`TMC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       14.37         3.42         2.10         1.32        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        11.77        21.37         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TMC2 MUTATED TMC2 WILD-TYPE 
          0.00           0.13 
  TMC2 MUTATED TMC2 WILD-TYPE 
         38.14         122.30 
  TMC2 MUTATED TMC2 WILD-TYPE 
          7.76          13.78 
[1] "0.0 - 38.1 (7.8)"   "0.1 - 122.3 (13.8)"
[1] "hr=" "1"  
D1220V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMC2 MUTATED         0        2        1        0         2         3
  TMC2 WILD-TYPE      10       18       45       31        82        80
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMC2 MUTATED           0          3          2          1        4         0
  TMC2 WILD-TYPE        29         81         60         38       39         4
D1220V3, multiclass
            clus
vv           TMC2 MUTATED TMC2 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             3             80
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              4             39
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  TMC2 MUTATED       2   3   8   6
  TMC2 WILD-TYPE    52 132 253  96
D1220V4, multiclass
       clus
vv      TMC2 MUTATED TMC2 WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3               8            253
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  TMC2 MUTATED     5   6   3   4
  TMC2 WILD-TYPE 190 167  86  81
D1220V5, multiclass
    clus
vv   TMC2 MUTATED TMC2 WILD-TYPE
  N0            5            190
  N1            6            167
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1220V6, binary
                cls
clus               0   1
  TMC2 MUTATED    12   3
  TMC2 WILD-TYPE 470  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED     12    3
  TMC2 WILD-TYPE  470   35
   clus
vv  TMC2 MUTATED TMC2 WILD-TYPE
  0           12            470
  1            3             35
[1] 2 2
[1] FALSE
D1220V7, binary
                cls
clus               0   1
  TMC2 MUTATED     6  13
  TMC2 WILD-TYPE 166 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED      6   13
  TMC2 WILD-TYPE  166  393
        clus
vv       TMC2 MUTATED TMC2 WILD-TYPE
  FEMALE            6            166
  MALE             13            393
[1] 2 2
[1] FALSE
D1220V8, binary
                cls
clus               0   1
  TMC2 MUTATED    13   2
  TMC2 WILD-TYPE 403 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED     13    2
  TMC2 WILD-TYPE  403  100
     clus
vv    TMC2 MUTATED TMC2 WILD-TYPE
  NO            13            403
  YES            2            100
[1] 2 2
[1] FALSE
D1220V9, continuous
D1220V10, continuous
[1] "Remove cluster labels:" "TMC2 MUTATED"          
clus
  TMC2 MUTATED TMC2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-LN-A8HZ     TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-R6-A6DN     TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-R6-A8W5     TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7 
"TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" "TMC2 WILD-TYPE" 
    TCGA-XP-A8T8 
"TMC2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TMC2 MUTATED       6                         0
  TMC2 WILD-TYPE   127                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMC2 MUTATED                                           0     9
  TMC2 WILD-TYPE                                         1   348
D1220V11, multiclass
                                           clus
vv                                          TMC2 MUTATED TMC2 WILD-TYPE
  ASIAN                                                6            127
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1220V12, binary
                cls
clus               0   1
  TMC2 MUTATED     0  13
  TMC2 WILD-TYPE  10 385
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED      0   13
  TMC2 WILD-TYPE   10  385
                        clus
vv                       TMC2 MUTATED TMC2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           13            385
[1] 2 2
[1] FALSE

Clustering(1221) Variable = XRCC5 MUTATION ANALYSIS
D1221V1, survival
                 sevent
clus2               0   1
  XRCC5 MUTATED     6   7
  XRCC5 WILD-TYPE 332 209
  XRCC5 MUTATED XRCC5 WILD-TYPE 
             13             541 
  XRCC5 MUTATED XRCC5 WILD-TYPE 
              7             209 
$`XRCC5 MUTATED`
TCGA-L5-A4OI TCGA-CG-4444 TCGA-L5-A8NM TCGA-VR-A8EX TCGA-VR-AA7B TCGA-BR-4184 
       19.99        47.05         7.76        28.11        11.24         6.97 
TCGA-BR-4256 TCGA-BR-8487 TCGA-CD-5801 TCGA-CD-A486 TCGA-CG-5728 TCGA-F1-6875 
        9.34         1.12        13.18         6.31        65.10        72.23 
TCGA-VQ-A8E2 
       43.36 

$`XRCC5 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        28.96         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  XRCC5 MUTATED XRCC5 WILD-TYPE 
           1.12            0.00 
  XRCC5 MUTATED XRCC5 WILD-TYPE 
          72.23          122.30 
  XRCC5 MUTATED XRCC5 WILD-TYPE 
          13.18           13.58 
[1] "1.1 - 72.2 (13.2)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1221V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XRCC5 MUTATED         0        1        1        0         2         1
  XRCC5 WILD-TYPE      10       19       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRCC5 MUTATED           0          3          1          1        1         1
  XRCC5 WILD-TYPE        29         81         61         38       42         3
D1221V3, multiclass
            clus
vv           XRCC5 MUTATED XRCC5 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  XRCC5 MUTATED       1   4   7   0
  XRCC5 WILD-TYPE    53 131 254 102
D1221V4, multiclass
       clus
vv      XRCC5 MUTATED XRCC5 WILD-TYPE
  T0+T1             1              53
  T2                4             131
  T3                7             254
  T4                0             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  XRCC5 MUTATED     4   5   2   2
  XRCC5 WILD-TYPE 191 168  87  83
D1221V5, multiclass
    clus
vv   XRCC5 MUTATED XRCC5 WILD-TYPE
  N0             4             191
  N1             5             168
  N2             2              87
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1221V6, binary
                 cls
clus                0   1
  XRCC5 MUTATED     9   2
  XRCC5 WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC5 MUTATED      9    2
  XRCC5 WILD-TYPE  473   36
   clus
vv  XRCC5 MUTATED XRCC5 WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D1221V7, binary
                 cls
clus                0   1
  XRCC5 MUTATED     4   9
  XRCC5 WILD-TYPE 168 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC5 MUTATED      4    9
  XRCC5 WILD-TYPE  168  397
        clus
vv       XRCC5 MUTATED XRCC5 WILD-TYPE
  FEMALE             4             168
  MALE               9             397
[1] 2 2
[1] FALSE
D1221V8, binary
                 cls
clus                0   1
  XRCC5 MUTATED    10   2
  XRCC5 WILD-TYPE 406 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC5 MUTATED     10    2
  XRCC5 WILD-TYPE  406  100
     clus
vv    XRCC5 MUTATED XRCC5 WILD-TYPE
  NO             10             406
  YES             2             100
[1] 2 2
[1] FALSE
D1221V9, continuous
[1] "Remove cluster labels:" "XRCC5 MUTATED"         
clus
  XRCC5 MUTATED XRCC5 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7D 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
D1221V10, continuous
[1] "Remove cluster labels:" "XRCC5 MUTATED"         
clus
  XRCC5 MUTATED XRCC5 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" "XRCC5 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XRCC5 MUTATED       3                         1
  XRCC5 WILD-TYPE   130                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XRCC5 MUTATED                                           0     6
  XRCC5 WILD-TYPE                                         1   351
D1221V11, multiclass
                                           clus
vv                                          XRCC5 MUTATED XRCC5 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1221V12, binary
                 cls
clus                0   1
  XRCC5 MUTATED     0   6
  XRCC5 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC5 MUTATED      0    6
  XRCC5 WILD-TYPE   10  392
                        clus
vv                       XRCC5 MUTATED XRCC5 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1222) Variable = ZNF828 MUTATION ANALYSIS
D1222V1, survival
                  sevent
clus2                0   1
  ZNF828 MUTATED     6   6
  ZNF828 WILD-TYPE 332 210
  ZNF828 MUTATED ZNF828 WILD-TYPE 
              12              542 
  ZNF828 MUTATED ZNF828 WILD-TYPE 
               6              210 
$`ZNF828 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GO TCGA-IC-A6RE TCGA-L5-A4OJ TCGA-L5-A8NI TCGA-V5-A7RB 
       21.99        16.24         7.69        21.01        13.48         5.29 
TCGA-VR-A8EX TCGA-CG-4305 TCGA-HF-A5NB TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-VQ-A8P2 
       28.11        15.95        30.51        11.77         0.10        38.14 

$`ZNF828 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94         4.21        32.45        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.75         3.02        55.50         2.66        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        37.41        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ZNF828 MUTATED ZNF828 WILD-TYPE 
             0.1              0.0 
  ZNF828 MUTATED ZNF828 WILD-TYPE 
           38.14           122.30 
  ZNF828 MUTATED ZNF828 WILD-TYPE 
          16.095           13.530 
[1] "0.1 - 38.1 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.3"
D1222V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF828 MUTATED         1        1        0        1         0         1
  ZNF828 WILD-TYPE       9       19       46       30        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF828 MUTATED           1          1          0          2        1
  ZNF828 WILD-TYPE        28         83         62         37       42
                  vv
clus               STAGE IVA
  ZNF828 MUTATED           2
  ZNF828 WILD-TYPE         2
D1222V3, multiclass
            clus
vv           ZNF828 MUTATED ZNF828 WILD-TYPE
  STAGE I                 1                9
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               1               28
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              2               37
  STAGE IV                1               42
  STAGE IVA               2                2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF828 MUTATED       5   1   2   4
  ZNF828 WILD-TYPE    49 134 259  98
D1222V4, multiclass
       clus
vv      ZNF828 MUTATED ZNF828 WILD-TYPE
  T0+T1              5               49
  T2                 1              134
  T3                 2              259
  T4                 4               98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF828 MUTATED     2   8   1   1
  ZNF828 WILD-TYPE 193 165  88  84
D1222V5, multiclass
    clus
vv   ZNF828 MUTATED ZNF828 WILD-TYPE
  N0              2              193
  N1              8              165
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1222V6, binary
                  cls
clus                 0   1
  ZNF828 MUTATED     8   3
  ZNF828 WILD-TYPE 474  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF828 MUTATED      8    3
  ZNF828 WILD-TYPE  474   35
   clus
vv  ZNF828 MUTATED ZNF828 WILD-TYPE
  0              8              474
  1              3               35
[1] 2 2
[1] FALSE
D1222V7, binary
                  cls
clus                 0   1
  ZNF828 MUTATED     3   9
  ZNF828 WILD-TYPE 169 397
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF828 MUTATED      3    9
  ZNF828 WILD-TYPE  169  397
        clus
vv       ZNF828 MUTATED ZNF828 WILD-TYPE
  FEMALE              3              169
  MALE                9              397
[1] 2 2
[1] FALSE
D1222V8, binary
                  cls
clus                 0   1
  ZNF828 MUTATED    10   2
  ZNF828 WILD-TYPE 406 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF828 MUTATED     10    2
  ZNF828 WILD-TYPE  406  100
     clus
vv    ZNF828 MUTATED ZNF828 WILD-TYPE
  NO              10              406
  YES              2              100
[1] 2 2
[1] FALSE
D1222V9, continuous
[1] "Remove cluster labels:" "ZNF828 MUTATED"        
clus
  ZNF828 MUTATED ZNF828 WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ZNF828 WILD-TYPE" "ZNF828 WILD-TYPE" 
D1222V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF828 MUTATED       2                         0
  ZNF828 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF828 MUTATED                                           0     4
  ZNF828 WILD-TYPE                                         1   353
D1222V11, multiclass
                                           clus
vv                                          ZNF828 MUTATED ZNF828 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1222V12, binary
                  cls
clus                 0   1
  ZNF828 MUTATED     1   3
  ZNF828 WILD-TYPE   9 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF828 MUTATED      1    3
  ZNF828 WILD-TYPE    9  395
                        clus
vv                       ZNF828 MUTATED ZNF828 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(1223) Variable = CHST4 MUTATION ANALYSIS
D1223V1, survival
                 sevent
clus2               0   1
  CHST4 MUTATED     4   3
  CHST4 WILD-TYPE 334 213
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             547 
  CHST4 MUTATED CHST4 WILD-TYPE 
              3             213 
$`CHST4 MUTATED`
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4H4 
       16.14         6.58        22.68        24.20         0.10        23.84 
TCGA-VQ-A8P2 
       38.14 

$`CHST4 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        21.44         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.26         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CHST4 MUTATED CHST4 WILD-TYPE 
            0.1             0.0 
  CHST4 MUTATED CHST4 WILD-TYPE 
          38.14          122.30 
  CHST4 MUTATED CHST4 WILD-TYPE 
          22.68           13.51 
[1] "0.1 - 38.1 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1223V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHST4 MUTATED         0        1        0        0         1         2
  CHST4 WILD-TYPE      10       19       46       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHST4 MUTATED           0          1          1          1        0         0
  CHST4 WILD-TYPE        29         83         61         38       43         4
D1223V3, multiclass
            clus
vv           CHST4 MUTATED CHST4 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CHST4 MUTATED       1   1   3   2
  CHST4 WILD-TYPE    53 134 258 100
D1223V4, multiclass
       clus
vv      CHST4 MUTATED CHST4 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                3             258
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CHST4 MUTATED     2   2   2   1
  CHST4 WILD-TYPE 193 171  87  84
D1223V5, multiclass
    clus
vv   CHST4 MUTATED CHST4 WILD-TYPE
  N0             2             193
  N1             2             171
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1223V6, binary
                 cls
clus                0   1
  CHST4 MUTATED     7   0
  CHST4 WILD-TYPE 475  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      7    0
  CHST4 WILD-TYPE  475   38
   clus
vv  CHST4 MUTATED CHST4 WILD-TYPE
  0             7             475
  1             0              38
[1] 2 2
[1] FALSE
D1223V7, binary
                 cls
clus                0   1
  CHST4 MUTATED     4   3
  CHST4 WILD-TYPE 168 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      4    3
  CHST4 WILD-TYPE  168  403
        clus
vv       CHST4 MUTATED CHST4 WILD-TYPE
  FEMALE             4             168
  MALE               3             403
[1] 2 2
[1] FALSE
D1223V8, binary
                 cls
clus                0   1
  CHST4 MUTATED     6   1
  CHST4 WILD-TYPE 410 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      6    1
  CHST4 WILD-TYPE  410  101
     clus
vv    CHST4 MUTATED CHST4 WILD-TYPE
  NO              6             410
  YES             1             101
[1] 2 2
[1] FALSE
D1223V9, continuous
D1223V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHST4 MUTATED       5                         0
  CHST4 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHST4 MUTATED                                           0     2
  CHST4 WILD-TYPE                                         1   355
D1223V11, multiclass
                                           clus
vv                                          CHST4 MUTATED CHST4 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1223V12, binary
                 cls
clus                0   1
  CHST4 MUTATED     0   6
  CHST4 WILD-TYPE  10 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      0    6
  CHST4 WILD-TYPE   10  392
                        clus
vv                       CHST4 MUTATED CHST4 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             6             392
[1] 2 2
[1] FALSE

Clustering(1224) Variable = SMARCC2 MUTATION ANALYSIS
D1224V1, survival
                   sevent
clus2                 0   1
  SMARCC2 MUTATED    12   9
  SMARCC2 WILD-TYPE 326 207
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               21               533 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                9               207 
$`SMARCC2 MUTATED`
TCGA-CG-4460 TCGA-2H-A9GI TCGA-2H-A9GK TCGA-LN-A4MQ TCGA-R6-A6XG TCGA-BR-4257 
       21.99        14.30         7.63        12.33        38.40         9.67 
TCGA-BR-7707 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-A4J2 
       35.84         3.45        29.59         0.26         1.12        14.17 
TCGA-CD-8526 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8572 TCGA-D7-A4YV 
       12.53        29.98         6.02        65.10        16.80         5.92 
TCGA-HF-7132 TCGA-HU-8243 TCGA-R5-A7ZF 
       77.29         5.92         8.52 

$`SMARCC2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.59        22.39        12.85        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.39        12.76        12.59         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       12.79        12.36        11.31        12.33        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
             0.26              0.00 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
            77.29            122.30 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
            12.53             13.58 
[1] "0.3 - 77.3 (12.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1224V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCC2 MUTATED         0        1        3        1         1         5
  SMARCC2 WILD-TYPE      10       19       43       30        83        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCC2 MUTATED           3          1          0          1        3
  SMARCC2 WILD-TYPE        26         83         62         38       40
                   vv
clus                STAGE IVA
  SMARCC2 MUTATED           0
  SMARCC2 WILD-TYPE         4
D1224V3, multiclass
            clus
vv           SMARCC2 MUTATED SMARCC2 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 1                19
  STAGE IB                 3                43
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                5                78
  STAGE III                3                26
  STAGE IIIA               1                83
  STAGE IIIB               0                62
  STAGE IIIC               1                38
  STAGE IV                 3                40
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  SMARCC2 MUTATED       1   5   7   6
  SMARCC2 WILD-TYPE    53 130 254  96
D1224V4, multiclass
       clus
vv      SMARCC2 MUTATED SMARCC2 WILD-TYPE
  T0+T1               1                53
  T2                  5               130
  T3                  7               254
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  SMARCC2 MUTATED     7  11   1   1
  SMARCC2 WILD-TYPE 188 162  88  84
D1224V5, multiclass
    clus
vv   SMARCC2 MUTATED SMARCC2 WILD-TYPE
  N0               7               188
  N1              11               162
  N2               1                88
  N3               1                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1224V6, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    19   2
  SMARCC2 WILD-TYPE 463  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     19    2
  SMARCC2 WILD-TYPE  463   36
   clus
vv  SMARCC2 MUTATED SMARCC2 WILD-TYPE
  0              19               463
  1               2                36
[1] 2 2
[1] FALSE
D1224V7, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    11  11
  SMARCC2 WILD-TYPE 161 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     11   11
  SMARCC2 WILD-TYPE  161  395
        clus
vv       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  FEMALE              11               161
  MALE                11               395
[1] 2 2
[1] FALSE
D1224V8, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    18   1
  SMARCC2 WILD-TYPE 398 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     18    1
  SMARCC2 WILD-TYPE  398  101
     clus
vv    SMARCC2 MUTATED SMARCC2 WILD-TYPE
  NO               18               398
  YES               1               101
[1] 2 2
[1] FALSE
D1224V9, continuous
[1] "Remove cluster labels:" "SMARCC2 MUTATED"       
clus
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A4A6        TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MR 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
D1224V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SMARCC2 MUTATED       4                         1
  SMARCC2 WILD-TYPE   129                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMARCC2 MUTATED                                           0    10
  SMARCC2 WILD-TYPE                                         1   347
D1224V11, multiclass
                                           clus
vv                                          SMARCC2 MUTATED SMARCC2 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               1                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1224V12, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED     0  15
  SMARCC2 WILD-TYPE  10 383
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      0   15
  SMARCC2 WILD-TYPE   10  383
                        clus
vv                       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              15               383
[1] 2 2
[1] FALSE

Clustering(1225) Variable = ZNF98 MUTATION ANALYSIS
D1225V1, survival
                 sevent
clus2               0   1
  ZNF98 MUTATED     9   7
  ZNF98 WILD-TYPE 329 209
  ZNF98 MUTATED ZNF98 WILD-TYPE 
             16             538 
  ZNF98 MUTATED ZNF98 WILD-TYPE 
              7             209 
$`ZNF98 MUTATED`
TCGA-CG-4444 TCGA-2H-A9GR TCGA-L5-A4OX TCGA-L5-A8NS TCGA-LN-A9FP TCGA-RE-A7BO 
       47.05        32.45         7.43        13.41        12.03         7.00 
TCGA-VR-A8EQ TCGA-BR-8680 TCGA-BR-A4PD TCGA-CD-8536 TCGA-D7-6526 TCGA-D7-6818 
       22.82        31.96        20.65        12.43        17.19        12.36 
TCGA-D7-A4YV TCGA-HF-7134 TCGA-HU-A4H4 TCGA-RD-A7BT 
        5.92        52.21        23.84         8.61 

$`ZNF98 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        9.30        15.78         2.89         2.30        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        63.06        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  ZNF98 MUTATED ZNF98 WILD-TYPE 
           5.92            0.00 
  ZNF98 MUTATED ZNF98 WILD-TYPE 
          52.21          122.30 
  ZNF98 MUTATED ZNF98 WILD-TYPE 
         15.300          13.565 
[1] "5.9 - 52.2 (15.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1"  
D1225V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF98 MUTATED         0        1        1        1         2         6
  ZNF98 WILD-TYPE      10       19       45       30        82        77
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF98 MUTATED           1          3          0          1        2         0
  ZNF98 WILD-TYPE        28         81         62         38       41         4
D1225V3, multiclass
            clus
vv           ZNF98 MUTATED ZNF98 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              6              77
  STAGE III              1              28
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               2              41
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ZNF98 MUTATED       2   6   7   3
  ZNF98 WILD-TYPE    52 129 254  99
D1225V4, multiclass
       clus
vv      ZNF98 MUTATED ZNF98 WILD-TYPE
  T0+T1             2              52
  T2                6             129
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ZNF98 MUTATED     7   4   4   3
  ZNF98 WILD-TYPE 188 169  85  82
D1225V5, multiclass
    clus
vv   ZNF98 MUTATED ZNF98 WILD-TYPE
  N0             7             188
  N1             4             169
  N2             4              85
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1225V6, binary
                 cls
clus                0   1
  ZNF98 MUTATED    17   1
  ZNF98 WILD-TYPE 465  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF98 MUTATED     17    1
  ZNF98 WILD-TYPE  465   37
   clus
vv  ZNF98 MUTATED ZNF98 WILD-TYPE
  0            17             465
  1             1              37
[1] 2 2
[1] FALSE
D1225V7, binary
                 cls
clus                0   1
  ZNF98 MUTATED     7  11
  ZNF98 WILD-TYPE 165 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF98 MUTATED      7   11
  ZNF98 WILD-TYPE  165  395
        clus
vv       ZNF98 MUTATED ZNF98 WILD-TYPE
  FEMALE             7             165
  MALE              11             395
[1] 2 2
[1] FALSE
D1225V8, binary
                 cls
clus                0   1
  ZNF98 MUTATED    12   5
  ZNF98 WILD-TYPE 404  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF98 MUTATED     12    5
  ZNF98 WILD-TYPE  404   97
     clus
vv    ZNF98 MUTATED ZNF98 WILD-TYPE
  NO             12             404
  YES             5              97
[1] 2 2
[1] FALSE
D1225V9, continuous
[1] "Remove cluster labels:" "ZNF98 MUTATED"         
clus
  ZNF98 MUTATED ZNF98 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" "ZNF98 WILD-TYPE" 
D1225V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF98 MUTATED       4                         0
  ZNF98 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF98 MUTATED                                           1     9
  ZNF98 WILD-TYPE                                         0   348
D1225V11, multiclass
                                           clus
vv                                          ZNF98 MUTATED ZNF98 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                 9             348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1225V12, binary
                 cls
clus                0   1
  ZNF98 MUTATED     0  11
  ZNF98 WILD-TYPE  10 387
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF98 MUTATED      0   11
  ZNF98 WILD-TYPE   10  387
                        clus
vv                       ZNF98 MUTATED ZNF98 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            11             387
[1] 2 2
[1] FALSE

Clustering(1226) Variable = RGS22 MUTATION ANALYSIS
D1226V1, survival
                 sevent
clus2               0   1
  RGS22 MUTATED    15   6
  RGS22 WILD-TYPE 323 210
  RGS22 MUTATED RGS22 WILD-TYPE 
             21             533 
  RGS22 MUTATED RGS22 WILD-TYPE 
              6             210 
$`RGS22 MUTATED`
TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6802 
      122.10        41.52        26.70        18.35        34.68        30.90 
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL 
       44.94        35.84        14.43        31.27        31.96        16.14 
TCGA-CG-4437 TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT 
        8.05        65.10        21.07        11.77         0.10         6.51 
TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-MX-A666 
        6.58        19.73        14.04 

$`RGS22 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
        3.42         2.10         1.32         2.66        19.73        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       40.21        31.20        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  RGS22 MUTATED RGS22 WILD-TYPE 
            0.1             0.0 
  RGS22 MUTATED RGS22 WILD-TYPE 
          122.1           122.3 
  RGS22 MUTATED RGS22 WILD-TYPE 
          21.07           13.41 
[1] "0.1 - 122.1 (21.1)" "0.0 - 122.3 (13.4)"
[1] "hr=" "2"  
D1226V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS22 MUTATED         1        1        3        1         5         2
  RGS22 WILD-TYPE       9       19       43       30        79        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS22 MUTATED           2          3          1          2        1         0
  RGS22 WILD-TYPE        27         81         61         37       42         4
D1226V3, multiclass
            clus
vv           RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               1              30
  STAGE IIA              5              79
  STAGE IIB              2              81
  STAGE III              2              27
  STAGE IIIA             3              81
  STAGE IIIB             1              61
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RGS22 MUTATED       2   6   9   5
  RGS22 WILD-TYPE    52 129 252  97
D1226V4, multiclass
       clus
vv      RGS22 MUTATED RGS22 WILD-TYPE
  T0+T1             2              52
  T2                6             129
  T3                9             252
  T4                5              97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RGS22 MUTATED    10   5   5   2
  RGS22 WILD-TYPE 185 168  84  83
D1226V5, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  N0            10             185
  N1             5             168
  N2             5              84
  N3             2              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1226V6, binary
                 cls
clus                0   1
  RGS22 MUTATED    21   1
  RGS22 WILD-TYPE 461  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     21    1
  RGS22 WILD-TYPE  461   37
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0            21             461
  1             1              37
[1] 2 2
[1] FALSE
D1226V7, binary
                 cls
clus                0   1
  RGS22 MUTATED     9  14
  RGS22 WILD-TYPE 163 392
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      9   14
  RGS22 WILD-TYPE  163  392
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  FEMALE             9             163
  MALE              14             392
[1] 2 2
[1] FALSE
D1226V8, binary
                 cls
clus                0   1
  RGS22 MUTATED    20   0
  RGS22 WILD-TYPE 396 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     20    0
  RGS22 WILD-TYPE  396  102
     clus
vv    RGS22 MUTATED RGS22 WILD-TYPE
  NO             20             396
  YES             0             102
[1] 2 2
[1] FALSE
D1226V9, continuous
D1226V10, continuous
[1] "Remove cluster labels:" "RGS22 MUTATED"         
clus
  RGS22 MUTATED RGS22 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-Z6-AAPN 
"RGS22 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RGS22 MUTATED       5                         0
  RGS22 WILD-TYPE   128                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS22 MUTATED                                           0    14
  RGS22 WILD-TYPE                                         1   343
D1226V11, multiclass
                                           clus
vv                                          RGS22 MUTATED RGS22 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1226V12, binary
                 cls
clus                0   1
  RGS22 MUTATED     0  17
  RGS22 WILD-TYPE  10 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      0   17
  RGS22 WILD-TYPE   10  381
                        clus
vv                       RGS22 MUTATED RGS22 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            17             381
[1] 2 2
[1] FALSE

Clustering(1227) Variable = ATOH1 MUTATION ANALYSIS
D1227V1, survival
                 sevent
clus2               0   1
  ATOH1 MUTATED     3   3
  ATOH1 WILD-TYPE 335 213
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             548 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              3             213 
$`ATOH1 MUTATED`
TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 
        6.61        44.94        29.59        16.14         6.02        28.96 

$`ATOH1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  ATOH1 MUTATED ATOH1 WILD-TYPE 
           6.02            0.00 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
          44.94          122.30 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
          22.55           13.53 
[1] "6.0 - 44.9 (22.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1227V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATOH1 MUTATED         0        1        0        0         1         1
  ATOH1 WILD-TYPE      10       19       46       31        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATOH1 MUTATED           1          0          1          0        1         0
  ATOH1 WILD-TYPE        28         84         61         39       42         4
D1227V3, multiclass
            clus
vv           ATOH1 MUTATED ATOH1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ATOH1 MUTATED       1   1   2   2
  ATOH1 WILD-TYPE    53 134 259 100
D1227V4, multiclass
       clus
vv      ATOH1 MUTATED ATOH1 WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ATOH1 MUTATED     3   2   0   1
  ATOH1 WILD-TYPE 192 171  89  84
D1227V5, multiclass
    clus
vv   ATOH1 MUTATED ATOH1 WILD-TYPE
  N0             3             192
  N1             2             171
  N2             0              89
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1227V6, binary
                 cls
clus                0   1
  ATOH1 MUTATED     6   0
  ATOH1 WILD-TYPE 476  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      6    0
  ATOH1 WILD-TYPE  476   38
   clus
vv  ATOH1 MUTATED ATOH1 WILD-TYPE
  0             6             476
  1             0              38
[1] 2 2
[1] FALSE
D1227V7, binary
                 cls
clus                0   1
  ATOH1 MUTATED     4   2
  ATOH1 WILD-TYPE 168 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      4    2
  ATOH1 WILD-TYPE  168  404
        clus
vv       ATOH1 MUTATED ATOH1 WILD-TYPE
  FEMALE             4             168
  MALE               2             404
[1] 2 2
[1] FALSE
D1227V8, binary
                 cls
clus                0   1
  ATOH1 MUTATED     5   0
  ATOH1 WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      5    0
  ATOH1 WILD-TYPE  411  102
     clus
vv    ATOH1 MUTATED ATOH1 WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D1227V9, continuous
D1227V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ATOH1 MUTATED       0                         0
  ATOH1 WILD-TYPE   133                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATOH1 MUTATED                                           0     4
  ATOH1 WILD-TYPE                                         1   353
D1227V11, multiclass
                                           clus
vv                                          ATOH1 MUTATED ATOH1 WILD-TYPE
  ASIAN                                                 0             133
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1227V12, binary
                 cls
clus                0   1
  ATOH1 MUTATED     0   4
  ATOH1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      0    4
  ATOH1 WILD-TYPE   10  394
                        clus
vv                       ATOH1 MUTATED ATOH1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1228) Variable = RBM33 MUTATION ANALYSIS
D1228V1, survival
                 sevent
clus2               0   1
  RBM33 MUTATED    15   5
  RBM33 WILD-TYPE 323 211
  RBM33 MUTATED RBM33 WILD-TYPE 
             20             534 
  RBM33 MUTATED RBM33 WILD-TYPE 
              5             211 
$`RBM33 MUTATED`
TCGA-L5-A8NM TCGA-L5-A8NV TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 
        7.76        52.57        34.68        32.25         0.26         4.31 
TCGA-BR-8372 TCGA-BR-8483 TCGA-BR-8680 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-D7-A4Z0 
       31.27         5.39        31.96         0.53        16.14        14.76 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HU-8249 TCGA-HU-A4G9 TCGA-HU-A4GQ 
       21.27        19.53        11.08        28.96        24.20         0.10 
TCGA-HU-A4GT TCGA-HU-A4H8 
        6.51        14.07 

$`RBM33 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       14.79         7.36        25.05         3.72        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98         0.72        14.17        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       25.81        11.77        21.37        29.98         8.98         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  RBM33 MUTATED RBM33 WILD-TYPE 
            0.1             0.0 
  RBM33 MUTATED RBM33 WILD-TYPE 
          52.57          122.30 
  RBM33 MUTATED RBM33 WILD-TYPE 
          15.45           13.51 
[1] "0.1 - 52.6 (15.4)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1228V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM33 MUTATED         0        1        3        0         4         4
  RBM33 WILD-TYPE      10       19       43       31        80        79
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM33 MUTATED           0          3          3          2        1         0
  RBM33 WILD-TYPE        29         81         59         37       42         4
D1228V3, multiclass
            clus
vv           RBM33 MUTATED RBM33 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               3              43
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              4              79
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             3              59
  STAGE IIIC             2              37
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RBM33 MUTATED       2   4   9   6
  RBM33 WILD-TYPE    52 131 252  96
D1228V4, multiclass
       clus
vv      RBM33 MUTATED RBM33 WILD-TYPE
  T0+T1             2              52
  T2                4             131
  T3                9             252
  T4                6              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RBM33 MUTATED     9   3   6   3
  RBM33 WILD-TYPE 186 170  83  82
D1228V5, multiclass
    clus
vv   RBM33 MUTATED RBM33 WILD-TYPE
  N0             9             186
  N1             3             170
  N2             6              83
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1228V6, binary
                 cls
clus                0   1
  RBM33 MUTATED    20   1
  RBM33 WILD-TYPE 462  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED     20    1
  RBM33 WILD-TYPE  462   37
   clus
vv  RBM33 MUTATED RBM33 WILD-TYPE
  0            20             462
  1             1              37
[1] 2 2
[1] FALSE
D1228V7, binary
                 cls
clus                0   1
  RBM33 MUTATED    10  11
  RBM33 WILD-TYPE 162 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED     10   11
  RBM33 WILD-TYPE  162  395
        clus
vv       RBM33 MUTATED RBM33 WILD-TYPE
  FEMALE            10             162
  MALE              11             395
[1] 2 2
[1] FALSE
D1228V8, binary
                 cls
clus                0   1
  RBM33 MUTATED    15   4
  RBM33 WILD-TYPE 401  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED     15    4
  RBM33 WILD-TYPE  401   98
     clus
vv    RBM33 MUTATED RBM33 WILD-TYPE
  NO             15             401
  YES             4              98
[1] 2 2
[1] FALSE
D1228V9, continuous
D1228V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RBM33 MUTATED       7                         1
  RBM33 WILD-TYPE   126                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBM33 MUTATED                                           0    13
  RBM33 WILD-TYPE                                         1   344
D1228V11, multiclass
                                           clus
vv                                          RBM33 MUTATED RBM33 WILD-TYPE
  ASIAN                                                 7             126
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1228V12, binary
                 cls
clus                0   1
  RBM33 MUTATED     1  18
  RBM33 WILD-TYPE   9 380
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      1   18
  RBM33 WILD-TYPE    9  380
                        clus
vv                       RBM33 MUTATED RBM33 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO            18             380
[1] 2 2
[1] FALSE

Clustering(1229) Variable = SLC22A16 MUTATION ANALYSIS
D1229V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED     9   2
  SLC22A16 WILD-TYPE 329 214
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                11                543 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 2                214 
$`SLC22A16 MUTATED`
TCGA-R6-A6KZ TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-8529 
        5.06        11.70         6.97        34.68        31.27        12.30 
TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-VQ-A8P2 
       14.47        22.32        22.68        29.98        38.14 

$`SLC22A16 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
              5.06               0.00 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             38.14             122.30 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             22.32              13.51 
[1] "5.1 - 38.1 (22.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.6"
D1229V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC22A16 MUTATED         0        0        2        0         2         2
  SLC22A16 WILD-TYPE      10       20       44       31        82        81
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           0          2          0          1        1
  SLC22A16 WILD-TYPE        29         82         62         38       42
                    vv
clus                 STAGE IVA
  SLC22A16 MUTATED           0
  SLC22A16 WILD-TYPE         4
D1229V3, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  0                 20
  STAGE IB                  2                 44
  STAGE II                  0                 31
  STAGE IIA                 2                 82
  STAGE IIB                 2                 81
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                0                 62
  STAGE IIIC                1                 38
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  SLC22A16 MUTATED       0   3   3   4
  SLC22A16 WILD-TYPE    54 132 258  98
D1229V4, multiclass
       clus
vv      SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T0+T1                0                 54
  T2                   3                132
  T3                   3                258
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  SLC22A16 MUTATED     5   4   0   1
  SLC22A16 WILD-TYPE 190 169  89  84
D1229V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0                5                190
  N1                4                169
  N2                0                 89
  N3                1                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1229V6, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     9   1
  SLC22A16 WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      9    1
  SLC22A16 WILD-TYPE  473   37
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D1229V7, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     4   8
  SLC22A16 WILD-TYPE 168 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      4    8
  SLC22A16 WILD-TYPE  168  398
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE                4                168
  MALE                  8                398
[1] 2 2
[1] FALSE
D1229V8, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     9   2
  SLC22A16 WILD-TYPE 407 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      9    2
  SLC22A16 WILD-TYPE  407  100
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                 9                407
  YES                2                100
[1] 2 2
[1] FALSE
D1229V9, continuous
D1229V10, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC22A16 MUTATED       4                         0
  SLC22A16 WILD-TYPE   129                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC22A16 MUTATED                                           0     8
  SLC22A16 WILD-TYPE                                         1   349
D1229V11, multiclass
                                           clus
vv                                          SLC22A16 MUTATED SLC22A16 WILD-TYPE
  ASIAN                                                    4                129
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1229V12, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     0  11
  SLC22A16 WILD-TYPE  10 387
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0   11
  SLC22A16 WILD-TYPE   10  387
                        clus
vv                       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                387
[1] 2 2
[1] FALSE

Clustering(1230) Variable = SMAD2 MUTATION ANALYSIS
D1230V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED     5   4
  SMAD2 WILD-TYPE 333 212
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             545 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              4             212 
$`SMAD2 MUTATED`
TCGA-CG-4444 TCGA-V5-A7RC TCGA-VR-A8ER TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-4462 
       47.05         3.42        12.43        34.68        16.14         0.00 
TCGA-F1-A448 TCGA-HU-8604 TCGA-HU-A4H3 
       21.27        22.82        29.00 

$`SMAD2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       72.23        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
            0.0             0.1 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          47.05          122.30 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          21.27           13.51 
[1] "0.0 - 47.0 (21.3)"  "0.1 - 122.3 (13.5)"
[1] "hr=" "1"  
D1230V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD2 MUTATED         0        0        0        0         2         1
  SMAD2 WILD-TYPE      10       20       46       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED           1          1          2          1        1         0
  SMAD2 WILD-TYPE        28         83         60         38       42         4
D1230V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SMAD2 MUTATED       0   2   5   3
  SMAD2 WILD-TYPE    54 133 256  99
D1230V4, multiclass
       clus
vv      SMAD2 MUTATED SMAD2 WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                5             256
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SMAD2 MUTATED     3   1   1   4
  SMAD2 WILD-TYPE 192 172  88  81
D1230V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             3             192
  N1             1             172
  N2             1              88
  N3             4              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1230V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED     9   1
  SMAD2 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      9    1
  SMAD2 WILD-TYPE  473   37
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D1230V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED     6   5
  SMAD2 WILD-TYPE 166 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      6    5
  SMAD2 WILD-TYPE  166  401
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             6             166
  MALE               5             401
[1] 2 2
[1] FALSE
D1230V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     4   4
  SMAD2 WILD-TYPE 412  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      4    4
  SMAD2 WILD-TYPE  412   98
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO              4             412
  YES             4              98
[1] 2 2
[1] FALSE
D1230V9, continuous
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2              66 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RE      TCGA-V5-AASV 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ET      TCGA-VR-A8EU      TCGA-VR-A8EW 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B      TCGA-VR-AA7D 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
D1230V10, continuous
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-LN-A8HZ      TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-R6-A6DN      TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-R6-A8W5      TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8EU 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD2 MUTATED       2                         1
  SMAD2 WILD-TYPE   131                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD2 MUTATED                                           0     5
  SMAD2 WILD-TYPE                                         1   352
D1230V11, multiclass
                                           clus
vv                                          SMAD2 MUTATED SMAD2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1230V12, binary
                 cls
clus                0   1
  SMAD2 MUTATED     1   7
  SMAD2 WILD-TYPE   9 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      1    7
  SMAD2 WILD-TYPE    9  391
                        clus
vv                       SMAD2 MUTATED SMAD2 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1231) Variable = FIGNL1 MUTATION ANALYSIS
D1231V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED     7   4
  FIGNL1 WILD-TYPE 331 212
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              11              543 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               4              212 
$`FIGNL1 MUTATED`
TCGA-L5-A8NE TCGA-L5-A8NM TCGA-VR-A8EX TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6802 
       55.50         7.76        28.11        26.70         6.97        30.90 
TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8682 TCGA-CD-A4MG TCGA-HU-8602 
       31.10         1.12        32.58         6.58        22.32 

$`FIGNL1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       22.82        12.43         1.55        18.31         8.12        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         1.32         2.66        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        31.96         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            1.12             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            55.5            122.3 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           26.70            13.51 
[1] "1.1 - 55.5 (26.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1231V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FIGNL1 MUTATED         0        0        0        0         2         5
  FIGNL1 WILD-TYPE      10       20       46       31        82        78
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           0          3          0          1        0
  FIGNL1 WILD-TYPE        29         81         62         38       43
                  vv
clus               STAGE IVA
  FIGNL1 MUTATED           1
  FIGNL1 WILD-TYPE         3
D1231V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               2               82
  STAGE IIB               5               78
  STAGE III               0               29
  STAGE IIIA              3               81
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               1                3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  FIGNL1 MUTATED       1   2   4   5
  FIGNL1 WILD-TYPE    53 133 257  97
D1231V4, multiclass
       clus
vv      FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 4              257
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  FIGNL1 MUTATED     6   4   2   0
  FIGNL1 WILD-TYPE 189 169  87  85
D1231V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0              6              189
  N1              4              169
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1231V6, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    10   1
  FIGNL1 WILD-TYPE 472  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     10    1
  FIGNL1 WILD-TYPE  472   37
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0             10              472
  1              1               37
[1] 2 2
[1] FALSE
D1231V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     6   6
  FIGNL1 WILD-TYPE 166 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      6    6
  FIGNL1 WILD-TYPE  166  400
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE              6              166
  MALE                6              400
[1] 2 2
[1] FALSE
D1231V8, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    11   0
  FIGNL1 WILD-TYPE 405 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     11    0
  FIGNL1 WILD-TYPE  405  102
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO              11              405
  YES              0              102
[1] 2 2
[1] FALSE
D1231V9, continuous
[1] "Remove cluster labels:" "FIGNL1 MUTATED"        
clus
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
D1231V10, continuous
[1] "Remove cluster labels:" "FIGNL1 MUTATED"        
clus
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" "FIGNL1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FIGNL1 MUTATED       3                         0
  FIGNL1 WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FIGNL1 MUTATED                                           0     8
  FIGNL1 WILD-TYPE                                         1   349
D1231V11, multiclass
                                           clus
vv                                          FIGNL1 MUTATED FIGNL1 WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1231V12, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     0   9
  FIGNL1 WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      0    9
  FIGNL1 WILD-TYPE   10  389
                        clus
vv                       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1232) Variable = KDELR2 MUTATION ANALYSIS
D1232V1, survival
                  sevent
clus2                0   1
  KDELR2 MUTATED     3   2
  KDELR2 WILD-TYPE 335 214
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               5              549 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               2              214 
$`KDELR2 MUTATED`
TCGA-LN-A9FP TCGA-XP-A8T7 TCGA-HJ-7597 TCGA-HU-8604 TCGA-R5-A7ZR 
       12.03        41.23        26.47        22.82         6.08 

$`KDELR2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38        13.18         0.13        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       11.24         9.17        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       14.04        45.67        18.21         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  KDELR2 MUTATED KDELR2 WILD-TYPE 
            6.08             0.00 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
           41.23           122.30 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
           22.82            13.55 
[1] "6.1 - 41.2 (22.8)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1232V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KDELR2 MUTATED         0        0        1        0         3         0
  KDELR2 WILD-TYPE      10       20       45       31        81        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KDELR2 MUTATED           1          0          0          0        0
  KDELR2 WILD-TYPE        28         84         62         39       43
                  vv
clus               STAGE IVA
  KDELR2 MUTATED           0
  KDELR2 WILD-TYPE         4
D1232V3, multiclass
            clus
vv           KDELR2 MUTATED KDELR2 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               3               81
  STAGE IIB               0               83
  STAGE III               1               28
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              0               39
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  KDELR2 MUTATED       0   3   2   0
  KDELR2 WILD-TYPE    54 132 259 102
D1232V4, multiclass
       clus
vv      KDELR2 MUTATED KDELR2 WILD-TYPE
  T0+T1              0               54
  T2                 3              132
  T3                 2              259
  T4                 0              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  KDELR2 MUTATED     4   0   0   0
  KDELR2 WILD-TYPE 191 173  89  85
D1232V5, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  N0              4              191
  N1              0              173
  N2              0               89
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1232V6, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     4   0
  KDELR2 WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      4    0
  KDELR2 WILD-TYPE  478   38
   clus
vv  KDELR2 MUTATED KDELR2 WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D1232V7, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     5   0
  KDELR2 WILD-TYPE 167 406
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      5    0
  KDELR2 WILD-TYPE  167  406
        clus
vv       KDELR2 MUTATED KDELR2 WILD-TYPE
  FEMALE              5              167
  MALE                0              406
[1] 2 2
[1] FALSE
D1232V8, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     4   1
  KDELR2 WILD-TYPE 412 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      4    1
  KDELR2 WILD-TYPE  412  101
     clus
vv    KDELR2 MUTATED KDELR2 WILD-TYPE
  NO               4              412
  YES              1              101
[1] 2 2
[1] FALSE
D1232V9, continuous
[1] "Remove cluster labels:" "KDELR2 MUTATED"        
clus
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
D1232V10, continuous
[1] "Remove cluster labels:" "KDELR2 MUTATED"        
clus
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T8 
"KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" "KDELR2 WILD-TYPE" 
      TCGA-Z6-AAPN 
"KDELR2 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KDELR2 MUTATED       2                         1
  KDELR2 WILD-TYPE   131                        13
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KDELR2 MUTATED                                           0     2
  KDELR2 WILD-TYPE                                         1   355
D1232V11, multiclass
                                           clus
vv                                          KDELR2 MUTATED KDELR2 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              1               13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1232V12, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     1   4
  KDELR2 WILD-TYPE   9 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      1    4
  KDELR2 WILD-TYPE    9  394
                        clus
vv                       KDELR2 MUTATED KDELR2 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              4              394
[1] 2 2
[1] FALSE

Clustering(1233) Variable = NOLC1 MUTATION ANALYSIS
D1233V1, survival
                 sevent
clus2               0   1
  NOLC1 MUTATED     7   6
  NOLC1 WILD-TYPE 331 210
  NOLC1 MUTATED NOLC1 WILD-TYPE 
             13             541 
  NOLC1 MUTATED NOLC1 WILD-TYPE 
              6             210 
$`NOLC1 MUTATED`
TCGA-CG-4460 TCGA-MX-A663 TCGA-IG-A6QS TCGA-JY-A93E TCGA-R6-A8W5 TCGA-BR-4256 
       21.99         9.86         9.96        25.22        15.78         9.34 
TCGA-BR-6452 TCGA-BR-6706 TCGA-CG-4305 TCGA-CG-5721 TCGA-HU-8604 TCGA-HU-A4GH 
       34.68        18.05        15.95         6.02        22.82        11.77 
TCGA-HU-A4H4 
       23.84 

$`NOLC1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
       16.24         0.23        20.15        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  NOLC1 MUTATED NOLC1 WILD-TYPE 
           6.02            0.00 
  NOLC1 MUTATED NOLC1 WILD-TYPE 
          34.68          122.30 
  NOLC1 MUTATED NOLC1 WILD-TYPE 
          15.95           13.51 
[1] "6.0 - 34.7 (15.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1233V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOLC1 MUTATED         0        1        0        1         3         3
  NOLC1 WILD-TYPE      10       19       46       30        81        80
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOLC1 MUTATED           0          3          0          0        2         1
  NOLC1 WILD-TYPE        29         81         62         39       41         3
D1233V3, multiclass
            clus
vv           NOLC1 MUTATED NOLC1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              3              80
  STAGE III              0              29
  STAGE IIIA             3              81
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               2              41
  STAGE IVA              1               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  NOLC1 MUTATED       1   3   7   3
  NOLC1 WILD-TYPE    53 132 254  99
D1233V4, multiclass
       clus
vv      NOLC1 MUTATED NOLC1 WILD-TYPE
  T0+T1             1              53
  T2                3             132
  T3                7             254
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  NOLC1 MUTATED     5   9   1   0
  NOLC1 WILD-TYPE 190 164  88  85
D1233V5, multiclass
    clus
vv   NOLC1 MUTATED NOLC1 WILD-TYPE
  N0             5             190
  N1             9             164
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1233V6, binary
                 cls
clus                0   1
  NOLC1 MUTATED    13   2
  NOLC1 WILD-TYPE 469  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOLC1 MUTATED     13    2
  NOLC1 WILD-TYPE  469   36
   clus
vv  NOLC1 MUTATED NOLC1 WILD-TYPE
  0            13             469
  1             2              36
[1] 2 2
[1] FALSE
D1233V7, binary
                 cls
clus                0   1
  NOLC1 MUTATED     4  11
  NOLC1 WILD-TYPE 168 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOLC1 MUTATED      4   11
  NOLC1 WILD-TYPE  168  395
        clus
vv       NOLC1 MUTATED NOLC1 WILD-TYPE
  FEMALE             4             168
  MALE              11             395
[1] 2 2
[1] FALSE
D1233V8, binary
                 cls
clus                0   1
  NOLC1 MUTATED    14   1
  NOLC1 WILD-TYPE 402 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOLC1 MUTATED     14    1
  NOLC1 WILD-TYPE  402  101
     clus
vv    NOLC1 MUTATED NOLC1 WILD-TYPE
  NO             14             402
  YES             1             101
[1] 2 2
[1] FALSE
D1233V9, continuous
D1233V10, continuous
[1] "Remove cluster labels:" "NOLC1 MUTATED"         
clus
  NOLC1 MUTATED NOLC1 WILD-TYPE 
              2              96 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W8 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB      TCGA-V5-A7RC 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8EU 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ      TCGA-VR-A8Q7 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-X8-AAAR 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
     TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8      TCGA-Z6-AAPN 
"NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" "NOLC1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NOLC1 MUTATED       3                         0
  NOLC1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOLC1 MUTATED                                           0     8
  NOLC1 WILD-TYPE                                         1   349
D1233V11, multiclass
                                           clus
vv                                          NOLC1 MUTATED NOLC1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1233V12, binary
                 cls
clus                0   1
  NOLC1 MUTATED     0  10
  NOLC1 WILD-TYPE  10 388
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOLC1 MUTATED      0   10
  NOLC1 WILD-TYPE   10  388
                        clus
vv                       NOLC1 MUTATED NOLC1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO            10             388
[1] 2 2
[1] FALSE

Clustering(1234) Variable = NF1 MUTATION ANALYSIS
D1234V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    14  14
  NF1 WILD-TYPE 324 202
  NF1 MUTATED NF1 WILD-TYPE 
           28           526 
  NF1 MUTATED NF1 WILD-TYPE 
           14           202 
$`NF1 MUTATED`
TCGA-L5-A4OI TCGA-IG-A5B8 TCGA-JY-A6FA TCGA-L5-A4OJ TCGA-L5-A8NE TCGA-R6-A6L4 
       19.99         0.79        44.75        21.01        55.50        16.31 
TCGA-R6-A8WG TCGA-VR-A8EO TCGA-BR-4256 TCGA-BR-8284 TCGA-BR-8363 TCGA-BR-8382 
       12.69        25.81         9.34         8.05         0.26        25.05 
TCGA-BR-8680 TCGA-BR-A44U TCGA-CD-A4MG TCGA-CG-4440 TCGA-CG-5721 TCGA-CG-5728 
       31.96        13.87         6.58         4.01         6.02        65.10 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.24        11.44        13.58        30.51         0.10         6.51 
TCGA-HU-A4H3 TCGA-RD-A8N1 TCGA-VQ-A8P2 TCGA-VQ-A91U 
       29.00       115.69        38.14         1.71 

$`NF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30        26.33        32.61        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
        3.42        16.44        15.35         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       29.59         9.60        32.25         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20         7.40         6.18        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79         7.36         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99         8.05        54.08        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         0.99         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        36.43        13.78        14.76        26.43        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       77.29        63.06        52.21        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       15.65        20.81        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  NF1 MUTATED NF1 WILD-TYPE 
          0.1           0.0 
  NF1 MUTATED NF1 WILD-TYPE 
       115.69        122.30 
  NF1 MUTATED NF1 WILD-TYPE 
       13.725        13.530 
[1] "0.1 - 115.7 (13.7)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.2"
D1234V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NF1 MUTATED         2        0        3        0         3         4
  NF1 WILD-TYPE       8       20       43       31        81        79
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF1 MUTATED           0          3          3          6        3         0
  NF1 WILD-TYPE        29         81         59         33       40         4
D1234V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              2             8
  STAGE IA             0            20
  STAGE IB             3            43
  STAGE II             0            31
  STAGE IIA            3            81
  STAGE IIB            4            79
  STAGE III            0            29
  STAGE IIIA           3            81
  STAGE IIIB           3            59
  STAGE IIIC           6            33
  STAGE IV             3            40
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  NF1 MUTATED       3   6  12   9
  NF1 WILD-TYPE    51 129 249  93
D1234V4, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  T0+T1           3            51
  T2              6           129
  T3             12           249
  T4              9            93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  NF1 MUTATED     8   9   4   8
  NF1 WILD-TYPE 187 164  85  77
D1234V5, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0           8           187
  N1           9           164
  N2           4            85
  N3           8            77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1234V6, binary
               cls
clus              0   1
  NF1 MUTATED    27   2
  NF1 WILD-TYPE 455  36
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     27    2
  NF1 WILD-TYPE  455   36
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          27           455
  1           2            36
[1] 2 2
[1] FALSE
D1234V7, binary
               cls
clus              0   1
  NF1 MUTATED    16  19
  NF1 WILD-TYPE 156 387
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     16   19
  NF1 WILD-TYPE  156  387
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          16           156
  MALE            19           387
[1] 2 2
[1] FALSE
D1234V8, binary
               cls
clus              0   1
  NF1 MUTATED    21   5
  NF1 WILD-TYPE 395  97
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     21    5
  NF1 WILD-TYPE  395   97
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           21           395
  YES           5            97
[1] 2 2
[1] FALSE
D1234V9, continuous
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            67 
   TCGA-IG-A3I8    TCGA-IG-A3QL    TCGA-IG-A3Y9    TCGA-IG-A3YA    TCGA-IG-A3YB 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-IG-A3YC    TCGA-IG-A51D    TCGA-IG-A5S3    TCGA-IG-A7DP    TCGA-KH-A6WC 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A49K    TCGA-LN-A49L    TCGA-LN-A49M    TCGA-LN-A49N    TCGA-LN-A49O 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A49P    TCGA-LN-A49R    TCGA-LN-A49S    TCGA-LN-A49U    TCGA-LN-A49V 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A49W    TCGA-LN-A49X    TCGA-LN-A49Y    TCGA-LN-A4A1    TCGA-LN-A4A2 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A4A3    TCGA-LN-A4A4    TCGA-LN-A4A5    TCGA-LN-A4A6    TCGA-LN-A4A8 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A4A9    TCGA-LN-A4MQ    TCGA-LN-A4MR    TCGA-LN-A5U5    TCGA-LN-A5U6 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A5U7    TCGA-LN-A7HV    TCGA-LN-A7HW    TCGA-LN-A7HX    TCGA-LN-A7HY 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-LN-A7HZ    TCGA-V5-A7RB    TCGA-V5-A7RC    TCGA-V5-A7RE    TCGA-V5-AASV 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-V5-AASW    TCGA-V5-AASX    TCGA-VR-A8EP    TCGA-VR-A8EQ    TCGA-VR-A8ER 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-VR-A8ET    TCGA-VR-A8EU    TCGA-VR-A8EW    TCGA-VR-A8EX    TCGA-VR-A8EY 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-VR-A8EZ    TCGA-VR-A8Q7    TCGA-VR-AA4D    TCGA-VR-AA4G    TCGA-VR-AA7B 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-VR-AA7D    TCGA-VR-AA7I    TCGA-XP-A8T6    TCGA-XP-A8T7    TCGA-XP-A8T8 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-Z6-A8JD    TCGA-Z6-A8JE 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" 
D1234V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NF1 MUTATED       7                         1
  NF1 WILD-TYPE   126                        13
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NF1 MUTATED                                           0    23
  NF1 WILD-TYPE                                         1   334
D1234V11, multiclass
                                           clus
vv                                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                                               7           126
  BLACK OR AFRICAN AMERICAN                           1            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              23           334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1234V12, binary
               cls
clus              0   1
  NF1 MUTATED     1  23
  NF1 WILD-TYPE   9 375
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   23
  NF1 WILD-TYPE    9  375
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             9
  NOT HISPANIC OR LATINO          23           375
[1] 2 2
[1] FALSE

Clustering(1235) Variable = GSDMB MUTATION ANALYSIS
D1235V1, survival
                 sevent
clus2               0   1
  GSDMB MUTATED     4   1
  GSDMB WILD-TYPE 334 215
  GSDMB MUTATED GSDMB WILD-TYPE 
              5             549 
  GSDMB MUTATED GSDMB WILD-TYPE 
              1             215 
$`GSDMB MUTATED`
TCGA-BR-8487 TCGA-BR-8680 TCGA-EQ-8122 TCGA-HU-A4GN TCGA-HU-A4H8 
        1.12        31.96         7.99        29.98        14.07 

$`GSDMB WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  GSDMB MUTATED GSDMB WILD-TYPE 
           1.12            0.00 
  GSDMB MUTATED GSDMB WILD-TYPE 
          31.96          122.30 
  GSDMB MUTATED GSDMB WILD-TYPE 
          14.07           13.55 
[1] "1.1 - 32.0 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.9"
D1235V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GSDMB MUTATED         0        0        1        0         2         1
  GSDMB WILD-TYPE      10       20       45       31        82        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSDMB MUTATED           0          0          0          0        1         0
  GSDMB WILD-TYPE        29         84         62         39       42         4
D1235V3, multiclass
            clus
vv           GSDMB MUTATED GSDMB WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              1              82
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GSDMB MUTATED       1   1   2   1
  GSDMB WILD-TYPE    53 134 259 101
D1235V4, multiclass
       clus
vv      GSDMB MUTATED GSDMB WILD-TYPE
  T0+T1             1              53
  T2                1             134
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GSDMB MUTATED     1   3   1   0
  GSDMB WILD-TYPE 194 170  88  85
D1235V5, multiclass
    clus
vv   GSDMB MUTATED GSDMB WILD-TYPE
  N0             1             194
  N1             3             170
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1235V6, binary
                 cls
clus                0   1
  GSDMB MUTATED     3   1
  GSDMB WILD-TYPE 479  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMB MUTATED      3    1
  GSDMB WILD-TYPE  479   37
   clus
vv  GSDMB MUTATED GSDMB WILD-TYPE
  0             3             479
  1             1              37
[1] 2 2
[1] FALSE
D1235V7, binary
                 cls
clus                0   1
  GSDMB MUTATED     2   3
  GSDMB WILD-TYPE 170 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMB MUTATED      2    3
  GSDMB WILD-TYPE  170  403
        clus
vv       GSDMB MUTATED GSDMB WILD-TYPE
  FEMALE             2             170
  MALE               3             403
[1] 2 2
[1] FALSE
D1235V8, binary
                 cls
clus                0   1
  GSDMB MUTATED     4   1
  GSDMB WILD-TYPE 412 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMB MUTATED      4    1
  GSDMB WILD-TYPE  412  101
     clus
vv    GSDMB MUTATED GSDMB WILD-TYPE
  NO              4             412
  YES             1             101
[1] 2 2
[1] FALSE
D1235V9, continuous
D1235V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GSDMB MUTATED       3                         0
  GSDMB WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GSDMB MUTATED                                           0     2
  GSDMB WILD-TYPE                                         1   355
D1235V11, multiclass
                                           clus
vv                                          GSDMB MUTATED GSDMB WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1235V12, binary
                 cls
clus                0   1
  GSDMB MUTATED     0   5
  GSDMB WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSDMB MUTATED      0    5
  GSDMB WILD-TYPE   10  393
                        clus
vv                       GSDMB MUTATED GSDMB WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1236) Variable = PPP1R12C MUTATION ANALYSIS
D1236V1, survival
                    sevent
clus2                  0   1
  PPP1R12C MUTATED     5   4
  PPP1R12C WILD-TYPE 333 212
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 9                545 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 4                212 
$`PPP1R12C MUTATED`
TCGA-L5-A4OE TCGA-L5-A4OX TCGA-BR-7703 TCGA-BR-8487 TCGA-BR-8680 TCGA-D7-A6EY 
       24.00         7.43        36.16         1.12        31.96        11.44 
TCGA-HU-A4G8 TCGA-VQ-A8P2 TCGA-VQ-AA6I 
       22.68        38.14        16.14 

$`PPP1R12C WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
              1.12               0.00 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             38.14             122.30 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             22.68              13.51 
[1] "1.1 - 38.1 (22.7)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1236V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R12C MUTATED         0        1        0        0         1         3
  PPP1R12C WILD-TYPE      10       19       46       31        83        80
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12C MUTATED           0          2          3          0        1
  PPP1R12C WILD-TYPE        29         82         59         39       42
                    vv
clus                 STAGE IVA
  PPP1R12C MUTATED           0
  PPP1R12C WILD-TYPE         4
D1236V3, multiclass
            clus
vv           PPP1R12C MUTATED PPP1R12C WILD-TYPE
  STAGE I                   0                 10
  STAGE IA                  1                 19
  STAGE IB                  0                 46
  STAGE II                  0                 31
  STAGE IIA                 1                 83
  STAGE IIB                 3                 80
  STAGE III                 0                 29
  STAGE IIIA                2                 82
  STAGE IIIB                3                 59
  STAGE IIIC                0                 39
  STAGE IV                  1                 42
  STAGE IVA                 0                  4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  PPP1R12C MUTATED       1   1   5   4
  PPP1R12C WILD-TYPE    53 134 256  98
D1236V4, multiclass
       clus
vv      PPP1R12C MUTATED PPP1R12C WILD-TYPE
  T0+T1                1                 53
  T2                   1                134
  T3                   5                256
  T4                   4                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  PPP1R12C MUTATED     4   3   2   2
  PPP1R12C WILD-TYPE 191 170  87  83
D1236V5, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  N0                4                191
  N1                3                170
  N2                2                 87
  N3                2                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1236V6, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     9   1
  PPP1R12C WILD-TYPE 473  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      9    1
  PPP1R12C WILD-TYPE  473   37
   clus
vv  PPP1R12C MUTATED PPP1R12C WILD-TYPE
  0                9                473
  1                1                 37
[1] 2 2
[1] FALSE
D1236V7, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     4   7
  PPP1R12C WILD-TYPE 168 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      4    7
  PPP1R12C WILD-TYPE  168  399
        clus
vv       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  FEMALE                4                168
  MALE                  7                399
[1] 2 2
[1] FALSE
D1236V8, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     9   1
  PPP1R12C WILD-TYPE 407 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      9    1
  PPP1R12C WILD-TYPE  407  101
     clus
vv    PPP1R12C MUTATED PPP1R12C WILD-TYPE
  NO                 9                407
  YES                1                101
[1] 2 2
[1] FALSE
D1236V9, continuous
D1236V10, continuous
[1] "Remove cluster labels:" "PPP1R12C MUTATED"      
clus
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 2                 96 
        TCGA-IC-A6RF         TCGA-L5-A43I         TCGA-L5-A43J 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A4OG         TCGA-L5-A4OI         TCGA-L5-A88T 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A88Y         TCGA-L5-A8NG         TCGA-L5-A8NT 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-Q9-A6FU         TCGA-IC-A6RE         TCGA-IG-A3QL 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IG-A3Y9         TCGA-IG-A3YA         TCGA-IG-A3YC 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IG-A4P3         TCGA-IG-A4QT         TCGA-IG-A50L 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IG-A5B8         TCGA-IG-A6QS         TCGA-IG-A8O2 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IG-A97H         TCGA-JY-A6FA         TCGA-JY-A6FE 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-JY-A6FG         TCGA-JY-A6FH         TCGA-KH-A6WC 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A43C         TCGA-L5-A43E         TCGA-L5-A43H 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A4OH         TCGA-L5-A4OM         TCGA-L5-A4ON 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A4OO         TCGA-L5-A4OP         TCGA-L5-A4OQ 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A4OT         TCGA-L5-A4OU         TCGA-L5-A4OW 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A88S         TCGA-L5-A88V         TCGA-L5-A893 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A8NE         TCGA-L5-A8NF         TCGA-L5-A8NK 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A8NN         TCGA-L5-A8NQ         TCGA-L5-A8NR 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-L5-A8NS         TCGA-L5-A8NW         TCGA-LN-A49O 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A49P         TCGA-LN-A49R         TCGA-LN-A49S 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A49U         TCGA-LN-A49V         TCGA-LN-A49W 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A4A3         TCGA-LN-A4A6         TCGA-LN-A4A9 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A5U6         TCGA-LN-A5U7         TCGA-LN-A7HV 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A7HW         TCGA-LN-A7HX         TCGA-LN-A7HZ 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LN-A8HZ         TCGA-LN-A8I0         TCGA-M9-A5M8 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-Q9-A6FW         TCGA-R6-A6DN         TCGA-R6-A6L4 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-R6-A6XQ         TCGA-R6-A6Y2         TCGA-R6-A8W5 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-R6-A8W8         TCGA-R6-A8WC         TCGA-RE-A7BO 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-V5-A7RB         TCGA-V5-A7RC         TCGA-V5-AASV 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-VR-A8EP         TCGA-VR-A8ER         TCGA-VR-A8EU 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-VR-A8EW         TCGA-VR-A8EX         TCGA-VR-A8EZ 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-VR-A8Q7         TCGA-VR-AA4G         TCGA-VR-AA7D 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-VR-AA7I         TCGA-X8-AAAR         TCGA-XP-A8T6 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-XP-A8T7         TCGA-XP-A8T8         TCGA-Z6-AAPN 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R12C MUTATED       2                         0
  PPP1R12C WILD-TYPE   131                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R12C MUTATED                                           0     9
  PPP1R12C WILD-TYPE                                         1   348
D1236V11, multiclass
                                           clus
vv                                          PPP1R12C MUTATED PPP1R12C WILD-TYPE
  ASIAN                                                    2                131
  BLACK OR AFRICAN AMERICAN                                0                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1236V12, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     0   7
  PPP1R12C WILD-TYPE  10 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      0    7
  PPP1R12C WILD-TYPE   10  391
                        clus
vv                       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO                7                391
[1] 2 2
[1] FALSE

Clustering(1237) Variable = PELI2 MUTATION ANALYSIS
D1237V1, survival
                 sevent
clus2               0   1
  PELI2 MUTATED     7   3
  PELI2 WILD-TYPE 331 213
  PELI2 MUTATED PELI2 WILD-TYPE 
             10             544 
  PELI2 MUTATED PELI2 WILD-TYPE 
              3             213 
$`PELI2 MUTATED`
TCGA-2H-A9GK TCGA-LN-A49P TCGA-LN-A9FQ TCGA-BR-4256 TCGA-BR-8360 TCGA-BR-8361 
        7.63        12.33        12.85         9.34         6.18        31.10 
TCGA-CG-4437 TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A4Z0 
        8.05        28.96        13.78        14.76 

$`PELI2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20         7.40         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PELI2 MUTATED PELI2 WILD-TYPE 
           6.18            0.00 
  PELI2 MUTATED PELI2 WILD-TYPE 
           31.1           122.3 
  PELI2 MUTATED PELI2 WILD-TYPE 
          12.59           13.63 
[1] "6.2 - 31.1 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1237V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PELI2 MUTATED         0        1        0        1         3         1
  PELI2 WILD-TYPE      10       19       46       30        81        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PELI2 MUTATED           1          0          1          1        0         0
  PELI2 WILD-TYPE        28         84         61         38       43         4
D1237V3, multiclass
            clus
vv           PELI2 MUTATED PELI2 WILD-TYPE
  STAGE I                0              10
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              3              81
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PELI2 MUTATED       1   2   5   1
  PELI2 WILD-TYPE    53 133 256 101
D1237V4, multiclass
       clus
vv      PELI2 MUTATED PELI2 WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                5             256
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PELI2 MUTATED     4   3   2   1
  PELI2 WILD-TYPE 191 170  87  84
D1237V5, multiclass
    clus
vv   PELI2 MUTATED PELI2 WILD-TYPE
  N0             4             191
  N1             3             170
  N2             2              87
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1237V6, binary
                 cls
clus                0   1
  PELI2 MUTATED    11   0
  PELI2 WILD-TYPE 471  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PELI2 MUTATED     11    0
  PELI2 WILD-TYPE  471   38
   clus
vv  PELI2 MUTATED PELI2 WILD-TYPE
  0            11             471
  1             0              38
[1] 2 2
[1] FALSE
D1237V7, binary
                 cls
clus                0   1
  PELI2 MUTATED     3   8
  PELI2 WILD-TYPE 169 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PELI2 MUTATED      3    8
  PELI2 WILD-TYPE  169  398
        clus
vv       PELI2 MUTATED PELI2 WILD-TYPE
  FEMALE             3             169
  MALE               8             398
[1] 2 2
[1] FALSE
D1237V8, binary
                 cls
clus                0   1
  PELI2 MUTATED     6   3
  PELI2 WILD-TYPE 410  99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PELI2 MUTATED      6    3
  PELI2 WILD-TYPE  410   99
     clus
vv    PELI2 MUTATED PELI2 WILD-TYPE
  NO              6             410
  YES             3              99
[1] 2 2
[1] FALSE
D1237V9, continuous
[1] "Remove cluster labels:" "PELI2 MUTATED"         
clus
  PELI2 MUTATED PELI2 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49R 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V      TCGA-LN-A49W 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
D1237V10, continuous
[1] "Remove cluster labels:" "PELI2 MUTATED"         
clus
  PELI2 MUTATED PELI2 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" "PELI2 WILD-TYPE" 
     TCGA-Z6-AAPN 
"PELI2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PELI2 MUTATED       2                         0
  PELI2 WILD-TYPE   131                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PELI2 MUTATED                                           0     6
  PELI2 WILD-TYPE                                         1   351
D1237V11, multiclass
                                           clus
vv                                          PELI2 MUTATED PELI2 WILD-TYPE
  ASIAN                                                 2             131
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1237V12, binary
                 cls
clus                0   1
  PELI2 MUTATED     0   8
  PELI2 WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PELI2 MUTATED      0    8
  PELI2 WILD-TYPE   10  390
                        clus
vv                       PELI2 MUTATED PELI2 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1238) Variable = UNC93B1 MUTATION ANALYSIS
D1238V1, survival
                   sevent
clus2                 0   1
  UNC93B1 MUTATED     5   4
  UNC93B1 WILD-TYPE 333 212
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                9               545 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                4               212 
$`UNC93B1 MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-IG-A3YA TCGA-L5-A8NL TCGA-R6-A6DQ TCGA-B7-A5TI 
       18.28         4.31        20.78        13.22         7.59        19.56 
TCGA-BR-8372 TCGA-CG-5733 TCGA-D7-5578 
       31.27        21.07        12.66 

$`UNC93B1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
             4.31              0.00 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            31.27            122.30 
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
            18.28             13.55 
[1] "4.3 - 31.3 (18.3)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1238V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UNC93B1 MUTATED         0        0        0        0         0         1
  UNC93B1 WILD-TYPE      10       20       46       31        84        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UNC93B1 MUTATED           1          4          0          2        0
  UNC93B1 WILD-TYPE        28         80         62         37       43
                   vv
clus                STAGE IVA
  UNC93B1 MUTATED           0
  UNC93B1 WILD-TYPE         4
D1238V3, multiclass
            clus
vv           UNC93B1 MUTATED UNC93B1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 0                46
  STAGE II                 0                31
  STAGE IIA                0                84
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               4                80
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  UNC93B1 MUTATED       0   1   4   3
  UNC93B1 WILD-TYPE    54 134 257  99
D1238V4, multiclass
       clus
vv      UNC93B1 MUTATED UNC93B1 WILD-TYPE
  T0+T1               0                54
  T2                  1               134
  T3                  4               257
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  UNC93B1 MUTATED     2   2   2   2
  UNC93B1 WILD-TYPE 193 171  87  83
D1238V5, multiclass
    clus
vv   UNC93B1 MUTATED UNC93B1 WILD-TYPE
  N0               2               193
  N1               2               171
  N2               2                87
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1238V6, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     6   0
  UNC93B1 WILD-TYPE 476  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      6    0
  UNC93B1 WILD-TYPE  476   38
   clus
vv  UNC93B1 MUTATED UNC93B1 WILD-TYPE
  0               6               476
  1               0                38
[1] 2 2
[1] FALSE
D1238V7, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     2   7
  UNC93B1 WILD-TYPE 170 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      2    7
  UNC93B1 WILD-TYPE  170  399
        clus
vv       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  FEMALE               2               170
  MALE                 7               399
[1] 2 2
[1] FALSE
D1238V8, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     5   1
  UNC93B1 WILD-TYPE 411 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      5    1
  UNC93B1 WILD-TYPE  411  101
     clus
vv    UNC93B1 MUTATED UNC93B1 WILD-TYPE
  NO                5               411
  YES               1               101
[1] 2 2
[1] FALSE
D1238V9, continuous
[1] "Remove cluster labels:" "UNC93B1 MUTATED"       
clus
  UNC93B1 MUTATED UNC93B1 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YB 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3        TCGA-IG-A7DP 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L        TCGA-LN-A49M 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1        TCGA-LN-A4A2 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5        TCGA-LN-A4A6 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" "UNC93B1 WILD-TYPE" 
D1238V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  UNC93B1 MUTATED       0                         0
  UNC93B1 WILD-TYPE   133                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UNC93B1 MUTATED                                           0     8
  UNC93B1 WILD-TYPE                                         1   349
D1238V11, multiclass
                                           clus
vv                                          UNC93B1 MUTATED UNC93B1 WILD-TYPE
  ASIAN                                                   0               133
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1238V12, binary
                   cls
clus                  0   1
  UNC93B1 MUTATED     0   5
  UNC93B1 WILD-TYPE  10 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UNC93B1 MUTATED      0    5
  UNC93B1 WILD-TYPE   10  393
                        clus
vv                       UNC93B1 MUTATED UNC93B1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               5               393
[1] 2 2
[1] FALSE

Clustering(1239) Variable = PRKCD MUTATION ANALYSIS
D1239V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED     7   4
  PRKCD WILD-TYPE 331 212
  PRKCD MUTATED PRKCD WILD-TYPE 
             11             543 
  PRKCD MUTATED PRKCD WILD-TYPE 
              4             212 
$`PRKCD MUTATED`
TCGA-CG-4460 TCGA-JY-A93C TCGA-VR-A8EQ TCGA-BR-4184 TCGA-BR-8680 TCGA-BR-A4QL 
       21.99        23.18        22.82         6.97        31.96        16.14 
TCGA-FP-7829 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HU-A4GN TCGA-VQ-A8P2 
       19.53         6.21        77.29        29.98        38.14 

$`PRKCD WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        20.02        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.52        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PRKCD MUTATED PRKCD WILD-TYPE 
           6.21            0.00 
  PRKCD MUTATED PRKCD WILD-TYPE 
          77.29          122.30 
  PRKCD MUTATED PRKCD WILD-TYPE 
          22.82           13.48 
[1] "6.2 - 77.3 (22.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1239V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRKCD MUTATED         0        0        0        1         1         1
  PRKCD WILD-TYPE      10       20       46       30        83        82
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCD MUTATED           1          2          2          0        3         0
  PRKCD WILD-TYPE        28         82         60         39       40         4
D1239V3, multiclass
            clus
vv           PRKCD MUTATED PRKCD WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              1              83
  STAGE IIB              1              82
  STAGE III              1              28
  STAGE IIIA             2              82
  STAGE IIIB             2              60
  STAGE IIIC             0              39
  STAGE IV               3              40
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  PRKCD MUTATED       1   2   5   4
  PRKCD WILD-TYPE    53 133 256  98
D1239V4, multiclass
       clus
vv      PRKCD MUTATED PRKCD WILD-TYPE
  T0+T1             1              53
  T2                2             133
  T3                5             256
  T4                4              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  PRKCD MUTATED     0   8   3   1
  PRKCD WILD-TYPE 195 165  86  84
D1239V5, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  N0             0             195
  N1             8             165
  N2             3              86
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1239V6, binary
                 cls
clus                0   1
  PRKCD MUTATED     9   2
  PRKCD WILD-TYPE 473  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      9    2
  PRKCD WILD-TYPE  473   36
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0             9             473
  1             2              36
[1] 2 2
[1] FALSE
D1239V7, binary
                 cls
clus                0   1
  PRKCD MUTATED     3   9
  PRKCD WILD-TYPE 169 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      3    9
  PRKCD WILD-TYPE  169  397
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             3             169
  MALE               9             397
[1] 2 2
[1] FALSE
D1239V8, binary
                 cls
clus                0   1
  PRKCD MUTATED     6   5
  PRKCD WILD-TYPE 410  97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      6    5
  PRKCD WILD-TYPE  410   97
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO              6             410
  YES             5              97
[1] 2 2
[1] FALSE
D1239V9, continuous
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
D1239V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRKCD MUTATED       3                         0
  PRKCD WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRKCD MUTATED                                           0     7
  PRKCD WILD-TYPE                                         1   350
D1239V11, multiclass
                                           clus
vv                                          PRKCD MUTATED PRKCD WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1239V12, binary
                 cls
clus                0   1
  PRKCD MUTATED     0   7
  PRKCD WILD-TYPE  10 391
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      0    7
  PRKCD WILD-TYPE   10  391
                        clus
vv                       PRKCD MUTATED PRKCD WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             7             391
[1] 2 2
[1] FALSE

Clustering(1240) Variable = TESK1 MUTATION ANALYSIS
D1240V1, survival
                 sevent
clus2               0   1
  TESK1 MUTATED     7   5
  TESK1 WILD-TYPE 331 211
  TESK1 MUTATED TESK1 WILD-TYPE 
             12             542 
  TESK1 MUTATED TESK1 WILD-TYPE 
              5             211 
$`TESK1 MUTATED`
TCGA-LN-A7HY TCGA-BR-6452 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5723 
       12.03        34.68         1.12         6.58         9.01       105.07 
TCGA-CG-5733 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ 
       21.07        11.44        21.27        24.20        29.98         0.10 

$`TESK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43        11.61        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        24.26        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT 
       22.75        25.81        11.77        21.37         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  TESK1 MUTATED TESK1 WILD-TYPE 
            0.1             0.0 
  TESK1 MUTATED TESK1 WILD-TYPE 
         105.07          122.30 
  TESK1 MUTATED TESK1 WILD-TYPE 
         16.550          13.565 
[1] "0.1 - 105.1 (16.6)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1240V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TESK1 MUTATED         1        1        0        1         4         0
  TESK1 WILD-TYPE       9       19       46       30        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TESK1 MUTATED           1          1          2          1        1         0
  TESK1 WILD-TYPE        28         83         60         38       42         4
D1240V3, multiclass
            clus
vv           TESK1 MUTATED TESK1 WILD-TYPE
  STAGE I                1               9
  STAGE IA               1              19
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              1              28
  STAGE IIIA             1              83
  STAGE IIIB             2              60
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  TESK1 MUTATED       2   3   6   2
  TESK1 WILD-TYPE    52 132 255 100
D1240V4, multiclass
       clus
vv      TESK1 MUTATED TESK1 WILD-TYPE
  T0+T1             2              52
  T2                3             132
  T3                6             255
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  TESK1 MUTATED     4   4   2   3
  TESK1 WILD-TYPE 191 169  87  82
D1240V5, multiclass
    clus
vv   TESK1 MUTATED TESK1 WILD-TYPE
  N0             4             191
  N1             4             169
  N2             2              87
  N3             3              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1240V6, binary
                 cls
clus                0   1
  TESK1 MUTATED    11   1
  TESK1 WILD-TYPE 471  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED     11    1
  TESK1 WILD-TYPE  471   37
   clus
vv  TESK1 MUTATED TESK1 WILD-TYPE
  0            11             471
  1             1              37
[1] 2 2
[1] FALSE
D1240V7, binary
                 cls
clus                0   1
  TESK1 MUTATED     6   7
  TESK1 WILD-TYPE 166 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      6    7
  TESK1 WILD-TYPE  166  399
        clus
vv       TESK1 MUTATED TESK1 WILD-TYPE
  FEMALE             6             166
  MALE               7             399
[1] 2 2
[1] FALSE
D1240V8, binary
                 cls
clus                0   1
  TESK1 MUTATED    11   1
  TESK1 WILD-TYPE 405 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED     11    1
  TESK1 WILD-TYPE  405  101
     clus
vv    TESK1 MUTATED TESK1 WILD-TYPE
  NO             11             405
  YES             1             101
[1] 2 2
[1] FALSE
D1240V9, continuous
[1] "Remove cluster labels:" "TESK1 MUTATED"         
clus
  TESK1 MUTATED TESK1 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"TESK1 WILD-TYPE" "TESK1 WILD-TYPE" "TESK1 WILD-TYPE" 
D1240V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TESK1 MUTATED       5                         1
  TESK1 WILD-TYPE   128                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TESK1 MUTATED                                           0     4
  TESK1 WILD-TYPE                                         1   353
D1240V11, multiclass
                                           clus
vv                                          TESK1 MUTATED TESK1 WILD-TYPE
  ASIAN                                                 5             128
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1240V12, binary
                 cls
clus                0   1
  TESK1 MUTATED     1   9
  TESK1 WILD-TYPE   9 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      1    9
  TESK1 WILD-TYPE    9  389
                        clus
vv                       TESK1 MUTATED TESK1 WILD-TYPE
  HISPANIC OR LATINO                 1               9
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1241) Variable = GLTPD1 MUTATION ANALYSIS
D1241V1, survival
                  sevent
clus2                0   1
  GLTPD1 MUTATED     2   2
  GLTPD1 WILD-TYPE 336 214
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              550 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               2              214 
$`GLTPD1 MUTATED`
TCGA-CG-5721 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4GQ 
        6.02        21.07        22.32         0.10 

$`GLTPD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
             0.1              0.0 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
           22.32           122.30 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
          13.545           13.565 
[1] "0.1 - 22.3 (13.5)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.8"
D1241V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLTPD1 MUTATED         0        0        0        0         0         1
  GLTPD1 WILD-TYPE      10       20       46       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTPD1 MUTATED           0          1          0          1        1
  GLTPD1 WILD-TYPE        29         83         62         38       42
                  vv
clus               STAGE IVA
  GLTPD1 MUTATED           0
  GLTPD1 WILD-TYPE         4
D1241V3, multiclass
            clus
vv           GLTPD1 MUTATED GLTPD1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GLTPD1 MUTATED       0   1   0   3
  GLTPD1 WILD-TYPE    54 134 261  99
D1241V4, multiclass
       clus
vv      GLTPD1 MUTATED GLTPD1 WILD-TYPE
  T0+T1              0               54
  T2                 1              134
  T3                 0              261
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GLTPD1 MUTATED     1   1   2   0
  GLTPD1 WILD-TYPE 194 172  87  85
D1241V5, multiclass
    clus
vv   GLTPD1 MUTATED GLTPD1 WILD-TYPE
  N0              1              194
  N1              1              172
  N2              2               87
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1241V6, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     4   0
  GLTPD1 WILD-TYPE 478  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      4    0
  GLTPD1 WILD-TYPE  478   38
   clus
vv  GLTPD1 MUTATED GLTPD1 WILD-TYPE
  0              4              478
  1              0               38
[1] 2 2
[1] FALSE
D1241V7, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     2   2
  GLTPD1 WILD-TYPE 170 404
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      2    2
  GLTPD1 WILD-TYPE  170  404
        clus
vv       GLTPD1 MUTATED GLTPD1 WILD-TYPE
  FEMALE              2              170
  MALE                2              404
[1] 2 2
[1] FALSE
D1241V8, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     4   0
  GLTPD1 WILD-TYPE 412 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      4    0
  GLTPD1 WILD-TYPE  412  102
     clus
vv    GLTPD1 MUTATED GLTPD1 WILD-TYPE
  NO               4              412
  YES              0              102
[1] 2 2
[1] FALSE
D1241V9, continuous
D1241V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLTPD1 MUTATED       2                         0
  GLTPD1 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLTPD1 MUTATED                                           0     0
  GLTPD1 WILD-TYPE                                         1   357
D1241V11, multiclass
[1] "Remove cluster labels:" "GLTPD1 MUTATED"        
clus
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               2              503 
      TCGA-IC-A6RF       TCGA-JY-A6FB       TCGA-JY-A938       TCGA-L5-A43I 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A43J       TCGA-L5-A4OE       TCGA-L5-A4OG       TCGA-L5-A4OI 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A88T       TCGA-L5-A88Y       TCGA-L5-A8NG       TCGA-L5-A8NT 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-Q9-A6FU       TCGA-S8-A6BV       TCGA-EQ-A4SO       TCGA-F1-6177 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-KB-A93G       TCGA-MX-A663       TCGA-IC-A6RE 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A4P3       TCGA-IG-A4QS 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A51D       TCGA-IG-A5B8 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IG-A5S3       TCGA-IG-A625       TCGA-IG-A6QS       TCGA-IG-A7DP 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-IG-A97I       TCGA-JY-A6F8 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-JY-A6FA       TCGA-JY-A6FD       TCGA-JY-A6FE       TCGA-JY-A6FG 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-JY-A6FH       TCGA-JY-A939       TCGA-JY-A93C       TCGA-JY-A93D 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-JY-A93E       TCGA-JY-A93F       TCGA-KH-A6WC       TCGA-L5-A43C 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OF       TCGA-L5-A4OH 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A4OJ       TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A4OP       TCGA-L5-A4OQ       TCGA-L5-A4OR       TCGA-L5-A4OS 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OX       TCGA-L5-A88S 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A88V       TCGA-L5-A88W       TCGA-L5-A88Z       TCGA-L5-A891 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A893       TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NH 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A8NI       TCGA-L5-A8NJ       TCGA-L5-A8NK       TCGA-L5-A8NL 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A8NM       TCGA-L5-A8NN       TCGA-L5-A8NQ       TCGA-L5-A8NS 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L5-A8NU       TCGA-L5-A8NV       TCGA-L5-A8NW       TCGA-L7-A56G 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-L7-A6VZ       TCGA-LN-A49K       TCGA-LN-A49L       TCGA-LN-A49M 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1       TCGA-LN-A4A2 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5       TCGA-LN-A4A6 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-LN-A8I1       TCGA-LN-A9FO 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-LN-A9FP       TCGA-LN-A9FQ       TCGA-LN-A9FR       TCGA-Q9-A6FW 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6DQ       TCGA-R6-A6KZ       TCGA-R6-A6L4 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R6-A6L6       TCGA-R6-A6XG       TCGA-R6-A6XQ       TCGA-R6-A6Y0 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R6-A8WG       TCGA-RE-A7BO       TCGA-S8-A6BW       TCGA-V5-A7RC 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-V5-A7RE       TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VR-A8EO       TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ET 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE       TCGA-Z6-A9VB 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-Z6-AAPN       TCGA-ZR-A9CJ       TCGA-B7-5816       TCGA-B7-5818 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-B7-A5TI       TCGA-B7-A5TJ       TCGA-B7-A5TK       TCGA-B7-A5TN 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4187       TCGA-BR-4188 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4201       TCGA-BR-4253       TCGA-BR-4255 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4256       TCGA-BR-4257       TCGA-BR-4267       TCGA-BR-4279 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4292       TCGA-BR-4294       TCGA-BR-4357 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4363       TCGA-BR-4366 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4368       TCGA-BR-4369       TCGA-BR-4370       TCGA-BR-4371 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6452       TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-5804       TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A6ET       TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A6EZ       TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A748       TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-EQ-8122       TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-F1-A72C       TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-A9TM       TCGA-HJ-7597       TCGA-HU-8238       TCGA-HU-8243 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8604       TCGA-HU-8608 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4GP       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-KB-A93J       TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-MX-A666 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R5-A7O7       TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R5-A7ZR       TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A7BT       TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A8MW       TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A8N4       TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-SW-A7EA       TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DU 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91U       TCGA-VQ-A92D 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA64       TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA6B       TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA6J       TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
D1241V12, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     0   2
  GLTPD1 WILD-TYPE  10 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      0    2
  GLTPD1 WILD-TYPE   10  396
                        clus
vv                       GLTPD1 MUTATED GLTPD1 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              2              396
[1] 2 2
[1] FALSE

Clustering(1242) Variable = ST8SIA6 MUTATION ANALYSIS
D1242V1, survival
                   sevent
clus2                 0   1
  ST8SIA6 MUTATED     6   2
  ST8SIA6 WILD-TYPE 332 214
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                8               546 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                2               214 
$`ST8SIA6 MUTATED`
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8372 TCGA-BR-8486 TCGA-HF-A5NB 
       32.78        35.84        14.43        31.27        20.22        30.51 
TCGA-HU-A4GN TCGA-HU-A4GQ 
       29.98         0.10 

$`ST8SIA6 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       52.21        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
              0.1               0.0 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
            35.84            122.30 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           30.245            13.495 
[1] "0.1 - 35.8 (30.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D1242V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ST8SIA6 MUTATED         0        2        2        0         2         0
  ST8SIA6 WILD-TYPE      10       18       44       31        82        83
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST8SIA6 MUTATED           1          0          0          3        0
  ST8SIA6 WILD-TYPE        28         84         62         36       43
                   vv
clus                STAGE IVA
  ST8SIA6 MUTATED           0
  ST8SIA6 WILD-TYPE         4
D1242V3, multiclass
            clus
vv           ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 2                18
  STAGE IB                 2                44
  STAGE II                 0                31
  STAGE IIA                2                82
  STAGE IIB                0                83
  STAGE III                1                28
  STAGE IIIA               0                84
  STAGE IIIB               0                62
  STAGE IIIC               3                36
  STAGE IV                 0                43
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  ST8SIA6 MUTATED       2   3   1   4
  ST8SIA6 WILD-TYPE    52 132 260  98
D1242V4, multiclass
       clus
vv      ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  T0+T1               2                52
  T2                  3               132
  T3                  1               260
  T4                  4                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  ST8SIA6 MUTATED     5   2   1   2
  ST8SIA6 WILD-TYPE 190 171  88  83
D1242V5, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  N0               5               190
  N1               2               171
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1242V6, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     9   0
  ST8SIA6 WILD-TYPE 473  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      9    0
  ST8SIA6 WILD-TYPE  473   38
   clus
vv  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  0               9               473
  1               0                38
[1] 2 2
[1] FALSE
D1242V7, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     5   5
  ST8SIA6 WILD-TYPE 167 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      5    5
  ST8SIA6 WILD-TYPE  167  401
        clus
vv       ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  FEMALE               5               167
  MALE                 5               401
[1] 2 2
[1] FALSE
D1242V8, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     7   3
  ST8SIA6 WILD-TYPE 409  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      7    3
  ST8SIA6 WILD-TYPE  409   99
     clus
vv    ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  NO                7               409
  YES               3                99
[1] 2 2
[1] FALSE
D1242V9, continuous
D1242V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ST8SIA6 MUTATED       3                         0
  ST8SIA6 WILD-TYPE   130                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ST8SIA6 MUTATED                                           0     5
  ST8SIA6 WILD-TYPE                                         1   352
D1242V11, multiclass
                                           clus
vv                                          ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  ASIAN                                                   3               130
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1242V12, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     0   8
  ST8SIA6 WILD-TYPE  10 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      0    8
  ST8SIA6 WILD-TYPE   10  390
                        clus
vv                       ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               8               390
[1] 2 2
[1] FALSE

Clustering(1243) Variable = ATP11B MUTATION ANALYSIS
D1243V1, survival
                  sevent
clus2                0   1
  ATP11B MUTATED     9   4
  ATP11B WILD-TYPE 329 212
  ATP11B MUTATED ATP11B WILD-TYPE 
              13              541 
  ATP11B MUTATED ATP11B WILD-TYPE 
               4              212 
$`ATP11B MUTATED`
TCGA-2H-A9GI TCGA-VR-AA7I TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8680 TCGA-CG-5721 
       14.30        15.91        34.68        31.10        31.96         6.02 
TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-IN-8663 
      105.07        22.32        24.20         0.10        20.25         3.39 
TCGA-MX-A666 
       14.04 

$`ATP11B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       20.05        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 
        2.66        19.96         2.20         7.40         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
        6.97        36.00         1.02         0.99         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  ATP11B MUTATED ATP11B WILD-TYPE 
             0.1              0.0 
  ATP11B MUTATED ATP11B WILD-TYPE 
          105.07           122.30 
  ATP11B MUTATED ATP11B WILD-TYPE 
           20.25            13.48 
[1] "0.1 - 105.1 (20.2)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1243V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP11B MUTATED         0        1        0        1         2         2
  ATP11B WILD-TYPE      10       19       46       30        82        81
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11B MUTATED           2          0          0          3        2
  ATP11B WILD-TYPE        27         84         62         36       41
                  vv
clus               STAGE IVA
  ATP11B MUTATED           0
  ATP11B WILD-TYPE         4
D1243V3, multiclass
            clus
vv           ATP11B MUTATED ATP11B WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               2               82
  STAGE IIB               2               81
  STAGE III               2               27
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              3               36
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ATP11B MUTATED       1   3   2   7
  ATP11B WILD-TYPE    53 132 259  95
D1243V4, multiclass
       clus
vv      ATP11B MUTATED ATP11B WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 2              259
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ATP11B MUTATED     4   3   5   0
  ATP11B WILD-TYPE 191 170  84  85
D1243V5, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  N0              4              191
  N1              3              170
  N2              5               84
  N3              0               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1243V6, binary
                  cls
clus                 0   1
  ATP11B MUTATED    11   1
  ATP11B WILD-TYPE 471  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     11    1
  ATP11B WILD-TYPE  471   37
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0             11              471
  1              1               37
[1] 2 2
[1] FALSE
D1243V7, binary
                  cls
clus                 0   1
  ATP11B MUTATED     5   8
  ATP11B WILD-TYPE 167 398
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      5    8
  ATP11B WILD-TYPE  167  398
        clus
vv       ATP11B MUTATED ATP11B WILD-TYPE
  FEMALE              5              167
  MALE                8              398
[1] 2 2
[1] FALSE
D1243V8, binary
                  cls
clus                 0   1
  ATP11B MUTATED    13   0
  ATP11B WILD-TYPE 403 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     13    0
  ATP11B WILD-TYPE  403  102
     clus
vv    ATP11B MUTATED ATP11B WILD-TYPE
  NO              13              403
  YES              0              102
[1] 2 2
[1] FALSE
D1243V9, continuous
[1] "Remove cluster labels:" "ATP11B MUTATED"        
clus
  ATP11B MUTATED ATP11B WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-V5-AASV       TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-A8EP       TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-AA7B       TCGA-VR-AA7D       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
D1243V10, continuous
[1] "Remove cluster labels:" "ATP11B MUTATED"        
clus
  ATP11B MUTATED ATP11B WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-L5-A8NQ       TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A49O       TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A49U       TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-LN-A8HZ       TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-R6-A6DN       TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-R6-A8W5       TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-VR-A8EZ       TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" "ATP11B WILD-TYPE" 
      TCGA-Z6-AAPN 
"ATP11B WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP11B MUTATED       5                         0
  ATP11B WILD-TYPE   128                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP11B MUTATED                                           0     5
  ATP11B WILD-TYPE                                         1   352
D1243V11, multiclass
                                           clus
vv                                          ATP11B MUTATED ATP11B WILD-TYPE
  ASIAN                                                  5              128
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1243V12, binary
                  cls
clus                 0   1
  ATP11B MUTATED     0   9
  ATP11B WILD-TYPE  10 389
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      0    9
  ATP11B WILD-TYPE   10  389
                        clus
vv                       ATP11B MUTATED ATP11B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              9              389
[1] 2 2
[1] FALSE

Clustering(1244) Variable = SRP68 MUTATION ANALYSIS
D1244V1, survival
                 sevent
clus2               0   1
  SRP68 MUTATED     4   4
  SRP68 WILD-TYPE 334 212
  SRP68 MUTATED SRP68 WILD-TYPE 
              8             546 
  SRP68 MUTATED SRP68 WILD-TYPE 
              4             212 
$`SRP68 MUTATED`
TCGA-R6-A8WG TCGA-VR-AA4D TCGA-BR-8363 TCGA-CD-8536 TCGA-HU-A4GQ TCGA-HU-A4GU 
       12.69        46.19         0.26        12.43         0.10         6.58 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`SRP68 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        33.70        18.18        52.27        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        8.52         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  SRP68 MUTATED SRP68 WILD-TYPE 
            0.1             0.0 
  SRP68 MUTATED SRP68 WILD-TYPE 
          74.53          122.30 
  SRP68 MUTATED SRP68 WILD-TYPE 
          12.56           13.63 
[1] "0.1 - 74.5 (12.6)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.3"
D1244V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRP68 MUTATED         0        0        2        1         0         2
  SRP68 WILD-TYPE      10       20       44       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRP68 MUTATED           0          0          0          1        1         0
  SRP68 WILD-TYPE        29         84         62         38       42         4
D1244V3, multiclass
            clus
vv           SRP68 MUTATED SRP68 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  SRP68 MUTATED       2   1   2   2
  SRP68 WILD-TYPE    52 134 259 100
D1244V4, multiclass
       clus
vv      SRP68 MUTATED SRP68 WILD-TYPE
  T0+T1             2              52
  T2                1             134
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  SRP68 MUTATED     2   4   1   0
  SRP68 WILD-TYPE 193 169  88  85
D1244V5, multiclass
    clus
vv   SRP68 MUTATED SRP68 WILD-TYPE
  N0             2             193
  N1             4             169
  N2             1              88
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1244V6, binary
                 cls
clus                0   1
  SRP68 MUTATED     6   1
  SRP68 WILD-TYPE 476  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP68 MUTATED      6    1
  SRP68 WILD-TYPE  476   37
   clus
vv  SRP68 MUTATED SRP68 WILD-TYPE
  0             6             476
  1             1              37
[1] 2 2
[1] FALSE
D1244V7, binary
                 cls
clus                0   1
  SRP68 MUTATED     2   6
  SRP68 WILD-TYPE 170 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP68 MUTATED      2    6
  SRP68 WILD-TYPE  170  400
        clus
vv       SRP68 MUTATED SRP68 WILD-TYPE
  FEMALE             2             170
  MALE               6             400
[1] 2 2
[1] FALSE
D1244V8, binary
                 cls
clus                0   1
  SRP68 MUTATED     7   1
  SRP68 WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP68 MUTATED      7    1
  SRP68 WILD-TYPE  409  101
     clus
vv    SRP68 MUTATED SRP68 WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D1244V9, continuous
[1] "Remove cluster labels:" "SRP68 MUTATED"         
clus
  SRP68 MUTATED SRP68 WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-LN-A7HZ      TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-V5-AASV      TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-VR-A8EP      TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-VR-A8EZ      TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7B 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"SRP68 WILD-TYPE" "SRP68 WILD-TYPE" "SRP68 WILD-TYPE" 
D1244V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SRP68 MUTATED       4                         0
  SRP68 WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRP68 MUTATED                                           0     4
  SRP68 WILD-TYPE                                         1   353
D1244V11, multiclass
                                           clus
vv                                          SRP68 MUTATED SRP68 WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1244V12, binary
                 cls
clus                0   1
  SRP68 MUTATED     2   5
  SRP68 WILD-TYPE   8 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP68 MUTATED      2    5
  SRP68 WILD-TYPE    8  393
                        clus
vv                       SRP68 MUTATED SRP68 WILD-TYPE
  HISPANIC OR LATINO                 2               8
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1245) Variable = ABCD1 MUTATION ANALYSIS
D1245V1, survival
                 sevent
clus2               0   1
  ABCD1 MUTATED     8   1
  ABCD1 WILD-TYPE 330 215
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              9             545 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
              1             215 
$`ABCD1 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8590 TCGA-BR-8680 TCGA-CD-5799 
       34.68        32.78        35.84         9.34        31.96        13.02 
TCGA-D7-6815 TCGA-HU-A4GU TCGA-VQ-A8P2 
       15.98         6.58        38.14 

$`ABCD1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10         9.17        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ABCD1 MUTATED ABCD1 WILD-TYPE 
           6.58            0.00 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
          38.14          122.30 
  ABCD1 MUTATED ABCD1 WILD-TYPE 
          31.96           13.51 
[1] "6.6 - 38.1 (32.0)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "4.8"
D1245V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCD1 MUTATED         0        0        1        1         2         2
  ABCD1 WILD-TYPE      10       20       45       30        82        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCD1 MUTATED           0          1          0          1        1         0
  ABCD1 WILD-TYPE        29         83         62         38       42         4
D1245V3, multiclass
            clus
vv           ABCD1 MUTATED ABCD1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               1              45
  STAGE II               1              30
  STAGE IIA              2              82
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  ABCD1 MUTATED       0   3   3   3
  ABCD1 WILD-TYPE    54 132 258  99
D1245V4, multiclass
       clus
vv      ABCD1 MUTATED ABCD1 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                3             258
  T4                3              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  ABCD1 MUTATED     3   3   3   0
  ABCD1 WILD-TYPE 192 170  86  85
D1245V5, multiclass
    clus
vv   ABCD1 MUTATED ABCD1 WILD-TYPE
  N0             3             192
  N1             3             170
  N2             3              86
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1245V6, binary
                 cls
clus                0   1
  ABCD1 MUTATED     9   1
  ABCD1 WILD-TYPE 473  37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      9    1
  ABCD1 WILD-TYPE  473   37
   clus
vv  ABCD1 MUTATED ABCD1 WILD-TYPE
  0             9             473
  1             1              37
[1] 2 2
[1] FALSE
D1245V7, binary
                 cls
clus                0   1
  ABCD1 MUTATED     5   5
  ABCD1 WILD-TYPE 167 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      5    5
  ABCD1 WILD-TYPE  167  401
        clus
vv       ABCD1 MUTATED ABCD1 WILD-TYPE
  FEMALE             5             167
  MALE               5             401
[1] 2 2
[1] FALSE
D1245V8, binary
                 cls
clus                0   1
  ABCD1 MUTATED     8   1
  ABCD1 WILD-TYPE 408 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      8    1
  ABCD1 WILD-TYPE  408  101
     clus
vv    ABCD1 MUTATED ABCD1 WILD-TYPE
  NO              8             408
  YES             1             101
[1] 2 2
[1] FALSE
D1245V9, continuous
D1245V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCD1 MUTATED       3                         0
  ABCD1 WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCD1 MUTATED                                           0     7
  ABCD1 WILD-TYPE                                         1   350
D1245V11, multiclass
                                           clus
vv                                          ABCD1 MUTATED ABCD1 WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1245V12, binary
                 cls
clus                0   1
  ABCD1 MUTATED     0   9
  ABCD1 WILD-TYPE  10 389
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD1 MUTATED      0    9
  ABCD1 WILD-TYPE   10  389
                        clus
vv                       ABCD1 MUTATED ABCD1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             9             389
[1] 2 2
[1] FALSE

Clustering(1246) Variable = MCTP1 MUTATION ANALYSIS
D1246V1, survival
                 sevent
clus2               0   1
  MCTP1 MUTATED     7   3
  MCTP1 WILD-TYPE 331 213
  MCTP1 MUTATED MCTP1 WILD-TYPE 
             10             544 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
              3             213 
$`MCTP1 MUTATED`
TCGA-L5-A4OI TCGA-L5-A8NM TCGA-BR-4184 TCGA-BR-8381 TCGA-CG-4466 TCGA-CG-5721 
       19.99         7.76         6.97         7.36        18.97         6.02 
TCGA-HU-A4GT TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA64 
        6.51        19.04        38.14        18.41 

$`MCTP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
       14.04         3.32        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       19.07        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         1.02         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.80        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        37.41        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  MCTP1 MUTATED MCTP1 WILD-TYPE 
           6.02            0.00 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
          38.14          122.30 
  MCTP1 MUTATED MCTP1 WILD-TYPE 
         13.085          13.565 
[1] "6.0 - 38.1 (13.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1246V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MCTP1 MUTATED         0        0        2        0         1         2
  MCTP1 WILD-TYPE      10       20       44       31        83        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCTP1 MUTATED           0          2          1          1        1         0
  MCTP1 WILD-TYPE        29         82         61         38       42         4
D1246V3, multiclass
            clus
vv           MCTP1 MUTATED MCTP1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              1              83
  STAGE IIB              2              81
  STAGE III              0              29
  STAGE IIIA             2              82
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               1              42
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  MCTP1 MUTATED       0   3   5   2
  MCTP1 WILD-TYPE    54 132 256 100
D1246V4, multiclass
       clus
vv      MCTP1 MUTATED MCTP1 WILD-TYPE
  T0+T1             0              54
  T2                3             132
  T3                5             256
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MCTP1 MUTATED     3   5   1   1
  MCTP1 WILD-TYPE 192 168  88  84
D1246V5, multiclass
    clus
vv   MCTP1 MUTATED MCTP1 WILD-TYPE
  N0             3             192
  N1             5             168
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1246V6, binary
                 cls
clus                0   1
  MCTP1 MUTATED     8   0
  MCTP1 WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      8    0
  MCTP1 WILD-TYPE  474   38
   clus
vv  MCTP1 MUTATED MCTP1 WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D1246V7, binary
                 cls
clus                0   1
  MCTP1 MUTATED     4   6
  MCTP1 WILD-TYPE 168 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      4    6
  MCTP1 WILD-TYPE  168  400
        clus
vv       MCTP1 MUTATED MCTP1 WILD-TYPE
  FEMALE             4             168
  MALE               6             400
[1] 2 2
[1] FALSE
D1246V8, binary
                 cls
clus                0   1
  MCTP1 MUTATED     8   2
  MCTP1 WILD-TYPE 408 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      8    2
  MCTP1 WILD-TYPE  408  100
     clus
vv    MCTP1 MUTATED MCTP1 WILD-TYPE
  NO              8             408
  YES             2             100
[1] 2 2
[1] FALSE
D1246V9, continuous
D1246V10, continuous
[1] "Remove cluster labels:" "MCTP1 MUTATED"         
clus
  MCTP1 MUTATED MCTP1 WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A88T      TCGA-L5-A88Y      TCGA-L5-A8NG 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE      TCGA-IG-A3QL 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC      TCGA-IG-A4P3 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8      TCGA-IG-A6QS 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA      TCGA-JY-A6FE 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC      TCGA-L5-A43C 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH      TCGA-L5-A4OM 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP      TCGA-L5-A4OQ 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW      TCGA-L5-A4OX 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893      TCGA-L5-A8NE 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN      TCGA-L5-A8NQ 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW      TCGA-LN-A49O 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" "MCTP1 WILD-TYPE" 
     TCGA-Z6-AAPN 
"MCTP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MCTP1 MUTATED       1                         0
  MCTP1 WILD-TYPE   132                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCTP1 MUTATED                                           0     7
  MCTP1 WILD-TYPE                                         1   350
D1246V11, multiclass
                                           clus
vv                                          MCTP1 MUTATED MCTP1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1246V12, binary
                 cls
clus                0   1
  MCTP1 MUTATED     0   4
  MCTP1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCTP1 MUTATED      0    4
  MCTP1 WILD-TYPE   10  394
                        clus
vv                       MCTP1 MUTATED MCTP1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1247) Variable = TCERG1 MUTATION ANALYSIS
D1247V1, survival
                  sevent
clus2                0   1
  TCERG1 MUTATED     7   4
  TCERG1 WILD-TYPE 331 212
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              11              543 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               4              212 
$`TCERG1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL 
       30.90        34.68         0.26        31.27        31.96        16.14 
TCGA-CG-5721 TCGA-CG-5726 TCGA-IN-8462 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        6.02        28.96        18.81        74.53        38.14 

$`TCERG1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TCERG1 MUTATED TCERG1 WILD-TYPE 
            0.26             0.00 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
           74.53           122.30 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
           30.90            13.48 
[1] "0.3 - 74.5 (30.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1247V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCERG1 MUTATED         0        1        1        0         1         1
  TCERG1 WILD-TYPE      10       19       45       31        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCERG1 MUTATED           0          1          1          1        3
  TCERG1 WILD-TYPE        29         83         61         38       40
                  vv
clus               STAGE IVA
  TCERG1 MUTATED           0
  TCERG1 WILD-TYPE         4
D1247V3, multiclass
            clus
vv           TCERG1 MUTATED TCERG1 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                0               31
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  TCERG1 MUTATED       1   3   3   5
  TCERG1 WILD-TYPE    53 132 258  97
D1247V4, multiclass
       clus
vv      TCERG1 MUTATED TCERG1 WILD-TYPE
  T0+T1              1               53
  T2                 3              132
  T3                 3              258
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  TCERG1 MUTATED     3   4   1   2
  TCERG1 WILD-TYPE 192 169  88  83
D1247V5, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  N0              3              192
  N1              4              169
  N2              1               88
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1247V6, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     9   2
  TCERG1 WILD-TYPE 473  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      9    2
  TCERG1 WILD-TYPE  473   36
   clus
vv  TCERG1 MUTATED TCERG1 WILD-TYPE
  0              9              473
  1              2               36
[1] 2 2
[1] FALSE
D1247V7, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     5   7
  TCERG1 WILD-TYPE 167 399
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      5    7
  TCERG1 WILD-TYPE  167  399
        clus
vv       TCERG1 MUTATED TCERG1 WILD-TYPE
  FEMALE              5              167
  MALE                7              399
[1] 2 2
[1] FALSE
D1247V8, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     9   1
  TCERG1 WILD-TYPE 407 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      9    1
  TCERG1 WILD-TYPE  407  101
     clus
vv    TCERG1 MUTATED TCERG1 WILD-TYPE
  NO               9              407
  YES              1              101
[1] 2 2
[1] FALSE
D1247V9, continuous
D1247V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TCERG1 MUTATED       1                         0
  TCERG1 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCERG1 MUTATED                                           0     9
  TCERG1 WILD-TYPE                                         1   348
D1247V11, multiclass
                                           clus
vv                                          TCERG1 MUTATED TCERG1 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1247V12, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     1   8
  TCERG1 WILD-TYPE   9 390
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      1    8
  TCERG1 WILD-TYPE    9  390
                        clus
vv                       TCERG1 MUTATED TCERG1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO              8              390
[1] 2 2
[1] FALSE

Clustering(1248) Variable = SETBP1 MUTATION ANALYSIS
D1248V1, survival
                  sevent
clus2                0   1
  SETBP1 MUTATED    24  19
  SETBP1 WILD-TYPE 314 197
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              43              511 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
              19              197 
$`SETBP1 MUTATED`
TCGA-JY-A6FB TCGA-L5-A8NG TCGA-2H-A9GL TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-KH-A6WC 
       60.39        35.97         5.92         0.85        18.64         6.28 
TCGA-L5-A4OT TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-R6-A8WG 
        4.90        16.47         7.76        21.37        52.57        12.69 
TCGA-RE-A7BO TCGA-V5-A7RE TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7703 
        7.00        16.44        11.01         9.67        34.68        36.16 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-A4QL 
        7.40         6.18         0.26         9.21        31.96        16.14 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4Z0 
        6.58        11.77         9.01        28.96        65.10        14.76 
TCGA-D7-A747 TCGA-FP-8099 TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-A4G8 TCGA-HU-A4GH 
        8.38        17.06        77.29        52.21        22.68        11.77 
TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-R5-A804 TCGA-VQ-A8DL 
       29.98         6.58        23.84        14.07         4.60         0.92 
TCGA-VQ-A8P2 
       38.14 

$`SETBP1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27        35.21        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
        0.79        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
        2.66        12.92        13.48        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        83.24        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78         2.89         2.30        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
        9.34         6.18         9.57         6.61        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        12.20        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         0.00        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44        20.32        22.29        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        63.06        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.80        21.17 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  SETBP1 MUTATED SETBP1 WILD-TYPE 
            0.26             0.00 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
           77.29           122.30 
  SETBP1 MUTATED SETBP1 WILD-TYPE 
           14.07            13.55 
[1] "0.3 - 77.3 (14.1)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D1248V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETBP1 MUTATED         2        5        4        1         8         9
  SETBP1 WILD-TYPE       8       15       42       30        76        74
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SETBP1 MUTATED           3          3          1          2        5
  SETBP1 WILD-TYPE        26         81         61         37       38
                  vv
clus               STAGE IVA
  SETBP1 MUTATED           0
  SETBP1 WILD-TYPE         4
D1248V3, multiclass
            clus
vv           SETBP1 MUTATED SETBP1 WILD-TYPE
  STAGE I                 2                8
  STAGE IA                5               15
  STAGE IB                4               42
  STAGE II                1               30
  STAGE IIA               8               76
  STAGE IIB               9               74
  STAGE III               3               26
  STAGE IIIA              3               81
  STAGE IIIB              1               61
  STAGE IIIC              2               37
  STAGE IV                5               38
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  SETBP1 MUTATED      10   9  16   8
  SETBP1 WILD-TYPE    44 126 245  94
D1248V4, multiclass
       clus
vv      SETBP1 MUTATED SETBP1 WILD-TYPE
  T0+T1             10               44
  T2                 9              126
  T3                16              245
  T4                 8               94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  SETBP1 MUTATED    17  16   5   4
  SETBP1 WILD-TYPE 178 157  84  81
D1248V5, multiclass
    clus
vv   SETBP1 MUTATED SETBP1 WILD-TYPE
  N0             17              178
  N1             16              157
  N2              5               84
  N3              4               81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1248V6, binary
                  cls
clus                 0   1
  SETBP1 MUTATED    40   4
  SETBP1 WILD-TYPE 442  34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     40    4
  SETBP1 WILD-TYPE  442   34
   clus
vv  SETBP1 MUTATED SETBP1 WILD-TYPE
  0             40              442
  1              4               34
[1] 2 2
[1] FALSE
D1248V7, binary
                  cls
clus                 0   1
  SETBP1 MUTATED    15  32
  SETBP1 WILD-TYPE 157 374
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     15   32
  SETBP1 WILD-TYPE  157  374
        clus
vv       SETBP1 MUTATED SETBP1 WILD-TYPE
  FEMALE             15              157
  MALE               32              374
[1] 2 2
[1] FALSE
D1248V8, binary
                  cls
clus                 0   1
  SETBP1 MUTATED    35   6
  SETBP1 WILD-TYPE 381  96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED     35    6
  SETBP1 WILD-TYPE  381   96
     clus
vv    SETBP1 MUTATED SETBP1 WILD-TYPE
  NO              35              381
  YES              6               96
[1] 2 2
[1] FALSE
D1248V9, continuous
D1248V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SETBP1 MUTATED       9                         2
  SETBP1 WILD-TYPE   124                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SETBP1 MUTATED                                           0    30
  SETBP1 WILD-TYPE                                         1   327
D1248V11, multiclass
                                           clus
vv                                          SETBP1 MUTATED SETBP1 WILD-TYPE
  ASIAN                                                  9              124
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 30              327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1248V12, binary
                  cls
clus                 0   1
  SETBP1 MUTATED     1  31
  SETBP1 WILD-TYPE   9 367
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETBP1 MUTATED      1   31
  SETBP1 WILD-TYPE    9  367
                        clus
vv                       SETBP1 MUTATED SETBP1 WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             31              367
[1] 2 2
[1] FALSE

Clustering(1249) Variable = WEE1 MUTATION ANALYSIS
D1249V1, survival
                sevent
clus2              0   1
  WEE1 MUTATED     7   0
  WEE1 WILD-TYPE 331 216
  WEE1 MUTATED WEE1 WILD-TYPE 
             7            547 
  WEE1 MUTATED WEE1 WILD-TYPE 
             0            216 
$`WEE1 MUTATED`
TCGA-L5-A8NK TCGA-BR-8360 TCGA-BR-8370 TCGA-BR-8591 TCGA-CD-A487 TCGA-VQ-A8DT 
       13.55         6.18         3.32        28.14        12.30        48.79 
TCGA-VQ-A8P2 
       38.14 

$`WEE1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.84        33.63        39.78        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       15.39        12.07        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.25        13.02        43.36        37.41        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  WEE1 MUTATED WEE1 WILD-TYPE 
          3.32           0.00 
  WEE1 MUTATED WEE1 WILD-TYPE 
         48.79         122.30 
  WEE1 MUTATED WEE1 WILD-TYPE 
         13.55          13.58 
[1] "3.3 - 48.8 (13.6)"  "0.0 - 122.3 (13.6)"
[1] "hr="     "9100000"
D1249V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WEE1 MUTATED         0        0        0        0         2         1
  WEE1 WILD-TYPE      10       20       46       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WEE1 MUTATED           0          1          2          1        0         0
  WEE1 WILD-TYPE        29         83         60         38       43         4
D1249V3, multiclass
            clus
vv           WEE1 MUTATED WEE1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              0             46
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            1             38
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  WEE1 MUTATED       0   0   5   2
  WEE1 WILD-TYPE    54 135 256 100
D1249V4, multiclass
       clus
vv      WEE1 MUTATED WEE1 WILD-TYPE
  T0+T1            0             54
  T2               0            135
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  WEE1 MUTATED     2   2   0   3
  WEE1 WILD-TYPE 193 171  89  82
D1249V5, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  N0            2            193
  N1            2            171
  N2            0             89
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1249V6, binary
                cls
clus               0   1
  WEE1 MUTATED     7   0
  WEE1 WILD-TYPE 475  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      7    0
  WEE1 WILD-TYPE  475   38
   clus
vv  WEE1 MUTATED WEE1 WILD-TYPE
  0            7            475
  1            0             38
[1] 2 2
[1] FALSE
D1249V7, binary
                cls
clus               0   1
  WEE1 MUTATED     1   6
  WEE1 WILD-TYPE 171 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      1    6
  WEE1 WILD-TYPE  171  400
        clus
vv       WEE1 MUTATED WEE1 WILD-TYPE
  FEMALE            1            171
  MALE              6            400
[1] 2 2
[1] FALSE
D1249V8, binary
                cls
clus               0   1
  WEE1 MUTATED     4   2
  WEE1 WILD-TYPE 412 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      4    2
  WEE1 WILD-TYPE  412  100
     clus
vv    WEE1 MUTATED WEE1 WILD-TYPE
  NO             4            412
  YES            2            100
[1] 2 2
[1] FALSE
D1249V9, continuous
D1249V10, continuous
[1] "Remove cluster labels:" "WEE1 MUTATED"          
clus
  WEE1 MUTATED WEE1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" "WEE1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"WEE1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WEE1 MUTATED       1                         0
  WEE1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WEE1 MUTATED                                           0     5
  WEE1 WILD-TYPE                                         1   352
D1249V11, multiclass
                                           clus
vv                                          WEE1 MUTATED WEE1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1249V12, binary
                cls
clus               0   1
  WEE1 MUTATED     0   4
  WEE1 WILD-TYPE  10 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      0    4
  WEE1 WILD-TYPE   10  394
                        clus
vv                       WEE1 MUTATED WEE1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            4            394
[1] 2 2
[1] FALSE

Clustering(1250) Variable = IGSF21 MUTATION ANALYSIS
D1250V1, survival
                  sevent
clus2                0   1
  IGSF21 MUTATED     4   1
  IGSF21 WILD-TYPE 334 215
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               5              549 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               1              215 
$`IGSF21 MUTATED`
TCGA-L5-A8NT TCGA-B7-A5TI TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GN 
       27.12        19.56       105.07        28.96        29.98 

$`IGSF21 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99        12.03        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  IGSF21 MUTATED IGSF21 WILD-TYPE 
           19.56             0.00 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
          105.07           122.30 
  IGSF21 MUTATED IGSF21 WILD-TYPE 
           28.96            13.51 
[1] "19.6 - 105.1 (29.0)" "0.0 - 122.3 (13.5)" 
[1] "hr=" "4"  
D1250V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGSF21 MUTATED         0        1        0        1         1         1
  IGSF21 WILD-TYPE      10       19       46       30        83        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGSF21 MUTATED           0          0          0          1        0
  IGSF21 WILD-TYPE        29         84         62         38       43
                  vv
clus               STAGE IVA
  IGSF21 MUTATED           0
  IGSF21 WILD-TYPE         4
D1250V3, multiclass
            clus
vv           IGSF21 MUTATED IGSF21 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                0               46
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  IGSF21 MUTATED       1   2   1   1
  IGSF21 WILD-TYPE    53 133 260 101
D1250V4, multiclass
       clus
vv      IGSF21 MUTATED IGSF21 WILD-TYPE
  T0+T1              1               53
  T2                 2              133
  T3                 1              260
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  IGSF21 MUTATED     2   2   0   1
  IGSF21 WILD-TYPE 193 171  89  84
D1250V5, multiclass
    clus
vv   IGSF21 MUTATED IGSF21 WILD-TYPE
  N0              2              193
  N1              2              171
  N2              0               89
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1250V6, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     5   0
  IGSF21 WILD-TYPE 477  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      5    0
  IGSF21 WILD-TYPE  477   38
   clus
vv  IGSF21 MUTATED IGSF21 WILD-TYPE
  0              5              477
  1              0               38
[1] 2 2
[1] FALSE
D1250V7, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     0   5
  IGSF21 WILD-TYPE 172 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      0    5
  IGSF21 WILD-TYPE  172  401
        clus
vv       IGSF21 MUTATED IGSF21 WILD-TYPE
  FEMALE              0              172
  MALE                5              401
[1] 2 2
[1] FALSE
D1250V8, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     3   1
  IGSF21 WILD-TYPE 413 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      3    1
  IGSF21 WILD-TYPE  413  101
     clus
vv    IGSF21 MUTATED IGSF21 WILD-TYPE
  NO               3              413
  YES              1              101
[1] 2 2
[1] FALSE
D1250V9, continuous
D1250V10, continuous
[1] "Remove cluster labels:" "IGSF21 MUTATED"        
clus
  IGSF21 MUTATED IGSF21 WILD-TYPE 
               1               97 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-Q9-A6FU       TCGA-IC-A6RE       TCGA-IG-A3QL 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC       TCGA-IG-A4P3 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8       TCGA-IG-A6QS 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA       TCGA-JY-A6FE 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC       TCGA-L5-A43C 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH       TCGA-L5-A4OM 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP       TCGA-L5-A4OQ 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW       TCGA-L5-A4OX 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893       TCGA-L5-A8NE 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NN       TCGA-L5-A8NQ 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A6 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-LN-A4A9       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-LN-A8I0       TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-R6-A6L4       TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-R6-A8W8       TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-V5-A7RC       TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-VR-A8EU       TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-X8-AAAR       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" "IGSF21 WILD-TYPE" 
      TCGA-Z6-AAPN 
"IGSF21 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGSF21 MUTATED       1                         0
  IGSF21 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGSF21 MUTATED                                           0     2
  IGSF21 WILD-TYPE                                         1   355
D1250V11, multiclass
                                           clus
vv                                          IGSF21 MUTATED IGSF21 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1250V12, binary
                  cls
clus                 0   1
  IGSF21 MUTATED     0   2
  IGSF21 WILD-TYPE  10 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF21 MUTATED      0    2
  IGSF21 WILD-TYPE   10  396
                        clus
vv                       IGSF21 MUTATED IGSF21 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              2              396
[1] 2 2
[1] FALSE

Clustering(1251) Variable = IBTK MUTATION ANALYSIS
D1251V1, survival
                sevent
clus2              0   1
  IBTK MUTATED    11   8
  IBTK WILD-TYPE 327 208
  IBTK MUTATED IBTK WILD-TYPE 
            19            535 
  IBTK MUTATED IBTK WILD-TYPE 
             8            208 
$`IBTK MUTATED`
TCGA-Q9-A6FU TCGA-IG-A50L TCGA-LN-A9FP TCGA-VR-A8ER TCGA-B7-5816 TCGA-BR-4184 
        5.16         0.53        12.03        12.43        26.70         6.97 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI 
       34.68        30.90        44.94         6.18        31.96        11.77 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ 
      105.07        21.07        11.44        11.08        22.32         0.10 
TCGA-VQ-A91U 
        1.71 

$`IBTK WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       18.35         3.32         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        19.73        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57         6.61        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8363 
        2.66        19.96         2.20         7.40        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 
       36.00         1.02         0.99         6.02         0.99        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V 
       22.19        17.85         1.87        15.65        20.81        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  IBTK MUTATED IBTK WILD-TYPE 
           0.1            0.0 
  IBTK MUTATED IBTK WILD-TYPE 
        105.07         122.30 
  IBTK MUTATED IBTK WILD-TYPE 
         12.03          13.68 
[1] "0.1 - 105.1 (12.0)" "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D1251V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IBTK MUTATED         0        0        1        1         5         2
  IBTK WILD-TYPE      10       20       45       30        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IBTK MUTATED           1          6          2          2        2         0
  IBTK WILD-TYPE        28         78         60         37       41         4
D1251V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            6             78
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  IBTK MUTATED       0   4  11   7
  IBTK WILD-TYPE    54 131 250  95
D1251V4, multiclass
       clus
vv      IBTK MUTATED IBTK WILD-TYPE
  T0+T1            0             54
  T2               4            131
  T3              11            250
  T4               7             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  IBTK MUTATED     8   6   6   2
  IBTK WILD-TYPE 187 167  83  83
D1251V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0            8            187
  N1            6            167
  N2            6             83
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1251V6, binary
                cls
clus               0   1
  IBTK MUTATED    21   1
  IBTK WILD-TYPE 461  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     21    1
  IBTK WILD-TYPE  461   37
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           21            461
  1            1             37
[1] 2 2
[1] FALSE
D1251V7, binary
                cls
clus               0   1
  IBTK MUTATED    10  13
  IBTK WILD-TYPE 162 393
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     10   13
  IBTK WILD-TYPE  162  393
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE           10            162
  MALE             13            393
[1] 2 2
[1] FALSE
D1251V8, binary
                cls
clus               0   1
  IBTK MUTATED    15   3
  IBTK WILD-TYPE 401  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     15    3
  IBTK WILD-TYPE  401   99
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO            15            401
  YES            3             99
[1] 2 2
[1] FALSE
D1251V9, continuous
[1] "Remove cluster labels:" "IBTK MUTATED"          
clus
  IBTK MUTATED IBTK WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ET     TCGA-VR-A8EU 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"IBTK WILD-TYPE" "IBTK WILD-TYPE" "IBTK WILD-TYPE" 
D1251V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IBTK MUTATED       7                         1
  IBTK WILD-TYPE   126                        13
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IBTK MUTATED                                           0    10
  IBTK WILD-TYPE                                         1   347
D1251V11, multiclass
                                           clus
vv                                          IBTK MUTATED IBTK WILD-TYPE
  ASIAN                                                7            126
  BLACK OR AFRICAN AMERICAN                            1             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1251V12, binary
                cls
clus               0   1
  IBTK MUTATED     0  17
  IBTK WILD-TYPE  10 381
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      0   17
  IBTK WILD-TYPE   10  381
                        clus
vv                       IBTK MUTATED IBTK WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           17            381
[1] 2 2
[1] FALSE

Clustering(1252) Variable = EEA1 MUTATION ANALYSIS
D1252V1, survival
                sevent
clus2              0   1
  EEA1 MUTATED    11   5
  EEA1 WILD-TYPE 327 211
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            538 
  EEA1 MUTATED EEA1 WILD-TYPE 
             5            211 
$`EEA1 MUTATED`
TCGA-LN-A4A9 TCGA-V5-A7RE TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8078 
       11.54        16.44         6.97        44.94        35.84        29.59 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5728 
        0.26         4.31        27.12        31.96        16.14        65.10 
TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-A4GU TCGA-RD-A7BW 
       77.29         1.51         6.58         5.13 

$`EEA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        31.20        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18        31.10        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       13.51        20.65        20.42         1.15        21.44         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19        10.26        15.22        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       26.47         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  EEA1 MUTATED EEA1 WILD-TYPE 
          0.26           0.00 
  EEA1 MUTATED EEA1 WILD-TYPE 
         77.29         122.30 
  EEA1 MUTATED EEA1 WILD-TYPE 
         16.29          13.53 
[1] "0.3 - 77.3 (16.3)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.5"
D1252V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EEA1 MUTATED         0        0        6        1         2         2
  EEA1 WILD-TYPE      10       20       40       30        82        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EEA1 MUTATED           0          1          2          0        1         0
  EEA1 WILD-TYPE        29         83         60         39       42         4
D1252V3, multiclass
            clus
vv           EEA1 MUTATED EEA1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              0             20
  STAGE IB              6             40
  STAGE II              1             30
  STAGE IIA             2             82
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            2             60
  STAGE IIIC            0             39
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  EEA1 MUTATED       1   7   5   3
  EEA1 WILD-TYPE    53 128 256  99
D1252V4, multiclass
       clus
vv      EEA1 MUTATED EEA1 WILD-TYPE
  T0+T1            1             53
  T2               7            128
  T3               5            256
  T4               3             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EEA1 MUTATED     9   4   2   1
  EEA1 WILD-TYPE 186 169  87  84
D1252V5, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  N0            9            186
  N1            4            169
  N2            2             87
  N3            1             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1252V6, binary
                cls
clus               0   1
  EEA1 MUTATED    14   1
  EEA1 WILD-TYPE 468  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     14    1
  EEA1 WILD-TYPE  468   37
   clus
vv  EEA1 MUTATED EEA1 WILD-TYPE
  0           14            468
  1            1             37
[1] 2 2
[1] FALSE
D1252V7, binary
                cls
clus               0   1
  EEA1 MUTATED     8   8
  EEA1 WILD-TYPE 164 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      8    8
  EEA1 WILD-TYPE  164  398
        clus
vv       EEA1 MUTATED EEA1 WILD-TYPE
  FEMALE            8            164
  MALE              8            398
[1] 2 2
[1] FALSE
D1252V8, binary
                cls
clus               0   1
  EEA1 MUTATED    12   3
  EEA1 WILD-TYPE 404  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     12    3
  EEA1 WILD-TYPE  404   99
     clus
vv    EEA1 MUTATED EEA1 WILD-TYPE
  NO            12            404
  YES            3             99
[1] 2 2
[1] FALSE
D1252V9, continuous
[1] "Remove cluster labels:" "EEA1 MUTATED"          
clus
  EEA1 MUTATED EEA1 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-V5-AASW 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP     TCGA-VR-A8EQ 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
D1252V10, continuous
[1] "Remove cluster labels:" "EEA1 MUTATED"          
clus
  EEA1 MUTATED EEA1 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A4OM     TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A4OQ     TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A4OX     TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A8NE     TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-L5-A8NQ     TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A49O     TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A49U     TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" "EEA1 WILD-TYPE" 
    TCGA-Z6-AAPN 
"EEA1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EEA1 MUTATED       4                         0
  EEA1 WILD-TYPE   129                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EEA1 MUTATED                                           0    10
  EEA1 WILD-TYPE                                         1   347
D1252V11, multiclass
                                           clus
vv                                          EEA1 MUTATED EEA1 WILD-TYPE
  ASIAN                                                4            129
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1252V12, binary
                cls
clus               0   1
  EEA1 MUTATED     0  14
  EEA1 WILD-TYPE  10 384
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      0   14
  EEA1 WILD-TYPE   10  384
                        clus
vv                       EEA1 MUTATED EEA1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           14            384
[1] 2 2
[1] FALSE

Clustering(1253) Variable = PBX2 MUTATION ANALYSIS
D1253V1, survival
                sevent
clus2              0   1
  PBX2 MUTATED     4   6
  PBX2 WILD-TYPE 334 210
  PBX2 MUTATED PBX2 WILD-TYPE 
            10            544 
  PBX2 MUTATED PBX2 WILD-TYPE 
             6            210 
$`PBX2 MUTATED`
TCGA-L5-A4OG TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8363 TCGA-BR-A4CS TCGA-CD-A4MG 
        4.70        34.68        19.33         0.26         1.48         6.58 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-HF-A5NB TCGA-HU-A4GY 
       11.77         1.02        30.51         0.26 

$`PBX2 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00        19.99        22.82         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        5.16        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        6.61        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       12.43        11.61        12.20        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
        8.98         0.10         6.51         6.58        20.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  PBX2 MUTATED PBX2 WILD-TYPE 
          0.26           0.00 
  PBX2 MUTATED PBX2 WILD-TYPE 
         34.68         122.30 
  PBX2 MUTATED PBX2 WILD-TYPE 
          5.64          13.73 
[1] "0.3 - 34.7 (5.6)"   "0.0 - 122.3 (13.7)"
[1] "hr=" "2.5"
D1253V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PBX2 MUTATED         1        0        1        0         2         1
  PBX2 WILD-TYPE       9       20       45       31        82        82
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PBX2 MUTATED           0          3          0          2        1         0
  PBX2 WILD-TYPE        29         81         62         37       42         4
D1253V3, multiclass
            clus
vv           PBX2 MUTATED PBX2 WILD-TYPE
  STAGE I               1              9
  STAGE IA              0             20
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             2             82
  STAGE IIB             1             82
  STAGE III             0             29
  STAGE IIIA            3             81
  STAGE IIIB            0             62
  STAGE IIIC            2             37
  STAGE IV              1             42
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PBX2 MUTATED       1   1   5   4
  PBX2 WILD-TYPE    53 134 256  98
D1253V4, multiclass
       clus
vv      PBX2 MUTATED PBX2 WILD-TYPE
  T0+T1            1             53
  T2               1            134
  T3               5            256
  T4               4             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PBX2 MUTATED     5   3   1   2
  PBX2 WILD-TYPE 190 170  88  83
D1253V5, multiclass
    clus
vv   PBX2 MUTATED PBX2 WILD-TYPE
  N0            5            190
  N1            3            170
  N2            1             88
  N3            2             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1253V6, binary
                cls
clus               0   1
  PBX2 MUTATED    10   1
  PBX2 WILD-TYPE 472  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED     10    1
  PBX2 WILD-TYPE  472   37
   clus
vv  PBX2 MUTATED PBX2 WILD-TYPE
  0           10            472
  1            1             37
[1] 2 2
[1] FALSE
D1253V7, binary
                cls
clus               0   1
  PBX2 MUTATED     7   4
  PBX2 WILD-TYPE 165 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      7    4
  PBX2 WILD-TYPE  165  402
        clus
vv       PBX2 MUTATED PBX2 WILD-TYPE
  FEMALE            7            165
  MALE              4            402
[1] 2 2
[1] FALSE
D1253V8, binary
                cls
clus               0   1
  PBX2 MUTATED     8   1
  PBX2 WILD-TYPE 408 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      8    1
  PBX2 WILD-TYPE  408  101
     clus
vv    PBX2 MUTATED PBX2 WILD-TYPE
  NO             8            408
  YES            1            101
[1] 2 2
[1] FALSE
D1253V9, continuous
D1253V10, continuous
[1] "Remove cluster labels:" "PBX2 MUTATED"          
clus
  PBX2 MUTATED PBX2 WILD-TYPE 
             1             97 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y     TCGA-L5-A8NG 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE     TCGA-IG-A3QL 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC     TCGA-IG-A4P3 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8     TCGA-IG-A6QS 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA     TCGA-JY-A6FE 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC     TCGA-L5-A43C 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH     TCGA-L5-A4OM 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-RE-A7BO     TCGA-V5-A7RB 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-V5-A7RC     TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-X8-AAAR     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" "PBX2 WILD-TYPE" 
    TCGA-Z6-AAPN 
"PBX2 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PBX2 MUTATED       3                         0
  PBX2 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PBX2 MUTATED                                           0     6
  PBX2 WILD-TYPE                                         1   351
D1253V11, multiclass
                                           clus
vv                                          PBX2 MUTATED PBX2 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1253V12, binary
                cls
clus               0   1
  PBX2 MUTATED     0   8
  PBX2 WILD-TYPE  10 390
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      0    8
  PBX2 WILD-TYPE   10  390
                        clus
vv                       PBX2 MUTATED PBX2 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            8            390
[1] 2 2
[1] FALSE

Clustering(1254) Variable = C2ORF67 MUTATION ANALYSIS
D1254V1, survival
                   sevent
clus2                 0   1
  C2ORF67 MUTATED    10   4
  C2ORF67 WILD-TYPE 328 212
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
               14               540 
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
                4               212 
$`C2ORF67 MUTATED`
TCGA-LN-A4A6 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 
       12.85        11.70        30.90        34.68        35.84        29.59 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-D7-8578 
       28.14        31.96        13.18         6.58        11.77        21.14 
TCGA-F1-6874 TCGA-HU-A4GT 
       14.47         6.51 

$`C2ORF67 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        18.35         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44         0.69         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43        11.61        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       12.03         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        14.66        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
             6.51              0.00 
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
            35.84            122.30 
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
           17.805            13.530 
[1] "6.5 - 35.8 (17.8)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1254V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF67 MUTATED         0        0        4        1         3         2
  C2ORF67 WILD-TYPE      10       20       42       30        81        81
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF67 MUTATED           0          3          0          2        1
  C2ORF67 WILD-TYPE        29         81         62         37       42
                   vv
clus                STAGE IVA
  C2ORF67 MUTATED           0
  C2ORF67 WILD-TYPE         4
D1254V3, multiclass
            clus
vv           C2ORF67 MUTATED C2ORF67 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 4                42
  STAGE II                 1                30
  STAGE IIA                3                81
  STAGE IIB                2                81
  STAGE III                0                29
  STAGE IIIA               3                81
  STAGE IIIB               0                62
  STAGE IIIC               2                37
  STAGE IV                 1                42
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  C2ORF67 MUTATED       0   6   5   6
  C2ORF67 WILD-TYPE    54 129 256  96
D1254V4, multiclass
       clus
vv      C2ORF67 MUTATED C2ORF67 WILD-TYPE
  T0+T1               0                54
  T2                  6               129
  T3                  5               256
  T4                  6                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  C2ORF67 MUTATED    11   2   1   2
  C2ORF67 WILD-TYPE 184 171  88  83
D1254V5, multiclass
    clus
vv   C2ORF67 MUTATED C2ORF67 WILD-TYPE
  N0              11               184
  N1               2               171
  N2               1                88
  N3               2                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1254V6, binary
                   cls
clus                  0   1
  C2ORF67 MUTATED    17   1
  C2ORF67 WILD-TYPE 465  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF67 MUTATED     17    1
  C2ORF67 WILD-TYPE  465   37
   clus
vv  C2ORF67 MUTATED C2ORF67 WILD-TYPE
  0              17               465
  1               1                37
[1] 2 2
[1] FALSE
D1254V7, binary
                   cls
clus                  0   1
  C2ORF67 MUTATED     8  10
  C2ORF67 WILD-TYPE 164 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF67 MUTATED      8   10
  C2ORF67 WILD-TYPE  164  396
        clus
vv       C2ORF67 MUTATED C2ORF67 WILD-TYPE
  FEMALE               8               164
  MALE                10               396
[1] 2 2
[1] FALSE
D1254V8, binary
                   cls
clus                  0   1
  C2ORF67 MUTATED    16   0
  C2ORF67 WILD-TYPE 400 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF67 MUTATED     16    0
  C2ORF67 WILD-TYPE  400  102
     clus
vv    C2ORF67 MUTATED C2ORF67 WILD-TYPE
  NO               16               400
  YES               0               102
[1] 2 2
[1] FALSE
D1254V9, continuous
[1] "Remove cluster labels:" "C2ORF67 MUTATED"       
clus
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
                1                67 
       TCGA-IG-A3I8        TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-IG-A3YB        TCGA-IG-A3YC        TCGA-IG-A51D        TCGA-IG-A5S3 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-IG-A7DP        TCGA-KH-A6WC        TCGA-LN-A49K        TCGA-LN-A49L 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A49M        TCGA-LN-A49N        TCGA-LN-A49O        TCGA-LN-A49P 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A49X        TCGA-LN-A49Y        TCGA-LN-A4A1 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A4A2        TCGA-LN-A4A3        TCGA-LN-A4A4        TCGA-LN-A4A5 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A4A8        TCGA-LN-A4A9        TCGA-LN-A4MQ        TCGA-LN-A4MR 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A5U5        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HY        TCGA-LN-A7HZ 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-V5-A7RB        TCGA-V5-A7RC        TCGA-V5-A7RE        TCGA-V5-AASV 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-V5-AASW        TCGA-V5-AASX        TCGA-VR-A8EO        TCGA-VR-A8EP 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-A8EQ        TCGA-VR-A8ER        TCGA-VR-A8ET        TCGA-VR-A8EU 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EY        TCGA-VR-A8EZ 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4D        TCGA-VR-AA4G        TCGA-VR-AA7B 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-XP-A8T6        TCGA-XP-A8T7 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-XP-A8T8        TCGA-Z6-A8JD        TCGA-Z6-A8JE 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
D1254V10, continuous
[1] "Remove cluster labels:" "C2ORF67 MUTATED"       
clus
  C2ORF67 MUTATED C2ORF67 WILD-TYPE 
                1                97 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-IG-A8O2        TCGA-IG-A97H        TCGA-JY-A6FA 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-JY-A6FE        TCGA-JY-A6FG        TCGA-JY-A6FH        TCGA-KH-A6WC 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A43C        TCGA-L5-A43E        TCGA-L5-A43H        TCGA-L5-A4OH 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A4OM        TCGA-L5-A4ON        TCGA-L5-A4OO        TCGA-L5-A4OP 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A4OQ        TCGA-L5-A4OT        TCGA-L5-A4OU        TCGA-L5-A4OW 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A4OX        TCGA-L5-A88S        TCGA-L5-A88V        TCGA-L5-A893 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A8NE        TCGA-L5-A8NF        TCGA-L5-A8NK        TCGA-L5-A8NN 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-L5-A8NQ        TCGA-L5-A8NR        TCGA-L5-A8NS        TCGA-L5-A8NW 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A49O        TCGA-LN-A49P        TCGA-LN-A49R        TCGA-LN-A49S 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A49U        TCGA-LN-A49V        TCGA-LN-A49W        TCGA-LN-A4A3 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A4A9        TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A7HW        TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-LN-A8I0        TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-R6-A6L4        TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-R6-A8W8        TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-V5-A7RC        TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-A8EU        TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-VR-A8Q7        TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-X8-AAAR        TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8 
"C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" "C2ORF67 WILD-TYPE" 
       TCGA-Z6-AAPN 
"C2ORF67 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C2ORF67 MUTATED       6                         0
  C2ORF67 WILD-TYPE   127                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2ORF67 MUTATED                                           0    12
  C2ORF67 WILD-TYPE                                         1   345
D1254V11, multiclass
                                           clus
vv                                          C2ORF67 MUTATED C2ORF67 WILD-TYPE
  ASIAN                                                   6               127
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1254V12, binary
                   cls
clus                  0   1
  C2ORF67 MUTATED     0  18
  C2ORF67 WILD-TYPE  10 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF67 MUTATED      0   18
  C2ORF67 WILD-TYPE   10  380
                        clus
vv                       C2ORF67 MUTATED C2ORF67 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              18               380
[1] 2 2
[1] FALSE

Clustering(1255) Variable = ZNF740 MUTATION ANALYSIS
D1255V1, survival
                  sevent
clus2                0   1
  ZNF740 MUTATED     3   0
  ZNF740 WILD-TYPE 335 216
  ZNF740 MUTATED ZNF740 WILD-TYPE 
               3              551 
  ZNF740 MUTATED ZNF740 WILD-TYPE 
               0              216 
$`ZNF740 MUTATED`
TCGA-BR-8591 TCGA-HU-A4G8 TCGA-MX-A5UJ 
       28.14        22.68        19.73 

$`ZNF740 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ZNF740 MUTATED ZNF740 WILD-TYPE 
           19.73             0.00 
  ZNF740 MUTATED ZNF740 WILD-TYPE 
           28.14           122.30 
  ZNF740 MUTATED ZNF740 WILD-TYPE 
           22.68            13.51 
[1] "19.7 - 28.1 (22.7)" "0.0 - 122.3 (13.5)"
[1] "hr="     "3300000"
D1255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF740 MUTATED         0        0        0        0         0         1
  ZNF740 WILD-TYPE      10       20       46       31        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF740 MUTATED           0          1          0          1        0
  ZNF740 WILD-TYPE        29         83         62         38       43
                  vv
clus               STAGE IVA
  ZNF740 MUTATED           0
  ZNF740 WILD-TYPE         4
D1255V3, multiclass
            clus
vv           ZNF740 MUTATED ZNF740 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                0               20
  STAGE IB                0               46
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              0               62
  STAGE IIIC              1               38
  STAGE IV                0               43
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ZNF740 MUTATED       0   0   2   1
  ZNF740 WILD-TYPE    54 135 259 101
D1255V4, multiclass
       clus
vv      ZNF740 MUTATED ZNF740 WILD-TYPE
  T0+T1              0               54
  T2                 0              135
  T3                 2              259
  T4                 1              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ZNF740 MUTATED     0   1   1   1
  ZNF740 WILD-TYPE 195 172  88  84
D1255V5, multiclass
    clus
vv   ZNF740 MUTATED ZNF740 WILD-TYPE
  N0              0              195
  N1              1              172
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1255V6, binary
                  cls
clus                 0   1
  ZNF740 MUTATED     3   0
  ZNF740 WILD-TYPE 479  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF740 MUTATED      3    0
  ZNF740 WILD-TYPE  479   38
   clus
vv  ZNF740 MUTATED ZNF740 WILD-TYPE
  0              3              479
  1              0               38
[1] 2 2
[1] FALSE
D1255V7, binary
                  cls
clus                 0   1
  ZNF740 MUTATED     2   1
  ZNF740 WILD-TYPE 170 405
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF740 MUTATED      2    1
  ZNF740 WILD-TYPE  170  405
        clus
vv       ZNF740 MUTATED ZNF740 WILD-TYPE
  FEMALE              2              170
  MALE                1              405
[1] 2 2
[1] FALSE
D1255V8, binary
                  cls
clus                 0   1
  ZNF740 MUTATED     3   0
  ZNF740 WILD-TYPE 413 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF740 MUTATED      3    0
  ZNF740 WILD-TYPE  413  102
     clus
vv    ZNF740 MUTATED ZNF740 WILD-TYPE
  NO               3              413
  YES              0              102
[1] 2 2
[1] FALSE
D1255V9, continuous
D1255V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF740 MUTATED       1                         0
  ZNF740 WILD-TYPE   132                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF740 MUTATED                                           0     2
  ZNF740 WILD-TYPE                                         1   355
D1255V11, multiclass
                                           clus
vv                                          ZNF740 MUTATED ZNF740 WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1255V12, binary
                  cls
clus                 0   1
  ZNF740 MUTATED     0   3
  ZNF740 WILD-TYPE  10 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF740 MUTATED      0    3
  ZNF740 WILD-TYPE   10  395
                        clus
vv                       ZNF740 MUTATED ZNF740 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              3              395
[1] 2 2
[1] FALSE

Clustering(1256) Variable = SLA MUTATION ANALYSIS
D1256V1, survival
               sevent
clus2             0   1
  SLA MUTATED     6   3
  SLA WILD-TYPE 332 213
  SLA MUTATED SLA WILD-TYPE 
            9           545 
  SLA MUTATED SLA WILD-TYPE 
            3           213 
$`SLA MUTATED`
TCGA-S8-A6BV TCGA-L5-A4OR TCGA-L5-A8NH TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 
       20.02         3.16        12.92        34.68        35.84         1.12 
TCGA-CG-5728 TCGA-D7-A6EY TCGA-HU-8602 
       65.10        11.44        22.32 

$`SLA WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
        9.34         9.67         6.18         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21        20.22        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  SLA MUTATED SLA WILD-TYPE 
         1.12          0.00 
  SLA MUTATED SLA WILD-TYPE 
         65.1         122.3 
  SLA MUTATED SLA WILD-TYPE 
        20.02         13.55 
[1] "1.1 - 65.1 (20.0)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.4"
D1256V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLA MUTATED         0        1        2        0         2         1
  SLA WILD-TYPE      10       19       44       31        82        82
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLA MUTATED           0          1          1          0        1         0
  SLA WILD-TYPE        29         83         61         39       42         4
D1256V3, multiclass
            clus
vv           SLA MUTATED SLA WILD-TYPE
  STAGE I              0            10
  STAGE IA             1            19
  STAGE IB             2            44
  STAGE II             0            31
  STAGE IIA            2            82
  STAGE IIB            1            82
  STAGE III            0            29
  STAGE IIIA           1            83
  STAGE IIIB           1            61
  STAGE IIIC           0            39
  STAGE IV             1            42
  STAGE IVA            0             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T0+T1  T2  T3  T4
  SLA MUTATED       2   2   4   1
  SLA WILD-TYPE    52 133 257 101
D1256V4, multiclass
       clus
vv      SLA MUTATED SLA WILD-TYPE
  T0+T1           2            52
  T2              2           133
  T3              4           257
  T4              1           101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2  N3
  SLA MUTATED     7   1   0   1
  SLA WILD-TYPE 188 172  89  84
D1256V5, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  N0           7           188
  N1           1           172
  N2           0            89
  N3           1            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1256V6, binary
               cls
clus              0   1
  SLA MUTATED     6   1
  SLA WILD-TYPE 476  37
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      6    1
  SLA WILD-TYPE  476   37
   clus
vv  SLA MUTATED SLA WILD-TYPE
  0           6           476
  1           1            37
[1] 2 2
[1] FALSE
D1256V7, binary
               cls
clus              0   1
  SLA MUTATED     6   3
  SLA WILD-TYPE 166 403
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      6    3
  SLA WILD-TYPE  166  403
        clus
vv       SLA MUTATED SLA WILD-TYPE
  FEMALE           6           166
  MALE             3           403
[1] 2 2
[1] FALSE
D1256V8, binary
               cls
clus              0   1
  SLA MUTATED     7   0
  SLA WILD-TYPE 409 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      7    0
  SLA WILD-TYPE  409  102
     clus
vv    SLA MUTATED SLA WILD-TYPE
  NO            7           409
  YES           0           102
[1] 2 2
[1] FALSE
D1256V9, continuous
D1256V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  SLA MUTATED       1                         0
  SLA WILD-TYPE   132                        14
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLA MUTATED                                           0     7
  SLA WILD-TYPE                                         1   350
D1256V11, multiclass
                                           clus
vv                                          SLA MUTATED SLA WILD-TYPE
  ASIAN                                               1           132
  BLACK OR AFRICAN AMERICAN                           0            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1256V12, binary
               cls
clus              0   1
  SLA MUTATED     0   6
  SLA WILD-TYPE  10 392
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      0    6
  SLA WILD-TYPE   10  392
                        clus
vv                       SLA MUTATED SLA WILD-TYPE
  HISPANIC OR LATINO               0            10
  NOT HISPANIC OR LATINO           6           392
[1] 2 2
[1] FALSE

Clustering(1257) Variable = CC2D2A MUTATION ANALYSIS
D1257V1, survival
                  sevent
clus2                0   1
  CC2D2A MUTATED    13   4
  CC2D2A WILD-TYPE 325 212
  CC2D2A MUTATED CC2D2A WILD-TYPE 
              17              537 
  CC2D2A MUTATED CC2D2A WILD-TYPE 
               4              212 
$`CC2D2A MUTATED`
TCGA-L5-A8NN TCGA-LN-A4A6 TCGA-VR-A8EQ TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-8361 
        5.49        12.85        22.82         6.97        36.16        31.10 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY 
       31.96        16.14        15.95         6.02       105.07        11.44 
TCGA-F1-6874 TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       14.47         6.58        19.73        74.53        38.14 

$`CC2D2A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.18        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        4.34        19.96         7.13         0.62         7.99        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        14.04        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  CC2D2A MUTATED CC2D2A WILD-TYPE 
            5.49             0.00 
  CC2D2A MUTATED CC2D2A WILD-TYPE 
          105.07           122.30 
  CC2D2A MUTATED CC2D2A WILD-TYPE 
           16.14            13.51 
[1] "5.5 - 105.1 (16.1)" "0.0 - 122.3 (13.5)"
[1] "hr=" "2.2"
D1257V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CC2D2A MUTATED         0        1        1        3         0         1
  CC2D2A WILD-TYPE      10       19       45       28        84        82
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CC2D2A MUTATED           2          3          2          1        3
  CC2D2A WILD-TYPE        27         81         60         38       40
                  vv
clus               STAGE IVA
  CC2D2A MUTATED           0
  CC2D2A WILD-TYPE         4
D1257V3, multiclass
            clus
vv           CC2D2A MUTATED CC2D2A WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                1               45
  STAGE II                3               28
  STAGE IIA               0               84
  STAGE IIB               1               82
  STAGE III               2               27
  STAGE IIIA              3               81
  STAGE IIIB              2               60
  STAGE IIIC              1               38
  STAGE IV                3               40
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  CC2D2A MUTATED       1   4   7   5
  CC2D2A WILD-TYPE    53 131 254  97
D1257V4, multiclass
       clus
vv      CC2D2A MUTATED CC2D2A WILD-TYPE
  T0+T1              1               53
  T2                 4              131
  T3                 7              254
  T4                 5               97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  CC2D2A MUTATED     3   9   3   2
  CC2D2A WILD-TYPE 192 164  86  83
D1257V5, multiclass
    clus
vv   CC2D2A MUTATED CC2D2A WILD-TYPE
  N0              3              192
  N1              9              164
  N2              3               86
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1257V6, binary
                  cls
clus                 0   1
  CC2D2A MUTATED    14   2
  CC2D2A WILD-TYPE 468  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CC2D2A MUTATED     14    2
  CC2D2A WILD-TYPE  468   36
   clus
vv  CC2D2A MUTATED CC2D2A WILD-TYPE
  0             14              468
  1              2               36
[1] 2 2
[1] FALSE
D1257V7, binary
                  cls
clus                 0   1
  CC2D2A MUTATED     5  12
  CC2D2A WILD-TYPE 167 394
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CC2D2A MUTATED      5   12
  CC2D2A WILD-TYPE  167  394
        clus
vv       CC2D2A MUTATED CC2D2A WILD-TYPE
  FEMALE              5              167
  MALE               12              394
[1] 2 2
[1] FALSE
D1257V8, binary
                  cls
clus                 0   1
  CC2D2A MUTATED    15   2
  CC2D2A WILD-TYPE 401 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CC2D2A MUTATED     15    2
  CC2D2A WILD-TYPE  401  100
     clus
vv    CC2D2A MUTATED CC2D2A WILD-TYPE
  NO              15              401
  YES              2              100
[1] 2 2
[1] FALSE
D1257V9, continuous
[1] "Remove cluster labels:" "CC2D2A MUTATED"        
clus
  CC2D2A MUTATED CC2D2A WILD-TYPE 
               2               66 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ       TCGA-LN-A4MR 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY       TCGA-LN-A7HZ 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-V5-A7RB       TCGA-V5-A7RC       TCGA-V5-A7RE       TCGA-V5-AASV 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU       TCGA-VR-A8EW 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B       TCGA-VR-AA7D 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
D1257V10, continuous
[1] "Remove cluster labels:" "CC2D2A MUTATED"        
clus
  CC2D2A MUTATED CC2D2A WILD-TYPE 
               2               96 
      TCGA-IC-A6RF       TCGA-L5-A43I       TCGA-L5-A43J       TCGA-L5-A4OE 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A4OG       TCGA-L5-A4OI       TCGA-L5-A88T       TCGA-L5-A88Y 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A8NG       TCGA-L5-A8NT       TCGA-Q9-A6FU       TCGA-IC-A6RE 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA       TCGA-IG-A3YC 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-IG-A4P3       TCGA-IG-A4QT       TCGA-IG-A50L       TCGA-IG-A5B8 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-IG-A6QS       TCGA-IG-A8O2       TCGA-IG-A97H       TCGA-JY-A6FA 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-JY-A6FE       TCGA-JY-A6FG       TCGA-JY-A6FH       TCGA-KH-A6WC 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A43C       TCGA-L5-A43E       TCGA-L5-A43H       TCGA-L5-A4OH 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A4OM       TCGA-L5-A4ON       TCGA-L5-A4OO       TCGA-L5-A4OP 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A4OQ       TCGA-L5-A4OT       TCGA-L5-A4OU       TCGA-L5-A4OW 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A4OX       TCGA-L5-A88S       TCGA-L5-A88V       TCGA-L5-A893 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A8NE       TCGA-L5-A8NF       TCGA-L5-A8NK       TCGA-L5-A8NQ 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-L5-A8NR       TCGA-L5-A8NS       TCGA-L5-A8NW       TCGA-LN-A49O 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A49P       TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A49V       TCGA-LN-A49W       TCGA-LN-A4A3       TCGA-LN-A4A9 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A5U6       TCGA-LN-A5U7       TCGA-LN-A7HV       TCGA-LN-A7HW 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-LN-A7HX       TCGA-LN-A7HZ       TCGA-LN-A8HZ       TCGA-LN-A8I0 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-M9-A5M8       TCGA-Q9-A6FW       TCGA-R6-A6DN       TCGA-R6-A6L4 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-R6-A6XQ       TCGA-R6-A6Y2       TCGA-R6-A8W5       TCGA-R6-A8W8 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-R6-A8WC       TCGA-RE-A7BO       TCGA-V5-A7RB       TCGA-V5-A7RC 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-V5-AASV       TCGA-VR-A8EP       TCGA-VR-A8ER       TCGA-VR-A8EU 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EZ       TCGA-VR-A8Q7 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-VR-AA4G       TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-X8-AAAR 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
      TCGA-XP-A8T6       TCGA-XP-A8T7       TCGA-XP-A8T8       TCGA-Z6-AAPN 
"CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" "CC2D2A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CC2D2A MUTATED       3                         0
  CC2D2A WILD-TYPE   130                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CC2D2A MUTATED                                           0    11
  CC2D2A WILD-TYPE                                         1   346
D1257V11, multiclass
                                           clus
vv                                          CC2D2A MUTATED CC2D2A WILD-TYPE
  ASIAN                                                  3              130
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1257V12, binary
                  cls
clus                 0   1
  CC2D2A MUTATED     1  10
  CC2D2A WILD-TYPE   9 388
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CC2D2A MUTATED      1   10
  CC2D2A WILD-TYPE    9  388
                        clus
vv                       CC2D2A MUTATED CC2D2A WILD-TYPE
  HISPANIC OR LATINO                  1                9
  NOT HISPANIC OR LATINO             10              388
[1] 2 2
[1] FALSE

Clustering(1258) Variable = GZF1 MUTATION ANALYSIS
D1258V1, survival
                sevent
clus2              0   1
  GZF1 MUTATED    12   8
  GZF1 WILD-TYPE 326 208
  GZF1 MUTATED GZF1 WILD-TYPE 
            20            534 
  GZF1 MUTATED GZF1 WILD-TYPE 
             8            208 
$`GZF1 MUTATED`
TCGA-L5-A43J TCGA-L5-A4OI TCGA-IG-A97H TCGA-JY-A6FD TCGA-LN-A4A4 TCGA-R6-A6XQ 
        4.31        19.99        14.50        68.02        12.59         6.35 
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-A4QL 
       19.56         6.97        32.25         4.31         1.12        16.14 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-KB-A93J 
       28.96        21.07        30.51         0.10        20.25        36.95 
TCGA-VQ-A8DL TCGA-VQ-A8P2 
        0.92        38.14 

$`GZF1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.62        12.46        12.59        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59         9.60         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96         2.20         7.40         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
        0.26        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        21.44         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        15.02        65.10         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        52.21        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         6.51         6.58         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        63.62         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        19.04         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       13.02        43.36        37.41        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GZF1 MUTATED GZF1 WILD-TYPE 
           0.1            0.0 
  GZF1 MUTATED GZF1 WILD-TYPE 
         68.02         122.30 
  GZF1 MUTATED GZF1 WILD-TYPE 
         17.85          13.51 
[1] "0.1 - 68.0 (17.9)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D1258V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GZF1 MUTATED         0        1        2        1         4         2
  GZF1 WILD-TYPE      10       19       44       30        80        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GZF1 MUTATED           1          3          1          5        0         0
  GZF1 WILD-TYPE        28         81         61         34       43         4
D1258V3, multiclass
            clus
vv           GZF1 MUTATED GZF1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              2             44
  STAGE II              1             30
  STAGE IIA             4             80
  STAGE IIB             2             81
  STAGE III             1             28
  STAGE IIIA            3             81
  STAGE IIIB            1             61
  STAGE IIIC            5             34
  STAGE IV              0             43
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  GZF1 MUTATED       1   4   9   6
  GZF1 WILD-TYPE    53 131 252  96
D1258V4, multiclass
       clus
vv      GZF1 MUTATED GZF1 WILD-TYPE
  T0+T1            1             53
  T2               4            131
  T3               9            252
  T4               6             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  GZF1 MUTATED     8   4   3   4
  GZF1 WILD-TYPE 187 169  86  81
D1258V5, multiclass
    clus
vv   GZF1 MUTATED GZF1 WILD-TYPE
  N0            8            187
  N1            4            169
  N2            3             86
  N3            4             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1258V6, binary
                cls
clus               0   1
  GZF1 MUTATED    17   0
  GZF1 WILD-TYPE 465  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZF1 MUTATED     17    0
  GZF1 WILD-TYPE  465   38
   clus
vv  GZF1 MUTATED GZF1 WILD-TYPE
  0           17            465
  1            0             38
[1] 2 2
[1] FALSE
D1258V7, binary
                cls
clus               0   1
  GZF1 MUTATED     9  12
  GZF1 WILD-TYPE 163 394
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZF1 MUTATED      9   12
  GZF1 WILD-TYPE  163  394
        clus
vv       GZF1 MUTATED GZF1 WILD-TYPE
  FEMALE            9            163
  MALE             12            394
[1] 2 2
[1] FALSE
D1258V8, binary
                cls
clus               0   1
  GZF1 MUTATED    13   4
  GZF1 WILD-TYPE 403  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZF1 MUTATED     13    4
  GZF1 WILD-TYPE  403   98
     clus
vv    GZF1 MUTATED GZF1 WILD-TYPE
  NO            13            403
  YES            4             98
[1] 2 2
[1] FALSE
D1258V9, continuous
[1] "Remove cluster labels:" "GZF1 MUTATED"          
clus
  GZF1 MUTATED GZF1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A5     TCGA-LN-A4A6 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ     TCGA-LN-A4MR 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY     TCGA-LN-A7HZ 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"GZF1 WILD-TYPE" "GZF1 WILD-TYPE" "GZF1 WILD-TYPE" 
D1258V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GZF1 MUTATED       5                         0
  GZF1 WILD-TYPE   128                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GZF1 MUTATED                                           0    12
  GZF1 WILD-TYPE                                         1   345
D1258V11, multiclass
                                           clus
vv                                          GZF1 MUTATED GZF1 WILD-TYPE
  ASIAN                                                5            128
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1258V12, binary
                cls
clus               0   1
  GZF1 MUTATED     0  11
  GZF1 WILD-TYPE  10 387
[1] "tbl2"
                cls
clus             [,1] [,2]
  GZF1 MUTATED      0   11
  GZF1 WILD-TYPE   10  387
                        clus
vv                       GZF1 MUTATED GZF1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           11            387
[1] 2 2
[1] FALSE

Clustering(1259) Variable = AGXT2L1 MUTATION ANALYSIS
D1259V1, survival
                   sevent
clus2                 0   1
  AGXT2L1 MUTATED     7   3
  AGXT2L1 WILD-TYPE 331 213
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               10               544 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
                3               213 
$`AGXT2L1 MUTATED`
TCGA-2H-A9GF TCGA-IG-A8O2 TCGA-IG-A97H TCGA-BR-4184 TCGA-BR-8680 TCGA-BR-A4PD 
       25.78         4.67        14.50         6.97        31.96        20.65 
TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5728 TCGA-KB-A6F7 
       12.43         6.02        65.10        63.62 

$`AGXT2L1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GG 
       79.07        16.24         0.23        20.15         9.86        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82         9.96        14.86        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       13.48        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.82         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53         5.56        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       38.14        37.22        22.19        17.85         1.87        15.65 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       20.81         1.71        42.64        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
             4.67              0.00 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
             65.1             122.3 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
           17.575            13.530 
[1] "4.7 - 65.1 (17.6)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.7"
D1259V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AGXT2L1 MUTATED         0        0        2        1         1         1
  AGXT2L1 WILD-TYPE      10       20       44       30        83        82
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGXT2L1 MUTATED           1          1          1          0        2
  AGXT2L1 WILD-TYPE        28         83         61         39       41
                   vv
clus                STAGE IVA
  AGXT2L1 MUTATED           0
  AGXT2L1 WILD-TYPE         4
D1259V3, multiclass
            clus
vv           AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  STAGE I                  0                10
  STAGE IA                 0                20
  STAGE IB                 2                44
  STAGE II                 1                30
  STAGE IIA                1                83
  STAGE IIB                1                82
  STAGE III                1                28
  STAGE IIIA               1                83
  STAGE IIIB               1                61
  STAGE IIIC               0                39
  STAGE IV                 2                41
  STAGE IVA                0                 4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  AGXT2L1 MUTATED       1   1   5   3
  AGXT2L1 WILD-TYPE    53 134 256  99
D1259V4, multiclass
       clus
vv      AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  T0+T1               1                53
  T2                  1               134
  T3                  5               256
  T4                  3                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  AGXT2L1 MUTATED     3   4   2   0
  AGXT2L1 WILD-TYPE 192 169  87  85
D1259V5, multiclass
    clus
vv   AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  N0               3               192
  N1               4               169
  N2               2                87
  N3               0                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1259V6, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED     8   1
  AGXT2L1 WILD-TYPE 474  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED      8    1
  AGXT2L1 WILD-TYPE  474   37
   clus
vv  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  0               8               474
  1               1                37
[1] 2 2
[1] FALSE
D1259V7, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED     3   7
  AGXT2L1 WILD-TYPE 169 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED      3    7
  AGXT2L1 WILD-TYPE  169  399
        clus
vv       AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  FEMALE               3               169
  MALE                 7               399
[1] 2 2
[1] FALSE
D1259V8, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED     6   1
  AGXT2L1 WILD-TYPE 410 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED      6    1
  AGXT2L1 WILD-TYPE  410  101
     clus
vv    AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  NO                6               410
  YES               1               101
[1] 2 2
[1] FALSE
D1259V9, continuous
D1259V10, continuous
[1] "Remove cluster labels:" "AGXT2L1 MUTATED"       
clus
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
                2                96 
       TCGA-IC-A6RF        TCGA-L5-A43I        TCGA-L5-A43J        TCGA-L5-A4OE 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A4OG        TCGA-L5-A4OI        TCGA-L5-A88T        TCGA-L5-A88Y 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A8NG        TCGA-L5-A8NT        TCGA-Q9-A6FU        TCGA-IC-A6RE 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-IG-A3QL        TCGA-IG-A3Y9        TCGA-IG-A3YA        TCGA-IG-A3YC 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-IG-A4P3        TCGA-IG-A4QT        TCGA-IG-A50L        TCGA-IG-A5B8 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-IG-A6QS        TCGA-JY-A6FA        TCGA-JY-A6FE        TCGA-JY-A6FG 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-JY-A6FH        TCGA-KH-A6WC        TCGA-L5-A43C        TCGA-L5-A43E 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A43H        TCGA-L5-A4OH        TCGA-L5-A4OM        TCGA-L5-A4ON 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A4OO        TCGA-L5-A4OP        TCGA-L5-A4OQ        TCGA-L5-A4OT 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A4OU        TCGA-L5-A4OW        TCGA-L5-A4OX        TCGA-L5-A88S 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A88V        TCGA-L5-A893        TCGA-L5-A8NE        TCGA-L5-A8NF 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A8NK        TCGA-L5-A8NN        TCGA-L5-A8NQ        TCGA-L5-A8NR 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-L5-A8NS        TCGA-L5-A8NW        TCGA-LN-A49O        TCGA-LN-A49P 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-LN-A49R        TCGA-LN-A49S        TCGA-LN-A49U        TCGA-LN-A49V 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-LN-A49W        TCGA-LN-A4A3        TCGA-LN-A4A6        TCGA-LN-A4A9 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-LN-A5U6        TCGA-LN-A5U7        TCGA-LN-A7HV        TCGA-LN-A7HW 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-LN-A7HX        TCGA-LN-A7HZ        TCGA-LN-A8HZ        TCGA-LN-A8I0 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-M9-A5M8        TCGA-Q9-A6FW        TCGA-R6-A6DN        TCGA-R6-A6L4 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-R6-A6XQ        TCGA-R6-A6Y2        TCGA-R6-A8W5        TCGA-R6-A8W8 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-R6-A8WC        TCGA-RE-A7BO        TCGA-V5-A7RB        TCGA-V5-A7RC 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-V5-AASV        TCGA-VR-A8EP        TCGA-VR-A8ER        TCGA-VR-A8EU 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-VR-A8EW        TCGA-VR-A8EX        TCGA-VR-A8EZ        TCGA-VR-A8Q7 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-VR-AA4G        TCGA-VR-AA7D        TCGA-VR-AA7I        TCGA-X8-AAAR 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
       TCGA-XP-A8T6        TCGA-XP-A8T7        TCGA-XP-A8T8        TCGA-Z6-AAPN 
"AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" "AGXT2L1 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  AGXT2L1 MUTATED       4                         0
  AGXT2L1 WILD-TYPE   129                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGXT2L1 MUTATED                                           0     2
  AGXT2L1 WILD-TYPE                                         1   355
D1259V11, multiclass
                                           clus
vv                                          AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  ASIAN                                                   4               129
  BLACK OR AFRICAN AMERICAN                               0                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1259V12, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED     0   6
  AGXT2L1 WILD-TYPE  10 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED      0    6
  AGXT2L1 WILD-TYPE   10  392
                        clus
vv                       AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO               6               392
[1] 2 2
[1] FALSE

Clustering(1260) Variable = EPN1 MUTATION ANALYSIS
D1260V1, survival
                sevent
clus2              0   1
  EPN1 MUTATED     7   5
  EPN1 WILD-TYPE 331 211
  EPN1 MUTATED EPN1 WILD-TYPE 
            12            542 
  EPN1 MUTATED EPN1 WILD-TYPE 
             5            211 
$`EPN1 MUTATED`
TCGA-IC-A6RF TCGA-L5-A4OI TCGA-CG-4460 TCGA-L5-A8NH TCGA-VR-AA7D TCGA-BR-6452 
       15.68        19.99        21.99        12.92         9.17        34.68 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8382 TCGA-BR-8487 TCGA-CG-5733 TCGA-HU-A4H8 
       44.94        36.16        25.05         1.12        21.07        14.07 

$`EPN1 WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        25.78        20.05        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50         2.66        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        8.71        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05        11.24        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         9.57         6.61        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       30.90        31.20        21.90         9.21        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       11.21        12.10        12.39        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       36.36         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        43.36        37.41        38.14        37.22 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U 
       22.19        17.85         1.87        15.65        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.64        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  EPN1 MUTATED EPN1 WILD-TYPE 
          1.12           0.00 
  EPN1 MUTATED EPN1 WILD-TYPE 
         44.94         122.30 
  EPN1 MUTATED EPN1 WILD-TYPE 
        20.530         13.495 
[1] "1.1 - 44.9 (20.5)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1260V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPN1 MUTATED         0        2        1        0         3         0
  EPN1 WILD-TYPE      10       18       45       31        81        83
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPN1 MUTATED           0          1          0          3        2         0
  EPN1 WILD-TYPE        29         83         62         36       41         4
D1260V3, multiclass
            clus
vv           EPN1 MUTATED EPN1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              2             18
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             3             81
  STAGE IIB             0             83
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            3             36
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  EPN1 MUTATED       4   1   5   2
  EPN1 WILD-TYPE    50 134 256 100
D1260V4, multiclass
       clus
vv      EPN1 MUTATED EPN1 WILD-TYPE
  T0+T1            4             50
  T2               1            134
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  EPN1 MUTATED     6   2   1   3
  EPN1 WILD-TYPE 189 171  88  82
D1260V5, multiclass
    clus
vv   EPN1 MUTATED EPN1 WILD-TYPE
  N0            6            189
  N1            2            171
  N2            1             88
  N3            3             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1260V6, binary
                cls
clus               0   1
  EPN1 MUTATED     9   2
  EPN1 WILD-TYPE 473  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      9    2
  EPN1 WILD-TYPE  473   36
   clus
vv  EPN1 MUTATED EPN1 WILD-TYPE
  0            9            473
  1            2             36
[1] 2 2
[1] FALSE
D1260V7, binary
                cls
clus               0   1
  EPN1 MUTATED     7   5
  EPN1 WILD-TYPE 165 401
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      7    5
  EPN1 WILD-TYPE  165  401
        clus
vv       EPN1 MUTATED EPN1 WILD-TYPE
  FEMALE            7            165
  MALE              5            401
[1] 2 2
[1] FALSE
D1260V8, binary
                cls
clus               0   1
  EPN1 MUTATED    10   1
  EPN1 WILD-TYPE 406 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED     10    1
  EPN1 WILD-TYPE  406  101
     clus
vv    EPN1 MUTATED EPN1 WILD-TYPE
  NO            10            406
  YES            1            101
[1] 2 2
[1] FALSE
D1260V9, continuous
[1] "Remove cluster labels:" "EPN1 MUTATED"          
clus
  EPN1 MUTATED EPN1 WILD-TYPE 
             1             67 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RB     TCGA-V5-A7RC     TCGA-V5-A7RE 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-VR-A8EP     TCGA-VR-A8EQ     TCGA-VR-A8ER     TCGA-VR-A8ET 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-VR-A8EU     TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EY 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-VR-A8EZ     TCGA-VR-A8Q7     TCGA-VR-AA4D     TCGA-VR-AA4G 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-VR-AA7B     TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
    TCGA-XP-A8T8     TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"EPN1 WILD-TYPE" "EPN1 WILD-TYPE" "EPN1 WILD-TYPE" 
D1260V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EPN1 MUTATED       1                         0
  EPN1 WILD-TYPE   132                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPN1 MUTATED                                           0     8
  EPN1 WILD-TYPE                                         1   349
D1260V11, multiclass
                                           clus
vv                                          EPN1 MUTATED EPN1 WILD-TYPE
  ASIAN                                                1            132
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1260V12, binary
                cls
clus               0   1
  EPN1 MUTATED     0   7
  EPN1 WILD-TYPE  10 391
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      0    7
  EPN1 WILD-TYPE   10  391
                        clus
vv                       EPN1 MUTATED EPN1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO            7            391
[1] 2 2
[1] FALSE

Clustering(1261) Variable = CCT6A MUTATION ANALYSIS
D1261V1, survival
                 sevent
clus2               0   1
  CCT6A MUTATED     5   4
  CCT6A WILD-TYPE 333 212
  CCT6A MUTATED CCT6A WILD-TYPE 
              9             545 
  CCT6A MUTATED CCT6A WILD-TYPE 
              4             212 
$`CCT6A MUTATED`
TCGA-LN-A49U TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG 
       15.35         6.97        34.68        35.84         1.12         6.58 
TCGA-CG-5728 TCGA-D7-A6EY TCGA-HU-A4GQ 
       65.10        11.44         0.10 

$`CCT6A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61        12.20        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.41        38.14        37.22        22.19        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T 
       15.65        20.81         1.71        42.64        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  CCT6A MUTATED CCT6A WILD-TYPE 
            0.1             0.0 
  CCT6A MUTATED CCT6A WILD-TYPE 
           65.1           122.3 
  CCT6A MUTATED CCT6A WILD-TYPE 
          11.44           13.58 
[1] "0.1 - 65.1 (11.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
D1261V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCT6A MUTATED         0        0        2        0         4         0
  CCT6A WILD-TYPE      10       20       44       31        80        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCT6A MUTATED           0          1          1          1        0         0
  CCT6A WILD-TYPE        29         83         61         38       43         4
D1261V3, multiclass
            clus
vv           CCT6A MUTATED CCT6A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               2              44
  STAGE II               0              31
  STAGE IIA              4              80
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             1              61
  STAGE IIIC             1              38
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  CCT6A MUTATED       0   2   6   1
  CCT6A WILD-TYPE    54 133 255 101
D1261V4, multiclass
       clus
vv      CCT6A MUTATED CCT6A WILD-TYPE
  T0+T1             0              54
  T2                2             133
  T3                6             255
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  CCT6A MUTATED     6   1   1   1
  CCT6A WILD-TYPE 189 172  88  84
D1261V5, multiclass
    clus
vv   CCT6A MUTATED CCT6A WILD-TYPE
  N0             6             189
  N1             1             172
  N2             1              88
  N3             1              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1261V6, binary
                 cls
clus                0   1
  CCT6A MUTATED     8   0
  CCT6A WILD-TYPE 474  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      8    0
  CCT6A WILD-TYPE  474   38
   clus
vv  CCT6A MUTATED CCT6A WILD-TYPE
  0             8             474
  1             0              38
[1] 2 2
[1] FALSE
D1261V7, binary
                 cls
clus                0   1
  CCT6A MUTATED     5   4
  CCT6A WILD-TYPE 167 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      5    4
  CCT6A WILD-TYPE  167  402
        clus
vv       CCT6A MUTATED CCT6A WILD-TYPE
  FEMALE             5             167
  MALE               4             402
[1] 2 2
[1] FALSE
D1261V8, binary
                 cls
clus                0   1
  CCT6A MUTATED     7   1
  CCT6A WILD-TYPE 409 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      7    1
  CCT6A WILD-TYPE  409  101
     clus
vv    CCT6A MUTATED CCT6A WILD-TYPE
  NO              7             409
  YES             1             101
[1] 2 2
[1] FALSE
D1261V9, continuous
[1] "Remove cluster labels:" "CCT6A MUTATED"         
clus
  CCT6A MUTATED CCT6A WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49V      TCGA-LN-A49W 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1      TCGA-LN-A4A2 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5      TCGA-LN-A4A6 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ      TCGA-LN-A4MR 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HY      TCGA-LN-A7HZ 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
D1261V10, continuous
[1] "Remove cluster labels:" "CCT6A MUTATED"         
clus
  CCT6A MUTATED CCT6A WILD-TYPE 
              1              97 
     TCGA-IC-A6RF      TCGA-L5-A43I      TCGA-L5-A43J      TCGA-L5-A4OE 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A4OG      TCGA-L5-A4OI      TCGA-L5-A88T      TCGA-L5-A88Y 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A8NG      TCGA-L5-A8NT      TCGA-Q9-A6FU      TCGA-IC-A6RE 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA      TCGA-IG-A3YC 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-IG-A4P3      TCGA-IG-A4QT      TCGA-IG-A50L      TCGA-IG-A5B8 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-IG-A6QS      TCGA-IG-A8O2      TCGA-IG-A97H      TCGA-JY-A6FA 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-JY-A6FE      TCGA-JY-A6FG      TCGA-JY-A6FH      TCGA-KH-A6WC 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A43C      TCGA-L5-A43E      TCGA-L5-A43H      TCGA-L5-A4OH 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A4OM      TCGA-L5-A4ON      TCGA-L5-A4OO      TCGA-L5-A4OP 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A4OQ      TCGA-L5-A4OT      TCGA-L5-A4OU      TCGA-L5-A4OW 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A4OX      TCGA-L5-A88S      TCGA-L5-A88V      TCGA-L5-A893 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A8NE      TCGA-L5-A8NF      TCGA-L5-A8NK      TCGA-L5-A8NN 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-L5-A8NQ      TCGA-L5-A8NR      TCGA-L5-A8NS      TCGA-L5-A8NW 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A49O      TCGA-LN-A49P      TCGA-LN-A49R      TCGA-LN-A49S 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A49V      TCGA-LN-A49W      TCGA-LN-A4A3      TCGA-LN-A4A6 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A4A9      TCGA-LN-A5U6      TCGA-LN-A5U7      TCGA-LN-A7HV 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ      TCGA-LN-A8HZ 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-LN-A8I0      TCGA-M9-A5M8      TCGA-Q9-A6FW      TCGA-R6-A6DN 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-R6-A6L4      TCGA-R6-A6XQ      TCGA-R6-A6Y2      TCGA-R6-A8W5 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-R6-A8W8      TCGA-R6-A8WC      TCGA-RE-A7BO      TCGA-V5-A7RB 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-V5-A7RC      TCGA-V5-AASV      TCGA-VR-A8EP      TCGA-VR-A8ER 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-A8EU      TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EZ 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4G      TCGA-VR-AA7D      TCGA-VR-AA7I 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-X8-AAAR      TCGA-XP-A8T6      TCGA-XP-A8T7      TCGA-XP-A8T8 
"CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" "CCT6A WILD-TYPE" 
     TCGA-Z6-AAPN 
"CCT6A WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CCT6A MUTATED       3                         0
  CCT6A WILD-TYPE   130                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCT6A MUTATED                                           0     5
  CCT6A WILD-TYPE                                         1   352
D1261V11, multiclass
                                           clus
vv                                          CCT6A MUTATED CCT6A WILD-TYPE
  ASIAN                                                 3             130
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1261V12, binary
                 cls
clus                0   1
  CCT6A MUTATED     0   8
  CCT6A WILD-TYPE  10 390
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      0    8
  CCT6A WILD-TYPE   10  390
                        clus
vv                       CCT6A MUTATED CCT6A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             8             390
[1] 2 2
[1] FALSE

Clustering(1262) Variable = PJA1 MUTATION ANALYSIS
D1262V1, survival
                sevent
clus2              0   1
  PJA1 MUTATED     6   5
  PJA1 WILD-TYPE 332 211
  PJA1 MUTATED PJA1 WILD-TYPE 
            11            543 
  PJA1 MUTATED PJA1 WILD-TYPE 
             5            211 
$`PJA1 MUTATED`
TCGA-L5-A4OM TCGA-RE-A7BO TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8487 TCGA-CD-A48A 
       47.93         7.00        34.68        18.15         1.12        12.43 
TCGA-CD-A4MG TCGA-D7-A4Z0 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-MX-A5UJ 
        6.58        14.76        26.47        29.98        19.73 

$`PJA1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        3.42         2.10         1.32         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       19.96         2.20         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
        3.72         5.39        25.18         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       36.43        13.78        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       20.32        22.29        15.65         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       59.54         5.03        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 
        6.21        77.29        63.06        52.21        30.51         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        21.37         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       15.68        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 
        2.53         5.56        63.62        36.95         3.72        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  PJA1 MUTATED PJA1 WILD-TYPE 
          1.12           0.00 
  PJA1 MUTATED PJA1 WILD-TYPE 
         47.93         122.30 
  PJA1 MUTATED PJA1 WILD-TYPE 
         18.15          13.51 
[1] "1.1 - 47.9 (18.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.1"
D1262V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PJA1 MUTATED         0        1        1        0         5         2
  PJA1 WILD-TYPE      10       19       45       31        79        81
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PJA1 MUTATED           0          1          0          0        2         0
  PJA1 WILD-TYPE        29         83         62         39       41         4
D1262V3, multiclass
            clus
vv           PJA1 MUTATED PJA1 WILD-TYPE
  STAGE I               0             10
  STAGE IA              1             19
  STAGE IB              1             45
  STAGE II              0             31
  STAGE IIA             5             79
  STAGE IIB             2             81
  STAGE III             0             29
  STAGE IIIA            1             83
  STAGE IIIB            0             62
  STAGE IIIC            0             39
  STAGE IV              2             41
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PJA1 MUTATED       2   3   5   2
  PJA1 WILD-TYPE    52 132 256 100
D1262V4, multiclass
       clus
vv      PJA1 MUTATED PJA1 WILD-TYPE
  T0+T1            2             52
  T2               3            132
  T3               5            256
  T4               2            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PJA1 MUTATED     6   3   3   0
  PJA1 WILD-TYPE 189 170  86  85
D1262V5, multiclass
    clus
vv   PJA1 MUTATED PJA1 WILD-TYPE
  N0            6            189
  N1            3            170
  N2            3             86
  N3            0             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1262V6, binary
                cls
clus               0   1
  PJA1 MUTATED    11   0
  PJA1 WILD-TYPE 471  38
[1] "tbl2"
                cls
clus             [,1] [,2]
  PJA1 MUTATED     11    0
  PJA1 WILD-TYPE  471   38
   clus
vv  PJA1 MUTATED PJA1 WILD-TYPE
  0           11            471
  1            0             38
[1] 2 2
[1] FALSE
D1262V7, binary
                cls
clus               0   1
  PJA1 MUTATED     9   4
  PJA1 WILD-TYPE 163 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  PJA1 MUTATED      9    4
  PJA1 WILD-TYPE  163  402
        clus
vv       PJA1 MUTATED PJA1 WILD-TYPE
  FEMALE            9            163
  MALE              4            402
[1] 2 2
[1] FALSE
D1262V8, binary
                cls
clus               0   1
  PJA1 MUTATED     9   2
  PJA1 WILD-TYPE 407 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  PJA1 MUTATED      9    2
  PJA1 WILD-TYPE  407  100
     clus
vv    PJA1 MUTATED PJA1 WILD-TYPE
  NO             9            407
  YES            2            100
[1] 2 2
[1] FALSE
D1262V9, continuous
D1262V10, continuous
[1] "Remove cluster labels:" "PJA1 MUTATED"          
clus
  PJA1 MUTATED PJA1 WILD-TYPE 
             2             96 
    TCGA-IC-A6RF     TCGA-L5-A43I     TCGA-L5-A43J     TCGA-L5-A4OE 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A4OG     TCGA-L5-A4OI     TCGA-L5-A88T     TCGA-L5-A88Y 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A8NG     TCGA-L5-A8NT     TCGA-Q9-A6FU     TCGA-IC-A6RE 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA     TCGA-IG-A3YC 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-IG-A4P3     TCGA-IG-A4QT     TCGA-IG-A50L     TCGA-IG-A5B8 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-IG-A6QS     TCGA-IG-A8O2     TCGA-IG-A97H     TCGA-JY-A6FA 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-JY-A6FE     TCGA-JY-A6FG     TCGA-JY-A6FH     TCGA-KH-A6WC 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A43C     TCGA-L5-A43E     TCGA-L5-A43H     TCGA-L5-A4OH 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A4ON     TCGA-L5-A4OO     TCGA-L5-A4OP     TCGA-L5-A4OQ 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A4OT     TCGA-L5-A4OU     TCGA-L5-A4OW     TCGA-L5-A4OX 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A88S     TCGA-L5-A88V     TCGA-L5-A893     TCGA-L5-A8NE 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A8NF     TCGA-L5-A8NK     TCGA-L5-A8NN     TCGA-L5-A8NQ 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-L5-A8NR     TCGA-L5-A8NS     TCGA-L5-A8NW     TCGA-LN-A49O 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-LN-A49P     TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-LN-A49V     TCGA-LN-A49W     TCGA-LN-A4A3     TCGA-LN-A4A6 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-LN-A4A9     TCGA-LN-A5U6     TCGA-LN-A5U7     TCGA-LN-A7HV 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HZ     TCGA-LN-A8HZ 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-LN-A8I0     TCGA-M9-A5M8     TCGA-Q9-A6FW     TCGA-R6-A6DN 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-R6-A6L4     TCGA-R6-A6XQ     TCGA-R6-A6Y2     TCGA-R6-A8W5 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-R6-A8W8     TCGA-R6-A8WC     TCGA-V5-A7RB     TCGA-V5-A7RC 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-V5-AASV     TCGA-VR-A8EP     TCGA-VR-A8ER     TCGA-VR-A8EU 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-VR-A8EW     TCGA-VR-A8EX     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-VR-AA4G     TCGA-VR-AA7D     TCGA-VR-AA7I     TCGA-X8-AAAR 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
    TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8     TCGA-Z6-AAPN 
"PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" "PJA1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PJA1 MUTATED       3                         0
  PJA1 WILD-TYPE   130                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PJA1 MUTATED                                           0    10
  PJA1 WILD-TYPE                                         1   347
D1262V11, multiclass
                                           clus
vv                                          PJA1 MUTATED PJA1 WILD-TYPE
  ASIAN                                                3            130
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1262V12, binary
                cls
clus               0   1
  PJA1 MUTATED     0  12
  PJA1 WILD-TYPE  10 386
[1] "tbl2"
                cls
clus             [,1] [,2]
  PJA1 MUTATED      0   12
  PJA1 WILD-TYPE   10  386
                        clus
vv                       PJA1 MUTATED PJA1 WILD-TYPE
  HISPANIC OR LATINO                0             10
  NOT HISPANIC OR LATINO           12            386
[1] 2 2
[1] FALSE

Clustering(1263) Variable = GALK1 MUTATION ANALYSIS
D1263V1, survival
                 sevent
clus2               0   1
  GALK1 MUTATED     1   1
  GALK1 WILD-TYPE 337 215
  GALK1 MUTATED GALK1 WILD-TYPE 
              2             552 
  GALK1 MUTATED GALK1 WILD-TYPE 
              1             215 
$`GALK1 MUTATED`
TCGA-CD-A4MG TCGA-FP-A4BE 
        6.58        11.08 

$`GALK1 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       31.96        32.58         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52        13.51        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.39        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.82        12.43         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       43.36        37.41        38.14        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D 
        1.87        15.65        20.81         1.71        42.64        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  GALK1 MUTATED GALK1 WILD-TYPE 
           6.58            0.00 
  GALK1 MUTATED GALK1 WILD-TYPE 
          11.08          122.30 
  GALK1 MUTATED GALK1 WILD-TYPE 
           8.83           13.63 
[1] "6.6 - 11.1 (8.8)"   "0.0 - 122.3 (13.6)"
[1] "Remove cluster labels:" "GALK1 MUTATED"         
D1263V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GALK1 MUTATED         0        0        0        0         2         0
  GALK1 WILD-TYPE      10       20       46       31        82        83
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GALK1 MUTATED           0          1          0          0        0         0
  GALK1 WILD-TYPE        29         83         62         39       43         4
D1263V3, multiclass
            clus
vv           GALK1 MUTATED GALK1 WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               0              31
  STAGE IIA              2              82
  STAGE IIB              0              83
  STAGE III              0              29
  STAGE IIIA             1              83
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  GALK1 MUTATED       0   0   2   1
  GALK1 WILD-TYPE    54 135 259 101
D1263V4, multiclass
       clus
vv      GALK1 MUTATED GALK1 WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                1             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  GALK1 MUTATED     3   0   0   0
  GALK1 WILD-TYPE 192 173  89  85
D1263V5, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  N0             3             192
  N1             0             173
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1263V6, binary
                 cls
clus                0   1
  GALK1 MUTATED     4   0
  GALK1 WILD-TYPE 478  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      4    0
  GALK1 WILD-TYPE  478   38
   clus
vv  GALK1 MUTATED GALK1 WILD-TYPE
  0             4             478
  1             0              38
[1] 2 2
[1] FALSE
D1263V7, binary
                 cls
clus                0   1
  GALK1 MUTATED     2   2
  GALK1 WILD-TYPE 170 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      2    2
  GALK1 WILD-TYPE  170  404
        clus
vv       GALK1 MUTATED GALK1 WILD-TYPE
  FEMALE             2             170
  MALE               2             404
[1] 2 2
[1] FALSE
D1263V8, binary
                 cls
clus                0   1
  GALK1 MUTATED     1   1
  GALK1 WILD-TYPE 415 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      1    1
  GALK1 WILD-TYPE  415  101
     clus
vv    GALK1 MUTATED GALK1 WILD-TYPE
  NO              1             415
  YES             1             101
[1] 2 2
[1] FALSE
D1263V9, continuous
D1263V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GALK1 MUTATED       1                         1
  GALK1 WILD-TYPE   132                        13
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GALK1 MUTATED                                           0     2
  GALK1 WILD-TYPE                                         1   355
D1263V11, multiclass
                                           clus
vv                                          GALK1 MUTATED GALK1 WILD-TYPE
  ASIAN                                                 1             132
  BLACK OR AFRICAN AMERICAN                             1              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1263V12, binary
                 cls
clus                0   1
  GALK1 MUTATED     0   4
  GALK1 WILD-TYPE  10 394
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      0    4
  GALK1 WILD-TYPE   10  394
                        clus
vv                       GALK1 MUTATED GALK1 WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             4             394
[1] 2 2
[1] FALSE

Clustering(1264) Variable = PEG3 MUTATION ANALYSIS
D1264V1, survival
                sevent
clus2              0   1
  PEG3 MUTATED    31  11
  PEG3 WILD-TYPE 307 205
  PEG3 MUTATED PEG3 WILD-TYPE 
            42            512 
  PEG3 MUTATED PEG3 WILD-TYPE 
            11            205 
$`PEG3 MUTATED`
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-2H-A9GM TCGA-L5-A43E TCGA-L5-A4OT TCGA-L5-A8NE 
        4.70        19.99        13.94        30.25         4.90        55.50 
TCGA-L5-A8NH TCGA-L5-A8NS TCGA-M9-A5M8 TCGA-V5-A7RB TCGA-VR-A8EQ TCGA-B7-A5TJ 
       12.92        13.41        33.11         5.29        22.82        11.01 
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8077 
        6.97        34.68        35.84        18.15        14.43         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4438 
       29.42         2.66        31.27         1.12        31.96        54.08 
TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-A4YY TCGA-D7-A4Z0 
        7.07         6.02        17.19        15.98        13.78        14.76 
TCGA-D7-A6F0 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GH 
       22.29        22.32        22.68        24.20        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A91V 
        8.98         6.51        16.67        19.04        38.14        42.64 

$`PEG3 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH 
        0.23        20.15         9.86        25.78        20.05        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.38         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04         3.32        11.80        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       12.10        12.39        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 
       18.54        18.61        17.85        13.35        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44         5.92        36.43        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       17.06        59.54         5.03        13.58         0.56        11.08 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.26         3.25 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        1.71        66.81        11.24        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  PEG3 MUTATED PEG3 WILD-TYPE 
          0.69           0.00 
  PEG3 MUTATED PEG3 WILD-TYPE 
          55.5          122.3 
  PEG3 MUTATED PEG3 WILD-TYPE 
        16.930         13.395 
[1] "0.7 - 55.5 (16.9)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.7"
D1264V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PEG3 MUTATED         2        2        4        1         5         9
  PEG3 WILD-TYPE       8       18       42       30        79        74
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PEG3 MUTATED           2          4          2          2        8         0
  PEG3 WILD-TYPE        27         80         60         37       35         4
D1264V3, multiclass
            clus
vv           PEG3 MUTATED PEG3 WILD-TYPE
  STAGE I               2              8
  STAGE IA              2             18
  STAGE IB              4             42
  STAGE II              1             30
  STAGE IIA             5             79
  STAGE IIB             9             74
  STAGE III             2             27
  STAGE IIIA            4             80
  STAGE IIIB            2             60
  STAGE IIIC            2             37
  STAGE IV              8             35
  STAGE IVA             0              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T0+T1  T2  T3  T4
  PEG3 MUTATED       8   8  16  11
  PEG3 WILD-TYPE    46 127 245  91
D1264V4, multiclass
       clus
vv      PEG3 MUTATED PEG3 WILD-TYPE
  T0+T1            8             46
  T2               8            127
  T3              16            245
  T4              11             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2  N3
  PEG3 MUTATED    16  14   6   5
  PEG3 WILD-TYPE 179 159  83  80
D1264V5, multiclass
    clus
vv   PEG3 MUTATED PEG3 WILD-TYPE
  N0           16            179
  N1           14            159
  N2            6             83
  N3            5             80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1264V6, binary
                cls
clus               0   1
  PEG3 MUTATED    36   4
  PEG3 WILD-TYPE 446  34
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED     36    4
  PEG3 WILD-TYPE  446   34
   clus
vv  PEG3 MUTATED PEG3 WILD-TYPE
  0           36            446
  1            4             34
[1] 2 2
[1] FALSE
D1264V7, binary
                cls
clus               0   1
  PEG3 MUTATED    16  27
  PEG3 WILD-TYPE 156 379
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED     16   27
  PEG3 WILD-TYPE  156  379
        clus
vv       PEG3 MUTATED PEG3 WILD-TYPE
  FEMALE           16            156
  MALE             27            379
[1] 2 2
[1] FALSE
D1264V8, binary
                cls
clus               0   1
  PEG3 MUTATED    32   6
  PEG3 WILD-TYPE 384  96
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED     32    6
  PEG3 WILD-TYPE  384   96
     clus
vv    PEG3 MUTATED PEG3 WILD-TYPE
  NO            32            384
  YES            6             96
[1] 2 2
[1] FALSE
D1264V9, continuous
[1] "Remove cluster labels:" "PEG3 MUTATED"          
clus
  PEG3 MUTATED PEG3 WILD-TYPE 
             2             66 
    TCGA-IG-A3I8     TCGA-IG-A3QL     TCGA-IG-A3Y9     TCGA-IG-A3YA 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-IG-A3YB     TCGA-IG-A3YC     TCGA-IG-A51D     TCGA-IG-A5S3 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-IG-A7DP     TCGA-KH-A6WC     TCGA-LN-A49K     TCGA-LN-A49L 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A49M     TCGA-LN-A49N     TCGA-LN-A49O     TCGA-LN-A49P 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A49R     TCGA-LN-A49S     TCGA-LN-A49U     TCGA-LN-A49V 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A49W     TCGA-LN-A49X     TCGA-LN-A49Y     TCGA-LN-A4A1 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A4A2     TCGA-LN-A4A3     TCGA-LN-A4A4     TCGA-LN-A4A5 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A4A6     TCGA-LN-A4A8     TCGA-LN-A4A9     TCGA-LN-A4MQ 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A4MR     TCGA-LN-A5U5     TCGA-LN-A5U6     TCGA-LN-A5U7 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A7HV     TCGA-LN-A7HW     TCGA-LN-A7HX     TCGA-LN-A7HY 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-LN-A7HZ     TCGA-V5-A7RC     TCGA-V5-A7RE     TCGA-V5-AASV 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-V5-AASW     TCGA-V5-AASX     TCGA-VR-A8EO     TCGA-VR-A8EP 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-VR-A8ER     TCGA-VR-A8ET     TCGA-VR-A8EU     TCGA-VR-A8EW 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-VR-A8EX     TCGA-VR-A8EY     TCGA-VR-A8EZ     TCGA-VR-A8Q7 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-VR-AA4D     TCGA-VR-AA4G     TCGA-VR-AA7B     TCGA-VR-AA7D 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-VR-AA7I     TCGA-XP-A8T6     TCGA-XP-A8T7     TCGA-XP-A8T8 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
    TCGA-Z6-A8JD     TCGA-Z6-A8JE 
"PEG3 WILD-TYPE" "PEG3 WILD-TYPE" 
D1264V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PEG3 MUTATED       8                         0
  PEG3 WILD-TYPE   125                        14
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PEG3 MUTATED                                           0    28
  PEG3 WILD-TYPE                                         1   329
D1264V11, multiclass
                                           clus
vv                                          PEG3 MUTATED PEG3 WILD-TYPE
  ASIAN                                                8            125
  BLACK OR AFRICAN AMERICAN                            0             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               28            329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1264V12, binary
                cls
clus               0   1
  PEG3 MUTATED     1  27
  PEG3 WILD-TYPE   9 371
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEG3 MUTATED      1   27
  PEG3 WILD-TYPE    9  371
                        clus
vv                       PEG3 MUTATED PEG3 WILD-TYPE
  HISPANIC OR LATINO                1              9
  NOT HISPANIC OR LATINO           27            371
[1] 2 2
[1] FALSE

Clustering(1265) Variable = GPR120 MUTATION ANALYSIS
D1265V1, survival
                  sevent
clus2                0   1
  GPR120 MUTATED     5   2
  GPR120 WILD-TYPE 333 214
  GPR120 MUTATED GPR120 WILD-TYPE 
               7              547 
  GPR120 MUTATED GPR120 WILD-TYPE 
               2              214 
$`GPR120 MUTATED`
TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 TCGA-F1-6874 
       27.12        31.96        16.14         6.02        28.96        14.47 
TCGA-HU-A4H8 
       14.07 

$`GPR120 WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 
       18.05        11.24         9.17        15.91        18.21        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.18         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.36        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       30.51        26.47         1.51         5.92        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.58        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        23.80        21.17        15.68        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  GPR120 MUTATED GPR120 WILD-TYPE 
            6.02             0.00 
  GPR120 MUTATED GPR120 WILD-TYPE 
           31.96           122.30 
  GPR120 MUTATED GPR120 WILD-TYPE 
           16.14            13.51 
[1] "6.0 - 32.0 (16.1)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.6"
D1265V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR120 MUTATED         0        1        2        0         0         0
  GPR120 WILD-TYPE      10       19       44       31        84        83
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR120 MUTATED           0          0          2          0        2
  GPR120 WILD-TYPE        29         84         60         39       41
                  vv
clus               STAGE IVA
  GPR120 MUTATED           0
  GPR120 WILD-TYPE         4
D1265V3, multiclass
            clus
vv           GPR120 MUTATED GPR120 WILD-TYPE
  STAGE I                 0               10
  STAGE IA                1               19
  STAGE IB                2               44
  STAGE II                0               31
  STAGE IIA               0               84
  STAGE IIB               0               83
  STAGE III               0               29
  STAGE IIIA              0               84
  STAGE IIIB              2               60
  STAGE IIIC              0               39
  STAGE IV                2               41
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  GPR120 MUTATED       2   1   1   3
  GPR120 WILD-TYPE    52 134 260  99
D1265V4, multiclass
       clus
vv      GPR120 MUTATED GPR120 WILD-TYPE
  T0+T1              2               52
  T2                 1              134
  T3                 1              260
  T4                 3               99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  GPR120 MUTATED     2   3   1   1
  GPR120 WILD-TYPE 193 170  88  84
D1265V5, multiclass
    clus
vv   GPR120 MUTATED GPR120 WILD-TYPE
  N0              2              193
  N1              3              170
  N2              1               88
  N3              1               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1265V6, binary
                  cls
clus                 0   1
  GPR120 MUTATED     6   1
  GPR120 WILD-TYPE 476  37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR120 MUTATED      6    1
  GPR120 WILD-TYPE  476   37
   clus
vv  GPR120 MUTATED GPR120 WILD-TYPE
  0              6              476
  1              1               37
[1] 2 2
[1] FALSE
D1265V7, binary
                  cls
clus                 0   1
  GPR120 MUTATED     1   6
  GPR120 WILD-TYPE 171 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR120 MUTATED      1    6
  GPR120 WILD-TYPE  171  400
        clus
vv       GPR120 MUTATED GPR120 WILD-TYPE
  FEMALE              1              171
  MALE                6              400
[1] 2 2
[1] FALSE
D1265V8, binary
                  cls
clus                 0   1
  GPR120 MUTATED     6   0
  GPR120 WILD-TYPE 410 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR120 MUTATED      6    0
  GPR120 WILD-TYPE  410  102
     clus
vv    GPR120 MUTATED GPR120 WILD-TYPE
  NO               6              410
  YES              0              102
[1] 2 2
[1] FALSE
D1265V9, continuous
D1265V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR120 MUTATED       2                         0
  GPR120 WILD-TYPE   131                        14
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR120 MUTATED                                           0     3
  GPR120 WILD-TYPE                                         1   354
D1265V11, multiclass
                                           clus
vv                                          GPR120 MUTATED GPR120 WILD-TYPE
  ASIAN                                                  2              131
  BLACK OR AFRICAN AMERICAN                              0               14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1265V12, binary
                  cls
clus                 0   1
  GPR120 MUTATED     0   5
  GPR120 WILD-TYPE  10 393
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR120 MUTATED      0    5
  GPR120 WILD-TYPE   10  393
                        clus
vv                       GPR120 MUTATED GPR120 WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO              5              393
[1] 2 2
[1] FALSE

Clustering(1266) Variable = RRP7A MUTATION ANALYSIS
D1266V1, survival
                 sevent
clus2               0   1
  RRP7A MUTATED     4   1
  RRP7A WILD-TYPE 334 215
  RRP7A MUTATED RRP7A WILD-TYPE 
              5             549 
  RRP7A MUTATED RRP7A WILD-TYPE 
              1             215 
$`RRP7A MUTATED`
TCGA-LN-A7HY TCGA-BR-4256 TCGA-BR-A4IY TCGA-CD-8536 TCGA-HU-8602 
       12.03         9.34        12.89        12.43        22.32 

$`RRP7A WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.05        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35        12.59        13.25        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       32.52        13.51        20.65        20.42         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.35        11.21        12.10        12.39        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       33.40        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.22        22.19        17.85         1.87        15.65        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        42.64        66.81        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RRP7A MUTATED RRP7A WILD-TYPE 
           9.34            0.00 
  RRP7A MUTATED RRP7A WILD-TYPE 
          22.32          122.30 
  RRP7A MUTATED RRP7A WILD-TYPE 
          12.43           13.68 
[1] "9.3 - 22.3 (12.4)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1.6"
D1266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRP7A MUTATED         0        0        0        1         0         2
  RRP7A WILD-TYPE      10       20       46       30        84        81
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRP7A MUTATED           1          0          0          0        0         0
  RRP7A WILD-TYPE        28         84         62         39       43         4
D1266V3, multiclass
            clus
vv           RRP7A MUTATED RRP7A WILD-TYPE
  STAGE I                0              10
  STAGE IA               0              20
  STAGE IB               0              46
  STAGE II               1              30
  STAGE IIA              0              84
  STAGE IIB              2              81
  STAGE III              1              28
  STAGE IIIA             0              84
  STAGE IIIB             0              62
  STAGE IIIC             0              39
  STAGE IV               0              43
  STAGE IVA              0               4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T0+T1  T2  T3  T4
  RRP7A MUTATED       0   0   2   2
  RRP7A WILD-TYPE    54 135 259 100
D1266V4, multiclass
       clus
vv      RRP7A MUTATED RRP7A WILD-TYPE
  T0+T1             0              54
  T2                0             135
  T3                2             259
  T4                2             100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  RRP7A MUTATED     3   2   0   0
  RRP7A WILD-TYPE 192 171  89  85
D1266V5, multiclass
    clus
vv   RRP7A MUTATED RRP7A WILD-TYPE
  N0             3             192
  N1             2             171
  N2             0              89
  N3             0              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1266V6, binary
                 cls
clus                0   1
  RRP7A MUTATED     5   0
  RRP7A WILD-TYPE 477  38
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP7A MUTATED      5    0
  RRP7A WILD-TYPE  477   38
   clus
vv  RRP7A MUTATED RRP7A WILD-TYPE
  0             5             477
  1             0              38
[1] 2 2
[1] FALSE
D1266V7, binary
                 cls
clus                0   1
  RRP7A MUTATED     1   4
  RRP7A WILD-TYPE 171 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP7A MUTATED      1    4
  RRP7A WILD-TYPE  171  402
        clus
vv       RRP7A MUTATED RRP7A WILD-TYPE
  FEMALE             1             171
  MALE               4             402
[1] 2 2
[1] FALSE
D1266V8, binary
                 cls
clus                0   1
  RRP7A MUTATED     5   0
  RRP7A WILD-TYPE 411 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP7A MUTATED      5    0
  RRP7A WILD-TYPE  411  102
     clus
vv    RRP7A MUTATED RRP7A WILD-TYPE
  NO              5             411
  YES             0             102
[1] 2 2
[1] FALSE
D1266V9, continuous
[1] "Remove cluster labels:" "RRP7A MUTATED"         
clus
  RRP7A MUTATED RRP7A WILD-TYPE 
              1              67 
     TCGA-IG-A3I8      TCGA-IG-A3QL      TCGA-IG-A3Y9      TCGA-IG-A3YA 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-IG-A3YB      TCGA-IG-A3YC      TCGA-IG-A51D      TCGA-IG-A5S3 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-IG-A7DP      TCGA-KH-A6WC      TCGA-LN-A49K      TCGA-LN-A49L 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A49M      TCGA-LN-A49N      TCGA-LN-A49O      TCGA-LN-A49P 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A49R      TCGA-LN-A49S      TCGA-LN-A49U      TCGA-LN-A49V 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A49W      TCGA-LN-A49X      TCGA-LN-A49Y      TCGA-LN-A4A1 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A4A2      TCGA-LN-A4A3      TCGA-LN-A4A4      TCGA-LN-A4A5 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A4A6      TCGA-LN-A4A8      TCGA-LN-A4A9      TCGA-LN-A4MQ 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A4MR      TCGA-LN-A5U5      TCGA-LN-A5U6      TCGA-LN-A5U7 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-LN-A7HV      TCGA-LN-A7HW      TCGA-LN-A7HX      TCGA-LN-A7HZ 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-V5-A7RB      TCGA-V5-A7RC      TCGA-V5-A7RE      TCGA-V5-AASV 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-V5-AASW      TCGA-V5-AASX      TCGA-VR-A8EO      TCGA-VR-A8EP 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-VR-A8EQ      TCGA-VR-A8ER      TCGA-VR-A8ET      TCGA-VR-A8EU 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-VR-A8EW      TCGA-VR-A8EX      TCGA-VR-A8EY      TCGA-VR-A8EZ 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-VR-A8Q7      TCGA-VR-AA4D      TCGA-VR-AA4G      TCGA-VR-AA7B 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-VR-AA7D      TCGA-VR-AA7I      TCGA-XP-A8T6      TCGA-XP-A8T7 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
     TCGA-XP-A8T8      TCGA-Z6-A8JD      TCGA-Z6-A8JE 
"RRP7A WILD-TYPE" "RRP7A WILD-TYPE" "RRP7A WILD-TYPE" 
D1266V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RRP7A MUTATED       4                         0
  RRP7A WILD-TYPE   129                        14
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRP7A MUTATED                                           0     1
  RRP7A WILD-TYPE                                         1   356
D1266V11, multiclass
                                           clus
vv                                          RRP7A MUTATED RRP7A WILD-TYPE
  ASIAN                                                 4             129
  BLACK OR AFRICAN AMERICAN                             0              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1266V12, binary
                 cls
clus                0   1
  RRP7A MUTATED     0   5
  RRP7A WILD-TYPE  10 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP7A MUTATED      0    5
  RRP7A WILD-TYPE   10  393
                        clus
vv                       RRP7A MUTATED RRP7A WILD-TYPE
  HISPANIC OR LATINO                 0              10
  NOT HISPANIC OR LATINO             5             393
[1] 2 2
[1] FALSE

Clustering(1267) Variable = ARID5B MUTATION ANALYSIS
D1267V1, survival
                  sevent
clus2                0   1
  ARID5B MUTATED    10   4
  ARID5B WILD-TYPE 328 212
  ARID5B MUTATED ARID5B WILD-TYPE 
              14              540 
  ARID5B MUTATED ARID5B WILD-TYPE 
               4              212 
$`ARID5B MUTATED`
TCGA-Q9-A6FU TCGA-V5-A7RC TCGA-Z6-AAPN TCGA-B7-5816 TCGA-BR-8284 TCGA-BR-8361 
        5.16         3.42         2.66        26.70         8.05        31.10 
TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4466 TCGA-CG-5721 TCGA-HU-8602 TCGA-IN-A6RI 
       31.27        15.95        18.97         6.02        22.32        18.38 
TCGA-IN-A6RR TCGA-VQ-A92D 
        6.74        66.81 

$`ARID5B WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12        20.02        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GG 
       16.24         0.23        20.15         9.86        25.78        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
        9.17        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10         1.32        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        36.16        35.24        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.15        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       13.58         0.56        11.08         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        28.96        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.58        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       33.40        36.36         3.45        18.81         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
       13.02        43.36        37.41        38.14        37.22        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       17.85         1.87        15.65        20.81         1.71        42.64 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  ARID5B MUTATED ARID5B WILD-TYPE 
            2.66             0.00 
  ARID5B MUTATED ARID5B WILD-TYPE 
           66.81           122.30 
  ARID5B MUTATED ARID5B WILD-TYPE 
          17.165           13.530 
[1] "2.7 - 66.8 (17.2)"  "0.0 - 122.3 (13.5)"
[1] "hr=" "1.4"
D1267V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID5B MUTATED         2        0        2        1         1         3
  ARID5B WILD-TYPE       8       20       44       30        83        80
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5B MUTATED           0          1          1          3        1
  ARID5B WILD-TYPE        29         83         61         36       42
                  vv
clus               STAGE IVA
  ARID5B MUTATED           0
  ARID5B WILD-TYPE         4
D1267V3, multiclass
            clus
vv           ARID5B MUTATED ARID5B WILD-TYPE
  STAGE I                 2                8
  STAGE IA                0               20
  STAGE IB                2               44
  STAGE II                1               30
  STAGE IIA               1               83
  STAGE IIB               3               80
  STAGE III               0               29
  STAGE IIIA              1               83
  STAGE IIIB              1               61
  STAGE IIIC              3               36
  STAGE IV                1               42
  STAGE IVA               0                4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T0+T1  T2  T3  T4
  ARID5B MUTATED       2   3   3   7
  ARID5B WILD-TYPE    52 132 258  95
D1267V4, multiclass
       clus
vv      ARID5B MUTATED ARID5B WILD-TYPE
  T0+T1              2               52
  T2                 3              132
  T3                 3              258
  T4                 7               95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2  N3
  ARID5B MUTATED     7   5   2   2
  ARID5B WILD-TYPE 188 168  87  83
D1267V5, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  N0              7              188
  N1              5              168
  N2              2               87
  N3              2               83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1267V6, binary
                  cls
clus                 0   1
  ARID5B MUTATED    16   0
  ARID5B WILD-TYPE 466  38
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     16    0
  ARID5B WILD-TYPE  466   38
   clus
vv  ARID5B MUTATED ARID5B WILD-TYPE
  0             16              466
  1              0               38
[1] 2 2
[1] FALSE
D1267V7, binary
                  cls
clus                 0   1
  ARID5B MUTATED     8  10
  ARID5B WILD-TYPE 164 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      8   10
  ARID5B WILD-TYPE  164  396
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  FEMALE              8              164
  MALE               10              396
[1] 2 2
[1] FALSE
D1267V8, binary
                  cls
clus                 0   1
  ARID5B MUTATED    15   1
  ARID5B WILD-TYPE 401 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     15    1
  ARID5B WILD-TYPE  401  101
     clus
vv    ARID5B MUTATED ARID5B WILD-TYPE
  NO              15              401
  YES              1              101
[1] 2 2
[1] FALSE
D1267V9, continuous
[1] "Remove cluster labels:" "ARID5B MUTATED"        
clus
  ARID5B MUTATED ARID5B WILD-TYPE 
               1               67 
      TCGA-IG-A3I8       TCGA-IG-A3QL       TCGA-IG-A3Y9       TCGA-IG-A3YA 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-IG-A3YB       TCGA-IG-A3YC       TCGA-IG-A51D       TCGA-IG-A5S3 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-IG-A7DP       TCGA-KH-A6WC       TCGA-LN-A49K       TCGA-LN-A49L 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A49M       TCGA-LN-A49N       TCGA-LN-A49O       TCGA-LN-A49P 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A49R       TCGA-LN-A49S       TCGA-LN-A49U       TCGA-LN-A49V 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A49W       TCGA-LN-A49X       TCGA-LN-A49Y       TCGA-LN-A4A1 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A4A2       TCGA-LN-A4A3       TCGA-LN-A4A4       TCGA-LN-A4A5 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A4A6       TCGA-LN-A4A8       TCGA-LN-A4A9       TCGA-LN-A4MQ 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A4MR       TCGA-LN-A5U5       TCGA-LN-A5U6       TCGA-LN-A5U7 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A7HV       TCGA-LN-A7HW       TCGA-LN-A7HX       TCGA-LN-A7HY 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-LN-A7HZ       TCGA-V5-A7RB       TCGA-V5-A7RE       TCGA-V5-AASV 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-V5-AASW       TCGA-V5-AASX       TCGA-VR-A8EO       TCGA-VR-A8EP 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-VR-A8EQ       TCGA-VR-A8ER       TCGA-VR-A8ET       TCGA-VR-A8EU 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-VR-A8EW       TCGA-VR-A8EX       TCGA-VR-A8EY       TCGA-VR-A8EZ 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-VR-A8Q7       TCGA-VR-AA4D       TCGA-VR-AA4G       TCGA-VR-AA7B 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-VR-AA7D       TCGA-VR-AA7I       TCGA-XP-A8T6       TCGA-XP-A8T7 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
      TCGA-XP-A8T8       TCGA-Z6-A8JD       TCGA-Z6-A8JE 
"ARID5B WILD-TYPE" "ARID5B WILD-TYPE" "ARID5B WILD-TYPE" 
D1267V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID5B MUTATED       1                         2
  ARID5B WILD-TYPE   132                        12
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID5B MUTATED                                           0    12
  ARID5B WILD-TYPE                                         1   345
D1267V11, multiclass
                                           clus
vv                                          ARID5B MUTATED ARID5B WILD-TYPE
  ASIAN                                                  1              132
  BLACK OR AFRICAN AMERICAN                              2               12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1267V12, binary
                  cls
clus                 0   1
  ARID5B MUTATED     0  14
  ARID5B WILD-TYPE  10 384
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      0   14
  ARID5B WILD-TYPE   10  384
                        clus
vv                       ARID5B MUTATED ARID5B WILD-TYPE
  HISPANIC OR LATINO                  0               10
  NOT HISPANIC OR LATINO             14              384
[1] 2 2
[1] FALSE
